Daily Papers

With the fast development of COVID-19 into a global pandemic, scientists around the globe are desperately searching for effective antiviral therapeutic agents. Bridging systems biology and drug discovery, we propose a deep learning framework for conditional de novo design of antiviral candidate drugs tailored against given protein targets. First, we train a multimodal ligand--protein binding affinity model on predicting affinities of antiviral compounds to target proteins and couple this model with pharmacological toxicity predictors. Exploiting this multi-objective as a reward function of a conditional molecular generator (consisting of two VAEs), we showcase a framework that navigates the chemical space toward regions with more antiviral molecules. Specifically, we explore a challenging setting of generating ligands against unseen protein targets by performing a leave-one-out-cross-validation on 41 SARS-CoV-2-related target proteins. Using deep RL, it is demonstrated that in 35 out of 41 cases, the generation is biased towards sampling more binding ligands, with an average increase of 83% comparing to an unbiased VAE. We present a case-study on a potential Envelope-protein inhibitor and perform a synthetic accessibility assessment of the best generated molecules is performed that resembles a viable roadmap towards a rapid in-vitro evaluation of potential SARS-CoV-2 inhibitors.

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.

Generative models have demonstrated substantial promise in Natural Language Processing (NLP) and have found application in designing molecules, as seen in General Pretrained Transformer (GPT) models. In our efforts to develop such a tool for exploring the organic chemical space in search of potentially electro-active compounds, we present "LLamol", a single novel generative transformer model based on the LLama 2 architecture, which was trained on a 13M superset of organic compounds drawn from diverse public sources. To allow for a maximum flexibility in usage and robustness in view of potentially incomplete data, we introduce "Stochastic Context Learning" as a new training procedure. We demonstrate that the resulting model adeptly handles single- and multi-conditional organic molecule generation with up to four conditions, yet more are possible. The model generates valid molecular structures in SMILES notation while flexibly incorporating three numerical and/or one token sequence into the generative process, just as requested. The generated compounds are very satisfactory in all scenarios tested. In detail, we showcase the model's capability to utilize token sequences for conditioning, either individually or in combination with numerical properties, making LLamol a potent tool for de novo molecule design, easily expandable with new properties.

Proteins are dynamic molecular machines whose biological functions, spanning enzymatic catalysis, signal transduction, and structural adaptation, are intrinsically linked to their motions. Designing proteins with targeted dynamic properties, however, remains a challenge due to the complex, degenerate relationships between sequence, structure, and molecular motion. Here, we introduce VibeGen, a generative AI framework that enables end-to-end de novo protein design conditioned on normal mode vibrations. VibeGen employs an agentic dual-model architecture, comprising a protein designer that generates sequence candidates based on specified vibrational modes and a protein predictor that evaluates their dynamic accuracy. This approach synergizes diversity, accuracy, and novelty during the design process. Via full-atom molecular simulations as direct validation, we demonstrate that the designed proteins accurately reproduce the prescribed normal mode amplitudes across the backbone while adopting various stable, functionally relevant structures. Notably, generated sequences are de novo, exhibiting no significant similarity to natural proteins, thereby expanding the accessible protein space beyond evolutionary constraints. Our work integrates protein dynamics into generative protein design, and establishes a direct, bidirectional link between sequence and vibrational behavior, unlocking new pathways for engineering biomolecules with tailored dynamical and functional properties. This framework holds broad implications for the rational design of flexible enzymes, dynamic scaffolds, and biomaterials, paving the way toward dynamics-informed AI-driven protein engineering.

The core challenge of de novo protein design lies in creating proteins with specific functions or properties, guided by certain conditions. Current models explore to generate protein using structural and evolutionary guidance, which only provide indirect conditions concerning functions and properties. However, textual annotations of proteins, especially the annotations for protein domains, which directly describe the protein's high-level functionalities, properties, and their correlation with target amino acid sequences, remain unexplored in the context of protein design tasks. In this paper, we propose Protein-Annotation Alignment Generation, PAAG, a multi-modality protein design framework that integrates the textual annotations extracted from protein database for controllable generation in sequence space. Specifically, within a multi-level alignment module, PAAG can explicitly generate proteins containing specific domains conditioned on the corresponding domain annotations, and can even design novel proteins with flexible combinations of different kinds of annotations. Our experimental results underscore the superiority of the aligned protein representations from PAAG over 7 prediction tasks. Furthermore, PAAG demonstrates a significant increase in generation success rate (24.7% vs 4.7% in zinc finger, and 54.3% vs 22.0% in the immunoglobulin domain) in comparison to the existing model. We anticipate that PAAG will broaden the horizons of protein design by leveraging the knowledge from between textual annotation and proteins.

