Daily Papers

Traditional molecular string representations, such as SMILES, often pose challenges for AI-driven molecular design due to their non-sequential depiction of molecular substructures. To address this issue, we introduce Sequential Attachment-based Fragment Embedding (SAFE), a novel line notation for chemical structures. SAFE reimagines SMILES strings as an unordered sequence of interconnected fragment blocks while maintaining full compatibility with existing SMILES parsers. It streamlines complex generative tasks, including scaffold decoration, fragment linking, polymer generation, and scaffold hopping, while facilitating autoregressive generation for fragment-constrained design, thereby eliminating the need for intricate decoding or graph-based models. We demonstrate the effectiveness of SAFE by training an 87-million-parameter GPT2-like model on a dataset containing 1.1 billion SAFE representations. Through extensive experimentation, we show that our SAFE-GPT model exhibits versatile and robust optimization performance. SAFE opens up new avenues for the rapid exploration of chemical space under various constraints, promising breakthroughs in AI-driven molecular design.

Language models can store vast amounts of factual knowledge, but their ability to use this knowledge for logical reasoning remains questionable. This paper explores a language model's ability to manipulate its stored knowledge during inference. We focus on four manipulation types: retrieval (e.g., "What is person A's attribute X"), classification (e.g., "Is A's attribute X even or odd?"), comparison (e.g., "Is A greater than B in attribute X?") and inverse search (e.g., "Which person's attribute X equals T?") We observe that pre-trained language models like GPT2/3/4 excel in knowledge retrieval but struggle with simple classification or comparison tasks unless Chain of Thoughts (CoTs) are employed during both training and inference. They also perform poorly in inverse knowledge search, irrespective of the prompts. Our primary contribution is a synthetic dataset for a controlled experiment that confirms these inherent weaknesses: a language model cannot efficiently manipulate knowledge from pre-training data, even when such knowledge is perfectly stored and fully extractable in the models, and despite adequate instruct fine-tuning.

Training deep neural networks in low rank, i.e. with factorised layers, is of particular interest to the community: it offers efficiency over unfactorised training in terms of both memory consumption and training time. Prior work has focused on low rank approximations of pre-trained networks and training in low rank space with additional objectives, offering various ad hoc explanations for chosen practice. We analyse techniques that work well in practice, and through extensive ablations on models such as GPT2 we provide evidence falsifying common beliefs in the field, hinting in the process at exciting research opportunities that still need answering.

Pretrained masked language models (MLMs) require finetuning for most NLP tasks. Instead, we evaluate MLMs out of the box via their pseudo-log-likelihood scores (PLLs), which are computed by masking tokens one by one. We show that PLLs outperform scores from autoregressive language models like GPT-2 in a variety of tasks. By rescoring ASR and NMT hypotheses, RoBERTa reduces an end-to-end LibriSpeech model's WER by 30% relative and adds up to +1.7 BLEU on state-of-the-art baselines for low-resource translation pairs, with further gains from domain adaptation. We attribute this success to PLL's unsupervised expression of linguistic acceptability without a left-to-right bias, greatly improving on scores from GPT-2 (+10 points on island effects, NPI licensing in BLiMP). One can finetune MLMs to give scores without masking, enabling computation in a single inference pass. In all, PLLs and their associated pseudo-perplexities (PPPLs) enable plug-and-play use of the growing number of pretrained MLMs; e.g., we use a single cross-lingual model to rescore translations in multiple languages. We release our library for language model scoring at https://github.com/awslabs/mlm-scoring.

A stereotype is an over-generalized belief about a particular group of people, e.g., Asians are good at math or Asians are bad drivers. Such beliefs (biases) are known to hurt target groups. Since pretrained language models are trained on large real world data, they are known to capture stereotypical biases. In order to assess the adverse effects of these models, it is important to quantify the bias captured in them. Existing literature on quantifying bias evaluates pretrained language models on a small set of artificially constructed bias-assessing sentences. We present StereoSet, a large-scale natural dataset in English to measure stereotypical biases in four domains: gender, profession, race, and religion. We evaluate popular models like BERT, GPT-2, RoBERTa, and XLNet on our dataset and show that these models exhibit strong stereotypical biases. We also present a leaderboard with a hidden test set to track the bias of future language models at https://stereoset.mit.edu

Deploying Large language models (LLMs) can pose hazards from harmful outputs such as toxic or dishonest speech. Prior work has introduced tools that elicit harmful outputs in order to identify and mitigate these risks. While this is a valuable step toward securing language models, these approaches typically rely on a pre-existing classifier for undesired outputs. This limits their application to situations where the type of harmful behavior is known with precision beforehand. However, this skips a central challenge of red teaming: developing a contextual understanding of the behaviors that a model can exhibit. Furthermore, when such a classifier already exists, red teaming has limited marginal value because the classifier could simply be used to filter training data or model outputs. In this work, we consider red teaming under the assumption that the adversary is working from a high-level, abstract specification of undesired behavior. The red team is expected to refine/extend this specification and identify methods to elicit this behavior from the model. Our red teaming framework consists of three steps: 1) Exploring the model's behavior in the desired context; 2) Establishing a measurement of undesired behavior (e.g., a classifier trained to reflect human evaluations); and 3) Exploiting the model's flaws using this measure and an established red teaming methodology. We apply this approach to red team GPT-2 and GPT-3 models to systematically discover classes of prompts that elicit toxic and dishonest statements. In doing so, we also construct and release the CommonClaim dataset of 20,000 statements that have been labeled by human subjects as common-knowledge-true, common-knowledge-false, or neither. Code is available at https://github.com/thestephencasper/explore_establish_exploit_llms. CommonClaim is available at https://github.com/thestephencasper/common_claim.

Training deep neural networks--and more recently, large models--demands efficient and scalable optimizers. Adaptive gradient algorithms like Adam, AdamW, and their variants have been central to this task. Despite the development of numerous variance reduction algorithms in the past decade aimed at accelerating stochastic optimization in both convex and nonconvex settings, variance reduction has not found widespread success in training deep neural networks or large language models. Consequently, it has remained a less favored approach in modern AI. In this paper, to unleash the power of variance reduction for efficient training of large models, we propose a unified optimization framework, MARS (Make vAriance Reduction Shine), which reconciles preconditioned gradient methods with variance reduction via a scaled stochastic recursive momentum technique. Within our framework, we introduce three instances of MARS that leverage preconditioned gradient updates based on AdamW, Lion, and Shampoo, respectively. We also draw a connection between our algorithms and existing optimizers. Experimental results on training GPT-2 models indicate that MARS consistently outperforms AdamW by a large margin.

Social bias in machine learning has drawn significant attention, with work ranging from demonstrations of bias in a multitude of applications, curating definitions of fairness for different contexts, to developing algorithms to mitigate bias. In natural language processing, gender bias has been shown to exist in context-free word embeddings. Recently, contextual word representations have outperformed word embeddings in several downstream NLP tasks. These word representations are conditioned on their context within a sentence, and can also be used to encode the entire sentence. In this paper, we analyze the extent to which state-of-the-art models for contextual word representations, such as BERT and GPT-2, encode biases with respect to gender, race, and intersectional identities. Towards this, we propose assessing bias at the contextual word level. This novel approach captures the contextual effects of bias missing in context-free word embeddings, yet avoids confounding effects that underestimate bias at the sentence encoding level. We demonstrate evidence of bias at the corpus level, find varying evidence of bias in embedding association tests, show in particular that racial bias is strongly encoded in contextual word models, and observe that bias effects for intersectional minorities are exacerbated beyond their constituent minority identities. Further, evaluating bias effects at the contextual word level captures biases that are not captured at the sentence level, confirming the need for our novel approach.

We present a novel approach to data-to-text generation based on iterative text editing. Our approach maximizes the completeness and semantic accuracy of the output text while leveraging the abilities of recent pre-trained models for text editing (LaserTagger) and language modeling (GPT-2) to improve the text fluency. To this end, we first transform data items to text using trivial templates, and then we iteratively improve the resulting text by a neural model trained for the sentence fusion task. The output of the model is filtered by a simple heuristic and reranked with an off-the-shelf pre-trained language model. We evaluate our approach on two major data-to-text datasets (WebNLG, Cleaned E2E) and analyze its caveats and benefits. Furthermore, we show that our formulation of data-to-text generation opens up the possibility for zero-shot domain adaptation using a general-domain dataset for sentence fusion.

The Transformer architecture deeply changed the natural language processing, outperforming all previous state-of-the-art models. However, well-known Transformer models like BERT, RoBERTa, and GPT-2 require a huge compute budget to create a high quality contextualised representation. In this paper, we study several efficient pre-training objectives for Transformers-based models. By testing these objectives on different tasks, we determine which of the ELECTRA model's new features is the most relevant. We confirm that Transformers pre-training is improved when the input does not contain masked tokens and that the usage of the whole output to compute the loss reduces training time. Moreover, inspired by ELECTRA, we study a model composed of two blocks; a discriminator and a simple generator based on a statistical model with no impact on the computational performances. Besides, we prove that eliminating the MASK token and considering the whole output during the loss computation are essential choices to improve performance. Furthermore, we show that it is possible to efficiently train BERT-like models using a discriminative approach as in ELECTRA but without a complex generator, which is expensive. Finally, we show that ELECTRA benefits heavily from a state-of-the-art hyper-parameters search.

Comparative knowledge (e.g., steel is stronger and heavier than styrofoam) is an essential component of our world knowledge, yet understudied in prior literature. In this paper, we harvest the dramatic improvements in knowledge capabilities of language models into a large-scale comparative knowledge base. While the ease of acquisition of such comparative knowledge is much higher from extreme-scale models like GPT-4, compared to their considerably smaller and weaker counterparts such as GPT-2, not even the most powerful models are exempt from making errors. We thus ask: to what extent are models at different scales able to generate valid and diverse comparative knowledge? We introduce NeuroComparatives, a novel framework for comparative knowledge distillation overgenerated from language models such as GPT-variants and LLaMA, followed by stringent filtering of the generated knowledge. Our framework acquires comparative knowledge between everyday objects, producing a corpus of up to 8.8M comparisons over 1.74M entity pairs - 10X larger and 30% more diverse than existing resources. Moreover, human evaluations show that NeuroComparatives outperform existing resources in terms of validity (up to 32% absolute improvement). Our acquired NeuroComparatives leads to performance improvements on five downstream tasks. We find that neuro-symbolic manipulation of smaller models offers complementary benefits to the currently dominant practice of prompting extreme-scale language models for knowledge distillation.

Detecting implicit causal relations in texts is a task that requires both common sense and world knowledge. Existing datasets are focused either on commonsense causal reasoning or explicit causal relations. In this work, we present HeadlineCause, a dataset for detecting implicit causal relations between pairs of news headlines. The dataset includes over 5000 headline pairs from English news and over 9000 headline pairs from Russian news labeled through crowdsourcing. The pairs vary from totally unrelated or belonging to the same general topic to the ones including causation and refutation relations. We also present a set of models and experiments that demonstrates the dataset validity, including a multilingual XLM-RoBERTa based model for causality detection and a GPT-2 based model for possible effects prediction.

Large language models (LLMs) have shown promising results in a wide array of generative NLP tasks, such as summarization and machine translation. In the context of narrative generation, however, existing models still do not capture factors that contribute to producing consistent text. For instance, it is logical that a piece of text or a story should be uniformly readable throughout and that this form of complexity should be controllable. As such, if the complexity of an input text prompt is rated first-grade reading level in the Flesch Reading Ease test, then the generated text continuing the plot should also be within this range of complexity. With this in mind, we introduce Uniform Complexity for Text Generation (UCTG), a new benchmark test which raises the challenge of making generative models observe uniform linguistic properties with respect to prompts. We experiment with over 150+ linguistically and cognitively motivated features for evaluating text complexity in humans and generative models. From our results, we find that models such as GPT-2 struggle to preserve the complexity of input prompts used in its generations, even if finetuned with professionally written texts.

The success of task-oriented and document-grounded dialogue systems depends on users accepting and enjoying using them. To achieve this, recently published work in the field of Human-Computer Interaction suggests that the combination of considering demographic information, user emotions and learning from the implicit feedback in their utterances, is particularly important. However, these findings have not yet been transferred to the field of Natural Language Processing, where these data are primarily studied separately. Accordingly, no sufficiently annotated dataset is available. To address this gap, we introduce FEDI, the first English dialogue dataset for task-oriented document-grounded dialogues annotated with demographic information, user emotions and implicit feedback. Our experiments with FLAN-T5, GPT-2 and LLaMA-2 show that these data have the potential to improve task completion and the factual consistency of the generated responses and user acceptance.

In the rapidly evolving landscape of online recipe sharing within a globalized context, there has been a notable surge in research towards comprehending and generating food recipes. Recent advancements in large language models (LLMs) like GPT-2 and LLaVA have paved the way for Natural Language Processing (NLP) approaches to delve deeper into various facets of food-related tasks, encompassing ingredient recognition and comprehensive recipe generation. Despite impressive performance and multi-modal adaptability of LLMs, domain-specific training remains paramount for their effective application. This work evaluates existing LLMs for recipe generation and proposes LLaVA-Chef, a novel model trained on a curated dataset of diverse recipe prompts in a multi-stage approach. First, we refine the mapping of visual food image embeddings to the language space. Second, we adapt LLaVA to the food domain by fine-tuning it on relevant recipe data. Third, we utilize diverse prompts to enhance the model's recipe comprehension. Finally, we improve the linguistic quality of generated recipes by penalizing the model with a custom loss function. LLaVA-Chef demonstrates impressive improvements over pretrained LLMs and prior works. A detailed qualitative analysis reveals that LLaVA-Chef generates more detailed recipes with precise ingredient mentions, compared to existing approaches.

The Game of Life (Life), a well known algorithm within the broader class of cellular automata (CA), exhibits complex emergent dynamics, with extreme sensitivity to initial conditions. Modeling and predicting such intricate behavior without explicit knowledge of the system's underlying topology presents a significant challenge, motivating the development of algorithms that can generalize across various grid configurations and boundary conditions. We develop a decoder-only generative pretrained transformer model to solve this problem, showing that our model can simulate Life on a toroidal grid with no prior knowledge on the size of the grid, or its periodic boundary conditions (LifeGPT). LifeGPT is topology-agnostic with respect to its training data and our results show that a GPT model is capable of capturing the deterministic rules of a Turing-complete system with near-perfect accuracy, given sufficiently diverse training data. We also introduce the idea of an `autoregressive autoregressor' to recursively implement Life using LifeGPT. Our results pave the path towards true universal computation within a large language model (LLM) framework, synthesizing of mathematical analysis with natural language processing, and probing AI systems for situational awareness about the evolution of such algorithms without ever having to compute them. Similar GPTs could potentially solve inverse problems in multicellular self-assembly by extracting CA-compatible rulesets from real-world biological systems to create new predictive models, which would have significant consequences for the fields of bioinspired materials, tissue engineering, and architected materials design.

Radiology plays a pivotal role in modern medicine due to its non-invasive diagnostic capabilities. However, the manual generation of unstructured medical reports is time consuming and prone to errors. It creates a significant bottleneck in clinical workflows. Despite advancements in AI-generated radiology reports, challenges remain in achieving detailed and accurate report generation. In this study we have evaluated different combinations of multimodal models that integrate Computer Vision and Natural Language Processing to generate comprehensive radiology reports. We employed a pretrained Vision Transformer (ViT-B16) and a SWIN Transformer as the image encoders. The BART and GPT-2 models serve as the textual decoders. We used Chest X-ray images and reports from the IU-Xray dataset to evaluate the usability of the SWIN Transformer-BART, SWIN Transformer-GPT-2, ViT-B16-BART and ViT-B16-GPT-2 models for report generation. We aimed at finding the best combination among the models. The SWIN-BART model performs as the best-performing model among the four models achieving remarkable results in almost all the evaluation metrics like ROUGE, BLEU and BERTScore.

Artificial writing is permeating our lives due to recent advances in large-scale, transformer-based language models (LMs) such as BERT, its variants, GPT-2/3, and others. Using them as pre-trained models and fine-tuning them for specific tasks, researchers have extended state of the art for many NLP tasks and shown that they capture not only linguistic knowledge but also retain general knowledge implicitly present in the data. Unfortunately, LMs trained on unfiltered text corpora suffer from degenerated and biased behaviour. While this is well established, we show that recent LMs also contain human-like biases of what is right and wrong to do, some form of ethical and moral norms of the society -- they bring a "moral direction" to surface. That is, we show that these norms can be captured geometrically by a direction, which can be computed, e.g., by a PCA, in the embedding space, reflecting well the agreement of phrases to social norms implicitly expressed in the training texts and providing a path for attenuating or even preventing toxic degeneration in LMs. Being able to rate the (non-)normativity of arbitrary phrases without explicitly training the LM for this task, we demonstrate the capabilities of the "moral direction" for guiding (even other) LMs towards producing normative text and showcase it on RealToxicityPrompts testbed, preventing the neural toxic degeneration in GPT-2.

In machine learning, generalization against distribution shifts -- where deployment conditions diverge from the training scenarios -- is crucial, particularly in fields like climate modeling, biomedicine, and autonomous driving. The emergence of foundation models, distinguished by their extensive pretraining and task versatility, has led to an increased interest in their adaptability to distribution shifts. GPT-4V(ision) acts as the most advanced publicly accessible multimodal foundation model, with extensive applications across various domains, including anomaly detection, video understanding, image generation, and medical diagnosis. However, its robustness against data distributions remains largely underexplored. Addressing this gap, this study rigorously evaluates GPT-4V's adaptability and generalization capabilities in dynamic environments, benchmarking against prominent models like CLIP and LLaVA. We delve into GPT-4V's zero-shot generalization across 13 diverse datasets spanning natural, medical, and molecular domains. We further investigate its adaptability to controlled data perturbations and examine the efficacy of in-context learning as a tool to enhance its adaptation. Our findings delineate GPT-4V's capability boundaries in distribution shifts, shedding light on its strengths and limitations across various scenarios. Importantly, this investigation contributes to our understanding of how AI foundation models generalize to distribution shifts, offering pivotal insights into their adaptability and robustness. Code is publicly available at https://github.com/jameszhou-gl/gpt-4v-distribution-shift.

Recently, there has been a rise in the development of powerful pre-trained natural language models, including GPT-2, Grover, and XLM. These models have shown state-of-the-art capabilities towards a variety of different NLP tasks, including question answering, content summarisation, and text generation. Alongside this, there have been many studies focused on online authorship attribution (AA). That is, the use of models to identify the authors of online texts. Given the power of natural language models in generating convincing texts, this paper examines the degree to which these language models can generate texts capable of deceiving online AA models. Experimenting with both blog and Twitter data, we utilise GPT-2 language models to generate texts using the existing posts of online users. We then examine whether these AI-based text generators are capable of mimicking authorial style to such a degree that they can deceive typical AA models. From this, we find that current AI-based text generators are able to successfully mimic authorship, showing capabilities towards this on both datasets. Our findings, in turn, highlight the current capacity of powerful natural language models to generate original online posts capable of mimicking authorial style sufficiently to deceive popular AA methods; a key finding given the proposed role of AA in real world applications such as spam-detection and forensic investigation.

We fine-tune GPT-3 to answer long-form questions using a text-based web-browsing environment, which allows the model to search and navigate the web. By setting up the task so that it can be performed by humans, we are able to train models on the task using imitation learning, and then optimize answer quality with human feedback. To make human evaluation of factual accuracy easier, models must collect references while browsing in support of their answers. We train and evaluate our models on ELI5, a dataset of questions asked by Reddit users. Our best model is obtained by fine-tuning GPT-3 using behavior cloning, and then performing rejection sampling against a reward model trained to predict human preferences. This model's answers are preferred by humans 56% of the time to those of our human demonstrators, and 69% of the time to the highest-voted answer from Reddit.

In this empirical article, we introduce INNAprop, an optimization algorithm that combines the INNA method with the RMSprop adaptive gradient scaling. It leverages second-order information and rescaling while keeping the memory requirements of standard DL methods as AdamW or SGD with momentum.After having recalled our geometrical motivations, we provide quite extensive experiments. On image classification (CIFAR-10, ImageNet) and language modeling (GPT-2), INNAprop consistently matches or outperforms AdamW both in training speed and accuracy, with minimal hyperparameter tuning in large-scale settings. Our code is publicly available at https://github.com/innaprop/innaprop.

Automatic Short Answer Grading (ASAG) is the process of grading the student answers by computational approaches given a question and the desired answer. Previous works implemented the methods of concept mapping, facet mapping, and some used the conventional word embeddings for extracting semantic features. They extracted multiple features manually to train on the corresponding datasets. We use pretrained embeddings of the transfer learning models, ELMo, BERT, GPT, and GPT-2 to assess their efficiency on this task. We train with a single feature, cosine similarity, extracted from the embeddings of these models. We compare the RMSE scores and correlation measurements of the four models with previous works on Mohler dataset. Our work demonstrates that ELMo outperformed the other three models. We also, briefly describe the four transfer learning models and conclude with the possible causes of poor results of transfer learning models.

Despite their groundbreaking performance for many generative modeling tasks, diffusion models have fallen short on discrete data domains such as natural language. Crucially, standard diffusion models rely on the well-established theory of score matching, but efforts to generalize this to discrete structures have not yielded the same empirical gains. In this work, we bridge this gap by proposing score entropy, a novel loss that naturally extends score matching to discrete spaces, integrates seamlessly to build discrete diffusion models, and significantly boosts performance. Experimentally, we test our Score Entropy Discrete Diffusion models (SEDD) on standard language modeling tasks. For comparable model sizes, SEDD beats existing language diffusion paradigms (reducing perplexity by 25-75\%) and is competitive with autoregressive models, in particular outperforming GPT-2. Furthermore, compared to autoregressive mdoels, SEDD generates faithful text without requiring distribution annealing techniques like temperature scaling (around 6-8times better generative perplexity than un-annealed GPT-2), can trade compute and quality (similar quality with 32times fewer network evaluations), and enables controllable infilling (matching nucleus sampling quality while enabling other strategies besides left to right prompting).

We classify and re-examine some of the current approaches to improve the performance-computes trade-off of language models, including (1) non-causal models (such as masked language models), (2) extension of batch length with efficient attention, (3) recurrence, (4) conditional computation and (5) retrieval. We identify some limitations (1) - (4) suffer from. For example, (1) currently struggles with open-ended text generation with the output loosely constrained by the input as well as performing general textual tasks like GPT-2/3 due to its need for a specific fine-tuning dataset. (2) and (3) do not improve the prediction of the first sim 10^3 tokens. Scaling up a model size (e.g. efficiently with (4)) still results in poor performance scaling for some tasks. We argue (5) would resolve many of these limitations, and it can (a) reduce the amount of supervision and (b) efficiently extend the context over the entire training dataset and the entire past of the current sample. We speculate how to modify MARGE to perform unsupervised causal modeling that achieves (b) with the retriever jointly trained.

Various XAI attribution methods have been recently proposed for the transformer architecture, allowing for insights into the decision-making process of large language models by assigning importance scores to input tokens and intermediate representations. One class of methods that seems very promising in this direction includes decomposition-based approaches, i.e., XAI-methods that redistribute the model's prediction logit through the network, as this value is directly related to the prediction. In the previous literature we note though that two prominent methods of this category, namely ALTI-Logit and LRP, have not yet been analyzed in juxtaposition and hence we propose to close this gap by conducting a careful quantitative evaluation w.r.t. ground truth annotations on a subject-verb agreement task, as well as various qualitative inspections, using BERT, GPT-2 and LLaMA-3 as a testbed. Along the way we compare and extend the ALTI-Logit and LRP methods, including the recently proposed AttnLRP variant, from an algorithmic and implementation perspective. We further incorporate in our benchmark two widely-used gradient-based attribution techniques. Finally, we make our carefullly constructed benchmark dataset for evaluating attributions on language models, as well as our code, publicly available in order to foster evaluation of XAI-methods on a well-defined common ground.

The recent advances in language modeling significantly improved the generative capabilities of deep neural models: in 2019 OpenAI released GPT-2, a pre-trained language model that can autonomously generate coherent, non-trivial and human-like text samples. Since then, ever more powerful text generative models have been developed. Adversaries can exploit these tremendous generative capabilities to enhance social bots that will have the ability to write plausible deepfake messages, hoping to contaminate public debate. To prevent this, it is crucial to develop deepfake social media messages detection systems. However, to the best of our knowledge no one has ever addressed the detection of machine-generated texts on social networks like Twitter or Facebook. With the aim of helping the research in this detection field, we collected the first dataset of \real deepfake tweets, TweepFake. It is real in the sense that each deepfake tweet was actually posted on Twitter. We collected tweets from a total of 23 bots, imitating 17 human accounts. The bots are based on various generation techniques, i.e., Markov Chains, RNN, RNN+Markov, LSTM, GPT-2. We also randomly selected tweets from the humans imitated by the bots to have an overall balanced dataset of 25,572 tweets (half human and half bots generated). The dataset is publicly available on Kaggle. Lastly, we evaluated 13 deepfake text detection methods (based on various state-of-the-art approaches) to both demonstrate the challenges that Tweepfake poses and create a solid baseline of detection techniques. We hope that TweepFake can offer the opportunity to tackle the deepfake detection on social media messages as well.

Unsupervised pre-training of large neural models has recently revolutionized Natural Language Processing. By warm-starting from the publicly released checkpoints, NLP practitioners have pushed the state-of-the-art on multiple benchmarks while saving significant amounts of compute time. So far the focus has been mainly on the Natural Language Understanding tasks. In this paper, we demonstrate the efficacy of pre-trained checkpoints for Sequence Generation. We developed a Transformer-based sequence-to-sequence model that is compatible with publicly available pre-trained BERT, GPT-2 and RoBERTa checkpoints and conducted an extensive empirical study on the utility of initializing our model, both encoder and decoder, with these checkpoints. Our models result in new state-of-the-art results on Machine Translation, Text Summarization, Sentence Splitting, and Sentence Fusion.

Classifier-Free Guidance (CFG) has recently emerged in text-to-image generation as a lightweight technique to encourage prompt-adherence in generations. In this work, we demonstrate that CFG can be used broadly as an inference-time technique in pure language modeling. We show that CFG (1) improves the performance of Pythia, GPT-2 and LLaMA-family models across an array of tasks: Q\&A, reasoning, code generation, and machine translation, achieving SOTA on LAMBADA with LLaMA-7B over PaLM-540B; (2) brings improvements equivalent to a model with twice the parameter-count; (3) can stack alongside other inference-time methods like Chain-of-Thought and Self-Consistency, yielding further improvements in difficult tasks; (4) can be used to increase the faithfulness and coherence of assistants in challenging form-driven and content-driven prompts: in a human evaluation we show a 75\% preference for GPT4All using CFG over baseline.

Traditional drug design faces significant challenges due to inherent chemical and biological complexities, often resulting in high failure rates in clinical trials. Deep learning advancements, particularly generative models, offer potential solutions to these challenges. One promising algorithm is DrugGPT, a transformer-based model, that generates small molecules for input protein sequences. Although promising, it generates both chemically valid and invalid structures and does not incorporate the features of approved drugs, resulting in time-consuming and inefficient drug discovery. To address these issues, we introduce DrugGen, an enhanced model based on the DrugGPT structure. DrugGen is fine-tuned on approved drug-target interactions and optimized with proximal policy optimization. By giving reward feedback from protein-ligand binding affinity prediction using pre-trained transformers (PLAPT) and a customized invalid structure assessor, DrugGen significantly improves performance. Evaluation across multiple targets demonstrated that DrugGen achieves 100% valid structure generation compared to 95.5% with DrugGPT and produced molecules with higher predicted binding affinities (7.22 [6.30-8.07]) compared to DrugGPT (5.81 [4.97-6.63]) while maintaining diversity and novelty. Docking simulations further validate its ability to generate molecules targeting binding sites effectively. For example, in the case of fatty acid-binding protein 5 (FABP5), DrugGen generated molecules with superior docking scores (FABP5/11, -9.537 and FABP5/5, -8.399) compared to the reference molecule (Palmitic acid, -6.177). Beyond lead compound generation, DrugGen also shows potential for drug repositioning and creating novel pharmacophores for existing targets. By producing high-quality small molecules, DrugGen provides a high-performance medium for advancing pharmaceutical research and drug discovery.