The Cambrian explosion of easily accessible pre-trained diffusion models suggests a demand for methods that combine multiple different pre-trained diffusion models without incurring the significant computational burden of re-training a larger combined model. In this paper, we cast the problem of combining multiple pre-trained diffusion models at the generation stage under a novel proposed framework termed superposition. Theoretically, we derive superposition from rigorous first principles stemming from the celebrated continuity equation and design two novel algorithms tailor-made for combining diffusion models in SuperDiff. SuperDiff leverages a new scalable It\^o density estimator for the log likelihood of the diffusion SDE which incurs no additional overhead compared to the well-known Hutchinson's estimator needed for divergence calculations. We demonstrate that SuperDiff is scalable to large pre-trained diffusion models as superposition is performed solely through composition during inference, and also enjoys painless implementation as it combines different pre-trained vector fields through an automated re-weighting scheme. Notably, we show that SuperDiff is efficient during inference time, and mimics traditional composition operators such as the logical OR and the logical AND. We empirically demonstrate the utility of using SuperDiff for generating more diverse images on CIFAR-10, more faithful prompt conditioned image editing using Stable Diffusion, and improved unconditional de novo structure design of proteins. https://github.com/necludov/super-diffusion

De novo design seeks to generate molecules with required property profiles by virtual design-make-test cycles. With the emergence of deep learning and neural generative models in many application areas, models for molecular design based on neural networks appeared recently and show promising results. However, the new models have not been profiled on consistent tasks, and comparative studies to well-established algorithms have only seldom been performed. To standardize the assessment of both classical and neural models for de novo molecular design, we propose an evaluation framework, GuacaMol, based on a suite of standardized benchmarks. The benchmark tasks encompass measuring the fidelity of the models to reproduce the property distribution of the training sets, the ability to generate novel molecules, the exploration and exploitation of chemical space, and a variety of single and multi-objective optimization tasks. The benchmarking open-source Python code, and a leaderboard can be found on https://benevolent.ai/guacamol

Recently, 3D generative models have shown promising performances in structure-based drug design by learning to generate ligands given target binding sites. However, only modeling the target-ligand distribution can hardly fulfill one of the main goals in drug discovery -- designing novel ligands with desired properties, e.g., high binding affinity, easily synthesizable, etc. This challenge becomes particularly pronounced when the target-ligand pairs used for training do not align with these desired properties. Moreover, most existing methods aim at solving de novo design task, while many generative scenarios requiring flexible controllability, such as R-group optimization and scaffold hopping, have received little attention. In this work, we propose DecompOpt, a structure-based molecular optimization method based on a controllable and decomposed diffusion model. DecompOpt presents a new generation paradigm which combines optimization with conditional diffusion models to achieve desired properties while adhering to the molecular grammar. Additionally, DecompOpt offers a unified framework covering both de novo design and controllable generation. To achieve so, ligands are decomposed into substructures which allows fine-grained control and local optimization. Experiments show that DecompOpt can efficiently generate molecules with improved properties than strong de novo baselines, and demonstrate great potential in controllable generation tasks.

Controllable layout generation refers to the process of creating a plausible visual arrangement of elements within a graphic design (e.g., document and web designs) with constraints representing design intentions. Although recent diffusion-based models have achieved state-of-the-art FID scores, they tend to exhibit more pronounced misalignment compared to earlier transformer-based models. In this work, we propose the LAyout Constraint diffusion modEl (LACE), a unified model to handle a broad range of layout generation tasks, such as arranging elements with specified attributes and refining or completing a coarse layout design. The model is based on continuous diffusion models. Compared with existing methods that use discrete diffusion models, continuous state-space design can enable the incorporation of differentiable aesthetic constraint functions in training. For conditional generation, we introduce conditions via masked input. Extensive experiment results show that LACE produces high-quality layouts and outperforms existing state-of-the-art baselines.

Recent studies have demonstrated the strong empirical performance of diffusion models on discrete sequences across domains from natural language to biological sequence generation. For example, in the protein inverse folding task, conditional diffusion models have achieved impressive results in generating natural-like sequences that fold back into the original structure. However, practical design tasks often require not only modeling a conditional distribution but also optimizing specific task objectives. For instance, we may prefer protein sequences with high stability. To address this, we consider the scenario where we have pre-trained discrete diffusion models that can generate natural-like sequences, as well as reward models that map sequences to task objectives. We then formulate the reward maximization problem within discrete diffusion models, analogous to reinforcement learning (RL), while minimizing the KL divergence against pretrained diffusion models to preserve naturalness. To solve this RL problem, we propose a novel algorithm, DRAKES, that enables direct backpropagation of rewards through entire trajectories generated by diffusion models, by making the originally non-differentiable trajectories differentiable using the Gumbel-Softmax trick. Our theoretical analysis indicates that our approach can generate sequences that are both natural-like and yield high rewards. While similar tasks have been recently explored in diffusion models for continuous domains, our work addresses unique algorithmic and theoretical challenges specific to discrete diffusion models, which arise from their foundation in continuous-time Markov chains rather than Brownian motion. Finally, we demonstrate the effectiveness of DRAKES in generating DNA and protein sequences that optimize enhancer activity and protein stability, respectively, important tasks for gene therapies and protein-based therapeutics.

Artificial intelligence (AI)-driven methods can vastly improve the historically costly drug design process, with various generative models already in widespread use. Generative models for de novo drug design, in particular, focus on the creation of novel biological compounds entirely from scratch, representing a promising future direction. Rapid development in the field, combined with the inherent complexity of the drug design process, creates a difficult landscape for new researchers to enter. In this survey, we organize de novo drug design into two overarching themes: small molecule and protein generation. Within each theme, we identify a variety of subtasks and applications, highlighting important datasets, benchmarks, and model architectures and comparing the performance of top models. We take a broad approach to AI-driven drug design, allowing for both micro-level comparisons of various methods within each subtask and macro-level observations across different fields. We discuss parallel challenges and approaches between the two applications and highlight future directions for AI-driven de novo drug design as a whole. An organized repository of all covered sources is available at https://github.com/gersteinlab/GenAI4Drug.

Layout design is an important task in various design fields, including user interface, document, and graphic design. As this task requires tedious manual effort by designers, prior works have attempted to automate this process using generative models, but commonly fell short of providing intuitive user controls and achieving design objectives. In this paper, we build a conditional latent diffusion model, PLay, that generates parametrically conditioned layouts in vector graphic space from user-specified guidelines, which are commonly used by designers for representing their design intents in current practices. Our method outperforms prior works across three datasets on metrics including FID and FD-VG, and in user study. Moreover, it brings a novel and interactive experience to professional layout design processes.

Content-aware visual-textual presentation layout aims at arranging spatial space on the given canvas for pre-defined elements, including text, logo, and underlay, which is a key to automatic template-free creative graphic design. In practical applications, e.g., poster designs, the canvas is originally non-empty, and both inter-element relationships as well as inter-layer relationships should be concerned when generating a proper layout. A few recent works deal with them simultaneously, but they still suffer from poor graphic performance, such as a lack of layout variety or spatial non-alignment. Since content-aware visual-textual presentation layout is a novel task, we first construct a new dataset named PosterLayout, which consists of 9,974 poster-layout pairs and 905 images, i.e., non-empty canvases. It is more challenging and useful for greater layout variety, domain diversity, and content diversity. Then, we propose design sequence formation (DSF) that reorganizes elements in layouts to imitate the design processes of human designers, and a novel CNN-LSTM-based conditional generative adversarial network (GAN) is presented to generate proper layouts. Specifically, the discriminator is design-sequence-aware and will supervise the "design" process of the generator. Experimental results verify the usefulness of the new benchmark and the effectiveness of the proposed approach, which achieves the best performance by generating suitable layouts for diverse canvases.

De novo drug design requires simultaneously generating novel molecules outside of training data and predicting their target properties, making it a hard task for generative models. To address this, we propose Joint Transformer that combines a Transformer decoder, Transformer encoder, and a predictor in a joint generative model with shared weights. We formulate a probabilistic black-box optimization algorithm that employs Joint Transformer to generate novel molecules with improved target properties and outperforms other SMILES-based optimization methods in de novo drug design.