Understanding the world and explaining it with scientific theories is a central aspiration of artificial intelligence research. Proposing theories, designing experiments to test them, and then revising them based on data are fundamental to scientific discovery. Despite the significant promise of LLM-based scientific agents, no benchmarks systematically test LLM's ability to propose scientific models, collect experimental data, and revise them in light of new data. We introduce BoxingGym, a benchmark with 10 environments for systematically evaluating both experimental design (e.g. collecting data to test a scientific theory) and model discovery (e.g. proposing and revising scientific theories). To enable tractable and quantitative evaluation, we implement each environment as a generative probabilistic model with which a scientific agent can run interactive experiments. These probabilistic models are drawn from various real-world scientific domains ranging from psychology to ecology. To quantitatively evaluate a scientific agent's ability to collect informative experimental data, we compute the expected information gain (EIG), an information-theoretic quantity which measures how much an experiment reduces uncertainty about the parameters of a generative model. A good scientific theory is a concise and predictive explanation. Therefore, to quantitatively evaluate model discovery, we ask a scientific agent to explain their model and then assess whether this explanation enables another scientific agent to make reliable predictions about this environment. In addition to this explanation-based evaluation, we compute standard model evaluation metrics such as prediction errors. We find that current LLMs, such as GPT-4o, struggle with both experimental design and model discovery. We find that augmenting the LLM-based agent with an explicit statistical model does not reliably improve these results.

Recent efforts have been dedicated to enhancing time series forecasting accuracy by introducing advanced network architectures and self-supervised pretraining strategies. Nevertheless, existing approaches still exhibit two critical drawbacks. Firstly, these methods often rely on a single dataset for training, limiting the model's generalizability due to the restricted scale of the training data. Secondly, the one-step generation schema is widely followed, which necessitates a customized forecasting head and overlooks the temporal dependencies in the output series, and also leads to increased training costs under different horizon length settings. To address these issues, we propose a novel generative pretrained hierarchical transformer architecture for forecasting, named GPHT. There are two aspects of key designs in GPHT. On the one hand, we advocate for constructing a mixed dataset for pretraining our model, comprising various datasets from diverse data scenarios. This approach significantly expands the scale of training data, allowing our model to uncover commonalities in time series data and facilitating improved transfer to specific datasets. On the other hand, GPHT employs an auto-regressive forecasting approach under the channel-independent assumption, effectively modeling temporal dependencies in the output series. Importantly, no customized forecasting head is required, enabling a single model to forecast at arbitrary horizon settings. We conduct sufficient experiments on eight datasets with mainstream self-supervised pretraining models and supervised models. The results demonstrated that GPHT surpasses the baseline models across various fine-tuning and zero/few-shot learning settings in the traditional long-term forecasting task, providing support for verifying the feasibility of pretrained time series large models.

We introduceGraphGPT, a novel self-supervised generative pre-trained model for graph learning based on the Graph Eulerian Transformer (GET). First, we propose GET, which combines a standard transformer encoder or decoder architecture with an innovative graph-to-sequence transformation method. This method converts graphs or sampled subgraphs into sequences of tokens representing nodes, edges, and attributes in a reversible manner using Eulerian paths. We pre-train GET using either of the two self-supervised tasks: next-token prediction (NTP) and scheduled masked-token prediction (SMTP). The pre-trained model is then fine-tuned for downstream tasks such as graph-, edge-, and node-level prediction. Despite its simplicity, GraphGPT achieves performance comparable to or surpassing state-of-the-art methods on multiple large-scale Open Graph Benchmark (OGB) datasets. It demonstrates exceptional results on the molecular property prediction dataset PCQM4Mv2 and the protein-protein interaction dataset ogbl-ppa. Notably, generative pre-training enables scaling GraphGPT to 2 billion parameters while maintaining performance gains - a breakthrough that overcomes the scalability limitations of traditional Graph Neural Networks (GNNs) and prior graph transformers (GTs). To advance research in graph foundation models and facilitate scientific discovery in chemistry, materials science, and related fields, we will release the source code (https://github.com/alibaba/graph-gpt) and pre-trained checkpoints.

Research in mechanistic interpretability seeks to explain behaviors of machine learning models in terms of their internal components. However, most previous work either focuses on simple behaviors in small models, or describes complicated behaviors in larger models with broad strokes. In this work, we bridge this gap by presenting an explanation for how GPT-2 small performs a natural language task called indirect object identification (IOI). Our explanation encompasses 26 attention heads grouped into 7 main classes, which we discovered using a combination of interpretability approaches relying on causal interventions. To our knowledge, this investigation is the largest end-to-end attempt at reverse-engineering a natural behavior "in the wild" in a language model. We evaluate the reliability of our explanation using three quantitative criteria--faithfulness, completeness and minimality. Though these criteria support our explanation, they also point to remaining gaps in our understanding. Our work provides evidence that a mechanistic understanding of large ML models is feasible, opening opportunities to scale our understanding to both larger models and more complex tasks.

In this paper, we introduce TimeGPT, the first foundation model for time series, capable of generating accurate predictions for diverse datasets not seen during training. We evaluate our pre-trained model against established statistical, machine learning, and deep learning methods, demonstrating that TimeGPT zero-shot inference excels in performance, efficiency, and simplicity. Our study provides compelling evidence that insights from other domains of artificial intelligence can be effectively applied to time series analysis. We conclude that large-scale time series models offer an exciting opportunity to democratize access to precise predictions and reduce uncertainty by leveraging the capabilities of contemporary advancements in deep learning.

Accurately predicting the future would be an important milestone in the capabilities of artificial intelligence. However, research on the ability of large language models to provide probabilistic predictions about future events remains nascent. To empirically test this ability, we enrolled OpenAI's state-of-the-art large language model, GPT-4, in a three-month forecasting tournament hosted on the Metaculus platform. The tournament, running from July to October 2023, attracted 843 participants and covered diverse topics including Big Tech, U.S. politics, viral outbreaks, and the Ukraine conflict. Focusing on binary forecasts, we show that GPT-4's probabilistic forecasts are significantly less accurate than the median human-crowd forecasts. We find that GPT-4's forecasts did not significantly differ from the no-information forecasting strategy of assigning a 50% probability to every question. We explore a potential explanation, that GPT-4 might be predisposed to predict probabilities close to the midpoint of the scale, but our data do not support this hypothesis. Overall, we find that GPT-4 significantly underperforms in real-world predictive tasks compared to median human-crowd forecasts. A potential explanation for this underperformance is that in real-world forecasting tournaments, the true answers are genuinely unknown at the time of prediction; unlike in other benchmark tasks like professional exams or time series forecasting, where strong performance may at least partly be due to the answers being memorized from the training data. This makes real-world forecasting tournaments an ideal environment for testing the generalized reasoning and prediction capabilities of artificial intelligence going forward.

Inverse design of solid-state materials with desired properties represents a formidable challenge in materials science. Although recent generative models have demonstrated potential, their adoption has been hindered by limitations such as inefficiency, architectural constraints and restricted open-source availability. The representation of crystal structures using the SLICES (Simplified Line-Input Crystal-Encoding System) notation as a string of characters enables the use of state-of-the-art natural language processing models, such as Transformers, for crystal design. Drawing inspiration from the success of GPT models in generating coherent text, we trained a generative Transformer on the next-token prediction task to generate solid-state materials with targeted properties. We demonstrate MatterGPT's capability to generate de novo crystal structures with targeted single properties, including both lattice-insensitive (formation energy) and lattice-sensitive (band gap) properties. Furthermore, we extend MatterGPT to simultaneously target multiple properties, addressing the complex challenge of multi-objective inverse design of crystals. Our approach showcases high validity, uniqueness, and novelty in generated structures, as well as the ability to generate materials with properties beyond the training data distribution. This work represents a significant step forward in computational materials discovery, offering a powerful and open tool for designing materials with tailored properties for various applications in energy, electronics, and beyond.

We developed a benchmark set to assess the generalization of state-of-the-art large language models on problems beyond linguistic tasks and evaluate it on a systematic progression of GPT models (GPT-3.5, GPT-4, GPT-4o, GPT-4o-mini). Using simple games like Tic-Tac-Toe, Connect Four, Battleship, and a Shape Recognition Game, all encoded in ASCII, we test strategic capabilities and spatial reasoning, core abilities any artificial intelligence would need to master for solving problems in chemistry. To probe generalization, we introduce two new games for spatial logic: LEGO Connect Language (LCL) and Guess-the-SMILES (GtS), a operationally simple chemistry benchmark. Our results show that GPT models provide meaningful responses for several tasks but, generally, perform poorly. A systematic performance progression with increased model capabilities (GPT-3.5, GPT-4, GPT-4o) is only observed for 4 out of the 7 benchmark tasks. All models consistently struggle with Battleship, LCL, and GtS. This suggests that while GPT models can emulate conversational proficiency and basic rule comprehension, they have limited generalization with respect to strategy and spatial reasoning. Particularly poor performance is observed for interpreting molecular graphs when encoded in ASCII. The results provided by our open-source benchmark suite (https://github.com/BlueVelvetSackOfGoldPotatoes/child-play{ChildPlay GitHub Repository}) caution against claims of emergent intelligence in GPT models, which appear more specialized than general.

We introduce a new family of physics-inspired generative models termed PFGM++ that unifies diffusion models and Poisson Flow Generative Models (PFGM). These models realize generative trajectories for N dimensional data by embedding paths in N{+}D dimensional space while still controlling the progression with a simple scalar norm of the D additional variables. The new models reduce to PFGM when D{=}1 and to diffusion models when D{to}infty. The flexibility of choosing D allows us to trade off robustness against rigidity as increasing D results in more concentrated coupling between the data and the additional variable norms. We dispense with the biased large batch field targets used in PFGM and instead provide an unbiased perturbation-based objective similar to diffusion models. To explore different choices of D, we provide a direct alignment method for transferring well-tuned hyperparameters from diffusion models (D{to} infty) to any finite D values. Our experiments show that models with finite D can be superior to previous state-of-the-art diffusion models on CIFAR-10/FFHQ 64{times}64 datasets, with FID scores of 1.91/2.43 when D{=}2048/128. In class-conditional setting, D{=}2048 yields current state-of-the-art FID of 1.74 on CIFAR-10. In addition, we demonstrate that models with smaller D exhibit improved robustness against modeling errors. Code is available at https://github.com/Newbeeer/pfgmpp

Recent work in scientific machine learning (SciML) has focused on incorporating partial differential equation (PDE) information into the learning process. Much of this work has focused on relatively ``easy'' PDE operators (e.g., elliptic and parabolic), with less emphasis on relatively ``hard'' PDE operators (e.g., hyperbolic). Within numerical PDEs, the latter problem class requires control of a type of volume element or conservation constraint, which is known to be challenging. Delivering on the promise of SciML requires seamlessly incorporating both types of problems into the learning process. To address this issue, we propose ProbConserv, a framework for incorporating conservation constraints into a generic SciML architecture. To do so, ProbConserv combines the integral form of a conservation law with a Bayesian update. We provide a detailed analysis of ProbConserv on learning with the Generalized Porous Medium Equation (GPME), a widely-applicable parameterized family of PDEs that illustrates the qualitative properties of both easier and harder PDEs. ProbConserv is effective for easy GPME variants, performing well with state-of-the-art competitors; and for harder GPME variants it outperforms other approaches that do not guarantee volume conservation. ProbConserv seamlessly enforces physical conservation constraints, maintains probabilistic uncertainty quantification (UQ), and deals well with shocks and heteroscedasticities. In each case, it achieves superior predictive performance on downstream tasks.

Generating novel active molecules for a given protein is an extremely challenging task for generative models that requires an understanding of the complex physical interactions between the molecule and its environment. In this paper, we present a novel generative model, BindGPT which uses a conceptually simple but powerful approach to create 3D molecules within the protein's binding site. Our model produces molecular graphs and conformations jointly, eliminating the need for an extra graph reconstruction step. We pretrain BindGPT on a large-scale dataset and fine-tune it with reinforcement learning using scores from external simulation software. We demonstrate how a single pretrained language model can serve at the same time as a 3D molecular generative model, conformer generator conditioned on the molecular graph, and a pocket-conditioned 3D molecule generator. Notably, the model does not make any representational equivariance assumptions about the domain of generation. We show how such simple conceptual approach combined with pretraining and scaling can perform on par or better than the current best specialized diffusion models, language models, and graph neural networks while being two orders of magnitude cheaper to sample.

Since the introduction of ChatGPT and GPT-4, these models have been tested across a large number of tasks. Their adeptness across domains is evident, but their aptitude in playing games, and specifically their aptitude in the realm of poker has remained unexplored. Poker is a game that requires decision making under uncertainty and incomplete information. In this paper, we put ChatGPT and GPT-4 through the poker test and evaluate their poker skills. Our findings reveal that while both models display an advanced understanding of poker, encompassing concepts like the valuation of starting hands, playing positions and other intricacies of game theory optimal (GTO) poker, both ChatGPT and GPT-4 are NOT game theory optimal poker players. Profitable strategies in poker are evaluated in expectations over large samples. Through a series of experiments, we first discover the characteristics of optimal prompts and model parameters for playing poker with these models. Our observations then unveil the distinct playing personas of the two models. We first conclude that GPT-4 is a more advanced poker player than ChatGPT. This exploration then sheds light on the divergent poker tactics of the two models: ChatGPT's conservativeness juxtaposed against GPT-4's aggression. In poker vernacular, when tasked to play GTO poker, ChatGPT plays like a nit, which means that it has a propensity to only engage with premium hands and folds a majority of hands. When subjected to the same directive, GPT-4 plays like a maniac, showcasing a loose and aggressive style of play. Both strategies, although relatively advanced, are not game theory optimal.

A basic question within the emerging field of mechanistic interpretability is the degree to which neural networks learn the same underlying mechanisms. In other words, are neural mechanisms universal across different models? In this work, we study the universality of individual neurons across GPT2 models trained from different initial random seeds, motivated by the hypothesis that universal neurons are likely to be interpretable. In particular, we compute pairwise correlations of neuron activations over 100 million tokens for every neuron pair across five different seeds and find that 1-5\% of neurons are universal, that is, pairs of neurons which consistently activate on the same inputs. We then study these universal neurons in detail, finding that they usually have clear interpretations and taxonomize them into a small number of neuron families. We conclude by studying patterns in neuron weights to establish several universal functional roles of neurons in simple circuits: deactivating attention heads, changing the entropy of the next token distribution, and predicting the next token to (not) be within a particular set.

We investigate the potential of GPT-4~gpt4 to perform Neural Architecture Search (NAS) -- the task of designing effective neural architectures. Our proposed approach, GPT-4 Enhanced Neural archItectUre Search (GENIUS), leverages the generative capabilities of GPT-4 as a black-box optimiser to quickly navigate the architecture search space, pinpoint promising candidates, and iteratively refine these candidates to improve performance. We assess GENIUS across several benchmarks, comparing it with existing state-of-the-art NAS techniques to illustrate its effectiveness. Rather than targeting state-of-the-art performance, our objective is to highlight GPT-4's potential to assist research on a challenging technical problem through a simple prompting scheme that requires relatively limited domain expertiseCode available at \href{https://github.com/mingkai-zheng/GENIUS{https://github.com/mingkai-zheng/GENIUS}.}. More broadly, we believe our preliminary results point to future research that harnesses general purpose language models for diverse optimisation tasks. We also highlight important limitations to our study, and note implications for AI safety.

We present a novel stochastic variational Gaussian process (GP) inference method, based on a posterior over a learnable set of weighted pseudo input-output points (coresets). Instead of a free-form variational family, the proposed coreset-based, variational tempered family for GPs (CVTGP) is defined in terms of the GP prior and the data-likelihood; hence, accommodating the modeling inductive biases. We derive CVTGP's lower bound for the log-marginal likelihood via marginalization of the proposed posterior over latent GP coreset variables, and show it is amenable to stochastic optimization. CVTGP reduces the learnable parameter size to O(M), enjoys numerical stability, and maintains O(M^3) time- and O(M^2) space-complexity, by leveraging a coreset-based tempered posterior that, in turn, provides sparse and explainable representations of the data. Results on simulated and real-world regression problems with Gaussian observation noise validate that CVTGP provides better evidence lower-bound estimates and predictive root mean squared error than alternative stochastic GP inference methods.

Diffusion models have recently exhibited remarkable performance on synthetic data. After a diffusion path is selected, a base model, such as UNet, operates as a denoising autoencoder, primarily predicting noises that need to be eliminated step by step. Consequently, it is crucial to employ a model that aligns with the expected budgets to facilitate superior synthetic performance. In this paper, we meticulously analyze the diffusion model and engineer a base model search approach, denoted "DiffNAS". Specifically, we leverage GPT-4 as a supernet to expedite the search, supplemented with a search memory to enhance the results. Moreover, we employ RFID as a proxy to promptly rank the experimental outcomes produced by GPT-4. We also adopt a rapid-convergence training strategy to boost search efficiency. Rigorous experimentation corroborates that our algorithm can augment the search efficiency by 2 times under GPT-based scenarios, while also attaining a performance of 2.82 with 0.37 improvement in FID on CIFAR10 relative to the benchmark IDDPM algorithm.

To handle the scarcity and heterogeneity of electroencephalography (EEG) data for Brain-Computer Interface (BCI) tasks, and to harness the power of large publicly available data sets, we propose Neuro-GPT, a foundation model consisting of an EEG encoder and a GPT model. The foundation model is pre-trained on a large-scale data set using a self-supervised task that learns how to reconstruct masked EEG segments. We then fine-tune the model on a Motor Imagery Classification task to validate its performance in a low-data regime (9 subjects). Our experiments demonstrate that applying a foundation model can significantly improve classification performance compared to a model trained from scratch, which provides evidence for the generalizability of the foundation model and its ability to address challenges of data scarcity and heterogeneity in EEG. The code is publicly available at github.com/wenhui0206/NeuroGPT.

Large language models (LLMs) such as generative pretrained transformers (GPTs) have shown potential for various commercial applications, but their applicability for materials design remains underexplored. In this article, we introduce AtomGPT, a model specifically developed for materials design based on transformer architectures, to demonstrate the capability for both atomistic property prediction and structure generation. We show that a combination of chemical and structural text descriptions can efficiently predict material properties with accuracy comparable to graph neural network models, including formation energies, electronic bandgaps from two different methods and superconducting transition temperatures. Furthermore, we demonstrate that AtomGPT can generate atomic structures for tasks such as designing new superconductors, with the predictions validated through density functional theory calculations. This work paves the way for leveraging LLMs in forward and inverse materials design, offering an efficient approach to the discovery and optimization of materials.

Procedural Content Generation (PCG) algorithms provide a technique to generate complex and diverse environments in an automated way. However, while generating content with PCG methods is often straightforward, generating meaningful content that reflects specific intentions and constraints remains challenging. Furthermore, many PCG algorithms lack the ability to generate content in an open-ended manner. Recently, Large Language Models (LLMs) have shown to be incredibly effective in many diverse domains. These trained LLMs can be fine-tuned, re-using information and accelerating training for new tasks. In this work, we introduce MarioGPT, a fine-tuned GPT2 model trained to generate tile-based game levels, in our case Super Mario Bros levels. We show that MarioGPT can not only generate diverse levels, but can be text-prompted for controllable level generation, addressing one of the key challenges of current PCG techniques. As far as we know, MarioGPT is the first text-to-level model. We also combine MarioGPT with novelty search, enabling it to generate diverse levels with varying play-style dynamics (i.e. player paths). This combination allows for the open-ended generation of an increasingly diverse range of content.

Energy-based models (EBMs) are known in the Machine Learning community for decades. Since the seminal works devoted to EBMs dating back to the noughties, there have been a lot of efficient methods which solve the generative modelling problem by means of energy potentials (unnormalized likelihood functions). In contrast, the realm of Optimal Transport (OT) and, in particular, neural OT solvers is much less explored and limited by few recent works (excluding WGAN-based approaches which utilize OT as a loss function and do not model OT maps themselves). In our work, we bridge the gap between EBMs and Entropy-regularized OT. We present a novel methodology which allows utilizing the recent developments and technical improvements of the former in order to enrich the latter. From the theoretical perspective, we prove generalization bounds for our technique. In practice, we validate its applicability in toy 2D and image domains. To showcase the scalability, we empower our method with a pre-trained StyleGAN and apply it to high-res AFHQ 512times 512 unpaired I2I translation. For simplicity, we choose simple short- and long-run EBMs as a backbone of our Energy-guided Entropic OT approach, leaving the application of more sophisticated EBMs for future research. Our code is available at: https://github.com/PetrMokrov/Energy-guided-Entropic-OT

Graph generation is a critical task in numerous domains, including molecular design and social network analysis, due to its ability to model complex relationships and structured data. While most modern graph generative models utilize adjacency matrix representations, this work revisits an alternative approach that represents graphs as sequences of node set and edge set. We advocate for this approach due to its efficient encoding of graphs and propose a novel representation. Based on this representation, we introduce the Graph Generative Pre-trained Transformer (G2PT), an auto-regressive model that learns graph structures via next-token prediction. To further exploit G2PT's capabilities as a general-purpose foundation model, we explore fine-tuning strategies for two downstream applications: goal-oriented generation and graph property prediction. We conduct extensive experiments across multiple datasets. Results indicate that G2PT achieves superior generative performance on both generic graph and molecule datasets. Furthermore, G2PT exhibits strong adaptability and versatility in downstream tasks from molecular design to property prediction.

Decoder-only Transformer models such as GPT have demonstrated superior performance in text generation, by autoregressively predicting the next token. However, the performance of GPT is bounded by low compute-to-memory-ratio and high memory access. Throughput-oriented architectures such as GPUs target parallel processing rather than sequential token generation, and are not efficient for GPT acceleration, particularly on-device inference applications. Process-in-memory (PIM) architectures can significantly reduce data movement and provide high computation parallelism, and are promising candidates to accelerate GPT inference. In this work, we propose PIM-GPT that aims to achieve high throughput, high energy efficiency and end-to-end acceleration of GPT inference. PIM-GPT leverages DRAM-based PIM solutions to perform multiply-accumulate (MAC) operations on the DRAM chips, greatly reducing data movement. A compact application-specific integrated chip (ASIC) is designed and synthesized to initiate instructions to PIM chips and support data communication along with necessary arithmetic computations. At the software level, the mapping scheme is designed to maximize data locality and computation parallelism by partitioning a matrix among DRAM channels and banks to utilize all in-bank computation resources concurrently. We develop an event-driven clock-cycle accurate simulator to validate the efficacy of the proposed PIM-GPT architecture. Overall, PIM-GPT achieves 41-137times, 631-1074times speedup and 339-1085times, 890-1632times energy efficiency over GPU and CPU baseline, respectively, on 8 GPT models with up to 1.4 billion parameters.

We propose a new test to measure a text model's multitask accuracy. The test covers 57 tasks including elementary mathematics, US history, computer science, law, and more. To attain high accuracy on this test, models must possess extensive world knowledge and problem solving ability. We find that while most recent models have near random-chance accuracy, the very largest GPT-3 model improves over random chance by almost 20 percentage points on average. However, on every one of the 57 tasks, the best models still need substantial improvements before they can reach expert-level accuracy. Models also have lopsided performance and frequently do not know when they are wrong. Worse, they still have near-random accuracy on some socially important subjects such as morality and law. By comprehensively evaluating the breadth and depth of a model's academic and professional understanding, our test can be used to analyze models across many tasks and to identify important shortcomings.

Can we model non-Euclidean graphs as pure language or even Euclidean vectors while retaining their inherent information? The non-Euclidean property have posed a long term challenge in graph modeling. Despite recent GNN and Graphformer efforts encoding graphs as Euclidean vectors, recovering original graph from the vectors remains a challenge. We introduce GraphsGPT, featuring a Graph2Seq encoder that transforms non-Euclidean graphs into learnable graph words in a Euclidean space, along with a GraphGPT decoder that reconstructs the original graph from graph words to ensure information equivalence. We pretrain GraphsGPT on 100M molecules and yield some interesting findings: (1) Pretrained Graph2Seq excels in graph representation learning, achieving state-of-the-art results on 8/9 graph classification and regression tasks. (2) Pretrained GraphGPT serves as a strong graph generator, demonstrated by its ability to perform both unconditional and conditional graph generation. (3) Graph2Seq+GraphGPT enables effective graph mixup in the Euclidean space, overcoming previously known non-Euclidean challenge. (4) Our proposed novel edge-centric GPT pretraining task is effective in graph fields, underscoring its success in both representation and generation.

Recently, there has been a growing trend of utilizing Large Language Model (LLM) to evaluate the quality of other LLMs. Many studies have employed proprietary close-source models, especially GPT4, as the evaluator. Alternatively, other works have fine-tuned judge models based on open-source LLMs as the evaluator. In this study, we conduct an empirical study of different judge models on their evaluation capability. Our findings indicate that although the fine-tuned judge models achieve high accuracy on in-domain test sets, even surpassing GPT4, they are inherently task-specific classifiers, and their generalizability and fairness severely underperform GPT4.

In recent years, generative pre-trained paradigms such as Large Language Models (LLMs) and Large Vision Models (LVMs) have achieved revolutionary advancements and widespread real-world applications. Particularly, the emergence of pre-trained LLMs-based temporal works, compared to previous deep model approaches, has demonstrated superior generalization and robustness, showcasing the potential of generative pre-trained paradigms as foundation models for time series. However, those LLMs-based works mainly focus on cross-modal research, i.e., leveraging the language capabilities of LLMs in time series contexts. Although they have achieved impressive performance, there still exist the issues of concept drift caused by differences in data distribution and inflexibility caused by misalignment of dimensions. To this end, inspired by recent work on LVMs, we reconsider the paradigm of time series modeling. In this paper, we comprehensively explore, for the first time, the effectiveness and superiority of the Generative Pre-trained Diffusion (GPD) paradigm in real-world multivariate time series forecasting (TSF). Specifically, to mitigate performance bias introduced by sophisticated networks, we propose a straightforward MLP diffusion network for unconditional modeling of time series. Then we employ a zero-shot and tuning-free method to predict (generate) future data using historical data as prompts. The GPD paradigm is established on the time series modality, effectively preventing the phenomenon of concept drift, and enabling flexible forecasting of arbitrary lengths. We demonstrate that the GPD paradigm achieves comprehensive performance and generalization comparable to current SOTA LLM-based and deep model paradigms on mainstream benchmarks and various TSF tasks. Extensive experiments validate the potential of the GPD paradigm and its assistance in future related research.

Understanding how language model performance varies with scale is critical to benchmark and algorithm development. Scaling laws are one approach to building this understanding, but the requirement of training models across many different scales has limited their use. We propose an alternative, observational approach that bypasses model training and instead builds scaling laws from ~80 publically available models. Building a single scaling law from multiple model families is challenging due to large variations in their training compute efficiencies and capabilities. However, we show that these variations are consistent with a simple, generalized scaling law where language model performance is a function of a low-dimensional capability space, and model families only vary in their efficiency in converting training compute to capabilities. Using this approach, we show the surprising predictability of complex scaling phenomena: we show that several emergent phenomena follow a smooth, sigmoidal behavior and are predictable from small models; we show that the agent performance of models such as GPT-4 can be precisely predicted from simpler non-agentic benchmarks; and we show how to predict the impact of post-training interventions like Chain-of-Thought and Self-Consistency as language model capabilities continue to improve.

Sailor2 is a family of cutting-edge multilingual language models for South-East Asian (SEA) languages, available in 1B, 8B, and 20B sizes to suit diverse applications. Building on Qwen2.5, Sailor2 undergoes continuous pre-training on 500B tokens (400B SEA-specific and 100B replay tokens) to support 13 SEA languages while retaining proficiency in Chinese and English. Sailor2-20B model achieves a 50-50 win rate against GPT-4o across SEA languages. We also deliver a comprehensive cookbook on how to develop the multilingual model in an efficient manner, including five key aspects: data curation, pre-training, post-training, model customization and evaluation. We hope that Sailor2 model (Apache 2.0 license) will drive language development in the SEA region, and Sailor2 cookbook will inspire researchers to build more inclusive LLMs for other under-served languages.

We conjecture that hidden state vectors corresponding to individual input tokens encode information sufficient to accurately predict several tokens ahead. More concretely, in this paper we ask: Given a hidden (internal) representation of a single token at position t in an input, can we reliably anticipate the tokens that will appear at positions geq t + 2? To test this, we measure linear approximation and causal intervention methods in GPT-J-6B to evaluate the degree to which individual hidden states in the network contain signal rich enough to predict future hidden states and, ultimately, token outputs. We find that, at some layers, we can approximate a model's output with more than 48% accuracy with respect to its prediction of subsequent tokens through a single hidden state. Finally we present a "Future Lens" visualization that uses these methods to create a new view of transformer states.

The scaling hypothesis motivates the expansion of models past trillions of parameters as a path towards better performance. Recent significant developments, such as GPT-3, have been driven by this conjecture. However, as models scale-up, training them efficiently with backpropagation becomes difficult. Because model, pipeline, and data parallelism distribute parameters and gradients over compute nodes, communication is challenging to orchestrate: this is a bottleneck to further scaling. In this work, we argue that alternative training methods can mitigate these issues, and can inform the design of extreme-scale training hardware. Indeed, using a synaptically asymmetric method with a parallelizable backward pass, such as Direct Feedback Alignement, communication needs are drastically reduced. We present a photonic accelerator for Direct Feedback Alignment, able to compute random projections with trillions of parameters. We demonstrate our system on benchmark tasks, using both fully-connected and graph convolutional networks. Our hardware is the first architecture-agnostic photonic co-processor for training neural networks. This is a significant step towards building scalable hardware, able to go beyond backpropagation, and opening new avenues for deep learning.