This paper presents a novel generative model for Computer Aided Design (CAD) that 1) represents high-level design concepts of a CAD model as a three-level hierarchical tree of neural codes, from global part arrangement down to local curve geometry; and 2) controls the generation or completion of CAD models by specifying the target design using a code tree. Concretely, a novel variant of a vector quantized VAE with "masked skip connection" extracts design variations as neural codebooks at three levels. Two-stage cascaded auto-regressive transformers learn to generate code trees from incomplete CAD models and then complete CAD models following the intended design. Extensive experiments demonstrate superior performance on conventional tasks such as random generation while enabling novel interaction capabilities on conditional generation tasks. The code is available at https://github.com/samxuxiang/hnc-cad.

This paper presents Representation-Conditioned image Generation (RCG), a simple yet effective image generation framework which sets a new benchmark in class-unconditional image generation. RCG does not condition on any human annotations. Instead, it conditions on a self-supervised representation distribution which is mapped from the image distribution using a pre-trained encoder. During generation, RCG samples from such representation distribution using a representation diffusion model (RDM), and employs a pixel generator to craft image pixels conditioned on the sampled representation. Such a design provides substantial guidance during the generative process, resulting in high-quality image generation. Tested on ImageNet 256times256, RCG achieves a Frechet Inception Distance (FID) of 3.31 and an Inception Score (IS) of 253.4. These results not only significantly improve the state-of-the-art of class-unconditional image generation but also rival the current leading methods in class-conditional image generation, bridging the long-standing performance gap between these two tasks. Code is available at https://github.com/LTH14/rcg.

Controllable layout generation aims at synthesizing plausible arrangement of element bounding boxes with optional constraints, such as type or position of a specific element. In this work, we try to solve a broad range of layout generation tasks in a single model that is based on discrete state-space diffusion models. Our model, named LayoutDM, naturally handles the structured layout data in the discrete representation and learns to progressively infer a noiseless layout from the initial input, where we model the layout corruption process by modality-wise discrete diffusion. For conditional generation, we propose to inject layout constraints in the form of masking or logit adjustment during inference. We show in the experiments that our LayoutDM successfully generates high-quality layouts and outperforms both task-specific and task-agnostic baselines on several layout tasks.

We introduce Multi-Objective Counterfactuals for Design (MCD), a novel method for counterfactual optimization in design problems. Counterfactuals are hypothetical situations that can lead to a different decision or choice. In this paper, the authors frame the counterfactual search problem as a design recommendation tool that can help identify modifications to a design, leading to better functional performance. MCD improves upon existing counterfactual search methods by supporting multi-objective queries, which are crucial in design problems, and by decoupling the counterfactual search and sampling processes, thus enhancing efficiency and facilitating objective tradeoff visualization. The paper demonstrates MCD's core functionality using a two-dimensional test case, followed by three case studies of bicycle design that showcase MCD's effectiveness in real-world design problems. In the first case study, MCD excels at recommending modifications to query designs that can significantly enhance functional performance, such as weight savings and improvements to the structural safety factor. The second case study demonstrates that MCD can work with a pre-trained language model to suggest design changes based on a subjective text prompt effectively. Lastly, the authors task MCD with increasing a query design's similarity to a target image and text prompt while simultaneously reducing weight and improving structural performance, demonstrating MCD's performance on a complex multimodal query. Overall, MCD has the potential to provide valuable recommendations for practitioners and design automation researchers looking for answers to their ``What if'' questions by exploring hypothetical design modifications and their impact on multiple design objectives. The code, test problems, and datasets used in the paper are available to the public at decode.mit.edu/projects/counterfactuals/.

Graphic design plays a vital role in visual communication across advertising, marketing, and multimedia entertainment. Prior work has explored automated graphic design generation using diffusion models, aiming to streamline creative workflows and democratize design capabilities. However, complex graphic design scenarios require accurately adhering to design intent specified by multiple heterogeneous user-provided elements (\eg images, layouts, and texts), which pose multi-condition control challenges for existing methods. Specifically, previous single-condition control models demonstrate effectiveness only within their specialized domains but fail to generalize to other conditions, while existing multi-condition methods often lack fine-grained control over each sub-condition and compromise overall compositional harmony. To address these limitations, we introduce CreatiDesign, a systematic solution for automated graphic design covering both model architecture and dataset construction. First, we design a unified multi-condition driven architecture that enables flexible and precise integration of heterogeneous design elements with minimal architectural modifications to the base diffusion model. Furthermore, to ensure that each condition precisely controls its designated image region and to avoid interference between conditions, we propose a multimodal attention mask mechanism. Additionally, we develop a fully automated pipeline for constructing graphic design datasets, and introduce a new dataset with 400K samples featuring multi-condition annotations, along with a comprehensive benchmark. Experimental results show that CreatiDesign outperforms existing models by a clear margin in faithfully adhering to user intent.

Graphic design is essential for visual communication with layouts being fundamental to composing attractive designs. Layout generation differs from pixel-level image synthesis and is unique in terms of the requirement of mutual relations among the desired components. We propose a method for design layout generation that can satisfy user-specified constraints. The proposed neural design network (NDN) consists of three modules. The first module predicts a graph with complete relations from a graph with user-specified relations. The second module generates a layout from the predicted graph. Finally, the third module fine-tunes the predicted layout. Quantitative and qualitative experiments demonstrate that the generated layouts are visually similar to real design layouts. We also construct real designs based on predicted layouts for a better understanding of the visual quality. Finally, we demonstrate a practical application on layout recommendation.

We introduce Cosmos-Transfer, a conditional world generation model that can generate world simulations based on multiple spatial control inputs of various modalities such as segmentation, depth, and edge. In the design, the spatial conditional scheme is adaptive and customizable. It allows weighting different conditional inputs differently at different spatial locations. This enables highly controllable world generation and finds use in various world-to-world transfer use cases, including Sim2Real. We conduct extensive evaluations to analyze the proposed model and demonstrate its applications for Physical AI, including robotics Sim2Real and autonomous vehicle data enrichment. We further demonstrate an inference scaling strategy to achieve real-time world generation with an NVIDIA GB200 NVL72 rack. To help accelerate research development in the field, we open-source our models and code at https://github.com/nvidia-cosmos/cosmos-transfer1.

Diffusion models have demonstrated remarkable success in various domains, including molecular generation. However, conditional molecular generation remains a fundamental challenge due to an intrinsic trade-off between targeting specific chemical properties and generating meaningful samples from the data distribution. In this work, we present Time-Aware Conditional Synthesis (TACS), a novel approach to conditional generation on diffusion models. It integrates adaptively controlled plug-and-play "online" guidance into a diffusion model, driving samples toward the desired properties while maintaining validity and stability. A key component of our algorithm is our new type of diffusion sampler, Time Correction Sampler (TCS), which is used to control guidance and ensure that the generated molecules remain on the correct manifold at each reverse step of the diffusion process at the same time. Our proposed method demonstrates significant performance in conditional 3D molecular generation and offers a promising approach towards inverse molecular design, potentially facilitating advancements in drug discovery, materials science, and other related fields.

Antibodies are Y-shaped proteins that neutralize pathogens and constitute the core of our adaptive immune system. De novo generation of new antibodies that target specific antigens holds the key to accelerating vaccine discovery. However, this co-design of the amino acid sequence and the 3D structure subsumes and accentuates some central challenges from multiple tasks, including protein folding (sequence to structure), inverse folding (structure to sequence), and docking (binding). We strive to surmount these challenges with a new generative model AbODE that extends graph PDEs to accommodate both contextual information and external interactions. Unlike existing approaches, AbODE uses a single round of full-shot decoding and elicits continuous differential attention that encapsulates and evolves with latent interactions within the antibody as well as those involving the antigen. We unravel fundamental connections between AbODE and temporal networks as well as graph-matching networks. The proposed model significantly outperforms existing methods on standard metrics across benchmarks.

Diffusion models, a powerful and universal generative AI technology, have achieved tremendous success in computer vision, audio, reinforcement learning, and computational biology. In these applications, diffusion models provide flexible high-dimensional data modeling, and act as a sampler for generating new samples under active guidance towards task-desired properties. Despite the significant empirical success, theory of diffusion models is very limited, potentially slowing down principled methodological innovations for further harnessing and improving diffusion models. In this paper, we review emerging applications of diffusion models, understanding their sample generation under various controls. Next, we overview the existing theories of diffusion models, covering their statistical properties and sampling capabilities. We adopt a progressive routine, beginning with unconditional diffusion models and connecting to conditional counterparts. Further, we review a new avenue in high-dimensional structured optimization through conditional diffusion models, where searching for solutions is reformulated as a conditional sampling problem and solved by diffusion models. Lastly, we discuss future directions about diffusion models. The purpose of this paper is to provide a well-rounded theoretical exposure for stimulating forward-looking theories and methods of diffusion models.