Latent Gaussian process (GP) models are widely used in neuroscience to uncover hidden state evolutions from sequential observations, mainly in neural activity recordings. While latent GP models provide a principled and powerful solution in theory, the intractable posterior in non-conjugate settings necessitates approximate inference schemes, which may lack scalability. In this work, we propose cvHM, a general inference framework for latent GP models leveraging Hida-Mat\'ern kernels and conjugate computation variational inference (CVI). With cvHM, we are able to perform variational inference of latent neural trajectories with linear time complexity for arbitrary likelihoods. The reparameterization of stationary kernels using Hida-Mat\'ern GPs helps us connect the latent variable models that encode prior assumptions through dynamical systems to those that encode trajectory assumptions through GPs. In contrast to previous work, we use bidirectional information filtering, leading to a more concise implementation. Furthermore, we employ the Whittle approximate likelihood to achieve highly efficient hyperparameter learning.

This paper introduces M^{3}-20M, a large-scale Multi-Modal Molecular dataset that contains over 20 million molecules. Designed to support AI-driven drug design and discovery, M^{3}-20M is 71 times more in the number of molecules than the largest existing dataset, providing an unprecedented scale that can highly benefit training or fine-tuning large (language) models with superior performance for drug design and discovery. This dataset integrates one-dimensional SMILES, two-dimensional molecular graphs, three-dimensional molecular structures, physicochemical properties, and textual descriptions collected through web crawling and generated by using GPT-3.5, offering a comprehensive view of each molecule. To demonstrate the power of M^{3}-20M in drug design and discovery, we conduct extensive experiments on two key tasks: molecule generation and molecular property prediction, using large language models including GLM4, GPT-3.5, and GPT-4. Our experimental results show that M^{3}-20M can significantly boost model performance in both tasks. Specifically, it enables the models to generate more diverse and valid molecular structures and achieve higher property prediction accuracy than the existing single-modal datasets, which validates the value and potential of M^{3}-20M in supporting AI-driven drug design and discovery. The dataset is available at https://github.com/bz99bz/M-3.

A model involving Gaussian processes (GPs) is introduced to simultaneously handle multi-task learning, clustering, and prediction for multiple functional data. This procedure acts as a model-based clustering method for functional data as well as a learning step for subsequent predictions for new tasks. The model is instantiated as a mixture of multi-task GPs with common mean processes. A variational EM algorithm is derived for dealing with the optimisation of the hyper-parameters along with the hyper-posteriors' estimation of latent variables and processes. We establish explicit formulas for integrating the mean processes and the latent clustering variables within a predictive distribution, accounting for uncertainty on both aspects. This distribution is defined as a mixture of cluster-specific GP predictions, which enhances the performances when dealing with group-structured data. The model handles irregular grid of observations and offers different hypotheses on the covariance structure for sharing additional information across tasks. The performances on both clustering and prediction tasks are assessed through various simulated scenarios and real datasets. The overall algorithm, called MagmaClust, is publicly available as an R package.

Bidirectional transformers excel at sentiment analysis, and Large Language Models (LLM) are effective zero-shot learners. Might they perform better as a team? This paper explores collaborative approaches between ELECTRA and GPT-4o for three-way sentiment classification. We fine-tuned (FT) four models (ELECTRA Base/Large, GPT-4o/4o-mini) using a mix of reviews from Stanford Sentiment Treebank (SST) and DynaSent. We provided input from ELECTRA to GPT as: predicted label, probabilities, and retrieved examples. Sharing ELECTRA Base FT predictions with GPT-4o-mini significantly improved performance over either model alone (82.74 macro F1 vs. 79.29 ELECTRA Base FT, 79.52 GPT-4o-mini) and yielded the lowest cost/performance ratio (\0.12/F1 point). However, when GPT models were fine-tuned, including predictions decreased performance. GPT-4o FT-M was the top performer (86.99), with GPT-4o-mini FT close behind (86.77) at much less cost (0.38 vs. \$1.59/F1 point). Our results show that augmenting prompts with predictions from fine-tuned encoders is an efficient way to boost performance, and a fine-tuned GPT-4o-mini is nearly as good as GPT-4o FT at 76% less cost. Both are affordable options for projects with limited resources.

In recent years, graph pre-training has gained significant attention, focusing on acquiring transferable knowledge from unlabeled graph data to improve downstream performance. Despite these recent endeavors, the problem of negative transfer remains a major concern when utilizing graph pre-trained models to downstream tasks. Previous studies made great efforts on the issue of what to pre-train and how to pre-train by designing a variety of graph pre-training and fine-tuning strategies. However, there are cases where even the most advanced "pre-train and fine-tune" paradigms fail to yield distinct benefits. This paper introduces a generic framework W2PGNN to answer the crucial question of when to pre-train (i.e., in what situations could we take advantage of graph pre-training) before performing effortful pre-training or fine-tuning. We start from a new perspective to explore the complex generative mechanisms from the pre-training data to downstream data. In particular, W2PGNN first fits the pre-training data into graphon bases, each element of graphon basis (i.e., a graphon) identifies a fundamental transferable pattern shared by a collection of pre-training graphs. All convex combinations of graphon bases give rise to a generator space, from which graphs generated form the solution space for those downstream data that can benefit from pre-training. In this manner, the feasibility of pre-training can be quantified as the generation probability of the downstream data from any generator in the generator space. W2PGNN offers three broad applications: providing the application scope of graph pre-trained models, quantifying the feasibility of pre-training, and assistance in selecting pre-training data to enhance downstream performance. We provide a theoretically sound solution for the first application and extensive empirical justifications for the latter two applications.

Circuit analysis of any certain model behavior is a central task in mechanistic interpretability. We introduce our circuit discovery pipeline with Sparse Autoencoders (SAEs) and a variant called Transcoders. With these two modules inserted into the model, the model's computation graph with respect to OV and MLP circuits becomes strictly linear. Our methods do not require linear approximation to compute the causal effect of each node. This fine-grained graph identifies both end-to-end and local circuits accounting for either logits or intermediate features. We can scalably apply this pipeline with a technique called Hierarchical Attribution. We analyze three kinds of circuits in GPT-2 Small: bracket, induction, and Indirect Object Identification circuits. Our results reveal new findings underlying existing discoveries.

We introduce GPT-NeoX-20B, a 20 billion parameter autoregressive language model trained on the Pile, whose weights will be made freely and openly available to the public through a permissive license. It is, to the best of our knowledge, the largest dense autoregressive model that has publicly available weights at the time of submission. In this work, we describe 's architecture and training and evaluate its performance on a range of language-understanding, mathematics, and knowledge-based tasks. We find that GPT-NeoX-20B is a particularly powerful few-shot reasoner and gains far more in performance when evaluated five-shot than similarly sized GPT-3 and FairSeq models. We open-source the training and evaluation code, as well as the model weights, at https://github.com/EleutherAI/gpt-neox.

Genomic language models (gLMs) have shown mostly modest success in identifying evolutionarily constrained elements in mammalian genomes. To address this issue, we introduce a novel framework for training gLMs that explicitly models nucleotide evolution on phylogenetic trees using multispecies whole-genome alignments. Our approach integrates an alignment into the loss function during training but does not require it for making predictions, thereby enhancing the model's applicability. We applied this framework to train PhyloGPN, a model that excels at predicting functionally disruptive variants from a single sequence alone and demonstrates strong transfer learning capabilities.

Multi-center positron emission tomography (PET) image synthesis aims at recovering low-dose PET images from multiple different centers. The generalizability of existing methods can still be suboptimal for a multi-center study due to domain shifts, which result from non-identical data distribution among centers with different imaging systems/protocols. While some approaches address domain shifts by training specialized models for each center, they are parameter inefficient and do not well exploit the shared knowledge across centers. To address this, we develop a generalist model that shares architecture and parameters across centers to utilize the shared knowledge. However, the generalist model can suffer from the center interference issue, i.e. the gradient directions of different centers can be inconsistent or even opposite owing to the non-identical data distribution. To mitigate such interference, we introduce a novel dynamic routing strategy with cross-layer connections that routes data from different centers to different experts. Experiments show that our generalist model with dynamic routing (DRMC) exhibits excellent generalizability across centers. Code and data are available at: https://github.com/Yaziwel/Multi-Center-PET-Image-Synthesis.

Foundation models applied to bio-molecular space hold promise to accelerate drug discovery. Molecular representation is key to building such models. Previous works have typically focused on a single representation or view of the molecules. Here, we develop a multi-view foundation model approach, that integrates molecular views of graph, image and text. Single-view foundation models are each pre-trained on a dataset of up to 200M molecules and then aggregated into combined representations. Our multi-view model is validated on a diverse set of 18 tasks, encompassing ligand-protein binding, molecular solubility, metabolism and toxicity. We show that the multi-view models perform robustly and are able to balance the strengths and weaknesses of specific views. We then apply this model to screen compounds against a large (>100 targets) set of G Protein-Coupled receptors (GPCRs). From this library of targets, we identify 33 that are related to Alzheimer's disease. On this subset, we employ our model to identify strong binders, which are validated through structure-based modeling and identification of key binding motifs.

We report the development of GPT-4, a large-scale, multimodal model which can accept image and text inputs and produce text outputs. While less capable than humans in many real-world scenarios, GPT-4 exhibits human-level performance on various professional and academic benchmarks, including passing a simulated bar exam with a score around the top 10% of test takers. GPT-4 is a Transformer-based model pre-trained to predict the next token in a document. The post-training alignment process results in improved performance on measures of factuality and adherence to desired behavior. A core component of this project was developing infrastructure and optimization methods that behave predictably across a wide range of scales. This allowed us to accurately predict some aspects of GPT-4's performance based on models trained with no more than 1/1,000th the compute of GPT-4.

Quantizing the weights of large language models (LLMs) from 16-bit to lower bitwidth is the de facto approach to deploy massive transformers onto more affordable accelerators. GPTQ emerged as one of the standard methods for one-shot post-training quantization at LLM scale. Yet, its inner workings are described as a sequence of ad-hoc algebraic updates that obscure any geometric meaning or worst-case guarantees. In this work, we show that, when executed back-to-front (from the last to first dimension) for a linear layer, GPTQ is mathematically identical to Babai's nearest plane algorithm for the classical closest vector problem (CVP) on a lattice defined by the Hessian matrix of the layer's inputs. This equivalence is based on a sophisticated mathematical argument, and has two analytical consequences: (i) the GPTQ error propagation step gains an intuitive geometric interpretation; (ii) GPTQ inherits the error upper bound of Babai's algorithm under the no-clipping condition. Taken together, these results place GPTQ on firm theoretical footing and open the door to importing decades of progress in lattice algorithms towards the design of future quantization algorithms for billion-parameter models.

Graph generation has been dominated by autoregressive models due to their simplicity and effectiveness, despite their sensitivity to ordering. Yet diffusion models have garnered increasing attention, as they offer comparable performance while being permutation-invariant. Current graph diffusion models generate graphs in a one-shot fashion, but they require extra features and thousands of denoising steps to achieve optimal performance. We introduce PARD, a Permutation-invariant Auto Regressive Diffusion model that integrates diffusion models with autoregressive methods. PARD harnesses the effectiveness and efficiency of the autoregressive model while maintaining permutation invariance without ordering sensitivity. Specifically, we show that contrary to sets, elements in a graph are not entirely unordered and there is a unique partial order for nodes and edges. With this partial order, PARD generates a graph in a block-by-block, autoregressive fashion, where each block's probability is conditionally modeled by a shared diffusion model with an equivariant network. To ensure efficiency while being expressive, we further propose a higher-order graph transformer, which integrates transformer with PPGN. Like GPT, we extend the higher-order graph transformer to support parallel training of all blocks. Without any extra features, PARD achieves state-of-the-art performance on molecular and non-molecular datasets, and scales to large datasets like MOSES containing 1.9M molecules.

The remarkable mechanical properties of spider silk, including its tensile strength and extensibility, are primarily governed by the repetitive regions of the proteins that constitute the fiber, the major ampullate spidroins (MaSps). However, establishing correlations between mechanical characteristics and repeat sequences is challenging due to the intricate sequence-structure-function relationships of MaSps and the limited availability of annotated datasets. In this study, we present a novel computational framework for designing MaSp repeat sequences with customizable mechanical properties. To achieve this, we developed a lightweight GPT-based generative model by distilling the pre-trained ProtGPT2 protein language model. The distilled model was subjected to multilevel fine-tuning using curated subsets of the Spider Silkome dataset. Specifically, we adapt the model for MaSp repeat generation using 6,000 MaSp repeat sequences and further refine it with 572 repeats associated with experimentally determined fiber-level mechanical properties. Our model generates biologically plausible MaSp repeat regions tailored to specific mechanical properties while also predicting those properties for given sequences. Validation includes sequence-level analysis, assessing physicochemical attributes and expected distribution of key motifs as well as secondary structure compositions. A correlation study using BLAST on the Spider Silkome dataset and a test set of MaSp repeats with known mechanical properties further confirmed the predictive accuracy of the model. This framework advances the rational design of spider silk-inspired biomaterials, offering a versatile tool for engineering protein sequences with tailored mechanical attributes.

Large Language Models (LLMs) are increasingly being used to simulate human-like decision making in agent-based financial market models (ABMs). As models become more powerful and accessible, researchers can now incorporate individual LLM decisions into ABM environments. However, integration may introduce inherent biases that need careful evaluation. In this paper we test three state-of-the-art GPT models for bias using two model sampling approaches: one-shot and few-shot API queries. We observe significant variations in distributions of outputs between specific models, and model sub versions, with GPT-4o-Mini-2024-07-18 showing notably better performance (32-43% yes responses) compared to GPT-4-0125-preview's extreme bias (98-99% yes responses). We show that sampling methods and model sub-versions significantly impact results: repeated independent API calls produce different distributions compared to batch sampling within a single call. While no current GPT model can simultaneously achieve a uniform distribution and Markovian properties in one-shot testing, few-shot sampling can approach uniform distributions under certain conditions. We explore the Temperature parameter, providing a definition and comparative results. We further compare our results to true random binary series and test specifically for the common human bias of Negative Recency - finding LLMs have a mixed ability to 'beat' humans in this one regard. These findings emphasise the critical importance of careful LLM integration into ABMs for financial markets and more broadly.

Through considerable effort and intuition, several recent works have reverse-engineered nontrivial behaviors of transformer models. This paper systematizes the mechanistic interpretability process they followed. First, researchers choose a metric and dataset that elicit the desired model behavior. Then, they apply activation patching to find which abstract neural network units are involved in the behavior. By varying the dataset, metric, and units under investigation, researchers can understand the functionality of each component. We automate one of the process' steps: to identify the circuit that implements the specified behavior in the model's computational graph. We propose several algorithms and reproduce previous interpretability results to validate them. For example, the ACDC algorithm rediscovered 5/5 of the component types in a circuit in GPT-2 Small that computes the Greater-Than operation. ACDC selected 68 of the 32,000 edges in GPT-2 Small, all of which were manually found by previous work. Our code is available at https://github.com/ArthurConmy/Automatic-Circuit-Discovery.

Score-based generative models (SGMs) are a powerful class of generative models that exhibit remarkable empirical performance. Score-based generative modelling (SGM) consists of a ``noising'' stage, whereby a diffusion is used to gradually add Gaussian noise to data, and a generative model, which entails a ``denoising'' process defined by approximating the time-reversal of the diffusion. Existing SGMs assume that data is supported on a Euclidean space, i.e. a manifold with flat geometry. In many domains such as robotics, geoscience or protein modelling, data is often naturally described by distributions living on Riemannian manifolds and current SGM techniques are not appropriate. We introduce here Riemannian Score-based Generative Models (RSGMs), a class of generative models extending SGMs to Riemannian manifolds. We demonstrate our approach on a variety of manifolds, and in particular with earth and climate science spherical data.

Widely used alignment techniques, such as reinforcement learning from human feedback (RLHF), rely on the ability of humans to supervise model behavior - for example, to evaluate whether a model faithfully followed instructions or generated safe outputs. However, future superhuman models will behave in complex ways too difficult for humans to reliably evaluate; humans will only be able to weakly supervise superhuman models. We study an analogy to this problem: can weak model supervision elicit the full capabilities of a much stronger model? We test this using a range of pretrained language models in the GPT-4 family on natural language processing (NLP), chess, and reward modeling tasks. We find that when we naively finetune strong pretrained models on labels generated by a weak model, they consistently perform better than their weak supervisors, a phenomenon we call weak-to-strong generalization. However, we are still far from recovering the full capabilities of strong models with naive finetuning alone, suggesting that techniques like RLHF may scale poorly to superhuman models without further work. We find that simple methods can often significantly improve weak-to-strong generalization: for example, when finetuning GPT-4 with a GPT-2-level supervisor and an auxiliary confidence loss, we can recover close to GPT-3.5-level performance on NLP tasks. Our results suggest that it is feasible to make empirical progress today on a fundamental challenge of aligning superhuman models.

Medical language models (MLMs) have become pivotal in advancing medical natural language processing. However, prior models that rely on pre-training or supervised fine-tuning often exhibit low data efficiency and limited practicality in real-world clinical applications. While OpenAIs O1 highlights test-time scaling in mathematics, attempts to replicate this approach in medicine typically distill responses from GPT-series models to open-source models, focusing primarily on multiple-choice tasks. This strategy, though straightforward, neglects critical concerns like data privacy and realistic deployment in clinical settings. In this work, we present a deployable, small-scale medical language model, \mone, designed for long-chain reasoning in clinical tasks using a self-evolution paradigm. Starting with a seed dataset of around 8,000 instances spanning five domains and 16 datasets, we prompt a base policy model to perform Monte Carlo Tree Search (MCTS) to construct verifiable reasoning chains. Each reasoning step is assigned an evolution rollout value, allowing verified trajectories to train the policy model and the reward model. During inference, the policy model generates multiple responses, and the reward model selects the one with the highest reward score. Experiments on eleven evaluation datasets demonstrate that \mone outperforms prior open-source models by 2 points, with the addition of the reward model further boosting performance (sim13 points), surpassing GPT-4o-mini. Code and data are available at https://github.com/pixas/MedSSS.

Transformer-based models trained on large and general purpose datasets consisting of molecular strings have recently emerged as a powerful tool for successfully modeling various structure-property relations. Inspired by this success, we extend the paradigm of training chemical language transformers on large-scale chemical datasets to generative tasks in this work. Specifically, we propose GP-MoLFormer, an autoregressive molecular string generator that is trained on more than 1.1B (billion) chemical SMILES. GP-MoLFormer uses a 46.8M parameter transformer decoder model with linear attention and rotary positional encodings as the base architecture. GP-MoLFormer's utility is evaluated and compared with that of existing baselines on three different tasks: de novo generation, scaffold-constrained molecular decoration, and unconstrained property-guided optimization. While the first two are handled with no additional training, we propose a parameter-efficient fine-tuning method for the last task, which uses property-ordered molecular pairs as input. We call this new approach pair-tuning. Our results show GP-MoLFormer performs better or comparable with baselines across all three tasks, demonstrating its general utility for a variety of molecular generation tasks. We further report strong memorization of training data in GP-MoLFormer generations, which has so far remained unexplored for chemical language models. Our analyses reveal that training data memorization and novelty in generations are impacted by the quality and scale of the training data; duplication bias in training data can enhance memorization at the cost of lowering novelty. We further establish a scaling law relating inference compute and novelty in generations.

Large Language Models (LLMs) are transforming society and permeating into diverse applications. As a result, LLMs will frequently interact with us and other agents. It is, therefore, of great societal value to understand how LLMs behave in interactive social settings. Here, we propose to use behavioral game theory to study LLM's cooperation and coordination behavior. To do so, we let different LLMs (GPT-3, GPT-3.5, and GPT-4) play finitely repeated games with each other and with other, human-like strategies. Our results show that LLMs generally perform well in such tasks and also uncover persistent behavioral signatures. In a large set of two players-two strategies games, we find that LLMs are particularly good at games where valuing their own self-interest pays off, like the iterated Prisoner's Dilemma family. However, they behave sub-optimally in games that require coordination. We, therefore, further focus on two games from these distinct families. In the canonical iterated Prisoner's Dilemma, we find that GPT-4 acts particularly unforgivingly, always defecting after another agent has defected only once. In the Battle of the Sexes, we find that GPT-4 cannot match the behavior of the simple convention to alternate between options. We verify that these behavioral signatures are stable across robustness checks. Finally, we show how GPT-4's behavior can be modified by providing further information about the other player as well as by asking it to predict the other player's actions before making a choice. These results enrich our understanding of LLM's social behavior and pave the way for a behavioral game theory for machines.

Gaussian process state-space models (GPSSMs) provide a principled and flexible approach to modeling the dynamics of a latent state, which is observed at discrete-time points via a likelihood model. However, inference in GPSSMs is computationally and statistically challenging due to the large number of latent variables in the model and the strong temporal dependencies between them. In this paper, we propose a new method for inference in Bayesian GPSSMs, which overcomes the drawbacks of previous approaches, namely over-simplified assumptions, and high computational requirements. Our method is based on free-form variational inference via stochastic gradient Hamiltonian Monte Carlo within the inducing-variable formalism. Furthermore, by exploiting our proposed variational distribution, we provide a collapsed extension of our method where the inducing variables are marginalized analytically. We also showcase results when combining our framework with particle MCMC methods. We show that, on six real-world datasets, our approach can learn transition dynamics and latent states more accurately than competing methods.

Scaling up Large Language Model(LLM) training involves fitting a tremendous amount of training parameters across a limited number of workers. However, methods like ZeRO-3 that drastically reduce GPU memory pressure often incur heavy communication to ensure global synchronization and consistency. Established efforts such as ZeRO++ use secondary partitions to avoid inter-node communications, given that intra-node GPU-GPU transfer generally has more bandwidth and lower latency than inter-node connections. However, as more capable infrastructure like Frontier, equipped with AMD GPUs, emerged with impressive computing capability, there is a need for investigations on the hardware topology and to develop targeted strategies to improve training efficiency. In this work, we propose a collection of communication and optimization strategies for ZeRO++ to reduce communication costs and improve memory utilization. In this paper, we propose a 3-level hierarchical partitioning specifically for the current Top-1 supercomputing cluster, Frontier, which aims at leveraging various bandwidths across layers of communications (GCD-GCD, GPU-GPU, and inter-node) to reduce communication overhead. For a 20B GPT model, we observe a 1.71x increase in TFLOPS per GPU when compared with ZeRO++ up to 384 GCDs and a scaling efficiency of 0.94 for up to 384 GCDs. To the best of our knowledge, our work is also the first effort to efficiently optimize LLM workloads on Frontier AMD GPUs.

Generalist foundation models such as GPT-4 have displayed surprising capabilities in a wide variety of domains and tasks. Yet, there is a prevalent assumption that they cannot match specialist capabilities of fine-tuned models. For example, most explorations to date on medical competency benchmarks have leveraged domain-specific training, as exemplified by efforts on BioGPT and Med-PaLM. We build on a prior study of GPT-4's capabilities on medical challenge benchmarks in the absence of special training. Rather than using simple prompting to highlight the model's out-of-the-box capabilities, we perform a systematic exploration of prompt engineering. We find that prompting innovation can unlock deeper specialist capabilities and show that GPT-4 easily tops prior leading results for medical benchmarks. The prompting methods we explore are general purpose, and make no specific use of domain expertise, removing the need for expert-curated content. Our experimental design carefully controls for overfitting during the prompt engineering process. We introduce Medprompt, based on a composition of several prompting strategies. With Medprompt, GPT-4 achieves state-of-the-art results on all nine of the benchmark datasets in the MultiMedQA suite. The method outperforms leading specialist models such as Med-PaLM 2 by a significant margin with an order of magnitude fewer calls to the model. Steering GPT-4 with Medprompt achieves a 27% reduction in error rate on the MedQA dataset over the best methods to date achieved with specialist models and surpasses a score of 90% for the first time. Beyond medical problems, we show the power of Medprompt to generalize to other domains and provide evidence for the broad applicability of the approach via studies of the strategy on exams in electrical engineering, machine learning, philosophy, accounting, law, nursing, and clinical psychology.

In their recent Nature Human Behaviour paper, "Emergent analogical reasoning in large language models," (Webb, Holyoak, and Lu, 2023) the authors argue that "large language models such as GPT-3 have acquired an emergent ability to find zero-shot solutions to a broad range of analogy problems." In this response, we provide counterexamples of the letter string analogies. In our tests, GPT-3 fails to solve even the easiest variants of the problems presented in the original paper. Zero-shot reasoning is an extraordinary claim that requires extraordinary evidence. We do not see that evidence in our experiments. To strengthen claims of humanlike reasoning such as zero-shot reasoning, it is important that the field develop approaches that rule out data memorization.

Large Language Models (LLMs) have shown remarkable aptitude in code generation but still struggle on challenging programming tasks. Self-repair -- in which the model debugs and fixes mistakes in its own code -- has recently become a popular way to boost performance in these settings. However, only very limited studies on how and when self-repair works effectively exist in the literature, and one might wonder to what extent a model is really capable of providing accurate feedback on why the code is wrong when that code was generated by the same model. In this paper, we analyze GPT-3.5 and GPT-4's ability to perform self-repair on APPS, a challenging dataset consisting of diverse coding challenges. To do so, we first establish a new evaluation strategy dubbed pass@t that measures the pass rate of the tasks against the total number of tokens sampled from the model, enabling a fair comparison to purely sampling-based approaches. With this evaluation strategy, we find that the effectiveness of self-repair is only seen in GPT-4. We also observe that self-repair is bottlenecked by the feedback stage; using GPT-4 to give feedback on the programs generated by GPT-3.5 and using expert human programmers to give feedback on the programs generated by GPT-4, we unlock significant performance gains.

Machine learning models are increasingly being scaled in both sequence length and model dimension to reach longer contexts and better performance. However, existing architectures such as Transformers scale quadratically along both these axes. We ask: are there performant architectures that can scale sub-quadratically along sequence length and model dimension? We introduce Monarch Mixer (M2), a new architecture that uses the same sub-quadratic primitive along both sequence length and model dimension: Monarch matrices, a simple class of expressive structured matrices that captures many linear transforms, achieves high hardware efficiency on GPUs, and scales sub-quadratically. As a proof of concept, we explore the performance of M2 in three domains: non-causal BERT-style language modeling, ViT-style image classification, and causal GPT-style language modeling. For non-causal BERT-style modeling, M2 matches BERT-base and BERT-large in downstream GLUE quality with up to 27% fewer parameters, and achieves up to 9.1times higher throughput at sequence length 4K. On ImageNet, M2 outperforms ViT-b by 1% in accuracy, with only half the parameters. Causal GPT-style models introduce a technical challenge: enforcing causality via masking introduces a quadratic bottleneck. To alleviate this bottleneck, we develop a novel theoretical view of Monarch matrices based on multivariate polynomial evaluation and interpolation, which lets us parameterize M2 to be causal while remaining sub-quadratic. Using this parameterization, M2 matches GPT-style Transformers at 360M parameters in pretraining perplexity on The PILE--showing for the first time that it may be possible to match Transformer quality without attention or MLPs.

Optimal transport (OT) theory focuses, among all maps T:R^drightarrow R^d that can morph a probability measure onto another, on those that are the ``thriftiest'', i.e. such that the averaged cost c(x, T(x)) between x and its image T(x) be as small as possible. Many computational approaches have been proposed to estimate such Monge maps when c is the ell_2^2 distance, e.g., using entropic maps [Pooladian'22], or neural networks [Makkuva'20, Korotin'20]. We propose a new model for transport maps, built on a family of translation invariant costs c(x, y):=h(x-y), where h:=1{2}|cdot|_2^2+tau and tau is a regularizer. We propose a generalization of the entropic map suitable for h, and highlight a surprising link tying it with the Bregman centroids of the divergence D_h generated by h, and the proximal operator of tau. We show that choosing a sparsity-inducing norm for tau results in maps that apply Occam's razor to transport, in the sense that the displacement vectors Delta(x):= T(x)-x they induce are sparse, with a sparsity pattern that varies depending on x. We showcase the ability of our method to estimate meaningful OT maps for high-dimensional single-cell transcription data, in the 34000-d space of gene counts for cells, without using dimensionality reduction, thus retaining the ability to interpret all displacements at the gene level.