Human organs constantly undergo anatomical changes due to a complex mix of short-term (e.g., heartbeat) and long-term (e.g., aging) factors. Evidently, prior knowledge of these factors will be beneficial when modeling their future state, i.e., via image generation. However, most of the medical image generation tasks only rely on the input from a single image, thus ignoring the sequential dependency even when longitudinal data is available. Sequence-aware deep generative models, where model input is a sequence of ordered and timestamped images, are still underexplored in the medical imaging domain that is featured by several unique challenges: 1) Sequences with various lengths; 2) Missing data or frame, and 3) High dimensionality. To this end, we propose a sequence-aware diffusion model (SADM) for the generation of longitudinal medical images. Recently, diffusion models have shown promising results in high-fidelity image generation. Our method extends this new technique by introducing a sequence-aware transformer as the conditional module in a diffusion model. The novel design enables learning longitudinal dependency even with missing data during training and allows autoregressive generation of a sequence of images during inference. Our extensive experiments on 3D longitudinal medical images demonstrate the effectiveness of SADM compared with baselines and alternative methods. The code is available at https://github.com/ubc-tea/SADM-Longitudinal-Medical-Image-Generation.

Layout generation aims to synthesize realistic graphic scenes consisting of elements with different attributes including category, size, position, and between-element relation. It is a crucial task for reducing the burden on heavy-duty graphic design works for formatted scenes, e.g., publications, documents, and user interfaces (UIs). Diverse application scenarios impose a big challenge in unifying various layout generation subtasks, including conditional and unconditional generation. In this paper, we propose a Layout Diffusion Generative Model (LDGM) to achieve such unification with a single decoupled diffusion model. LDGM views a layout of arbitrary missing or coarse element attributes as an intermediate diffusion status from a completed layout. Since different attributes have their individual semantics and characteristics, we propose to decouple the diffusion processes for them to improve the diversity of training samples and learn the reverse process jointly to exploit global-scope contexts for facilitating generation. As a result, our LDGM can generate layouts either from scratch or conditional on arbitrary available attributes. Extensive qualitative and quantitative experiments demonstrate our proposed LDGM outperforms existing layout generation models in both functionality and performance.

Designing de novo proteins beyond those found in nature holds significant promise for advancements in both scientific and engineering applications. Current methodologies for protein design often rely on AI-based models, such as surrogate models that address end-to-end problems by linking protein structure to material properties or vice versa. However, these models frequently focus on specific material objectives or structural properties, limiting their flexibility when incorporating out-of-domain knowledge into the design process or comprehensive data analysis is required. In this study, we introduce ProtAgents, a platform for de novo protein design based on Large Language Models (LLMs), where multiple AI agents with distinct capabilities collaboratively address complex tasks within a dynamic environment. The versatility in agent development allows for expertise in diverse domains, including knowledge retrieval, protein structure analysis, physics-based simulations, and results analysis. The dynamic collaboration between agents, empowered by LLMs, provides a versatile approach to tackling protein design and analysis problems, as demonstrated through diverse examples in this study. The problems of interest encompass designing new proteins, analyzing protein structures and obtaining new first-principles data -- natural vibrational frequencies -- via physics simulations. The concerted effort of the system allows for powerful automated and synergistic design of de novo proteins with targeted mechanical properties. The flexibility in designing the agents, on one hand, and their capacity in autonomous collaboration through the dynamic LLM-based multi-agent environment on the other hand, unleashes great potentials of LLMs in addressing multi-objective materials problems and opens up new avenues for autonomous materials discovery and design.