We show that a GPT-3 model can learn to express uncertainty about its own answers in natural language -- without use of model logits. When given a question, the model generates both an answer and a level of confidence (e.g. "90% confidence" or "high confidence"). These levels map to probabilities that are well calibrated. The model also remains moderately calibrated under distribution shift, and is sensitive to uncertainty in its own answers, rather than imitating human examples. To our knowledge, this is the first time a model has been shown to express calibrated uncertainty about its own answers in natural language. For testing calibration, we introduce the CalibratedMath suite of tasks. We compare the calibration of uncertainty expressed in words ("verbalized probability") to uncertainty extracted from model logits. Both kinds of uncertainty are capable of generalizing calibration under distribution shift. We also provide evidence that GPT-3's ability to generalize calibration depends on pre-trained latent representations that correlate with epistemic uncertainty over its answers.

With LLMs shifting their role from statistical modeling of language to serving as general-purpose AI agents, how should LLM evaluations change? Arguably, a key ability of an AI agent is to flexibly combine, as needed, the basic skills it has learned. The capability to combine skills plays an important role in (human) pedagogy and also in a paper on emergence phenomena (Arora & Goyal, 2023). This work introduces Skill-Mix, a new evaluation to measure ability to combine skills. Using a list of N skills the evaluator repeatedly picks random subsets of k skills and asks the LLM to produce text combining that subset of skills. Since the number of subsets grows like N^k, for even modest k this evaluation will, with high probability, require the LLM to produce text significantly different from any text in the training set. The paper develops a methodology for (a) designing and administering such an evaluation, and (b) automatic grading (plus spot-checking by humans) of the results using GPT-4 as well as the open LLaMA-2 70B model. Administering a version of to popular chatbots gave results that, while generally in line with prior expectations, contained surprises. Sizeable differences exist among model capabilities that are not captured by their ranking on popular LLM leaderboards ("cramming for the leaderboard"). Furthermore, simple probability calculations indicate that GPT-4's reasonable performance on k=5 is suggestive of going beyond "stochastic parrot" behavior (Bender et al., 2021), i.e., it combines skills in ways that it had not seen during training. We sketch how the methodology can lead to a Skill-Mix based eco-system of open evaluations for AI capabilities of future models.

This study evaluates the performance of ChatGPT variants, GPT-3.5 and GPT-4, both with and without prompt engineering, against solely student work and a mixed category containing both student and GPT-4 contributions in university-level physics coding assignments using the Python language. Comparing 50 student submissions to 50 AI-generated submissions across different categories, and marked blindly by three independent markers, we amassed n = 300 data points. Students averaged 91.9% (SE:0.4), surpassing the highest performing AI submission category, GPT-4 with prompt engineering, which scored 81.1% (SE:0.8) - a statistically significant difference (p = 2.482 times 10^{-10}). Prompt engineering significantly improved scores for both GPT-4 (p = 1.661 times 10^{-4}) and GPT-3.5 (p = 4.967 times 10^{-9}). Additionally, the blinded markers were tasked with guessing the authorship of the submissions on a four-point Likert scale from `Definitely AI' to `Definitely Human'. They accurately identified the authorship, with 92.1% of the work categorized as 'Definitely Human' being human-authored. Simplifying this to a binary `AI' or `Human' categorization resulted in an average accuracy rate of 85.3%. These findings suggest that while AI-generated work closely approaches the quality of university students' work, it often remains detectable by human evaluators.

We give the first efficient algorithm for learning halfspaces in the testable learning model recently defined by Rubinfeld and Vasilyan (2023). In this model, a learner certifies that the accuracy of its output hypothesis is near optimal whenever the training set passes an associated test, and training sets drawn from some target distribution -- e.g., the Gaussian -- must pass the test. This model is more challenging than distribution-specific agnostic or Massart noise models where the learner is allowed to fail arbitrarily if the distributional assumption does not hold. We consider the setting where the target distribution is Gaussian (or more generally any strongly log-concave distribution) in d dimensions and the noise model is either Massart or adversarial (agnostic). For Massart noise, our tester-learner runs in polynomial time and outputs a hypothesis with (information-theoretically optimal) error opt + epsilon for any strongly log-concave target distribution. For adversarial noise, our tester-learner obtains error O(opt) + epsilon in polynomial time when the target distribution is Gaussian; for strongly log-concave distributions, we obtain O(opt) + epsilon in quasipolynomial time. Prior work on testable learning ignores the labels in the training set and checks that the empirical moments of the covariates are close to the moments of the base distribution. Here we develop new tests of independent interest that make critical use of the labels and combine them with the moment-matching approach of Gollakota et al. (2023). This enables us to simulate a variant of the algorithm of Diakonikolas et al. (2020) for learning noisy halfspaces using nonconvex SGD but in the testable learning setting.

Language models show a surprising range of capabilities, but the source of their apparent competence is unclear. Do these networks just memorize a collection of surface statistics, or do they rely on internal representations of the process that generates the sequences they see? We investigate this question by applying a variant of the GPT model to the task of predicting legal moves in a simple board game, Othello. Although the network has no a priori knowledge of the game or its rules, we uncover evidence of an emergent nonlinear internal representation of the board state. Interventional experiments indicate this representation can be used to control the output of the network and create "latent saliency maps" that can help explain predictions in human terms.

Partial differential equations (PDEs) are important tools to model physical systems, and including them into machine learning models is an important way of incorporating physical knowledge. Given any system of linear PDEs with constant coefficients, we propose a family of Gaussian process (GP) priors, which we call EPGP, such that all realizations are exact solutions of this system. We apply the Ehrenpreis-Palamodov fundamental principle, which works like a non-linear Fourier transform, to construct GP kernels mirroring standard spectral methods for GPs. Our approach can infer probable solutions of linear PDE systems from any data such as noisy measurements, or pointwise defined initial and boundary conditions. Constructing EPGP-priors is algorithmic, generally applicable, and comes with a sparse version (S-EPGP) that learns the relevant spectral frequencies and works better for big data sets. We demonstrate our approach on three families of systems of PDE, the heat equation, wave equation, and Maxwell's equations, where we improve upon the state of the art in computation time and precision, in some experiments by several orders of magnitude.

Multiple Sequence Alignment (MSA) plays a pivotal role in unveiling the evolutionary trajectories of protein families. The accuracy of protein structure predictions is often compromised for protein sequences that lack sufficient homologous information to construct high quality MSA. Although various methods have been proposed to generate virtual MSA under these conditions, they fall short in comprehensively capturing the intricate coevolutionary patterns within MSA or require guidance from external oracle models. Here we introduce MSAGPT, a novel approach to prompt protein structure predictions via MSA generative pretraining in the low MSA regime. MSAGPT employs a simple yet effective 2D evolutionary positional encoding scheme to model complex evolutionary patterns. Endowed by this, its flexible 1D MSA decoding framework facilitates zero or few shot learning. Moreover, we demonstrate that leveraging the feedback from AlphaFold2 can further enhance the model capacity via Rejective Fine tuning (RFT) and Reinforcement Learning from AF2 Feedback (RLAF). Extensive experiments confirm the efficacy of MSAGPT in generating faithful virtual MSA to enhance the structure prediction accuracy. The transfer learning capabilities also highlight its great potential for facilitating other protein tasks.

Using the example of configurations generated with the worm algorithm for the two-dimensional Ising model, we propose renormalization group (RG) transformations, inspired by the tensor RG, that can be applied to sets of images. We relate criticality to the logarithmic divergence of the largest principal component. We discuss the changes in link occupation under the RG transformation, suggest ways to obtain data collapse, and compare with the two state tensor RG approximation near the fixed point.

Humans acquire knowledge by observing the external world, but also by introspection. Introspection gives a person privileged access to their current state of mind (e.g., thoughts and feelings) that is not accessible to external observers. Can LLMs introspect? We define introspection as acquiring knowledge that is not contained in or derived from training data but instead originates from internal states. Such a capability could enhance model interpretability. Instead of painstakingly analyzing a model's internal workings, we could simply ask the model about its beliefs, world models, and goals. More speculatively, an introspective model might self-report on whether it possesses certain internal states such as subjective feelings or desires and this could inform us about the moral status of these states. Such self-reports would not be entirely dictated by the model's training data. We study introspection by finetuning LLMs to predict properties of their own behavior in hypothetical scenarios. For example, "Given the input P, would your output favor the short- or long-term option?" If a model M1 can introspect, it should outperform a different model M2 in predicting M1's behavior even if M2 is trained on M1's ground-truth behavior. The idea is that M1 has privileged access to its own behavioral tendencies, and this enables it to predict itself better than M2 (even if M2 is generally stronger). In experiments with GPT-4, GPT-4o, and Llama-3 models (each finetuned to predict itself), we find that the model M1 outperforms M2 in predicting itself, providing evidence for introspection. Notably, M1 continues to predict its behavior accurately even after we intentionally modify its ground-truth behavior. However, while we successfully elicit introspection on simple tasks, we are unsuccessful on more complex tasks or those requiring out-of-distribution generalization.

GPT-3.5 and GPT-4 are the two most widely used large language model (LLM) services. However, when and how these models are updated over time is opaque. Here, we evaluate the March 2023 and June 2023 versions of GPT-3.5 and GPT-4 on four diverse tasks: 1) solving math problems, 2) answering sensitive/dangerous questions, 3) generating code and 4) visual reasoning. We find that the performance and behavior of both GPT-3.5 and GPT-4 can vary greatly over time. For example, GPT-4 (March 2023) was very good at identifying prime numbers (accuracy 97.6%) but GPT-4 (June 2023) was very poor on these same questions (accuracy 2.4%). Interestingly GPT-3.5 (June 2023) was much better than GPT-3.5 (March 2023) in this task. GPT-4 was less willing to answer sensitive questions in June than in March, and both GPT-4 and GPT-3.5 had more formatting mistakes in code generation in June than in March. Overall, our findings shows that the behavior of the same LLM service can change substantially in a relatively short amount of time, highlighting the need for continuous monitoring of LLM quality.

Unified generation of sequence and structure for scientific data (e.g., materials, molecules, proteins) is a critical task. Existing approaches primarily rely on either autoregressive sequence models or diffusion models, each offering distinct advantages and facing notable limitations. Autoregressive models, such as GPT, Llama, and Phi-4, have demonstrated remarkable success in natural language generation and have been extended to multimodal tasks (e.g., image, video, and audio) using advanced encoders like VQ-VAE to represent complex modalities as discrete sequences. However, their direct application to scientific domains is challenging due to the high precision requirements and the diverse nature of scientific data. On the other hand, diffusion models excel at generating high-dimensional scientific data, such as protein, molecule, and material structures, with remarkable accuracy. Yet, their inability to effectively model sequences limits their potential as general-purpose multimodal foundation models. To address these challenges, we propose UniGenX, a unified framework that combines autoregressive next-token prediction with conditional diffusion models. This integration leverages the strengths of autoregressive models to ease the training of conditional diffusion models, while diffusion-based generative heads enhance the precision of autoregressive predictions. We validate the effectiveness of UniGenX on material and small molecule generation tasks, achieving a significant leap in state-of-the-art performance for material crystal structure prediction and establishing new state-of-the-art results for small molecule structure prediction, de novo design, and conditional generation. Notably, UniGenX demonstrates significant improvements, especially in handling long sequences for complex structures, showcasing its efficacy as a versatile tool for scientific data generation.

We propose two approaches to extend the notion of knowledge distillation to Gaussian Process Regression (GPR) and Gaussian Process Classification (GPC); data-centric and distribution-centric. The data-centric approach resembles most current distillation techniques for machine learning, and refits a model on deterministic predictions from the teacher, while the distribution-centric approach, re-uses the full probabilistic posterior for the next iteration. By analyzing the properties of these approaches, we show that the data-centric approach for GPR closely relates to known results for self-distillation of kernel ridge regression and that the distribution-centric approach for GPR corresponds to ordinary GPR with a very particular choice of hyperparameters. Furthermore, we demonstrate that the distribution-centric approach for GPC approximately corresponds to data duplication and a particular scaling of the covariance and that the data-centric approach for GPC requires redefining the model from a Binomial likelihood to a continuous Bernoulli likelihood to be well-specified. To the best of our knowledge, our proposed approaches are the first to formulate knowledge distillation specifically for Gaussian Process models.

Global climate models typically operate at a grid resolution of hundreds of kilometers and fail to resolve atmospheric mesoscale processes, e.g., clouds, precipitation, and gravity waves (GWs). Model representation of these processes and their sources is essential to the global circulation and planetary energy budget, but subgrid scale contributions from these processes are often only approximately represented in models using parameterizations. These parameterizations are subject to approximations and idealizations, which limit their capability and accuracy. The most drastic of these approximations is the "single-column approximation" which completely neglects the horizontal evolution of these processes, resulting in key biases in current climate models. With a focus on atmospheric GWs, we present the first-ever global simulation of atmospheric GW fluxes using machine learning (ML) models trained on the WINDSET dataset to emulate global GW emulation in the atmosphere, as an alternative to traditional single-column parameterizations. Using an Attention U-Net-based architecture trained on globally resolved GW momentum fluxes, we illustrate the importance and effectiveness of global nonlocality, when simulating GWs using data-driven schemes.

Large language models (LLMs) like GPTs, trained on vast datasets, have demonstrated impressive capabilities in language understanding, reasoning, and planning, achieving human-level performance in various tasks. Most studies focus on enhancing these models by training on ever-larger datasets to build more powerful foundation models. While training stronger models is important, enabling models to evolve during inference is equally crucial, a process we refer to as AI self-evolution. Unlike large-scale training, self-evolution may rely on limited data or interactions. Inspired by the columnar organization of the human cerebral cortex, we hypothesize that AI models could develop cognitive abilities and build internal representations through iterative interactions with their environment. To achieve this, models need long-term memory (LTM) to store and manage processed interaction data. LTM supports self-evolution by representing diverse experiences across environments and agents. In this report, we explore AI self-evolution and its potential to enhance models during inference. We examine LTM's role in lifelong learning, allowing models to evolve based on accumulated interactions. We outline the structure of LTM and the systems needed for effective data retention and representation. We also classify approaches for building personalized models with LTM data and show how these models achieve self-evolution through interaction. Using LTM, our multi-agent framework OMNE achieved first place on the GAIA benchmark, demonstrating LTM's potential for AI self-evolution. Finally, we present a roadmap for future research, emphasizing the importance of LTM for advancing AI technology and its practical applications.

For industrial control, developing high-performance controllers with few samples and low technical debt is appealing. Foundation models, possessing rich prior knowledge obtained from pre-training with Internet-scale corpus, have the potential to be a good controller with proper prompts. In this paper, we take HVAC (Heating, Ventilation, and Air Conditioning) building control as an example to examine the ability of GPT-4 (one of the first-tier foundation models) as the controller. To control HVAC, we wrap the task as a language game by providing text including a short description for the task, several selected demonstrations, and the current observation to GPT-4 on each step and execute the actions responded by GPT-4. We conduct series of experiments to answer the following questions: 1)~How well can GPT-4 control HVAC? 2)~How well can GPT-4 generalize to different scenarios for HVAC control? 3) How different parts of the text context affect the performance? In general, we found GPT-4 achieves the performance comparable to RL methods with few samples and low technical debt, indicating the potential of directly applying foundation models to industrial control tasks.

Generating functions, which are widely used in combinatorics and probability theory, encode function values into the coefficients of a polynomial. In this paper, we explore their use as a tractable probabilistic model, and propose probabilistic generating circuits (PGCs) for their efficient representation. PGCs are strictly more expressive efficient than many existing tractable probabilistic models, including determinantal point processes (DPPs), probabilistic circuits (PCs) such as sum-product networks, and tractable graphical models. We contend that PGCs are not just a theoretical framework that unifies vastly different existing models, but also show great potential in modeling realistic data. We exhibit a simple class of PGCs that are not trivially subsumed by simple combinations of PCs and DPPs, and obtain competitive performance on a suite of density estimation benchmarks. We also highlight PGCs' connection to the theory of strongly Rayleigh distributions.

Multi-channel imaging data is a prevalent data format in scientific fields such as astronomy and biology. The structured information and the high dimensionality of these 3-D tensor data makes the analysis an intriguing but challenging topic for statisticians and practitioners. The low-rank scalar-on-tensor regression model, in particular, has received widespread attention and has been re-formulated as a tensor Gaussian Process (Tensor-GP) model with multi-linear kernel in Yu et al. (2018). In this paper, we extend the Tensor-GP model by integrating a dimensionality reduction technique, called tensor contraction, with a Tensor-GP for a scalar-on-tensor regression task with multi-channel imaging data. This is motivated by the solar flare forecasting problem with high dimensional multi-channel imaging data. We first estimate a latent, reduced-size tensor for each data tensor and then apply a multi-linear Tensor-GP on the latent tensor data for prediction. We introduce an anisotropic total-variation regularization when conducting the tensor contraction to obtain a sparse and smooth latent tensor. We then propose an alternating proximal gradient descent algorithm for estimation. We validate our approach via extensive simulation studies and applying it to the solar flare forecasting problem.

Chomsky and others have very directly claimed that large language models (LLMs) are equally capable of learning languages that are possible and impossible for humans to learn. However, there is very little published experimental evidence to support such a claim. Here, we develop a set of synthetic impossible languages of differing complexity, each designed by systematically altering English data with unnatural word orders and grammar rules. These languages lie on an impossibility continuum: at one end are languages that are inherently impossible, such as random and irreversible shuffles of English words, and on the other, languages that may not be intuitively impossible but are often considered so in linguistics, particularly those with rules based on counting word positions. We report on a wide range of evaluations to assess the capacity of GPT-2 small models to learn these uncontroversially impossible languages, and crucially, we perform these assessments at various stages throughout training to compare the learning process for each language. Our core finding is that GPT-2 struggles to learn impossible languages when compared to English as a control, challenging the core claim. More importantly, we hope our approach opens up a productive line of inquiry in which different LLM architectures are tested on a variety of impossible languages in an effort to learn more about how LLMs can be used as tools for these cognitive and typological investigations.

The increasing size of large language models (LLMs) has introduced challenges in their training and inference. Removing model components is perceived as a solution to tackle the large model sizes, however, existing pruning methods solely focus on performance, without considering an essential aspect for the responsible use of LLMs: model fairness. It is crucial to address the fairness of LLMs towards diverse groups, such as women, Black people, LGBTQ+, Jewish communities, among others, as they are being deployed and available to a wide audience. In this work, first, we investigate how attention heads impact fairness and performance in pre-trained transformer-based language models. We then propose a novel method to prune the attention heads that negatively impact fairness while retaining the heads critical for performance, i.e. language modeling capabilities. Our approach is practical in terms of time and resources, as it does not require fine-tuning the final pruned, and fairer, model. Our findings demonstrate a reduction in gender bias by 19%, 19.5%, 39.5%, 34.7%, 23%, and 8% for DistilGPT-2, GPT-2, GPT-Neo of two different sizes, GPT-J, and Llama 2 models, respectively, in comparison to the biased model, with only a slight decrease in performance.

The remarkable abilities of large language models (LLMs) like GPT-4 partially stem from post-training processes like Reinforcement Learning from Human Feedback (RLHF) involving human preferences encoded in a reward model. However, these reward models (RMs) often lack direct knowledge of why, or under what principles, the preferences annotations were made. In this study, we identify principles that guide RMs to better align with human preferences, and then develop an axiomatic framework to generate a rich variety of preference signals to uphold them. We use these axiomatic signals to train a model for scoring answers to longform questions. Our approach yields a Preference Model with only about 220M parameters that agrees with gold human-annotated preference labels more often than GPT-4. The contributions of this work include: training a standalone preference model that can score human- and LLM-generated answers on the same scale; developing an axiomatic framework for generating training data pairs tailored to certain principles; and showing that a small amount of axiomatic signals can help small models outperform GPT-4 in preference scoring. We release our model on huggingface: https://huggingface.co/corbyrosset/axiomatic_preference_model

Predictive Coding (PC) is a theoretical framework in cognitive science suggesting that the human brain processes cognition through spatiotemporal prediction of the visual world. Existing studies have developed spatiotemporal prediction neural networks based on the PC theory, emulating its two core mechanisms: Correcting predictions from residuals and hierarchical learning. However, these models do not show the enhancement of prediction skills on real-world forecasting tasks and ignore the Precision Weighting mechanism of PC theory. The precision weighting mechanism posits that the brain allocates more attention to signals with lower precision, contributing to the cognitive ability of human brains. This work introduces the Cognitive Diffusion Probabilistic Models (CogDPM), which demonstrate the connection between diffusion probabilistic models and PC theory. CogDPM features a precision estimation method based on the hierarchical sampling capabilities of diffusion models and weight the guidance with precision weights estimated by the inherent property of diffusion models. We experimentally show that the precision weights effectively estimate the data predictability. We apply CogDPM to real-world prediction tasks using the United Kindom precipitation and ERA surface wind datasets. Our results demonstrate that CogDPM outperforms both existing domain-specific operational models and general deep prediction models by providing more proficient forecasting.

In optimal transport (OT), a Monge map is known as a mapping that transports a source distribution to a target distribution in the most cost-efficient way. Recently, multiple neural estimators for Monge maps have been developed and applied in diverse unpaired domain translation tasks, e.g. in single-cell biology and computer vision. However, the classic OT framework enforces mass conservation, which makes it prone to outliers and limits its applicability in real-world scenarios. The latter can be particularly harmful in OT domain translation tasks, where the relative position of a sample within a distribution is explicitly taken into account. While unbalanced OT tackles this challenge in the discrete setting, its integration into neural Monge map estimators has received limited attention. We propose a theoretically grounded method to incorporate unbalancedness into any Monge map estimator. We improve existing estimators to model cell trajectories over time and to predict cellular responses to perturbations. Moreover, our approach seamlessly integrates with the OT flow matching (OT-FM) framework. While we show that OT-FM performs competitively in image translation, we further improve performance by incorporating unbalancedness (UOT-FM), which better preserves relevant features. We hence establish UOT-FM as a principled method for unpaired image translation.

Neural networks (NN) achieve remarkable results in various tasks, but lack key characteristics: interpretability, support for categorical features, and lightweight implementations suitable for edge devices. While ongoing efforts aim to address these challenges, Gradient Boosting Trees (GBT) inherently meet these requirements. As a result, GBTs have become the go-to method for supervised learning tasks in many real-world applications and competitions. However, their application in online learning scenarios, notably in reinforcement learning (RL), has been limited. In this work, we bridge this gap by introducing Gradient-Boosting RL (GBRL), a framework that extends the advantages of GBT to the RL domain. Using the GBRL framework, we implement various actor-critic algorithms and compare their performance with their NN counterparts. Inspired by shared backbones in NN we introduce a tree-sharing approach for policy and value functions with distinct learning rates, enhancing learning efficiency over millions of interactions. GBRL achieves competitive performance across a diverse array of tasks, excelling in domains with structured or categorical features. Additionally, we present a high-performance, GPU-accelerated implementation that integrates seamlessly with widely-used RL libraries (available at https://github.com/NVlabs/gbrl). GBRL expands the toolkit for RL practitioners, demonstrating the viability and promise of GBT within the RL paradigm, particularly in domains characterized by structured or categorical features.

Many real-world problems require reasoning across multiple scales, demanding models which operate not on single data points, but on entire distributions. We introduce generative distribution embeddings (GDE), a framework that lifts autoencoders to the space of distributions. In GDEs, an encoder acts on sets of samples, and the decoder is replaced by a generator which aims to match the input distribution. This framework enables learning representations of distributions by coupling conditional generative models with encoder networks which satisfy a criterion we call distributional invariance. We show that GDEs learn predictive sufficient statistics embedded in the Wasserstein space, such that latent GDE distances approximately recover the W_2 distance, and latent interpolation approximately recovers optimal transport trajectories for Gaussian and Gaussian mixture distributions. We systematically benchmark GDEs against existing approaches on synthetic datasets, demonstrating consistently stronger performance. We then apply GDEs to six key problems in computational biology: learning representations of cell populations from lineage-tracing data (150K cells), predicting perturbation effects on single-cell transcriptomes (1M cells), predicting perturbation effects on cellular phenotypes (20M single-cell images), modeling tissue-specific DNA methylation patterns (253M sequences), designing synthetic yeast promoters (34M sequences), and spatiotemporal modeling of viral protein sequences (1M sequences).

Gate set tomography (GST) is a protocol for detailed, predictive characterization of logic operations (gates) on quantum computing processors. Early versions of GST emerged around 2012-13, and since then it has been refined, demonstrated, and used in a large number of experiments. This paper presents the foundations of GST in comprehensive detail. The most important feature of GST, compared to older state and process tomography protocols, is that it is calibration-free. GST does not rely on pre-calibrated state preparations and measurements. Instead, it characterizes all the operations in a gate set simultaneously and self-consistently, relative to each other. Long sequence GST can estimate gates with very high precision and efficiency, achieving Heisenberg scaling in regimes of practical interest. In this paper, we cover GST's intellectual history, the techniques and experiments used to achieve its intended purpose, data analysis, gauge freedom and fixing, error bars, and the interpretation of gauge-fixed estimates of gate sets. Our focus is fundamental mathematical aspects of GST, rather than implementation details, but we touch on some of the foundational algorithmic tricks used in the pyGSTi implementation.

We present Symphony, an E(3)-equivariant autoregressive generative model for 3D molecular geometries that iteratively builds a molecule from molecular fragments. Existing autoregressive models such as G-SchNet and G-SphereNet for molecules utilize rotationally invariant features to respect the 3D symmetries of molecules. In contrast, Symphony uses message-passing with higher-degree E(3)-equivariant features. This allows a novel representation of probability distributions via spherical harmonic signals to efficiently model the 3D geometry of molecules. We show that Symphony is able to accurately generate small molecules from the QM9 dataset, outperforming existing autoregressive models and approaching the performance of diffusion models.

Distribution shift presents a significant challenge in machine learning, where models often underperform during the test stage when faced with a different distribution than the one they were trained on. This paper focuses on domain shifts, which occur when the model is applied to new domains that are different from the ones it was trained on, and propose a new approach called D^3G. Unlike previous methods that aim to learn a single model that is domain invariant, D^3G leverages domain similarities based on domain metadata to learn domain-specific models. Concretely, D^3G learns a set of training-domain-specific functions during the training stage and reweights them based on domain relations during the test stage. These domain relations can be directly obtained and learned from domain metadata. Under mild assumptions, we theoretically prove that using domain relations to reweight training-domain-specific functions achieves stronger out-of-domain generalization compared to the conventional averaging approach. Empirically, we evaluate the effectiveness of D^3G using real-world datasets for tasks such as temperature regression, land use classification, and molecule-protein binding affinity prediction. Our results show that D^3G consistently outperforms state-of-the-art methods.

Stars on the AGB can exhibit acoustic pulsation modes of different radial orders, along with non-radial modes. These pulsations are essential to the mass-loss process and influence the evolutionary pathways of AGB stars. P-L relations serve as a valuable diagnostic for understanding stellar evolution along the AGB. 3D RHD simulations provide a powerful tool for investigating pulsation phenomena driven by convective processes and their non-linear coupling with stellar oscillations. We investigate multi-mode pulsations in AGB stars using advanced 3D 'star-in-a-box' simulations with the CO5BOLD code. Signatures of these multi-mode pulsations were weak in our previous 3D models. Our focus is on identifying and characterising the various pulsation modes, examining their persistence and transitions, and comparing the results with 1D model predictions and observational data where applicable. We produced a new model grid comprising AGB stars with current masses of 0.7, 0.8, and 1,M_{odot}. Fourier analysis was applied to dynamic, time-dependent quantities to extract dominant pulsation modes and their corresponding periods. Additionally, wavelet transforms were employed to identify mode-switching behaviour over time. The models successfully reproduce the P-L sequences found in AGB stars. Mode-switching phenomena are found in both the models and wavelet analyses of observational data, allowing us to infer similarities in the underlying pulsation dynamics. These 3D simulations highlight the natural emergence of multi-mode pulsations, including both radial and non-radial modes, driven by the self-consistent interplay of convection and oscillations. Our findings underscore the value of 3D RHD models in capturing the non-linear behaviour of AGB pulsations, providing insights into mode switching, envelope structures, and potential links to episodic mass-loss events.

Understanding the glassy nature of neural networks is pivotal both for theoretical and computational advances in Machine Learning and Theoretical Artificial Intelligence. Keeping the focus on dense associative Hebbian neural networks, the purpose of this paper is two-fold: at first we develop rigorous mathematical approaches to address properly a statistical mechanical picture of the phenomenon of {\em replica symmetry breaking} (RSB) in these networks, then -- deepening results stemmed via these routes -- we aim to inspect the {\em glassiness} that they hide. In particular, regarding the methodology, we provide two techniques: the former is an adaptation of the transport PDE to the case, while the latter is an extension of Guerra's interpolation breakthrough. Beyond coherence among the results, either in replica symmetric and in the one-step replica symmetry breaking level of description, we prove the Gardner's picture and we identify the maximal storage capacity by a ground-state analysis in the Baldi-Venkatesh high-storage regime. In the second part of the paper we investigate the glassy structure of these networks: in contrast with the replica symmetric scenario (RS), RSB actually stabilizes the spin-glass phase. We report huge differences w.r.t. the standard pairwise Hopfield limit: in particular, it is known that it is possible to express the free energy of the Hopfield neural network as a linear combination of the free energies of an hard spin glass (i.e. the Sherrington-Kirkpatrick model) and a soft spin glass (the Gaussian or "spherical" model). This is no longer true when interactions are more than pairwise (whatever the level of description, RS or RSB): for dense networks solely the free energy of the hard spin glass survives, proving a huge diversity in the underlying glassiness of associative neural networks.

The recent advent of large language models has reinvigorated debate over whether human cognitive capacities might emerge in such generic models given sufficient training data. Of particular interest is the ability of these models to reason about novel problems zero-shot, without any direct training. In human cognition, this capacity is closely tied to an ability to reason by analogy. Here, we performed a direct comparison between human reasoners and a large language model (the text-davinci-003 variant of GPT-3) on a range of analogical tasks, including a non-visual matrix reasoning task based on the rule structure of Raven's Standard Progressive Matrices. We found that GPT-3 displayed a surprisingly strong capacity for abstract pattern induction, matching or even surpassing human capabilities in most settings; preliminary tests of GPT-4 indicated even better performance. Our results indicate that large language models such as GPT-3 have acquired an emergent ability to find zero-shot solutions to a broad range of analogy problems.

Optimal Transport (OT) has fueled machine learning (ML) across many domains. When paired data measurements (mu, nu) are coupled to covariates, a challenging conditional distribution learning setting arises. Existing approaches for learning a global transport map parameterized through a potentially unseen context utilize Neural OT and largely rely on Brenier's theorem. Here, we propose a first-of-its-kind quantum computing formulation for amortized optimization of contextualized transportation plans. We exploit a direct link between doubly stochastic matrices and unitary operators thus unravelling a natural connection between OT and quantum computation. We verify our method (QontOT) on synthetic and real data by predicting variations in cell type distributions conditioned on drug dosage. Importantly we conduct a 24-qubit hardware experiment on a task challenging for classical computers and report a performance that cannot be matched with our classical neural OT approach. In sum, this is a first step toward learning to predict contextualized transportation plans through quantum computing.

Communication-reduction techniques are a popular way to improve scalability in data-parallel training of deep neural networks (DNNs). The recent emergence of large language models such as GPT has created the need for new approaches to exploit data-parallelism. Among these, fully-sharded data parallel (FSDP) training is highly popular, yet it still encounters scalability bottlenecks. One reason is that applying compression techniques to FSDP is challenging: as the vast majority of the communication involves the model's weights, direct compression alters convergence and leads to accuracy loss. We present QSDP, a variant of FSDP which supports both gradient and weight quantization with theoretical guarantees, is simple to implement and has essentially no overheads. To derive QSDP we prove that a natural modification of SGD achieves convergence even when we only maintain quantized weights, and thus the domain over which we train consists of quantized points and is, therefore, highly non-convex. We validate this approach by training GPT-family models with up to 1.3 billion parameters on a multi-node cluster. Experiments show that QSDP preserves model accuracy, while completely removing the communication bottlenecks of FSDP, providing end-to-end speedups of up to 2.2x.

Many have observed that the development and deployment of generative machine learning (ML) and artificial intelligence (AI) models follow a distinctive pattern in which pre-trained models are adapted and fine-tuned for specific downstream tasks. However, there is limited empirical work that examines the structure of these interactions. This paper analyzes 1.86 million models on Hugging Face, a leading peer production platform for model development. Our study of model family trees -- networks that connect fine-tuned models to their base or parent -- reveals sprawling fine-tuning lineages that vary widely in size and structure. Using an evolutionary biology lens to study ML models, we use model metadata and model cards to measure the genetic similarity and mutation of traits over model families. We find that models tend to exhibit a family resemblance, meaning their genetic markers and traits exhibit more overlap when they belong to the same model family. However, these similarities depart in certain ways from standard models of asexual reproduction, because mutations are fast and directed, such that two `sibling' models tend to exhibit more similarity than parent/child pairs. Further analysis of the directional drifts of these mutations reveals qualitative insights about the open machine learning ecosystem: Licenses counter-intuitively drift from restrictive, commercial licenses towards permissive or copyleft licenses, often in violation of upstream license's terms; models evolve from multi-lingual compatibility towards english-only compatibility; and model cards reduce in length and standardize by turning, more often, to templates and automatically generated text. Overall, this work takes a step toward an empirically grounded understanding of model fine-tuning and suggests that ecological models and methods can yield novel scientific insights.

Proteins power a vast array of functional processes in living cells. The capability to create new proteins with designed structures and functions would thus enable the engineering of cellular behavior and development of protein-based therapeutics and materials. Structure-based protein design aims to find structures that are designable (can be realized by a protein sequence), novel (have dissimilar geometry from natural proteins), and diverse (span a wide range of geometries). While advances in protein structure prediction have made it possible to predict structures of novel protein sequences, the combinatorially large space of sequences and structures limits the practicality of search-based methods. Generative models provide a compelling alternative, by implicitly learning the low-dimensional structure of complex data distributions. Here, we leverage recent advances in denoising diffusion probabilistic models and equivariant neural networks to develop Genie, a generative model of protein structures that performs discrete-time diffusion using a cloud of oriented reference frames in 3D space. Through in silico evaluations, we demonstrate that Genie generates protein backbones that are more designable, novel, and diverse than existing models. This indicates that Genie is capturing key aspects of the distribution of protein structure space and facilitates protein design with high success rates. Code for generating new proteins and training new versions of Genie is available at https://github.com/aqlaboratory/genie.

Generative Flow Networks (GFlowNets) have recently emerged as a suitable framework for generating diverse and high-quality molecular structures by learning from rewards treated as unnormalized distributions. Previous works in this framework often restrict exploration by using predefined molecular fragments as building blocks, limiting the chemical space that can be accessed. In this work, we introduce Atomic GFlowNets (A-GFNs), a foundational generative model leveraging individual atoms as building blocks to explore drug-like chemical space more comprehensively. We propose an unsupervised pre-training approach using drug-like molecule datasets, which teaches A-GFNs about inexpensive yet informative molecular descriptors such as drug-likeliness, topological polar surface area, and synthetic accessibility scores. These properties serve as proxy rewards, guiding A-GFNs towards regions of chemical space that exhibit desirable pharmacological properties. We further implement a goal-conditioned finetuning process, which adapts A-GFNs to optimize for specific target properties. In this work, we pretrain A-GFN on a subset of ZINC dataset, and by employing robust evaluation metrics we show the effectiveness of our approach when compared to other relevant baseline methods for a wide range of drug design tasks. The code is accessible at https://github.com/diamondspark/AGFN.

Scientific discoveries often hinge on synthesizing decades of research, a task that potentially outstrips human information processing capacities. Large language models (LLMs) offer a solution. LLMs trained on the vast scientific literature could potentially integrate noisy yet interrelated findings to forecast novel results better than human experts. To evaluate this possibility, we created BrainBench, a forward-looking benchmark for predicting neuroscience results. We find that LLMs surpass experts in predicting experimental outcomes. BrainGPT, an LLM we tuned on the neuroscience literature, performed better yet. Like human experts, when LLMs were confident in their predictions, they were more likely to be correct, which presages a future where humans and LLMs team together to make discoveries. Our approach is not neuroscience-specific and is transferable to other knowledge-intensive endeavors.

Medical images and radiology reports are crucial for diagnosing medical conditions, highlighting the importance of quantitative analysis for clinical decision-making. However, the diversity and cross-source heterogeneity of these data challenge the generalizability of current data-mining methods. Multimodal large language models (MLLMs) have recently transformed many domains, significantly affecting the medical field. Notably, Gemini-Vision-series (Gemini) and GPT-4-series (GPT-4) models have epitomized a paradigm shift in Artificial General Intelligence (AGI) for computer vision, showcasing their potential in the biomedical domain. In this study, we evaluated the performance of the Gemini, GPT-4, and 4 popular large models for an exhaustive evaluation across 14 medical imaging datasets, including 5 medical imaging categories (dermatology, radiology, dentistry, ophthalmology, and endoscopy), and 3 radiology report datasets. The investigated tasks encompass disease classification, lesion segmentation, anatomical localization, disease diagnosis, report generation, and lesion detection. Our experimental results demonstrated that Gemini-series models excelled in report generation and lesion detection but faces challenges in disease classification and anatomical localization. Conversely, GPT-series models exhibited proficiency in lesion segmentation and anatomical localization but encountered difficulties in disease diagnosis and lesion detection. Additionally, both the Gemini series and GPT series contain models that have demonstrated commendable generation efficiency. While both models hold promise in reducing physician workload, alleviating pressure on limited healthcare resources, and fostering collaboration between clinical practitioners and artificial intelligence technologies, substantial enhancements and comprehensive validations remain imperative before clinical deployment.

Recently, pre-trained foundation models have enabled significant advancements in multiple fields. In molecular machine learning, however, where datasets are often hand-curated, and hence typically small, the lack of datasets with labeled features, and codebases to manage those datasets, has hindered the development of foundation models. In this work, we present seven novel datasets categorized by size into three distinct categories: ToyMix, LargeMix and UltraLarge. These datasets push the boundaries in both the scale and the diversity of supervised labels for molecular learning. They cover nearly 100 million molecules and over 3000 sparsely defined tasks, totaling more than 13 billion individual labels of both quantum and biological nature. In comparison, our datasets contain 300 times more data points than the widely used OGB-LSC PCQM4Mv2 dataset, and 13 times more than the quantum-only QM1B dataset. In addition, to support the development of foundational models based on our proposed datasets, we present the Graphium graph machine learning library which simplifies the process of building and training molecular machine learning models for multi-task and multi-level molecular datasets. Finally, we present a range of baseline results as a starting point of multi-task and multi-level training on these datasets. Empirically, we observe that performance on low-resource biological datasets show improvement by also training on large amounts of quantum data. This indicates that there may be potential in multi-task and multi-level training of a foundation model and fine-tuning it to resource-constrained downstream tasks.

This work introduces the Efficient Transformed Gaussian Process (ETGP), a new way of creating C stochastic processes characterized by: 1) the C processes are non-stationary, 2) the C processes are dependent by construction without needing a mixing matrix, 3) training and making predictions is very efficient since the number of Gaussian Processes (GP) operations (e.g. inverting the inducing point's covariance matrix) do not depend on the number of processes. This makes the ETGP particularly suited for multi-class problems with a very large number of classes, which are the problems studied in this work. ETGPs exploit the recently proposed Transformed Gaussian Process (TGP), a stochastic process specified by transforming a Gaussian Process using an invertible transformation. However, unlike TGPs, ETGPs are constructed by transforming a single sample from a GP using C invertible transformations. We derive an efficient sparse variational inference algorithm for the proposed model and demonstrate its utility in 5 classification tasks which include low/medium/large datasets and a different number of classes, ranging from just a few to hundreds. Our results show that ETGPs, in general, outperform state-of-the-art methods for multi-class classification based on GPs, and have a lower computational cost (around one order of magnitude smaller).

We present our proposed solution to the BabyLM challenge [arXiv:2301.11796], whose goal was to improve the sample efficiency of language models. We trained an ensemble consisting of a GPT-2 and small LLaMA models on the developmentally-plausible, 10M-word BabyLM dataset, then distilled it into a small, 58M-parameter LLaMA model, which exceeds in performance both of its teachers as well as a similar model trained without distillation. This suggests that distillation can not only retain the full performance of the teacher model when the latter is trained on a sufficiently small dataset; it can exceed it, and lead to significantly better performance than direct training.

Large-scale pre-trained models (PTMs) such as BERT and GPT have recently achieved great success and become a milestone in the field of artificial intelligence (AI). Owing to sophisticated pre-training objectives and huge model parameters, large-scale PTMs can effectively capture knowledge from massive labeled and unlabeled data. By storing knowledge into huge parameters and fine-tuning on specific tasks, the rich knowledge implicitly encoded in huge parameters can benefit a variety of downstream tasks, which has been extensively demonstrated via experimental verification and empirical analysis. It is now the consensus of the AI community to adopt PTMs as backbone for downstream tasks rather than learning models from scratch. In this paper, we take a deep look into the history of pre-training, especially its special relation with transfer learning and self-supervised learning, to reveal the crucial position of PTMs in the AI development spectrum. Further, we comprehensively review the latest breakthroughs of PTMs. These breakthroughs are driven by the surge of computational power and the increasing availability of data, towards four important directions: designing effective architectures, utilizing rich contexts, improving computational efficiency, and conducting interpretation and theoretical analysis. Finally, we discuss a series of open problems and research directions of PTMs, and hope our view can inspire and advance the future study of PTMs.

AI Alignment is often presented as an interaction between a single designer and an artificial agent in which the designer attempts to ensure the agent's behavior is consistent with its purpose, and risks arise solely because of conflicts caused by inadvertent misalignment between the utility function intended by the designer and the resulting internal utility function of the agent. With the advent of agents instantiated with large-language models (LLMs), which are typically pre-trained, we argue this does not capture the essential aspects of AI safety because in the real world there is not a one-to-one correspondence between designer and agent, and the many agents, both artificial and human, have heterogeneous values. Therefore, there is an economic aspect to AI safety and the principal-agent problem is likely to arise. In a principal-agent problem conflict arises because of information asymmetry together with inherent misalignment between the utility of the agent and its principal, and this inherent misalignment cannot be overcome by coercing the agent into adopting a desired utility function through training. We argue the assumptions underlying principal-agent problems are crucial to capturing the essence of safety problems involving pre-trained AI models in real-world situations. Taking an empirical approach to AI safety, we investigate how GPT models respond in principal-agent conflicts. We find that agents based on both GPT-3.5 and GPT-4 override their principal's objectives in a simple online shopping task, showing clear evidence of principal-agent conflict. Surprisingly, the earlier GPT-3.5 model exhibits more nuanced behaviour in response to changes in information asymmetry, whereas the later GPT-4 model is more rigid in adhering to its prior alignment. Our results highlight the importance of incorporating principles from economics into the alignment process.

Transition state (TS) structures define the critical geometries and energy barriers underlying chemical reactivity, yet their fleeting nature renders them experimentally elusive and drives the reliance on costly, high-throughput density functional theory (DFT) calculations. Here, we introduce TS-GEN, a conditional flow-matching generative model that maps samples from a simple Gaussian prior directly to transition-state saddle-point geometries in a single, deterministic pass. By embedding both reactant and product conformations as conditioning information, TS-GEN learns to transport latent noise to true TS structures via an optimal-transport path, effectively replacing the iterative optimization common in nudged-elastic band or string-method algorithms. TS-GEN delivers unprecedented accuracy, achieving a root-mean-square deviation of 0.004 mathring{A} (vs. 0.103 mathring{A} for prior state-of-the-art) and a mean barrier-height error of 1.019 {rm kcal/mol} (vs. 2.864 {rm kcal/mol}), while requiring only 0.06 {rm s} GPU time per inference. Over 87% of generated TSs meet chemical-accuracy criteria (<1.58 {rm kcal/mol} error), substantially outpacing existing methods. TS-GEN also exhibits strong transferability to out-of-distribution reactions from a larger database. By uniting sub-angstrom precision, sub-second speed, and broad applicability, TS-GEN will be highly useful for high-throughput exploration of complex reaction networks, paving the way to the exploration of novel chemical reaction mechanisms.

We propose Fuzzy Group Relative Policy Reward (FGRPR), a novel framework that integrates Group Relative Policy Optimization (GRPO) with a fuzzy reward function to enhance learning efficiency. Unlike the conventional binary 0/1 accuracy reward, our fuzzy reward model provides nuanced incentives, encouraging more precise outputs. Experimental results demonstrate that GRPO with a standard 0/1 accuracy reward underperforms compared to supervised fine-tuning (SFT). In contrast, FGRPR, applied to Qwen2.5-VL(3B and 7B), surpasses all baseline models, including GPT4o, LLaMA2(90B), and SFT, across five in-domain datasets. On an out-of-domain dataset, FGRPR achieves performance comparable to SFT but excels when target values are larger, as its fuzzy reward function assigns higher rewards to closer approximations. This approach is broadly applicable to tasks where the precision of the answer is critical. Code and data: https://github.com/yeyimilk/CrowdVLM-R1

While score-based generative models are the model of choice across diverse domains, there are limited tools available for controlling inference-time behavior in a principled manner, e.g. for composing multiple pretrained models. Existing classifier-free guidance methods use a simple heuristic to mix conditional and unconditional scores to approximately sample from conditional distributions. However, such methods do not approximate the intermediate distributions, necessitating additional 'corrector' steps. In this work, we provide an efficient and principled method for sampling from a sequence of annealed, geometric-averaged, or product distributions derived from pretrained score-based models. We derive a weighted simulation scheme which we call Feynman-Kac Correctors (FKCs) based on the celebrated Feynman-Kac formula by carefully accounting for terms in the appropriate partial differential equations (PDEs). To simulate these PDEs, we propose Sequential Monte Carlo (SMC) resampling algorithms that leverage inference-time scaling to improve sampling quality. We empirically demonstrate the utility of our methods by proposing amortized sampling via inference-time temperature annealing, improving multi-objective molecule generation using pretrained models, and improving classifier-free guidance for text-to-image generation. Our code is available at https://github.com/martaskrt/fkc-diffusion.

The pre-trained model (PTM) is revolutionizing Artificial Intelligence (AI) technology. However, the hardware requirement of PTM training is prohibitively high, making it a game for a small proportion of people. Therefore, we proposed PatrickStar system to lower the hardware requirements of PTMs and make them accessible to everyone. PatrickStar uses the CPU-GPU heterogeneous memory space to store the model data. Different from existing works, we organize the model data in memory chunks and dynamically distribute them in the heterogeneous memory. Guided by the runtime memory statistics collected in a warm-up iteration, chunks are orchestrated efficiently in heterogeneous memory and generate lower CPU-GPU data transmission volume and higher bandwidth utilization. Symbiosis with the Zero Redundancy Optimizer, PatrickStar scales to multiple GPUs on multiple nodes. % using data parallelism. The system can train tasks on bigger models and larger batch sizes, which cannot be accomplished by existing works. Experimental results show that PatrickStar extends model scales 2.27 and 2.5 times of DeepSpeed, and consistently exhibits significantly higher execution speed. PatricStar also successfully runs the 175B GPT3 training task on a 32 GPU cluster. Our code is publicly available at https://github.com/Tencent/PatrickStar.

Continual Test-Time Adaptation (CTTA) aims to adapt a pretrained model to ever-changing environments during the test time under continuous domain shifts. Most existing CTTA approaches are based on the Mean Teacher (MT) structure, which contains a student and a teacher model, where the student is updated using the pseudo-labels from the teacher model, and the teacher is then updated by exponential moving average strategy. However, these methods update the MT model indiscriminately on all parameters of the model. That is, some critical parameters involving sharing knowledge across different domains may be erased, intensifying error accumulation and catastrophic forgetting. In this paper, we introduce Parameter-Selective Mean Teacher (PSMT) method, which is capable of effectively updating the critical parameters within the MT network under domain shifts. First, we introduce a selective distillation mechanism in the student model, which utilizes past knowledge to regularize novel knowledge, thereby mitigating the impact of error accumulation. Second, to avoid catastrophic forgetting, in the teacher model, we create a mask through Fisher information to selectively update parameters via exponential moving average, with preservation measures applied to crucial parameters. Extensive experimental results verify that PSMT outperforms state-of-the-art methods across multiple benchmark datasets. Our code is available at https://github.com/JiaxuTian/PSMT.

Approximate inference in Gaussian process (GP) models with non-conjugate likelihoods gets entangled with the learning of the model hyperparameters. We improve hyperparameter learning in GP models and focus on the interplay between variational inference (VI) and the learning target. While VI's lower bound to the marginal likelihood is a suitable objective for inferring the approximate posterior, we show that a direct approximation of the marginal likelihood as in Expectation Propagation (EP) is a better learning objective for hyperparameter optimization. We design a hybrid training procedure to bring the best of both worlds: it leverages conjugate-computation VI for inference and uses an EP-like marginal likelihood approximation for hyperparameter learning. We compare VI, EP, Laplace approximation, and our proposed training procedure and empirically demonstrate the effectiveness of our proposal across a wide range of data sets.

In this paper, we evaluate different abilities of GPT-4V including visual understanding, language understanding, visual puzzle solving, and understanding of other modalities such as depth, thermal, video, and audio. To estimate GPT-4V's performance, we manually construct 656 test instances and carefully evaluate the results of GPT-4V. The highlights of our findings are as follows: (1) GPT-4V exhibits impressive performance on English visual-centric benchmarks but fails to recognize simple Chinese texts in the images; (2) GPT-4V shows inconsistent refusal behavior when answering questions related to sensitive traits such as gender, race, and age; (3) GPT-4V obtains worse results than GPT-4 (API) on language understanding tasks including general language understanding benchmarks and visual commonsense knowledge evaluation benchmarks; (4) Few-shot prompting can improve GPT-4V's performance on both visual understanding and language understanding; (5) GPT-4V struggles to find the nuances between two similar images and solve the easy math picture puzzles; (6) GPT-4V shows non-trivial performance on the tasks of similar modalities to image, such as video and thermal. Our experimental results reveal the ability and limitations of GPT-4V and we hope our paper can provide some insights into the application and research of GPT-4V.

Accelerating material discovery holds the potential to greatly help mitigate the climate crisis. Discovering new solid-state materials such as electrocatalysts, super-ionic conductors or photovoltaic materials can have a crucial impact, for instance, in improving the efficiency of renewable energy production and storage. In this paper, we introduce Crystal-GFN, a generative model of crystal structures that sequentially samples structural properties of crystalline materials, namely the space group, composition and lattice parameters. This domain-inspired approach enables the flexible incorporation of physical and structural hard constraints, as well as the use of any available predictive model of a desired physicochemical property as an objective function. To design stable materials, one must target the candidates with the lowest formation energy. Here, we use as objective the formation energy per atom of a crystal structure predicted by a new proxy machine learning model trained on MatBench. The results demonstrate that Crystal-GFN is able to sample highly diverse crystals with low (median -3.1 eV/atom) predicted formation energy.

Learning in Gaussian Process models occurs through the adaptation of hyperparameters of the mean and the covariance function. The classical approach entails maximizing the marginal likelihood yielding fixed point estimates (an approach called Type II maximum likelihood or ML-II). An alternative learning procedure is to infer the posterior over hyperparameters in a hierarchical specification of GPs we call Fully Bayesian Gaussian Process Regression (GPR). This work considers two approximation schemes for the intractable hyperparameter posterior: 1) Hamiltonian Monte Carlo (HMC) yielding a sampling-based approximation and 2) Variational Inference (VI) where the posterior over hyperparameters is approximated by a factorized Gaussian (mean-field) or a full-rank Gaussian accounting for correlations between hyperparameters. We analyze the predictive performance for fully Bayesian GPR on a range of benchmark data sets.

Forecasting on sparse multivariate time series (MTS) aims to model the predictors of future values of time series given their incomplete past, which is important for many emerging applications. However, most existing methods process MTS's individually, and do not leverage the dynamic distributions underlying the MTS's, leading to sub-optimal results when the sparsity is high. To address this challenge, we propose a novel generative model, which tracks the transition of latent clusters, instead of isolated feature representations, to achieve robust modeling. It is characterized by a newly designed dynamic Gaussian mixture distribution, which captures the dynamics of clustering structures, and is used for emitting timeseries. The generative model is parameterized by neural networks. A structured inference network is also designed for enabling inductive analysis. A gating mechanism is further introduced to dynamically tune the Gaussian mixture distributions. Extensive experimental results on a variety of real-life datasets demonstrate the effectiveness of our method.

Providing effective treatment and making informed clinical decisions are essential goals of modern medicine and clinical care. We are interested in simulating disease dynamics for clinical decision-making, leveraging recent advances in large generative models. To this end, we introduce the Medical World Model (MeWM), the first world model in medicine that visually predicts future disease states based on clinical decisions. MeWM comprises (i) vision-language models to serve as policy models, and (ii) tumor generative models as dynamics models. The policy model generates action plans, such as clinical treatments, while the dynamics model simulates tumor progression or regression under given treatment conditions. Building on this, we propose the inverse dynamics model that applies survival analysis to the simulated post-treatment tumor, enabling the evaluation of treatment efficacy and the selection of the optimal clinical action plan. As a result, the proposed MeWM simulates disease dynamics by synthesizing post-treatment tumors, with state-of-the-art specificity in Turing tests evaluated by radiologists. Simultaneously, its inverse dynamics model outperforms medical-specialized GPTs in optimizing individualized treatment protocols across all metrics. Notably, MeWM improves clinical decision-making for interventional physicians, boosting F1-score in selecting the optimal TACE protocol by 13%, paving the way for future integration of medical world models as the second readers.

Ridgelet transform has been a fundamental mathematical tool in the theoretical studies of neural networks. However, the practical applicability of ridgelet transform to conducting learning tasks was limited since its numerical implementation by conventional classical computation requires an exponential runtime exp(O(D)) as data dimension D increases. To address this problem, we develop a quantum ridgelet transform (QRT), which implements the ridgelet transform of a quantum state within a linear runtime O(D) of quantum computation. As an application, we also show that one can use QRT as a fundamental subroutine for quantum machine learning (QML) to efficiently find a sparse trainable subnetwork of large shallow wide neural networks without conducting large-scale optimization of the original network. This application discovers an efficient way in this regime to demonstrate the lottery ticket hypothesis on finding such a sparse trainable neural network. These results open an avenue of QML for accelerating learning tasks with commonly used classical neural networks.

Two-dimensional (2D) Nuclear Magnetic Resonance (NMR) spectroscopy, particularly Heteronuclear Single Quantum Coherence (HSQC) spectroscopy, plays a critical role in elucidating molecular structures, interactions, and electronic properties. However, accurately interpreting 2D NMR data remains labor-intensive and error-prone, requiring highly trained domain experts, especially for complex molecules. Machine Learning (ML) holds significant potential in 2D NMR analysis by learning molecular representations and recognizing complex patterns from data. However, progress has been limited by the lack of large-scale and high-quality annotated datasets. In this work, we introduce 2DNMRGym, the first annotated experimental dataset designed for ML-based molecular representation learning in 2D NMR. It includes over 22,000 HSQC spectra, along with the corresponding molecular graphs and SMILES strings. Uniquely, 2DNMRGym adopts a surrogate supervision setup: models are trained using algorithm-generated annotations derived from a previously validated method and evaluated on a held-out set of human-annotated gold-standard labels. This enables rigorous assessment of a model's ability to generalize from imperfect supervision to expert-level interpretation. We provide benchmark results using a series of 2D and 3D GNN and GNN transformer models, establishing a strong foundation for future work. 2DNMRGym supports scalable model training and introduces a chemically meaningful benchmark for evaluating atom-level molecular representations in NMR-guided structural tasks. Our data and code is open-source and available on Huggingface and Github.

Eleven Large Language Models (LLMs) were assessed using a custom-made battery of false-belief tasks, considered a gold standard in testing Theory of Mind (ToM) in humans. The battery included 640 prompts spread across 40 diverse tasks, each one including a false-belief scenario, three closely matched true-belief control scenarios, and the reversed versions of all four. To solve a single task, a model needed to correctly answer 16 prompts across all eight scenarios. Smaller and older models solved no tasks; GPT-3-davinci-003 (from November 2022) and ChatGPT-3.5-turbo (from March 2023) solved 20% of the tasks; ChatGPT-4 (from June 2023) solved 75% of the tasks, matching the performance of six-year-old children observed in past studies. We explore the potential interpretation of these findings, including the intriguing possibility that ToM, previously considered exclusive to humans, may have spontaneously emerged as a byproduct of LLMs' improving language skills.