Flow matching in the continuous simplex has emerged as a promising strategy for DNA sequence design, but struggles to scale to higher simplex dimensions required for peptide and protein generation. We introduce Gumbel-Softmax Flow and Score Matching, a generative framework on the simplex based on a novel Gumbel-Softmax interpolant with a time-dependent temperature. Using this interpolant, we introduce Gumbel-Softmax Flow Matching by deriving a parameterized velocity field that transports from smooth categorical distributions to distributions concentrated at a single vertex of the simplex. We alternatively present Gumbel-Softmax Score Matching which learns to regress the gradient of the probability density. Our framework enables high-quality, diverse generation and scales efficiently to higher-dimensional simplices. To enable training-free guidance, we propose Straight-Through Guided Flows (STGFlow), a classifier-based guidance method that leverages straight-through estimators to steer the unconditional velocity field toward optimal vertices of the simplex. STGFlow enables efficient inference-time guidance using classifiers pre-trained on clean sequences, and can be used with any discrete flow method. Together, these components form a robust framework for controllable de novo sequence generation. We demonstrate state-of-the-art performance in conditional DNA promoter design, sequence-only protein generation, and target-binding peptide design for rare disease treatment.

This paper pursues the insight that large language models (LLMs) trained to generate code can vastly improve the effectiveness of mutation operators applied to programs in genetic programming (GP). Because such LLMs benefit from training data that includes sequential changes and modifications, they can approximate likely changes that humans would make. To highlight the breadth of implications of such evolution through large models (ELM), in the main experiment ELM combined with MAP-Elites generates hundreds of thousands of functional examples of Python programs that output working ambulating robots in the Sodarace domain, which the original LLM had never seen in pre-training. These examples then help to bootstrap training a new conditional language model that can output the right walker for a particular terrain. The ability to bootstrap new models that can output appropriate artifacts for a given context in a domain where zero training data was previously available carries implications for open-endedness, deep learning, and reinforcement learning. These implications are explored here in depth in the hope of inspiring new directions of research now opened up by ELM.

One of the most critical tasks for startups is to validate their business model. Therefore, entrepreneurs try to collect information such as feedback from other actors to assess the validity of their assumptions and make decisions. However, previous work on decisional guidance for business model validation provides no solution for the highly uncertain and complex context of earlystage startups. The purpose of this paper is, thus, to develop design principles for a Hybrid Intelligence decision support system (HI-DSS) that combines the complementary capabilities of human and machine intelligence. We follow a design science research approach to design a prototype artifact and a set of design principles. Our study provides prescriptive knowledge for HI-DSS and contributes to previous work on decision support for business models, the applications of complementary strengths of humans and machines for making decisions, and support systems for extremely uncertain decision-making problems.

A well-known limitation of existing molecular generative models is that the generated molecules highly resemble those in the training set. To generate truly novel molecules that may have even better properties for de novo drug discovery, more powerful exploration in the chemical space is necessary. To this end, we propose Molecular Out-Of-distribution Diffusion(MOOD), a score-based diffusion scheme that incorporates out-of-distribution (OOD) control in the generative stochastic differential equation (SDE) with simple control of a hyperparameter, thus requires no additional costs. Since some novel molecules may not meet the basic requirements of real-world drugs, MOOD performs conditional generation by utilizing the gradients from a property predictor that guides the reverse-time diffusion process to high-scoring regions according to target properties such as protein-ligand interactions, drug-likeness, and synthesizability. This allows MOOD to search for novel and meaningful molecules rather than generating unseen yet trivial ones. We experimentally validate that MOOD is able to explore the chemical space beyond the training distribution, generating molecules that outscore ones found with existing methods, and even the top 0.01% of the original training pool. Our code is available at https://github.com/SeulLee05/MOOD.

Conditional generative models typically demand large annotated training sets to achieve high-quality synthesis. As a result, there has been significant interest in designing models that perform plug-and-play generation, i.e., to use a predefined or pretrained model, which is not explicitly trained on the generative task, to guide the generative process (e.g., using language). However, such guidance is typically useful only towards synthesizing high-level semantics rather than editing fine-grained details as in image-to-image translation tasks. To this end, and capitalizing on the powerful fine-grained generative control offered by the recent diffusion-based generative models, we introduce Steered Diffusion, a generalized framework for photorealistic zero-shot conditional image generation using a diffusion model trained for unconditional generation. The key idea is to steer the image generation of the diffusion model at inference time via designing a loss using a pre-trained inverse model that characterizes the conditional task. This loss modulates the sampling trajectory of the diffusion process. Our framework allows for easy incorporation of multiple conditions during inference. We present experiments using steered diffusion on several tasks including inpainting, colorization, text-guided semantic editing, and image super-resolution. Our results demonstrate clear qualitative and quantitative improvements over state-of-the-art diffusion-based plug-and-play models while adding negligible additional computational cost.