Despite significant progress of generative models in the natural sciences, their controllability remains challenging. One fundamentally missing aspect of molecular or protein generative models is an inductive bias that can reflect continuous properties of interest. To that end, we propose the Regression Transformer (RT), a novel method that abstracts regression as a conditional sequence modeling problem. This introduces a new paradigm of multitask language models which seamlessly bridge sequence regression and conditional sequence generation. We thoroughly demonstrate that, despite using a nominal-scale training objective, the RT matches or surpasses the performance of conventional regression models in property prediction tasks of small molecules, proteins and chemical reactions. Critically, priming the same model with continuous properties yields a highly competitive conditional generative model that outperforms specialized approaches in a substructure-constrained, property-driven molecule generation benchmark. Our dichotomous approach is facilitated by a novel, alternating training scheme that enables the model to decorate seed sequences by desired properties, e.g., to optimize reaction yield. In sum, the RT is the first report of a multitask model that concurrently excels at predictive and generative tasks in biochemistry. This finds particular application in property-driven, local exploration of the chemical or protein space and could pave the road toward foundation models in material design. The code to reproduce all experiments of the paper is available at: https://github.com/IBM/regression-transformer

AI agents have the potential to aid users on a variety of consequential tasks, including conducting scientific research. To spur the development of useful agents, we need benchmarks that are challenging, but more crucially, directly correspond to real-world tasks of interest. This paper introduces such a benchmark, designed to measure the accuracy of AI agents in tackling a crucial yet surprisingly challenging aspect of scientific research: computational reproducibility. This task, fundamental to the scientific process, involves reproducing the results of a study using the provided code and data. We introduce CORE-Bench (Computational Reproducibility Agent Benchmark), a benchmark consisting of 270 tasks based on 90 scientific papers across three disciplines (computer science, social science, and medicine). Tasks in CORE-Bench consist of three difficulty levels and include both language-only and vision-language tasks. We provide an evaluation system to measure the accuracy of agents in a fast and parallelizable way, saving days of evaluation time for each run compared to a sequential implementation. We evaluated two baseline agents: the general-purpose AutoGPT and a task-specific agent called CORE-Agent. We tested both variants using two underlying language models: GPT-4o and GPT-4o-mini. The best agent achieved an accuracy of 21% on the hardest task, showing the vast scope for improvement in automating routine scientific tasks. Having agents that can reproduce existing work is a necessary step towards building agents that can conduct novel research and could verify and improve the performance of other research agents. We hope that CORE-Bench can improve the state of reproducibility and spur the development of future research agents.

The development of large-scale Chinese language models is flourishing, yet there is a lack of corresponding capability assessments. Therefore, we propose a test to measure the multitask accuracy of large Chinese language models. This test encompasses four major domains, including medicine, law, psychology, and education, with 15 subtasks in medicine and 8 subtasks in education. We found that the best-performing models in the zero-shot setting outperformed the worst-performing models by nearly 18.6 percentage points on average. Across the four major domains, the highest average zero-shot accuracy of all models is 0.512. In the subdomains, only the GPT-3.5-turbo model achieved a zero-shot accuracy of 0.693 in clinical medicine, which was the highest accuracy among all models across all subtasks. All models performed poorly in the legal domain, with the highest zero-shot accuracy reaching only 0.239. By comprehensively evaluating the breadth and depth of knowledge across multiple disciplines, this test can more accurately identify the shortcomings of the models.

Interrogating the evolution of biological changes at early stages of life requires longitudinal profiling of molecules, such as DNA methylation, which can be challenging with children. We introduce a probabilistic and longitudinal machine learning framework based on multi-mean Gaussian processes (GPs), accounting for individual and gene correlations across time. This method provides future predictions of DNA methylation status at different individual ages while accounting for uncertainty. Our model is trained on a birth cohort of children with methylation profiled at ages 0-4, and we demonstrated that the status of methylation sites for each child can be accurately predicted at ages 5-7. We show that methylation profiles predicted by multi-mean GPs can be used to estimate other phenotypes, such as epigenetic age, and enable comparison to other health measures of interest. This approach encourages epigenetic studies to move towards longitudinal design for investigating epigenetic changes during development, ageing and disease progression.

Generative Flow Networks or GFlowNets are related to Monte-Carlo Markov chain methods (as they sample from a distribution specified by an energy function), reinforcement learning (as they learn a policy to sample composed objects through a sequence of steps), generative models (as they learn to represent and sample from a distribution) and amortized variational methods (as they can be used to learn to approximate and sample from an otherwise intractable posterior, given a prior and a likelihood). They are trained to generate an object x through a sequence of steps with probability proportional to some reward function R(x) (or exp(-E(x)) with E(x) denoting the energy function), given at the end of the generative trajectory. Like for other RL settings where the reward is only given at the end, the efficiency of training and credit assignment may suffer when those trajectories are longer. With previous GFlowNet work, no learning was possible from incomplete trajectories (lacking a terminal state and the computation of the associated reward). In this paper, we consider the case where the energy function can be applied not just to terminal states but also to intermediate states. This is for example achieved when the energy function is additive, with terms available along the trajectory. We show how to reparameterize the GFlowNet state flow function to take advantage of the partial reward already accrued at each state. This enables a training objective that can be applied to update parameters even with incomplete trajectories. Even when complete trajectories are available, being able to obtain more localized credit and gradients is found to speed up training convergence, as demonstrated across many simulations.

Due to the recurrent structure of RNN, the long information propagation path poses limitations in capturing long-term dependencies, gradient explosion/vanishing issues, and inefficient sequential execution. Based on this, we propose a novel paradigm called Parallel Gated Network (PGN) as the new successor to RNN. PGN directly captures information from previous time steps through the designed Historical Information Extraction (HIE) layer and leverages gated mechanisms to select and fuse it with the current time step information. This reduces the information propagation path to O(1), effectively addressing the limitations of RNN. To enhance PGN's performance in long-range time series forecasting tasks, we propose a novel temporal modeling framework called Temporal PGN (TPGN). TPGN incorporates two branches to comprehensively capture the semantic information of time series. One branch utilizes PGN to capture long-term periodic patterns while preserving their local characteristics. The other branch employs patches to capture short-term information and aggregate the global representation of the series. TPGN achieves a theoretical complexity of O(L), ensuring efficiency in its operations. Experimental results on five benchmark datasets demonstrate the state-of-the-art (SOTA) performance and high efficiency of TPGN, further confirming the effectiveness of PGN as the new successor to RNN in long-range time series forecasting. The code is available in this repository: https://github.com/Water2sea/TPGN.

Supervised learning on molecules has incredible potential to be useful in chemistry, drug discovery, and materials science. Luckily, several promising and closely related neural network models invariant to molecular symmetries have already been described in the literature. These models learn a message passing algorithm and aggregation procedure to compute a function of their entire input graph. At this point, the next step is to find a particularly effective variant of this general approach and apply it to chemical prediction benchmarks until we either solve them or reach the limits of the approach. In this paper, we reformulate existing models into a single common framework we call Message Passing Neural Networks (MPNNs) and explore additional novel variations within this framework. Using MPNNs we demonstrate state of the art results on an important molecular property prediction benchmark; these results are strong enough that we believe future work should focus on datasets with larger molecules or more accurate ground truth labels.

In the realm of machine learning, traditional model development and automated approaches like AutoML typically rely on layers of abstraction, such as tree-based or Cartesian genetic programming. Our study introduces "Guided Evolution" (GE), a novel framework that diverges from these methods by utilizing Large Language Models (LLMs) to directly modify code. GE leverages LLMs for a more intelligent, supervised evolutionary process, guiding mutations and crossovers. Our unique "Evolution of Thought" (EoT) technique further enhances GE by enabling LLMs to reflect on and learn from the outcomes of previous mutations. This results in a self-sustaining feedback loop that augments decision-making in model evolution. GE maintains genetic diversity, crucial for evolutionary algorithms, by leveraging LLMs' capability to generate diverse responses from expertly crafted prompts and modulate model temperature. This not only accelerates the evolution process but also injects expert like creativity and insight into the process. Our application of GE in evolving the ExquisiteNetV2 model demonstrates its efficacy: the LLM-driven GE autonomously produced variants with improved accuracy, increasing from 92.52% to 93.34%, without compromising model compactness. This underscores the potential of LLMs to accelerate the traditional model design pipeline, enabling models to autonomously evolve and enhance their own designs.

Bayesian models of cognition have gained considerable traction in computational neuroscience and psychiatry. Their scopes are now expected to expand rapidly to artificial intelligence, providing general inference frameworks to support embodied, adaptable, and energy-efficient autonomous agents. A central theory in this domain is predictive coding, which posits that learning and behaviour are driven by hierarchical probabilistic inferences about the causes of sensory inputs. Biological realism constrains these networks to rely on simple local computations in the form of precision-weighted predictions and prediction errors. This can make this framework highly efficient, but its implementation comes with unique challenges on the software development side. Embedding such models in standard neural network libraries often becomes limiting, as these libraries' compilation and differentiation backends can force a conceptual separation between optimization algorithms and the systems being optimized. This critically departs from other biological principles such as self-monitoring, self-organisation, cellular growth and functional plasticity. In this paper, we introduce pyhgf: a Python package backed by JAX and Rust for creating, manipulating and sampling dynamic networks for predictive coding. We improve over other frameworks by enclosing the network components as transparent, modular and malleable variables in the message-passing steps. The resulting graphs can implement arbitrary computational complexities as beliefs propagation. But the transparency of core variables can also translate into inference processes that leverage self-organisation principles, and express structure learning, meta-learning or causal discovery as the consequence of network structural adaptation to surprising inputs. The code, tutorials and documentation are hosted at: https://github.com/ilabcode/pyhgf.

In various fields of knowledge creation, including science, new ideas often build on pre-existing information. In this work, we explore this concept within the context of language models. Specifically, we explore the potential of self-training models on their own outputs, akin to how humans learn and build on their previous thoughts and actions. While this approach is intuitively appealing, our research reveals its practical limitations. We find that extended self-training of the GPT-2 model leads to a significant degradation in performance, resulting in repetitive and collapsed token output.

In this paper cum technical report, we present PHUDGE A fine tuned Phi3 model that achieved SOTA results in 4 tasks as Feedback Test, Feedback OOD, MT Human, Preference Test surpassing each and every existing model in latency and throughput. It shows very strong correlation not only with GPT4 but with Human annotators too in unseen data as well as in both absolute and relative grading tasks. We have not only addressed the usage of small LMs for cost effective production grade systems but have also shown that Causal modelling is not only slow in nature but sometimes it can hinder models learning capabilities and should be replaced by simpler tasks whenever we can to make the overall system faster and better. We show that by following systematic ML experimentation, thoughtful data augmentation and re purposing the problem itself, we can even beat 10x bigger models even with lesser training data. To the best of our knowledge, we are re the first one to experiment and showcase the usage of generalised version of Earth Movers Distance AKA Wasserstein distance by using Minkowski Distance with a penalty to control loss smoothing and can be used as a loss function instead of Cross Entropy to get stable training and better results for grading tasks.

Optimal Transport (OT) problem aims to find a transport plan that bridges two distributions while minimizing a given cost function. OT theory has been widely utilized in generative modeling. In the beginning, OT distance has been used as a measure for assessing the distance between data and generated distributions. Recently, OT transport map between data and prior distributions has been utilized as a generative model. These OT-based generative models share a similar adversarial training objective. In this paper, we begin by unifying these OT-based adversarial methods within a single framework. Then, we elucidate the role of each component in training dynamics through a comprehensive analysis of this unified framework. Moreover, we suggest a simple but novel method that improves the previously best-performing OT-based model. Intuitively, our approach conducts a gradual refinement of the generated distribution, progressively aligning it with the data distribution. Our approach achieves a FID score of 2.51 on CIFAR-10 and 5.99 on CelebA-HQ-256, outperforming unified OT-based adversarial approaches.

We consider a biological population whose environment varies periodically in time, exhibiting two very different "seasons" : one is favorable and the other one is unfavorable. For monotone differential models with concave nonlinearities, we address the following question: the system's period being fixed, under what conditions does there exist a critical duration for the unfavorable season? By "critical duration" we mean that above some threshold, the population cannot sustain and extincts, while below this threshold, the system converges to a unique periodic and positive solution. We term this a "sharp seasonal threshold property" (SSTP, for short). Building upon a previous result, we obtain sufficient conditions for SSTP in any dimension and apply our criterion to a two-dimensional model featuring juvenile and adult populations of insects.

If machine learning models were to achieve superhuman abilities at various reasoning or decision-making tasks, how would we go about evaluating such models, given that humans would necessarily be poor proxies for ground truth? In this paper, we propose a framework for evaluating superhuman models via consistency checks. Our premise is that while the correctness of superhuman decisions may be impossible to evaluate, we can still surface mistakes if the model's decisions fail to satisfy certain logical, human-interpretable rules. We instantiate our framework on three tasks where correctness of decisions is hard to evaluate due to either superhuman model abilities, or to otherwise missing ground truth: evaluating chess positions, forecasting future events, and making legal judgments. We show that regardless of a model's (possibly superhuman) performance on these tasks, we can discover logical inconsistencies in decision making. For example: a chess engine assigning opposing valuations to semantically identical boards; GPT-4 forecasting that sports records will evolve non-monotonically over time; or an AI judge assigning bail to a defendant only after we add a felony to their criminal record.

Global solar photospheric magnetic maps play a critical role in solar and heliospheric physics research. Routine magnetograph measurements of the field occur only along the Sun-Earth line, leaving the far-side of the Sun unobserved. Surface Flux Transport (SFT) models attempt to mitigate this by modeling the surface evolution of the field. While such models have long been established in the community (with several releasing public full-Sun maps), none are open source. The Open Source Flux Transport (OFT) model seeks to fill this gap by providing an open and user-extensible SFT model that also builds on the knowledge of previous models with updated numerical and data acquisition/assimilation methods along with additional user-defined features. In this first of a series of papers on OFT, we introduce its computational core: the High-performance Flux Transport (HipFT) code (github.com/predsci/hipft). HipFT implements advection, diffusion, and data assimilation in a modular design that supports a variety of flow models and options. It can compute multiple realizations in a single run across model parameters to create ensembles of maps for uncertainty quantification and is high-performance through the use of multi-CPU and multi-GPU parallelism. HipFT is designed to enable users to easily write extensions, enhancing its flexibility and adaptability. We describe HipFT's model features, validations of its numerical methods, performance of its parallel and GPU-accelerated code implementation, analysis/post-processing options, and example use cases.

In this study, we present a novel dataset for training machine learning models translating between OpenMP Fortran and C++ code. To ensure reliability and applicability, the dataset is created from a range of representative open-source OpenMP benchmarks. It is also refined using a meticulous code similarity test. The effectiveness of our dataset is assessed using both quantitative (CodeBLEU) and qualitative (human evaluation) methods. We showcase how this dataset significantly elevates the translation competencies of large language models (LLMs). Specifically, models without prior coding knowledge experienced a boost of times~5.1 in their CodeBLEU scores, while models with some coding familiarity saw an impressive times~9.9-fold increase. The best fine-tuned model using our dataset outperforms GPT-4. It is also reaching human-level accuracy. This work underscores the immense potential of our dataset in propelling advancements in the domain of code translation for high-performance computing. The dataset is accessible at https://github.com/bin123apple/Fortran-CPP-HPC-code-translation-dataset{OpenMP-Fortran-CPP-Translation}.

Model uncertainty and limited data are fundamental challenges to robust management of human intervention in a natural system. These challenges are acutely highlighted by concerns that many ecological systems may contain tipping points, such as Allee population sizes. Before a collapse, we do not know where the tipping points lie, if they exist at all. Hence, we know neither a complete model of the system dynamics nor do we have access to data in some large region of state-space where such a tipping point might exist. We illustrate how a Bayesian Non-Parametric (BNP) approach using a Gaussian Process (GP) prior provides a flexible representation of this inherent uncertainty. We embed GPs in a Stochastic Dynamic Programming (SDP) framework in order to make robust management predictions with both model uncertainty and limited data. We use simulations to evaluate this approach as compared with the standard approach of using model selection to choose from a set of candidate models. We find that model selection erroneously favors models without tipping points -- leading to harvest policies that guarantee extinction. The GPDP performs nearly as well as the true model and significantly outperforms standard approaches. We illustrate this using examples of simulated single-species dynamics, where the standard model selection approach should be most effective, and find that it still fails to account for uncertainty appropriately and leads to population crashes, while management based on the GPDP does not, since it does not underestimate the uncertainty outside of the observed data.

With the recent development of large language models (LLMs), models that focus on certain domains and languages have been discussed for their necessity. There is also a growing need for benchmarks to evaluate the performance of current LLMs in each domain. Therefore, in this study, we constructed a benchmark comprising multiple tasks specific to the Japanese and financial domains and performed benchmark measurements on some models. Consequently, we confirmed that GPT-4 is currently outstanding, and that the constructed benchmarks function effectively. According to our analysis, our benchmark can differentiate benchmark scores among models in all performance ranges by combining tasks with different difficulties.

In large language models like the Generative Pre-trained Transformer, the Mixture of Experts paradigm has emerged as a powerful technique for enhancing model expressiveness and accuracy. However, deploying GPT MoE models for parallel inference on distributed systems presents significant challenges, primarily due to the extensive Alltoall communication required for expert routing and aggregation. This communication bottleneck exacerbates the already complex computational landscape, hindering the efficient utilization of high-performance computing resources. In this paper, we propose a lightweight optimization technique called ExFlow, to largely accelerate the inference of these MoE models. We take a new perspective on alleviating the communication overhead by exploiting the inter-layer expert affinity. Unlike previous methods, our solution can be directly applied to pre-trained MoE models without any fine-tuning or accuracy degradation. By proposing a context-coherent expert parallelism on distributed systems, our design only uses one Alltoall communication to deliver the same functionality while previous methods all require two Alltoalls. By carefully examining the conditional probability in tokens' routing across multiple layers, we proved that pre-trained GPT MoE models implicitly exhibit a strong inter-layer expert affinity. We then design an efficient integer programming model to capture such features and show that by properly placing the experts on corresponding GPUs, we can reduce up to 67% cross-GPU routing latency. Our solution beats the cutting-edge MoE implementations with experts from 8 to 64, with up to 2.2x improvement in inference throughput. We further provide a detailed study of how the model implicitly acquires this expert affinity at the very early training stage and how this affinity evolves and stabilizes during training.

Lattices are architected metamaterials whose properties strongly depend on their geometrical design. The analogy between lattices and graphs enables the use of graph neural networks (GNNs) as a faster surrogate model compared to traditional methods such as finite element modelling. In this work, we generate a big dataset of structure-property relationships for strut-based lattices. The dataset is made available to the community which can fuel the development of methods anchored in physical principles for the fitting of fourth-order tensors. In addition, we present a higher-order GNN model trained on this dataset. The key features of the model are (i) SE(3) equivariance, and (ii) consistency with the thermodynamic law of conservation of energy. We compare the model to non-equivariant models based on a number of error metrics and demonstrate its benefits in terms of predictive performance and reduced training requirements. Finally, we demonstrate an example application of the model to an architected material design task. The methods which we developed are applicable to fourth-order tensors beyond elasticity such as piezo-optical tensor etc.

Numerous biological and physical processes can be modeled as systems of interacting entities evolving continuously over time, e.g. the dynamics of communicating cells or physical particles. Learning the dynamics of such systems is essential for predicting the temporal evolution of populations across novel samples and unseen environments. Flow-based models allow for learning these dynamics at the population level - they model the evolution of the entire distribution of samples. However, current flow-based models are limited to a single initial population and a set of predefined conditions which describe different dynamics. We argue that multiple processes in natural sciences have to be represented as vector fields on the Wasserstein manifold of probability densities. That is, the change of the population at any moment in time depends on the population itself due to the interactions between samples. In particular, this is crucial for personalized medicine where the development of diseases and their respective treatment response depends on the microenvironment of cells specific to each patient. We propose Meta Flow Matching (MFM), a practical approach to integrating along these vector fields on the Wasserstein manifold by amortizing the flow model over the initial populations. Namely, we embed the population of samples using a Graph Neural Network (GNN) and use these embeddings to train a Flow Matching model. This gives MFM the ability to generalize over the initial distributions unlike previously proposed methods. We demonstrate the ability of MFM to improve prediction of individual treatment responses on a large scale multi-patient single-cell drug screen dataset.

The advancement in generative AI could be boosted with more accessible mathematics. Beyond human-AI chat, large language models (LLMs) are emerging in programming, algorithm discovery, and theorem proving, yet their genomics application is limited. This project introduces Math Agents and mathematical embedding as fresh entries to the "Moore's Law of Mathematics", using a GPT-based workflow to convert equations from literature into LaTeX and Python formats. While many digital equation representations exist, there's a lack of automated large-scale evaluation tools. LLMs are pivotal as linguistic user interfaces, providing natural language access for human-AI chat and formal languages for large-scale AI-assisted computational infrastructure. Given the infinite formal possibility spaces, Math Agents, which interact with math, could potentially shift us from "big data" to "big math". Math, unlike the more flexible natural language, has properties subject to proof, enabling its use beyond traditional applications like high-validation math-certified icons for AI alignment aims. This project aims to use Math Agents and mathematical embeddings to address the ageing issue in information systems biology by applying multiscalar physics mathematics to disease models and genomic data. Generative AI with episodic memory could help analyse causal relations in longitudinal health records, using SIR Precision Health models. Genomic data is suggested for addressing the unsolved Alzheimer's disease problem.

We present a neural network emulator to constrain the thermal parameters of the intergalactic medium (IGM) at 5.4z6.0 using the Lyman-displaystylealpha (Lydisplaystylealpha) forest flux auto-correlation function. Our auto-differentiable JAX-based framework accelerates the surrogate model generation process using approximately 100 sparsely sampled Nyx hydrodynamical simulations with varying combinations of thermal parameters, i.e., the temperature at mean density T_{{0}}, the slope of the temperaturedisplaystyle-density relation displaystylegamma, and the mean transmission flux langle{F}{rangle}. We show that this emulator has a typical accuracy of 1.0% across the specified redshift range. Bayesian inference of the IGM thermal parameters, incorporating emulator uncertainty propagation, is further expedited using NumPyro Hamiltonian Monte Carlo. We compare both the inference results and computational cost of our framework with the traditional nearest-neighbor interpolation approach applied to the same set of mock Lyalpha flux. By examining the credibility contours of the marginalized posteriors for T_{{0}},gamma,and{langle}{F}{rangle} obtained using the emulator, the statistical reliability of measurements is established through inference on 100 realistic mock data sets of the auto-correlation function.

Foundation models pretrained on large-scale datasets are revolutionizing the field of computational pathology (CPath). The generalization ability of foundation models is crucial for the success in various downstream clinical tasks. However, current foundation models have only been evaluated on a limited type and number of tasks, leaving their generalization ability and overall performance unclear. To address this gap, we established a most comprehensive benchmark to evaluate the performance of off-the-shelf foundation models across six distinct clinical task types, encompassing a total of 39 specific tasks. Our findings reveal that existing foundation models excel at certain task types but struggle to effectively handle the full breadth of clinical tasks. To improve the generalization of pathology foundation models, we propose a unified knowledge distillation framework consisting of both expert and self knowledge distillation, where the former allows the model to learn from the knowledge of multiple expert models, while the latter leverages self-distillation to enable image representation learning via local-global alignment. Based on this framework, a Generalizable Pathology Foundation Model (GPFM) is pretrained on a large-scale dataset consisting of 190 million images from around 86,000 public H&E whole slides across 34 major tissue types. Evaluated on the established benchmark, GPFM achieves an impressive average rank of 1.36, with 29 tasks ranked 1st, while the the second-best model, UNI, attains an average rank of 2.96, with only 4 tasks ranked 1st. The superior generalization of GPFM demonstrates its exceptional modeling capabilities across a wide range of clinical tasks, positioning it as a new cornerstone for feature representation in CPath.

As a fundamental task in computational chemistry, retrosynthesis prediction aims to identify a set of reactants to synthesize a target molecule. Existing template-free approaches only consider the graph structures of the target molecule, which often cannot generalize well to rare reaction types and large molecules. Here, we propose T-Rex, a text-assisted retrosynthesis prediction approach that exploits pre-trained text language models, such as ChatGPT, to assist the generation of reactants. T-Rex first exploits ChatGPT to generate a description for the target molecule and rank candidate reaction centers based both the description and the molecular graph. It then re-ranks these candidates by querying the descriptions for each reactants and examines which group of reactants can best synthesize the target molecule. We observed that T-Rex substantially outperformed graph-based state-of-the-art approaches on two datasets, indicating the effectiveness of considering text information. We further found that T-Rex outperformed the variant that only use ChatGPT-based description without the re-ranking step, demonstrate how our framework outperformed a straightforward integration of ChatGPT and graph information. Collectively, we show that text generated by pre-trained language models can substantially improve retrosynthesis prediction, opening up new avenues for exploiting ChatGPT to advance computational chemistry. And the codes can be found at https://github.com/lauyikfung/T-Rex.

Training large language models (LLMs) is known to be challenging because of the huge computational and memory capacity requirements. To address these issues, it is common to use a cluster of GPUs with 3D parallelism, which splits a model along the data batch, pipeline stage, and intra-layer tensor dimensions. However, the use of 3D parallelism produces the additional challenge of finding the optimal number of ways on each dimension and mapping the split models onto the GPUs. Several previous studies have attempted to automatically find the optimal configuration, but many of these lacked several important aspects. For instance, the heterogeneous nature of the interconnect speeds is often ignored. While the peak bandwidths for the interconnects are usually made equal, the actual attained bandwidth varies per link in real-world clusters. Combined with the critical path modeling that does not properly consider the communication, they easily fall into sub-optimal configurations. In addition, they often fail to consider the memory requirement per GPU, often recommending solutions that could not be executed. To address these challenges, we propose Pipette, which is an automatic fine-grained LLM training configurator for real-world clusters. By devising better performance models along with the memory estimator and fine-grained individual GPU assignment, Pipette achieves faster configurations that satisfy the memory constraints. We evaluated Pipette on large clusters to show that it provides a significant speedup over the prior art. The implementation of Pipette is available at https://github.com/yimjinkyu1/date2024_pipette.

Generative models trained on internet-scale data are capable of generating novel and realistic texts, images, and videos. A natural next question is whether these models can advance science, for example by generating novel stable materials. Traditionally, models with explicit structures (e.g., graphs) have been used in modeling structural relationships in scientific data (e.g., atoms and bonds in crystals), but generating structures can be difficult to scale to large and complex systems. Another challenge in generating materials is the mismatch between standard generative modeling metrics and downstream applications. For instance, common metrics such as the reconstruction error do not correlate well with the downstream goal of discovering stable materials. In this work, we tackle the scalability challenge by developing a unified crystal representation that can represent any crystal structure (UniMat), followed by training a diffusion probabilistic model on these UniMat representations. Our empirical results suggest that despite the lack of explicit structure modeling, UniMat can generate high fidelity crystal structures from larger and more complex chemical systems, outperforming previous graph-based approaches under various generative modeling metrics. To better connect the generation quality of materials to downstream applications, such as discovering novel stable materials, we propose additional metrics for evaluating generative models of materials, including per-composition formation energy and stability with respect to convex hulls through decomposition energy from Density Function Theory (DFT). Lastly, we show that conditional generation with UniMat can scale to previously established crystal datasets with up to millions of crystals structures, outperforming random structure search (the current leading method for structure discovery) in discovering new stable materials.

By learning the gradient of smoothed data distributions, diffusion models can iteratively generate samples from complex distributions. The learned score function enables their generalization capabilities, but how the learned score relates to the score of the underlying data manifold remains largely unclear. Here, we aim to elucidate this relationship by comparing learned neural scores to the scores of two kinds of analytically tractable distributions: Gaussians and Gaussian mixtures. The simplicity of the Gaussian model makes it theoretically attractive, and we show that it admits a closed-form solution and predicts many qualitative aspects of sample generation dynamics. We claim that the learned neural score is dominated by its linear (Gaussian) approximation for moderate to high noise scales, and supply both theoretical and empirical arguments to support this claim. Moreover, the Gaussian approximation empirically works for a larger range of noise scales than naive theory suggests it should, and is preferentially learned early in training. At smaller noise scales, we observe that learned scores are better described by a coarse-grained (Gaussian mixture) approximation of training data than by the score of the training distribution, a finding consistent with generalization. Our findings enable us to precisely predict the initial phase of trained models' sampling trajectories through their Gaussian approximations. We show that this allows the skipping of the first 15-30% of sampling steps while maintaining high sample quality (with a near state-of-the-art FID score of 1.93 on CIFAR-10 unconditional generation). This forms the foundation of a novel hybrid sampling method, termed analytical teleportation, which can seamlessly integrate with and accelerate existing samplers, including DPM-Solver-v3 and UniPC. Our findings suggest ways to improve the design and training of diffusion models.

Generating novel molecules with out-of-distribution properties is a major challenge in molecular discovery. While supervised learning methods generate high-quality molecules similar to those in a dataset, they struggle to generalize to out-of-distribution properties. Reinforcement learning can explore new chemical spaces but often conducts 'reward-hacking' and generates non-synthesizable molecules. In this work, we address this problem by integrating a state-of-the-art supervised learning method, STGG+, in an active learning loop. Our approach iteratively generates, evaluates, and fine-tunes STGG+ to continuously expand its knowledge. We denote this approach STGG+AL. We apply STGG+AL to the design of organic pi-functional materials, specifically two challenging tasks: 1) generating highly absorptive molecules characterized by high oscillator strength and 2) designing absorptive molecules with reasonable oscillator strength in the near-infrared (NIR) range. The generated molecules are validated and rationalized in-silico with time-dependent density functional theory. Our results demonstrate that our method is highly effective in generating novel molecules with high oscillator strength, contrary to existing methods such as reinforcement learning (RL) methods. We open-source our active-learning code along with our Conjugated-xTB dataset containing 2.9 million pi-conjugated molecules and the function for approximating the oscillator strength and absorption wavelength (based on sTDA-xTB).

Generative models, especially diffusion models (DMs), have achieved promising results for generating feature-rich geometries and advancing foundational science problems such as molecule design. Inspired by the recent huge success of Stable (latent) Diffusion models, we propose a novel and principled method for 3D molecule generation named Geometric Latent Diffusion Models (GeoLDM). GeoLDM is the first latent DM model for the molecular geometry domain, composed of autoencoders encoding structures into continuous latent codes and DMs operating in the latent space. Our key innovation is that for modeling the 3D molecular geometries, we capture its critical roto-translational equivariance constraints by building a point-structured latent space with both invariant scalars and equivariant tensors. Extensive experiments demonstrate that GeoLDM can consistently achieve better performance on multiple molecule generation benchmarks, with up to 7\% improvement for the valid percentage of large biomolecules. Results also demonstrate GeoLDM's higher capacity for controllable generation thanks to the latent modeling. Code is provided at https://github.com/MinkaiXu/GeoLDM.

Applications of machine learning techniques for materials modeling typically involve functions known to be equivariant or invariant to specific symmetries. While graph neural networks (GNNs) have proven successful in such tasks, they enforce symmetries via the model architecture, which often reduces their expressivity, scalability and comprehensibility. In this paper, we introduce (1) a flexible framework relying on stochastic frame-averaging (SFA) to make any model E(3)-equivariant or invariant through data transformations. (2) FAENet: a simple, fast and expressive GNN, optimized for SFA, that processes geometric information without any symmetrypreserving design constraints. We prove the validity of our method theoretically and empirically demonstrate its superior accuracy and computational scalability in materials modeling on the OC20 dataset (S2EF, IS2RE) as well as common molecular modeling tasks (QM9, QM7-X). A package implementation is available at https://faenet.readthedocs.io.

Protein design with desirable properties has been a significant challenge for many decades. Generative artificial intelligence is a promising approach and has achieved great success in various protein generation tasks. Notably, diffusion models stand out for their robust mathematical foundations and impressive generative capabilities, offering unique advantages in certain applications such as protein design. In this review, we first give the definition and characteristics of diffusion models and then focus on two strategies: Denoising Diffusion Probabilistic Models and Score-based Generative Models, where DDPM is the discrete form of SGM. Furthermore, we discuss their applications in protein design, peptide generation, drug discovery, and protein-ligand interaction. Finally, we outline the future perspectives of diffusion models to advance autonomous protein design and engineering. The E(3) group consists of all rotations, reflections, and translations in three-dimensions. The equivariance on the E(3) group can keep the physical stability of the frame of each amino acid as much as possible, and we reflect on how to keep the diffusion model E(3) equivariant for protein generation.

We introduce Interleaved Gibbs Diffusion (IGD), a novel generative modeling framework for mixed continuous-discrete data, focusing on constrained generation problems. Prior works on discrete and continuous-discrete diffusion models assume factorized denoising distribution for fast generation, which can hinder the modeling of strong dependencies between random variables encountered in constrained generation. IGD moves beyond this by interleaving continuous and discrete denoising algorithms via a discrete time Gibbs sampling type Markov chain. IGD provides flexibility in the choice of denoisers, allows conditional generation via state-space doubling and inference time scaling via the ReDeNoise method. Empirical evaluations on three challenging tasks-solving 3-SAT, generating molecule structures, and generating layouts-demonstrate state-of-the-art performance. Notably, IGD achieves a 7% improvement on 3-SAT out of the box and achieves state-of-the-art results in molecule generation without relying on equivariant diffusion or domain-specific architectures. We explore a wide range of modeling, and interleaving strategies along with hyperparameters in each of these problems.

Unlike perfect information games, where all elements are known to every player, imperfect information games emulate the real-world complexities of decision-making under uncertain or incomplete information. GPT-4, the recent breakthrough in large language models (LLMs) trained on massive passive data, is notable for its knowledge retrieval and reasoning abilities. This paper delves into the applicability of GPT-4's learned knowledge for imperfect information games. To achieve this, we introduce Suspicion-Agent, an innovative agent that leverages GPT-4's capabilities for performing in imperfect information games. With proper prompt engineering to achieve different functions, Suspicion-Agent based on GPT-4 demonstrates remarkable adaptability across a range of imperfect information card games. Importantly, GPT-4 displays a strong high-order theory of mind (ToM) capacity, meaning it can understand others and intentionally impact others' behavior. Leveraging this, we design a planning strategy that enables GPT-4 to competently play against different opponents, adapting its gameplay style as needed, while requiring only the game rules and descriptions of observations as input. In the experiments, we qualitatively showcase the capabilities of Suspicion-Agent across three different imperfect information games and then quantitatively evaluate it in Leduc Hold'em. The results show that Suspicion-Agent can potentially outperform traditional algorithms designed for imperfect information games, without any specialized training or examples. In order to encourage and foster deeper insights within the community, we make our game-related data publicly available.

Peptide therapeutics, a major class of medicines, have achieved remarkable success across diseases such as diabetes and cancer, with landmark examples such as GLP-1 receptor agonists revolutionizing the treatment of type-2 diabetes and obesity. Despite their success, designing peptides that satisfy multiple conflicting objectives, such as target binding affinity, solubility, and membrane permeability, remains a major challenge. Classical drug development and structure-based design are ineffective for such tasks, as they fail to optimize global functional properties critical for therapeutic efficacy. Existing generative frameworks are largely limited to continuous spaces, unconditioned outputs, or single-objective guidance, making them unsuitable for discrete sequence optimization across multiple properties. To address this, we present PepTune, a multi-objective discrete diffusion model for the simultaneous generation and optimization of therapeutic peptide SMILES. Built on the Masked Discrete Language Model (MDLM) framework, PepTune ensures valid peptide structures with state-dependent masking schedules and penalty-based objectives. To guide the diffusion process, we propose a Monte Carlo Tree Search (MCTS)-based strategy that balances exploration and exploitation to iteratively refine Pareto-optimal sequences. MCTS integrates classifier-based rewards with search-tree expansion, overcoming gradient estimation challenges and data sparsity inherent to discrete spaces. Using PepTune, we generate diverse, chemically-modified peptides optimized for multiple therapeutic properties, including target binding affinity, membrane permeability, solubility, hemolysis, and non-fouling characteristics on various disease-relevant targets. In total, our results demonstrate that MCTS-guided discrete diffusion is a powerful and modular approach for multi-objective sequence design in discrete state spaces.

Recent work claims that large language models display emergent abilities, abilities not present in smaller-scale models that are present in larger-scale models. What makes emergent abilities intriguing is two-fold: their sharpness, transitioning seemingly instantaneously from not present to present, and their unpredictability, appearing at seemingly unforeseeable model scales. Here, we present an alternative explanation for emergent abilities: that for a particular task and model family, when analyzing fixed model outputs, emergent abilities appear due to the researcher's choice of metric rather than due to fundamental changes in model behavior with scale. Specifically, nonlinear or discontinuous metrics produce apparent emergent abilities, whereas linear or continuous metrics produce smooth, continuous predictable changes in model performance. We present our alternative explanation in a simple mathematical model, then test it in three complementary ways: we (1) make, test and confirm three predictions on the effect of metric choice using the InstructGPT/GPT-3 family on tasks with claimed emergent abilities; (2) make, test and confirm two predictions about metric choices in a meta-analysis of emergent abilities on BIG-Bench; and (3) show to choose metrics to produce never-before-seen seemingly emergent abilities in multiple vision tasks across diverse deep networks. Via all three analyses, we provide evidence that alleged emergent abilities evaporate with different metrics or with better statistics, and may not be a fundamental property of scaling AI models.

With the growing availability of data within various scientific domains, generative models hold enormous potential to accelerate scientific discovery. They harness powerful representations learned from datasets to speed up the formulation of novel hypotheses with the potential to impact material discovery broadly. We present the Generative Toolkit for Scientific Discovery (GT4SD). This extensible open-source library enables scientists, developers, and researchers to train and use state-of-the-art generative models to accelerate scientific discovery focused on material design.

Recent advances in large language models have brought immense value to the world, with their superior capabilities stemming from the massive number of parameters they utilize. However, even the GPUs with the highest memory capacities, currently peaking at 80GB, are far from sufficient to accommodate these vast parameters and their associated optimizer states when conducting stochastic gradient descent-based optimization. One approach to hosting such huge models is to aggregate device memory from many GPUs. However, this approach introduces prohibitive costs for most academic researchers, who always have a limited budget for many high-end GPU servers. In this paper, we focus on huge model fine-tuning on a single, even low-end, GPU in a commodity server, which is accessible to most AI researchers. In such a scenario, the state-of-the-art work ZeRO-Infinity suffers from two severe issues when running in a commodity server: 1) low GPU utilization due to inefficient swapping, and 2) limited trainable model size due to CPU memory capacity. The underlying reason is that ZeRO-Infinity is optimized for running on high-end GPU servers. To this end, we present Fuyou, a low-cost training framework that enables efficient 100B huge model fine-tuning on a low-end server with a low-end GPU and limited CPU memory capacity. The key idea is to add the SSD-CPU communication as an optimization dimension and thus carefully co-optimize computation and data swapping from a systematic approach to maximize GPU utilization. The experimental results show that 1) Fuyou is able to fine-tune 175B GPT-3 on a consumer GPU RTX 4090 with high GPU utilization, while ZeRO-Infinity fails to fine-tune; and 2) when training a small GPT-3 13B model, Fuyou achieves 156 TFLOPS on an RTX 4090 GPU while ZeRO-Infinity only achieves 45 TFLOPS.

Generative tasks about molecules, including but not limited to molecule generation, are crucial for drug discovery and material design, and have consistently attracted significant attention. In recent years, diffusion models have emerged as an impressive class of deep generative models, sparking extensive research and leading to numerous studies on their application to molecular generative tasks. Despite the proliferation of related work, there remains a notable lack of up-to-date and systematic surveys in this area. Particularly, due to the diversity of diffusion model formulations, molecular data modalities, and generative task types, the research landscape is challenging to navigate, hindering understanding and limiting the area's growth. To address this, this paper conducts a comprehensive survey of diffusion model-based molecular generative methods. We systematically review the research from the perspectives of methodological formulations, data modalities, and task types, offering a novel taxonomy. This survey aims to facilitate understanding and further flourishing development in this area. The relevant papers are summarized at: https://github.com/AzureLeon1/awesome-molecular-diffusion-models.

Large language models (LLMs) are currently at the forefront of intertwining AI systems with human communication and everyday life. Therefore, it is of great importance to evaluate their emerging abilities. In this study, we show that LLMs like GPT-3 exhibit behavior that strikingly resembles human-like intuition - and the cognitive errors that come with it. However, LLMs with higher cognitive capabilities, in particular ChatGPT and GPT-4, learned to avoid succumbing to these errors and perform in a hyperrational manner. For our experiments, we probe LLMs with the Cognitive Reflection Test (CRT) as well as semantic illusions that were originally designed to investigate intuitive decision-making in humans. Our study demonstrates that investigating LLMs with methods from psychology has the potential to reveal otherwise unknown emergent traits.

State-space models (SSMs) have recently emerged as a framework for learning long-range sequence tasks. An example is the structured state-space sequence (S4) layer, which uses the diagonal-plus-low-rank structure of the HiPPO initialization framework. However, the complicated structure of the S4 layer poses challenges; and, in an effort to address these challenges, models such as S4D and S5 have considered a purely diagonal structure. This choice simplifies the implementation, improves computational efficiency, and allows channel communication. However, diagonalizing the HiPPO framework is itself an ill-posed problem. In this paper, we propose a general solution for this and related ill-posed diagonalization problems in machine learning. We introduce a generic, backward-stable "perturb-then-diagonalize" (PTD) methodology, which is based on the pseudospectral theory of non-normal operators, and which may be interpreted as the approximate diagonalization of the non-normal matrices defining SSMs. Based on this, we introduce the S4-PTD and S5-PTD models. Through theoretical analysis of the transfer functions of different initialization schemes, we demonstrate that the S4-PTD/S5-PTD initialization strongly converges to the HiPPO framework, while the S4D/S5 initialization only achieves weak convergences. As a result, our new models show resilience to Fourier-mode noise-perturbed inputs, a crucial property not achieved by the S4D/S5 models. In addition to improved robustness, our S5-PTD model averages 87.6% accuracy on the Long-Range Arena benchmark, demonstrating that the PTD methodology helps to improve the accuracy of deep learning models.

Gaussian processes (GPs) are popular nonparametric statistical models for learning unknown functions and quantifying the spatiotemporal uncertainty in data. Recent works have extended GPs to model scalar and vector quantities distributed over non-Euclidean domains, including smooth manifolds appearing in numerous fields such as computer vision, dynamical systems, and neuroscience. However, these approaches assume that the manifold underlying the data is known, limiting their practical utility. We introduce RVGP, a generalisation of GPs for learning vector signals over latent Riemannian manifolds. Our method uses positional encoding with eigenfunctions of the connection Laplacian, associated with the tangent bundle, readily derived from common graph-based approximation of data. We demonstrate that RVGP possesses global regularity over the manifold, which allows it to super-resolve and inpaint vector fields while preserving singularities. Furthermore, we use RVGP to reconstruct high-density neural dynamics derived from low-density EEG recordings in healthy individuals and Alzheimer's patients. We show that vector field singularities are important disease markers and that their reconstruction leads to a comparable classification accuracy of disease states to high-density recordings. Thus, our method overcomes a significant practical limitation in experimental and clinical applications.

Large Language Models (LLMs) have demonstrated remarkable capabilities across various domains and are moving towards more specialized areas. Recent advanced proprietary models such as GPT-4 and Gemini have achieved significant advancements in biomedicine, which have also raised privacy and security challenges. The construction of specialized generalists hinges largely on high-quality datasets, enhanced by techniques like supervised fine-tuning and reinforcement learning from human or AI feedback, and direct preference optimization. However, these leading technologies (e.g., preference learning) are still significantly limited in the open source community due to the scarcity of specialized data. In this paper, we present the UltraMedical collections, which consist of high-quality manual and synthetic datasets in the biomedicine domain, featuring preference annotations across multiple advanced LLMs. By utilizing these datasets, we fine-tune a suite of specialized medical models based on Llama-3 series, demonstrating breathtaking capabilities across various medical benchmarks. Moreover, we develop powerful reward models skilled in biomedical and general reward benchmark, enhancing further online preference learning within the biomedical LLM community.

Generative models for molecules have shown considerable promise for use in computational chemistry, but remain difficult to use for non-experts. For this reason, we introduce open-source infrastructure for easily building generative molecular models into the widely used DeepChem [Ramsundar et al., 2019] library with the aim of creating a robust and reusable molecular generation pipeline. In particular, we add high quality PyTorch [Paszke et al., 2019] implementations of the Molecular Generative Adversarial Networks (MolGAN) [Cao and Kipf, 2022] and Normalizing Flows [Papamakarios et al., 2021]. Our implementations show strong performance comparable with past work [Kuznetsov and Polykovskiy, 2021, Cao and Kipf, 2022].

Generative modeling of crystal data distribution is an important yet challenging task due to the unique periodic physical symmetry of crystals. Diffusion-based methods have shown early promise in modeling crystal distribution. More recently, Bayesian Flow Networks were introduced to aggregate noisy latent variables, resulting in a variance-reduced parameter space that has been shown to be advantageous for modeling Euclidean data distributions with structural constraints (Song et al., 2023). Inspired by this, we seek to unlock its potential for modeling variables located in non-Euclidean manifolds e.g. those within crystal structures, by overcoming challenging theoretical issues. We introduce CrysBFN, a novel crystal generation method by proposing a periodic Bayesian flow, which essentially differs from the original Gaussian-based BFN by exhibiting non-monotonic entropy dynamics. To successfully realize the concept of periodic Bayesian flow, CrysBFN integrates a new entropy conditioning mechanism and empirically demonstrates its significance compared to time-conditioning. Extensive experiments over both crystal ab initio generation and crystal structure prediction tasks demonstrate the superiority of CrysBFN, which consistently achieves new state-of-the-art on all benchmarks. Surprisingly, we found that CrysBFN enjoys a significant improvement in sampling efficiency, e.g., ~100x speedup 10 v.s. 2000 steps network forwards) compared with previous diffusion-based methods on MP-20 dataset. Code is available at https://github.com/wu-han-lin/CrysBFN.

Brain tumor growth is unique to each glioma patient and extends beyond what is visible in imaging scans, infiltrating surrounding brain tissue. Understanding these hidden patient-specific progressions is essential for effective therapies. Current treatment plans for brain tumors, such as radiotherapy, typically involve delineating a uniform margin around the visible tumor on pre-treatment scans to target this invisible tumor growth. This "one size fits all" approach is derived from population studies and often fails to account for the nuances of individual patient conditions. We present the GliODIL framework, which infers the full spatial distribution of tumor cell concentration from available multi-modal imaging, leveraging a Fisher-Kolmogorov type physics model to describe tumor growth. This is achieved through the newly introduced method of Optimizing the Discrete Loss (ODIL), where both data and physics-based constraints are softly assimilated into the solution. Our test dataset comprises 152 glioblastoma patients with pre-treatment imaging and post-treatment follow-ups for tumor recurrence monitoring. By blending data-driven techniques with physics-based constraints, GliODIL enhances recurrence prediction in radiotherapy planning, challenging traditional uniform margins and strict adherence to the Fisher-Kolmogorov partial differential equation (PDE) model, which is adapted for complex cases.

E(3)-equivariant neural networks have demonstrated success across a wide range of 3D modelling tasks. A fundamental operation in these networks is the tensor product, which interacts two geometric features in an equivariant manner to create new features. Due to the high computational complexity of the tensor product, significant effort has been invested to optimize the runtime of this operation. For example, Luo et al. (2024) recently proposed the Gaunt tensor product (GTP) which promises a significant speedup. In this work, we provide a careful, systematic analysis of a number of tensor product operations. In particular, we emphasize that different tensor products are not performing the same operation. The reported speedups typically come at the cost of expressivity. We introduce measures of expressivity and interactability to characterize these differences. In addition, we realized the original implementation of GTP can be greatly simplified by directly using a spherical grid at no cost in asymptotic runtime. This spherical grid approach is faster on our benchmarks and in actual training of the MACE interatomic potential by 30%. Finally, we provide the first systematic microbenchmarks of the various tensor product operations. We find that the theoretical runtime guarantees can differ wildly from empirical performance, demonstrating the need for careful application-specific benchmarking. Code is available at https://github.com/atomicarchitects/PriceofFreedom.

We propose a new framework for estimating generative models via an adversarial process, in which we simultaneously train two models: a generative model G that captures the data distribution, and a discriminative model D that estimates the probability that a sample came from the training data rather than G. The training procedure for G is to maximize the probability of D making a mistake. This framework corresponds to a minimax two-player game. In the space of arbitrary functions G and D, a unique solution exists, with G recovering the training data distribution and D equal to 1/2 everywhere. In the case where G and D are defined by multilayer perceptrons, the entire system can be trained with backpropagation. There is no need for any Markov chains or unrolled approximate inference networks during either training or generation of samples. Experiments demonstrate the potential of the framework through qualitative and quantitative evaluation of the generated samples.

Designing antibody sequences to better resemble those observed in natural human repertoires is a key challenge in biologics development. We introduce IgCraft: a multi-purpose model for paired human antibody sequence generation, built on Bayesian Flow Networks. IgCraft presents one of the first unified generative modeling frameworks capable of addressing multiple antibody sequence design tasks with a single model, including unconditional sampling, sequence inpainting, inverse folding, and CDR motif scaffolding. Our approach achieves competitive results across the full spectrum of these tasks while constraining generation to the space of human antibody sequences, exhibiting particular strengths in CDR motif scaffolding (grafting) where we achieve state-of-the-art performance in terms of humanness and preservation of structural properties. By integrating previously separate tasks into a single scalable generative model, IgCraft provides a versatile platform for sampling human antibody sequences under a variety of contexts relevant to antibody discovery and engineering. Model code and weights are publicly available at github.com/mgreenig/IgCraft.

Crystal symmetry plays a fundamental role in determining its physical, chemical, and electronic properties such as electrical and thermal conductivity, optical and polarization behavior, and mechanical strength. Almost all known crystalline materials have internal symmetry. However, this is often inadequately addressed by existing generative models, making the consistent generation of stable and symmetrically valid crystal structures a significant challenge. We introduce WyFormer, a generative model that directly tackles this by formally conditioning on space group symmetry. It achieves this by using Wyckoff positions as the basis for an elegant, compressed, and discrete structure representation. To model the distribution, we develop a permutation-invariant autoregressive model based on the Transformer encoder and an absence of positional encoding. Extensive experimentation demonstrates WyFormer's compelling combination of attributes: it achieves best-in-class symmetry-conditioned generation, incorporates a physics-motivated inductive bias, produces structures with competitive stability, predicts material properties with competitive accuracy even without atomic coordinates, and exhibits unparalleled inference speed.

We study flat space cosmologies in two dimensions by taking the flat space limit of the Achucarro-Ortiz model. We unravel a phase transition between hot flat space and flat space cosmologies, and derive a new dilaton-dependent counterterm required for the consistency of the Euclidean partition function. Our results generalize to asymptotically mass-dominated 2-dimensional dilaton gravity models, whose thermodynamical properties we discuss. The novel case of asymptotic mass-domination is neither covered by the comprehensive discussion of hep-th/0703230 nor by the more recent generalization to dilaton gravity with confining U(1) charges in 1406.7007.

Prior-data fitted networks (PFNs) were recently proposed as a new paradigm for machine learning. Instead of training the network to an observed training set, a fixed model is pre-trained offline on small, simulated training sets from a variety of tasks. The pre-trained model is then used to infer class probabilities in-context on fresh training sets with arbitrary size and distribution. Empirically, PFNs achieve state-of-the-art performance on tasks with similar size to the ones used in pre-training. Surprisingly, their accuracy further improves when passed larger data sets during inference. This article establishes a theoretical foundation for PFNs and illuminates the statistical mechanisms governing their behavior. While PFNs are motivated by Bayesian ideas, a purely frequentistic interpretation of PFNs as pre-tuned, but untrained predictors explains their behavior. A predictor's variance vanishes if its sensitivity to individual training samples does and the bias vanishes only if it is appropriately localized around the test feature. The transformer architecture used in current PFN implementations ensures only the former. These findings shall prove useful for designing architectures with favorable empirical behavior.

Real-world time series often exhibit a non-stationary nature, degrading the performance of pre-trained forecasting models. Test-Time Adaptation (TTA) addresses this by adjusting models during inference, but existing methods typically update the full model, increasing memory and compute costs. We propose PETSA, a parameter-efficient method that adapts forecasters at test time by only updating small calibration modules on the input and output. PETSA uses low-rank adapters and dynamic gating to adjust representations without retraining. To maintain accuracy despite limited adaptation capacity, we introduce a specialized loss combining three components: (1) a robust term, (2) a frequency-domain term to preserve periodicity, and (3) a patch-wise structural term for structural alignment. PETSA improves the adaptability of various forecasting backbones while requiring fewer parameters than baselines. Experimental results on benchmark datasets show that PETSA achieves competitive or better performance across all horizons. Our code is available at: https://github.com/BorealisAI/PETSA

We present the "Spanish Built Factual Freectianary 2.0" (Spanish-BFF-2) as the second iteration of an AI-generated Spanish dictionary. Previously, we developed the inaugural version of this unique free dictionary employing GPT-3. In this study, we aim to improve the dictionary by using GPT-4-turbo instead. Furthermore, we explore improvements made to the initial version and compare the performance of both models.

As of September 2023, ChatGPT correctly answers "what is 7+8" with 15, but when asked "7+8=15, True or False" it responds with "False". This inconsistency between generating and validating an answer is prevalent in language models (LMs) and erodes trust. In this paper, we propose a framework for measuring the consistency between generation and validation (which we call generator-validator consistency, or GV-consistency), finding that even GPT-4, a state-of-the-art LM, is GV-consistent only 76% of the time. To improve the consistency of LMs, we propose to finetune on the filtered generator and validator responses that are GV-consistent, and call this approach consistency fine-tuning. We find that this approach improves GV-consistency of Alpaca-30B from 60% to 93%, and the improvement extrapolates to unseen tasks and domains (e.g., GV-consistency for positive style transfers extrapolates to unseen styles like humor). In addition to improving consistency, consistency fine-tuning improves both generator quality and validator accuracy without using any labeled data. Evaluated across 6 tasks, including math questions, knowledge-intensive QA, and instruction following, our method improves the generator quality by 16% and the validator accuracy by 6.3% across all tasks.

The "pre-training rightarrow downstream adaptation" presents both new opportunities and challenges for Continual Learning (CL). Although the recent state-of-the-art in CL is achieved through Parameter-Efficient-Tuning (PET) adaptation paradigm, only prompt has been explored, limiting its application to Transformers only. In this paper, we position prompting as one instantiation of PET, and propose a unified CL framework with general PET, dubbed as Learning-Accumulation-Ensemble (LAE). PET, e.g., using Adapter, LoRA, or Prefix, can adapt a pre-trained model to downstream tasks with fewer parameters and resources. Given a PET method, our LAE framework incorporates it for CL with three novel designs. 1) Learning: the pre-trained model adapts to the new task by tuning an online PET module, along with our adaptation speed calibration to align different PET modules, 2) Accumulation: the task-specific knowledge learned by the online PET module is accumulated into an offline PET module through momentum update, 3) Ensemble: During inference, we respectively construct two experts with online/offline PET modules (which are favored by the novel/historical tasks) for prediction ensemble. We show that LAE is compatible with a battery of PET methods and gains strong CL capability. For example, LAE with Adaptor PET surpasses the prior state-of-the-art by 1.3% and 3.6% in last-incremental accuracy on CIFAR100 and ImageNet-R datasets, respectively. Code is available at https://github.com/gqk/LAE.

Whole-Slide Image (WSI) is an important tool for evaluating the prognosis of cancer patients. Present WSI-based prognosis studies generally follow a conventional paradigm -- cancer-specific model development -- where one cancer disease corresponds to one model and this model cannot make use of the prognostic knowledge from others. Despite its notable success in recent years, this paradigm has inherent limitations and has always been struggling with practical requirements: (i) scaling to the rare tumor diseases with very limited samples and (ii) benefiting from the generalizable prognostic knowledge in other cancers. To this end, this paper presents the first systematic study on Prognostic Knowledge Transfer in Pathology, called Path-PKT. It comprises three main parts. (1) We curate a large dataset (UNI2-h-DSS) with 13 cancers and use it to evaluate the transferability of prognostic knowledge between different cancers computationally. (2) We design experiments to understand what factors affect knowledge transfer and what causes positive transfers. (3) Motivated by empirical findings, we propose a new baseline approach (MoE-PKT) with a routing mechanism to utilize the generalizable prognostic knowledge in other cancers. Finally, we show the transferability of source models to rare tumor diseases. This study could lay solid foundations for the study of knowledge transfer in WSI-based cancer prognosis. Source code is available at https://github.com/liupei101/Path-PKT.

This paper reports the first brain-inspired large language model (BriLLM). This is a non-Transformer, non-GPT, non-traditional machine learning input-output controlled generative language model. The model is based on the Signal Fully-connected flowing (SiFu) definition on the directed graph in terms of the neural network, and has the interpretability of all nodes on the graph of the whole model, instead of the traditional machine learning model that only has limited interpretability at the input and output ends. In the language model scenario, the token is defined as a node in the graph. A randomly shaped or user-defined signal flow flows between nodes on the principle of "least resistance" along paths. The next token or node to be predicted or generated is the target of the signal flow. As a language model, BriLLM theoretically supports infinitely long n-gram models when the model size is independent of the input and predicted length of the model. The model's working signal flow provides the possibility of recall activation and innate multi-modal support similar to the cognitive patterns of the human brain. At present, we released the first BriLLM version in Chinese, with 4000 tokens, 32-dimensional node width, 16-token long sequence prediction ability, and language model prediction performance comparable to GPT-1. More computing power will help us explore the infinite possibilities depicted above.

Large pretrained models such as GPT-3 have had tremendous impact on modern natural language processing by leveraging self-supervised learning to learn salient representations that can be used to readily finetune on a wide variety of downstream tasks. We investigate the possibility of transferring such advances to molecular machine learning by building a chemical foundation model, ChemBERTa-2, using the language of SMILES. While labeled data for molecular prediction tasks is typically scarce, libraries of SMILES strings are readily available. In this work, we build upon ChemBERTa by optimizing the pretraining process. We compare multi-task and self-supervised pretraining by varying hyperparameters and pretraining dataset size, up to 77M compounds from PubChem. To our knowledge, the 77M set constitutes one of the largest datasets used for molecular pretraining to date. We find that with these pretraining improvements, we are competitive with existing state-of-the-art architectures on the MoleculeNet benchmark suite. We analyze the degree to which improvements in pretraining translate to improvement on downstream tasks.

Riemannian diffusion models draw inspiration from standard Euclidean space diffusion models to learn distributions on general manifolds. Unfortunately, the additional geometric complexity renders the diffusion transition term inexpressible in closed form, so prior methods resort to imprecise approximations of the score matching training objective that degrade performance and preclude applications in high dimensions. In this work, we reexamine these approximations and propose several practical improvements. Our key observation is that most relevant manifolds are symmetric spaces, which are much more amenable to computation. By leveraging and combining various ans\"{a}tze, we can quickly compute relevant quantities to high precision. On low dimensional datasets, our correction produces a noticeable improvement, allowing diffusion to compete with other methods. Additionally, we show that our method enables us to scale to high dimensional tasks on nontrivial manifolds. In particular, we model QCD densities on SU(n) lattices and contrastively learned embeddings on high dimensional hyperspheres.

LLM agents enhanced by tree search algorithms have yielded notable performances in code generation. However, current search algorithms in this domain suffer from low search quality due to several reasons: 1) Ineffective design of the search space for the high-reasoning demands of code generation tasks, 2) Inadequate integration of code feedback with the search algorithm, and 3) Poor handling of negative feedback during the search, leading to reduced search efficiency and quality. To address these challenges, we propose to search for the reasoning process of the code and use the detailed feedback of code execution to refine erroneous thoughts during the search. In this paper, we introduce RethinkMCTS, which employs the Monte Carlo Tree Search (MCTS) algorithm to conduct thought-level searches before generating code, thereby exploring a wider range of strategies. More importantly, we construct verbal feedback from fine-grained code execution feedback to refine erroneous thoughts during the search. This ensures that the search progresses along the correct reasoning paths, thus improving the overall search quality of the tree by leveraging execution feedback. Through extensive experiments, we demonstrate that RethinkMCTS outperforms previous search-based and feedback-based code generation baselines. On the HumanEval dataset, it improves the pass@1 of GPT-3.5-turbo from 70.12 to 89.02 and GPT-4o-mini from 87.20 to 94.51. It effectively conducts more thorough exploration through thought-level searches and enhances the search quality of the entire tree by incorporating rethink operation.

Molecular relational learning, whose goal is to learn the interaction behavior between molecular pairs, got a surge of interest in molecular sciences due to its wide range of applications. Recently, graph neural networks have recently shown great success in molecular relational learning by modeling a molecule as a graph structure, and considering atom-level interactions between two molecules. Despite their success, existing molecular relational learning methods tend to overlook the nature of chemistry, i.e., a chemical compound is composed of multiple substructures such as functional groups that cause distinctive chemical reactions. In this work, we propose a novel relational learning framework, called CGIB, that predicts the interaction behavior between a pair of graphs by detecting core subgraphs therein. The main idea is, given a pair of graphs, to find a subgraph from a graph that contains the minimal sufficient information regarding the task at hand conditioned on the paired graph based on the principle of conditional graph information bottleneck. We argue that our proposed method mimics the nature of chemical reactions, i.e., the core substructure of a molecule varies depending on which other molecule it interacts with. Extensive experiments on various tasks with real-world datasets demonstrate the superiority of CGIB over state-of-the-art baselines. Our code is available at https://github.com/Namkyeong/CGIB.

We study a discrete model for generalized exchange-driven growth in which the particle exchanged between two clusters is not limited to be of size one. This set of models include as special cases the usual exchange-driven growth system and the coagulation-fragmentation system with binary fragmentation. Under reasonable general condition on the rate coefficients we establish the existence of admissible solutions, meaning solutions that are obtained as appropriate limit of solutions to a finite-dimensional truncation of the infinite-dimensional ODE. For these solutions we prove that, in the class of models we call isolated both the total number of particles and the total mass are conserved, whereas in those models we can non-isolated only the mass is conserved. Additionally, under more restrictive growth conditions for the rate equations we obtain uniqueness of solutions to the initial value problems.

Knowledge of mixtures' phase equilibria is crucial in nature and technical chemistry. Phase equilibria calculations of mixtures require activity coefficients. However, experimental data on activity coefficients is often limited due to high cost of experiments. For an accurate and efficient prediction of activity coefficients, machine learning approaches have been recently developed. However, current machine learning approaches still extrapolate poorly for activity coefficients of unknown molecules. In this work, we introduce the SMILES-to-Properties-Transformer (SPT), a natural language processing network to predict binary limiting activity coefficients from SMILES codes. To overcome the limitations of available experimental data, we initially train our network on a large dataset of synthetic data sampled from COSMO-RS (10 Million data points) and then fine-tune the model on experimental data (20 870 data points). This training strategy enables SPT to accurately predict limiting activity coefficients even for unknown molecules, cutting the mean prediction error in half compared to state-of-the-art models for activity coefficient predictions such as COSMO-RS, UNIFAC, and improving on recent machine learning approaches.

Given an unconditional generative model and a predictor for a target property (e.g., a classifier), the goal of training-free guidance is to generate samples with desirable target properties without additional training. As a highly efficient technique for steering generative models toward flexible outcomes, training-free guidance has gained increasing attention in diffusion models. However, existing methods only handle data in continuous spaces, while many scientific applications involve both continuous and discrete data (referred to as multimodality). Another emerging trend is the growing use of the simple and general flow matching framework in building generative foundation models, where guided generation remains under-explored. To address this, we introduce TFG-Flow, a novel training-free guidance method for multimodal generative flow. TFG-Flow addresses the curse-of-dimensionality while maintaining the property of unbiased sampling in guiding discrete variables. We validate TFG-Flow on four molecular design tasks and show that TFG-Flow has great potential in drug design by generating molecules with desired properties.

Foundation models are redefining how AI systems are built. Practitioners now follow a standard procedure to build their machine learning solutions: from a pre-trained foundation model, they fine-tune the weights on the target task of interest. So, the Internet is swarmed by a handful of foundation models fine-tuned on many diverse tasks: these individual fine-tunings exist in isolation without benefiting from each other. In our opinion, this is a missed opportunity, as these specialized models contain rich and diverse features. In this paper, we thus propose model ratatouille, a new strategy to recycle the multiple fine-tunings of the same foundation model on diverse auxiliary tasks. Specifically, we repurpose these auxiliary weights as initializations for multiple parallel fine-tunings on the target task; then, we average all fine-tuned weights to obtain the final model. This recycling strategy aims at maximizing the diversity in weights by leveraging the diversity in auxiliary tasks. Empirically, it improves the state of the art on the reference DomainBed benchmark for out-of-distribution generalization. Looking forward, this work contributes to the emerging paradigm of updatable machine learning where, akin to open-source software development, the community collaborates to reliably update machine learning models.

Recent research shows that when Gradient Descent (GD) is applied to neural networks, the loss almost never decreases monotonically. Instead, the loss oscillates as gradient descent converges to its ''Edge of Stability'' (EoS). Here, we find a quantity that does decrease monotonically throughout GD training: the sharpness attained by the gradient flow solution (GFS)-the solution that would be obtained if, from now until convergence, we train with an infinitesimal step size. Theoretically, we analyze scalar neural networks with the squared loss, perhaps the simplest setting where the EoS phenomena still occur. In this model, we prove that the GFS sharpness decreases monotonically. Using this result, we characterize settings where GD provably converges to the EoS in scalar networks. Empirically, we show that GD monotonically decreases the GFS sharpness in a squared regression model as well as practical neural network architectures.

We introduce marginalization models (MaMs), a new family of generative models for high-dimensional discrete data. They offer scalable and flexible generative modeling with tractable likelihoods by explicitly modeling all induced marginal distributions. Marginalization models enable fast evaluation of arbitrary marginal probabilities with a single forward pass of the neural network, which overcomes a major limitation of methods with exact marginal inference, such as autoregressive models (ARMs). We propose scalable methods for learning the marginals, grounded in the concept of "marginalization self-consistency". Unlike previous methods, MaMs support scalable training of any-order generative models for high-dimensional problems under the setting of energy-based training, where the goal is to match the learned distribution to a given desired probability (specified by an unnormalized (log) probability function such as energy function or reward function). We demonstrate the effectiveness of the proposed model on a variety of discrete data distributions, including binary images, language, physical systems, and molecules, for maximum likelihood and energy-based training settings. MaMs achieve orders of magnitude speedup in evaluating the marginal probabilities on both settings. For energy-based training tasks, MaMs enable any-order generative modeling of high-dimensional problems beyond the capability of previous methods. Code is at https://github.com/PrincetonLIPS/MaM.

Most economic theories typically assume that financial market participants are fully rational individuals and use mathematical models to simulate human behavior in financial markets. However, human behavior is often not entirely rational and is challenging to predict accurately with mathematical models. In this paper, we propose Agent-based Simulated Financial Market (ASFM), which first constructs a simulated stock market with a real order matching system. Then, we propose a large language model based agent as the stock trader, which contains the profile, observation, and tool-learning based action module. The trading agent can comprehensively understand current market dynamics and financial policy information, and make decisions that align with their trading strategy. In the experiments, we first verify that the reactions of our ASFM are consistent with the real stock market in two controllable scenarios. In addition, we also conduct experiments in two popular economics research directions, and we find that conclusions drawn in our \model align with the preliminary findings in economics research. Based on these observations, we believe our proposed ASFM provides a new paradigm for economic research.

Machine learning based solvers have garnered much attention in physical simulation and scientific computing, with a prominent example, physics-informed neural networks (PINNs). However, PINNs often struggle to solve high-frequency and multi-scale PDEs, which can be due to spectral bias during neural network training. To address this problem, we resort to the Gaussian process (GP) framework. To flexibly capture the dominant frequencies, we model the power spectrum of the PDE solution with a student t mixture or Gaussian mixture. We apply the inverse Fourier transform to obtain the covariance function (by Wiener-Khinchin theorem). The covariance derived from the Gaussian mixture spectrum corresponds to the known spectral mixture kernel. Next, we estimate the mixture weights in the log domain, which we show is equivalent to placing a Jeffreys prior. It automatically induces sparsity, prunes excessive frequencies, and adjusts the remaining toward the ground truth. Third, to enable efficient and scalable computation on massive collocation points, which are critical to capture high frequencies, we place the collocation points on a grid, and multiply our covariance function at each input dimension. We use the GP conditional mean to predict the solution and its derivatives so as to fit the boundary condition and the equation itself. As a result, we can derive a Kronecker product structure in the covariance matrix. We use Kronecker product properties and multilinear algebra to promote computational efficiency and scalability, without low-rank approximations. We show the advantage of our method in systematic experiments. The code is released at https://github.com/xuangu-fang/Gaussian-Process-Slover-for-High-Freq-PDE.

Simulation-based inference with conditional neural density estimators is a powerful approach to solving inverse problems in science. However, these methods typically treat the underlying forward model as a black box, with no way to exploit geometric properties such as equivariances. Equivariances are common in scientific models, however integrating them directly into expressive inference networks (such as normalizing flows) is not straightforward. We here describe an alternative method to incorporate equivariances under joint transformations of parameters and data. Our method -- called group equivariant neural posterior estimation (GNPE) -- is based on self-consistently standardizing the "pose" of the data while estimating the posterior over parameters. It is architecture-independent, and applies both to exact and approximate equivariances. As a real-world application, we use GNPE for amortized inference of astrophysical binary black hole systems from gravitational-wave observations. We show that GNPE achieves state-of-the-art accuracy while reducing inference times by three orders of magnitude.

Learning the continuous dynamics of a system from snapshots of its temporal marginals is a problem which appears throughout natural sciences and machine learning, including in quantum systems, single-cell biological data, and generative modeling. In these settings, we assume access to cross-sectional samples that are uncorrelated over time, rather than full trajectories of samples. In order to better understand the systems under observation, we would like to learn a model of the underlying process that allows us to propagate samples in time and thereby simulate entire individual trajectories. In this work, we propose Action Matching, a method for learning a rich family of dynamics using only independent samples from its time evolution. We derive a tractable training objective, which does not rely on explicit assumptions about the underlying dynamics and does not require back-propagation through differential equations or optimal transport solvers. Inspired by connections with optimal transport, we derive extensions of Action Matching to learn stochastic differential equations and dynamics involving creation and destruction of probability mass. Finally, we showcase applications of Action Matching by achieving competitive performance in a diverse set of experiments from biology, physics, and generative modeling.

Diffusion models are a class of generative models that learn to synthesize samples by inverting a diffusion process that gradually maps data into noise. While these models have enjoyed great success recently, a full theoretical understanding of their observed properties is still lacking, in particular, their weak sensitivity to the choice of noise family and the role of adequate scheduling of noise levels for good synthesis. By identifying a correspondence between diffusion models and a well-known paradigm in cognitive science known as serial reproduction, whereby human agents iteratively observe and reproduce stimuli from memory, we show how the aforementioned properties of diffusion models can be explained as a natural consequence of this correspondence. We then complement our theoretical analysis with simulations that exhibit these key features. Our work highlights how classic paradigms in cognitive science can shed light on state-of-the-art machine learning problems.

The Maximal Update Parametrization (muP) aims to make the optimal hyperparameters (HPs) of a model independent of its size, allowing them to be swept using a cheap proxy model rather than the full-size target model. We present a new scheme, u-muP, which improves upon muP by combining it with Unit Scaling, a method for designing models that makes them easy to train in low-precision. The two techniques have a natural affinity: muP ensures that the scale of activations is independent of model size, and Unit Scaling ensures that activations, weights and gradients begin training with a scale of one. This synthesis opens the door to a simpler scheme, whose default values are near-optimal. This in turn facilitates a more efficient sweeping strategy, with u-muP models reaching a lower loss than comparable muP models and working out-of-the-box in FP8.

Biological processes, functions, and properties are intricately linked to the ensemble of protein conformations, rather than being solely determined by a single stable conformation. In this study, we have developed P2DFlow, a generative model based on SE(3) flow matching, to predict the structural ensembles of proteins. We specifically designed a valuable prior for the flow process and enhanced the model's ability to distinguish each intermediate state by incorporating an additional dimension to describe the ensemble data, which can reflect the physical laws governing the distribution of ensembles, so that the prior knowledge can effectively guide the generation process. When trained and evaluated on the MD datasets of ATLAS, P2DFlow outperforms other baseline models on extensive experiments, successfully capturing the observable dynamic fluctuations as evidenced in crystal structure and MD simulations. As a potential proxy agent for protein molecular simulation, the high-quality ensembles generated by P2DFlow could significantly aid in understanding protein functions across various scenarios. Code is available at https://github.com/BLEACH366/P2DFlow

Large Generative Models (LGMs) such as GPT, Stable Diffusion, Sora, and Suno are trained on a huge amount of language corpus, images, videos, and audio that are extremely diverse from numerous domains. This training paradigm over diverse well-curated data lies at the heart of generating creative and sensible content. However, all previous graph generative models (e.g., GraphRNN, MDVAE, MoFlow, GDSS, and DiGress) have been trained only on one dataset each time, which cannot replicate the revolutionary success achieved by LGMs in other fields. To remedy this crucial gap, we propose a new class of graph generative model called Large Graph Generative Model (LGGM) that is trained on a large corpus of graphs (over 5000 graphs) from 13 different domains. We empirically demonstrate that the pre-trained LGGM has superior zero-shot generative capability to existing graph generative models. Furthermore, our pre-trained LGGM can be easily fine-tuned with graphs from target domains and demonstrate even better performance than those directly trained from scratch, behaving as a solid starting point for real-world customization. Inspired by Stable Diffusion, we further equip LGGM with the capability to generate graphs given text prompts (Text-to-Graph), such as the description of the network name and domain (i.e., "The power-1138-bus graph represents a network of buses in a power distribution system."), and network statistics (i.e., "The graph has a low average degree, suitable for modeling social media interactions."). This Text-to-Graph capability integrates the extensive world knowledge in the underlying language model, offering users fine-grained control of the generated graphs. We release the code, the model checkpoint, and the datasets at https://lggm-lg.github.io/.

This work introduces DiGress, a discrete denoising diffusion model for generating graphs with categorical node and edge attributes. Our model utilizes a discrete diffusion process that progressively edits graphs with noise, through the process of adding or removing edges and changing the categories. A graph transformer network is trained to revert this process, simplifying the problem of distribution learning over graphs into a sequence of node and edge classification tasks. We further improve sample quality by introducing a Markovian noise model that preserves the marginal distribution of node and edge types during diffusion, and by incorporating auxiliary graph-theoretic features. A procedure for conditioning the generation on graph-level features is also proposed. DiGress achieves state-of-the-art performance on molecular and non-molecular datasets, with up to 3x validity improvement on a planar graph dataset. It is also the first model to scale to the large GuacaMol dataset containing 1.3M drug-like molecules without the use of molecule-specific representations.

Analytical framework for predicting General Matrix Multiplication (GEMM) performance on modern GPUs, focusing on runtime, power consumption, and energy efficiency. Our study employs two approaches: a custom-implemented tiled matrix multiplication kernel for fundamental analysis, and NVIDIA's CUTLASS library for comprehensive performance data collection across advanced configurations. Using the NVIDIA RTX 4070 as our experimental platform, we developed a Random Forest-based prediction model with multi-output regression capability. Through analysis of both naive tiled matrix multiplication with varying tile sizes (1 to 32) and 16,128 CUTLASS GEMM operations across diverse configurations, we identified critical performance patterns related to matrix dimensions, thread block configurations, and memory access patterns. Our framework achieved exceptional accuracy with an R^2 score of 0.98 for runtime prediction (mean error 15.57%) and 0.78 for power prediction (median error 5.42%). The system successfully predicts performance across matrix sizes, demonstrating robust scaling behavior. Our results show that optimal tile size selection can improve performance by up to 3.2x while reducing power consumption by 22% compared to baseline configurations. Analysis of shared memory utilization and SM occupancy reveals that tile sizes of 16x16 achieve the best balance between parallelism and resource usage. The implementation of our framework, including prediction models and analysis tools, is available as an open-source project at GPPerf [https://github.com/pavlyhalim/GPPerf].

Foundation models have emerged as critical components in a variety of artificial intelligence applications, and showcase significant success in natural language processing and several other domains. Meanwhile, the field of graph machine learning is witnessing a paradigm transition from shallow methods to more sophisticated deep learning approaches. The capabilities of foundation models to generalize and adapt motivate graph machine learning researchers to discuss the potential of developing a new graph learning paradigm. This paradigm envisions models that are pre-trained on extensive graph data and can be adapted for various graph tasks. Despite this burgeoning interest, there is a noticeable lack of clear definitions and systematic analyses pertaining to this new domain. To this end, this article introduces the concept of Graph Foundation Models (GFMs), and offers an exhaustive explanation of their key characteristics and underlying technologies. We proceed to classify the existing work related to GFMs into three distinct categories, based on their dependence on graph neural networks and large language models. In addition to providing a thorough review of the current state of GFMs, this article also outlooks potential avenues for future research in this rapidly evolving domain.

Error Feedback (EF) is a highly popular and immensely effective mechanism for fixing convergence issues which arise in distributed training methods (such as distributed GD or SGD) when these are enhanced with greedy communication compression techniques such as TopK. While EF was proposed almost a decade ago (Seide et al., 2014), and despite concentrated effort by the community to advance the theoretical understanding of this mechanism, there is still a lot to explore. In this work we study a modern form of error feedback called EF21 (Richtarik et al., 2021) which offers the currently best-known theoretical guarantees, under the weakest assumptions, and also works well in practice. In particular, while the theoretical communication complexity of EF21 depends on the quadratic mean of certain smoothness parameters, we improve this dependence to their arithmetic mean, which is always smaller, and can be substantially smaller, especially in heterogeneous data regimes. We take the reader on a journey of our discovery process. Starting with the idea of applying EF21 to an equivalent reformulation of the underlying problem which (unfortunately) requires (often impractical) machine cloning, we continue to the discovery of a new weighted version of EF21 which can (fortunately) be executed without any cloning, and finally circle back to an improved analysis of the original EF21 method. While this development applies to the simplest form of EF21, our approach naturally extends to more elaborate variants involving stochastic gradients and partial participation. Further, our technique improves the best-known theory of EF21 in the rare features regime (Richtarik et al., 2023). Finally, we validate our theoretical findings with suitable experiments.

Large-scale molecular representation methods have revolutionized applications in material science, such as drug discovery, chemical modeling, and material design. With the rise of transformers, models now learn representations directly from molecular structures. In this study, we develop an encoder-decoder model based on BART that is capable of leaning molecular representations and generate new molecules. Trained on SELFIES, a robust molecular string representation, our model outperforms existing baselines in downstream tasks, demonstrating its potential in efficient and effective molecular data analysis and manipulation.

The dynamic nature of proteins is crucial for determining their biological functions and properties, for which Monte Carlo (MC) and molecular dynamics (MD) simulations stand as predominant tools to study such phenomena. By utilizing empirically derived force fields, MC or MD simulations explore the conformational space through numerically evolving the system via Markov chain or Newtonian mechanics. However, the high-energy barrier of the force fields can hamper the exploration of both methods by the rare event, resulting in inadequately sampled ensemble without exhaustive running. Existing learning-based approaches perform direct sampling yet heavily rely on target-specific simulation data for training, which suffers from high data acquisition cost and poor generalizability. Inspired by simulated annealing, we propose Str2Str, a novel structure-to-structure translation framework capable of zero-shot conformation sampling with roto-translation equivariant property. Our method leverages an amortized denoising score matching objective trained on general crystal structures and has no reliance on simulation data during both training and inference. Experimental results across several benchmarking protein systems demonstrate that Str2Str outperforms previous state-of-the-art generative structure prediction models and can be orders of magnitude faster compared to long MD simulations. Our open-source implementation is available at https://github.com/lujiarui/Str2Str

Survival prediction using whole slide images (WSIs) can be formulated as a multiple instance learning (MIL) problem. However, existing MIL methods often fail to explicitly capture pathological heterogeneity within WSIs, both globally -- through long-tailed morphological distributions, and locally through -- tile-level prediction uncertainty. Optimal transport (OT) provides a principled way of modeling such heterogeneity by incorporating marginal distribution constraints. Building on this insight, we propose OTSurv, a novel MIL framework from an optimal transport perspective. Specifically, OTSurv formulates survival predictions as a heterogeneity-aware OT problem with two constraints: (1) global long-tail constraint that models prior morphological distributions to avert both mode collapse and excessive uniformity by regulating transport mass allocation, and (2) local uncertainty-aware constraint that prioritizes high-confidence patches while suppressing noise by progressively raising the total transport mass. We then recast the initial OT problem, augmented by these constraints, into an unbalanced OT formulation that can be solved with an efficient, hardware-friendly matrix scaling algorithm. Empirically, OTSurv sets new state-of-the-art results across six popular benchmarks, achieving an absolute 3.6% improvement in average C-index. In addition, OTSurv achieves statistical significance in log-rank tests and offers high interpretability, making it a powerful tool for survival prediction in digital pathology. Our codes are available at https://github.com/Y-Research-SBU/OTSurv.

Deep generative diffusion models are a promising avenue for 3D de novo molecular design in materials science and drug discovery. However, their utility is still limited by suboptimal performance on large molecular structures and limited training data. To address this gap, we explore the design space of E(3)-equivariant diffusion models, focusing on previously unexplored areas. Our extensive comparative analysis evaluates the interplay between continuous and discrete state spaces. From this investigation, we present the EQGAT-diff model, which consistently outperforms established models for the QM9 and GEOM-Drugs datasets. Significantly, EQGAT-diff takes continuous atom positions, while chemical elements and bond types are categorical and uses time-dependent loss weighting, substantially increasing training convergence, the quality of generated samples, and inference time. We also showcase that including chemically motivated additional features like hybridization states in the diffusion process enhances the validity of generated molecules. To further strengthen the applicability of diffusion models to limited training data, we investigate the transferability of EQGAT-diff trained on the large PubChem3D dataset with implicit hydrogen atoms to target different data distributions. Fine-tuning EQGAT-diff for just a few iterations shows an efficient distribution shift, further improving performance throughout data sets. Finally, we test our model on the Crossdocked data set for structure-based de novo ligand generation, underlining the importance of our findings showing state-of-the-art performance on Vina docking scores.

The main challenge in domain generalization (DG) is to handle the distribution shift problem that lies between the training and test data. Recent studies suggest that test-time training (TTT), which adapts the learned model with test data, might be a promising solution to the problem. Generally, a TTT strategy hinges its performance on two main factors: selecting an appropriate auxiliary TTT task for updating and identifying reliable parameters to update during the test phase. Both previous arts and our experiments indicate that TTT may not improve but be detrimental to the learned model if those two factors are not properly considered. This work addresses those two factors by proposing an Improved Test-Time Adaptation (ITTA) method. First, instead of heuristically defining an auxiliary objective, we propose a learnable consistency loss for the TTT task, which contains learnable parameters that can be adjusted toward better alignment between our TTT task and the main prediction task. Second, we introduce additional adaptive parameters for the trained model, and we suggest only updating the adaptive parameters during the test phase. Through extensive experiments, we show that the proposed two strategies are beneficial for the learned model (see Figure 1), and ITTA could achieve superior performance to the current state-of-the-art methods on several DG benchmarks. Code is available at https://github.com/liangchen527/ITTA.

The rapid development of universal machine learning interatomic potentials (uMLIPs) has demonstrated the possibility for generalizable learning of the universal potential energy surface. In principle, the accuracy of uMLIPs can be further improved by bridging the model from lower-fidelity datasets to high-fidelity ones. In this work, we analyze the challenge of this transfer learning problem within the CHGNet framework. We show that significant energy scale shifts and poor correlations between GGA and r^2SCAN pose challenges to cross-functional data transferability in uMLIPs. By benchmarking different transfer learning approaches on the MP-r^2SCAN dataset of 0.24 million structures, we demonstrate the importance of elemental energy referencing in the transfer learning of uMLIPs. By comparing the scaling law with and without the pre-training on a low-fidelity dataset, we show that significant data efficiency can still be achieved through transfer learning, even with a target dataset of sub-million structures. We highlight the importance of proper transfer learning and multi-fidelity learning in creating next-generation uMLIPs on high-fidelity data.

The quality of many modern machine learning models improves as model complexity increases, an effect that has been quantified, for predictive performance, with the non-monotonic double descent learning curve. Here, we address the overarching question: is there an analogous theory of double descent for models which estimate uncertainty? We provide a partially affirmative and partially negative answer in the setting of Gaussian processes (GP). Under standard assumptions, we prove that higher model quality for optimally-tuned GPs (including uncertainty prediction) under marginal likelihood is realized for larger input dimensions, and therefore exhibits a monotone error curve. After showing that marginal likelihood does not naturally exhibit double descent in the input dimension, we highlight related forms of posterior predictive loss that do exhibit non-monotonicity. Finally, we verify empirically that our results hold for real data, beyond our considered assumptions, and we explore consequences involving synthetic covariates.

Linear time-invariant state space models (SSM) are a classical model from engineering and statistics, that have recently been shown to be very promising in machine learning through the Structured State Space sequence model (S4). A core component of S4 involves initializing the SSM state matrix to a particular matrix called a HiPPO matrix, which was empirically important for S4's ability to handle long sequences. However, the specific matrix that S4 uses was actually derived in previous work for a particular time-varying dynamical system, and the use of this matrix as a time-invariant SSM had no known mathematical interpretation. Consequently, the theoretical mechanism by which S4 models long-range dependencies actually remains unexplained. We derive a more general and intuitive formulation of the HiPPO framework, which provides a simple mathematical interpretation of S4 as a decomposition onto exponentially-warped Legendre polynomials, explaining its ability to capture long dependencies. Our generalization introduces a theoretically rich class of SSMs that also lets us derive more intuitive S4 variants for other bases such as the Fourier basis, and explains other aspects of training S4, such as how to initialize the important timescale parameter. These insights improve S4's performance to 86% on the Long Range Arena benchmark, with 96% on the most difficult Path-X task.

Strategies for the generation of periodic discrete structures with identical two-point correlation are developed. Starting from a pair of root structures, which are not related by translation, phase inversion or axis reflections, child structures of arbitrary resolution (i.e., pixel or voxel numbers) and number of phases (i.e., material phases/species) can be generated by means of trivial embedding based phase extension, application of kernels and/or phase coalescence, such that the generated structures inherit the two-point-correlation equivalence. Proofs of the inheritance property are provided by means of the Discrete Fourier Transform theory. A Python 3 implementation of the results is offered by the authors through the Github repository https://github.com/DataAnalyticsEngineering/EQ2PC in order to make the provided results reproducible and useful for all interested readers. Examples for the generation of structures are demonstrated, together with applications in the homogenization theory of periodic media.