Beam search is the default decoding strategy for many sequence generation tasks in NLP. The set of approximate K-best items returned by the algorithm is a useful summary of the distribution for many applications; however, the candidates typically exhibit high overlap and may give a highly biased estimate for expectations under our model. These problems can be addressed by instead using stochastic decoding strategies. In this work, we propose a new method for turning beam search into a stochastic process: Conditional Poisson stochastic beam search. Rather than taking the maximizing set at each iteration, we sample K candidates without replacement according to the conditional Poisson sampling design. We view this as a more natural alternative to Kool et. al. 2019's stochastic beam search (SBS). Furthermore, we show how samples generated under the CPSBS design can be used to build consistent estimators and sample diverse sets from sequence models. In our experiments, we observe CPSBS produces lower variance and more efficient estimators than SBS, even showing improvements in high entropy settings.

Inverse design refers to the problem of optimizing the input of an objective function in order to enact a target outcome. For many real-world engineering problems, the objective function takes the form of a simulator that predicts how the system state will evolve over time, and the design challenge is to optimize the initial conditions that lead to a target outcome. Recent developments in learned simulation have shown that graph neural networks (GNNs) can be used for accurate, efficient, differentiable estimation of simulator dynamics, and support high-quality design optimization with gradient- or sampling-based optimization procedures. However, optimizing designs from scratch requires many expensive model queries, and these procedures exhibit basic failures on either non-convex or high-dimensional problems.In this work, we show how denoising diffusion models (DDMs) can be used to solve inverse design problems efficiently and propose a particle sampling algorithm for further improving their efficiency. We perform experiments on a number of fluid dynamics design challenges, and find that our approach substantially reduces the number of calls to the simulator compared to standard techniques.

While conditional diffusion models are known to have good coverage of the data distribution, they still face limitations in output diversity, particularly when sampled with a high classifier-free guidance scale for optimal image quality or when trained on small datasets. We attribute this problem to the role of the conditioning signal in inference and offer an improved sampling strategy for diffusion models that can increase generation diversity, especially at high guidance scales, with minimal loss of sample quality. Our sampling strategy anneals the conditioning signal by adding scheduled, monotonically decreasing Gaussian noise to the conditioning vector during inference to balance diversity and condition alignment. Our Condition-Annealed Diffusion Sampler (CADS) can be used with any pretrained model and sampling algorithm, and we show that it boosts the diversity of diffusion models in various conditional generation tasks. Further, using an existing pretrained diffusion model, CADS achieves a new state-of-the-art FID of 1.70 and 2.31 for class-conditional ImageNet generation at 256times256 and 512times512 respectively.

Generating novel molecules with higher properties than the training space, namely the out-of-distribution generation, is important for {de~novo} drug design. However, it is not easy for distribution learning-based models, for example diffusion models, to solve this challenge as these methods are designed to fit the distribution of training data as close as possible. In this paper, we show that Bayesian flow network is capable of effortlessly generating high quality out-of-distribution samples that meet several scenarios. We introduce a semi-autoregressive training/sampling method that helps to enhance the model performance and surpass the state-of-the-art models.

Inverse protein folding -- the task of predicting a protein sequence from its backbone atom coordinates -- has surfaced as an important problem in the "top down", de novo design of proteins. Contemporary approaches have cast this problem as a conditional generative modelling problem, where a large generative model over protein sequences is conditioned on the backbone. While these generative models very rapidly produce promising sequences, independent draws from generative models may fail to produce sequences that reliably fold to the correct backbone. Furthermore, it is challenging to adapt pure generative approaches to other settings, e.g., when constraints exist. In this paper, we cast the problem of improving generated inverse folds as an optimization problem that we solve using recent advances in "deep" or "latent space" Bayesian optimization. Our approach consistently produces protein sequences with greatly reduced structural error to the target backbone structure as measured by TM score and RMSD while using fewer computational resources. Additionally, we demonstrate other advantages of an optimization-based approach to the problem, such as the ability to handle constraints.

Protein design, a grand challenge of the day, involves optimization on a fitness landscape, and leading methods adopt a model-based approach where a model is trained on a training set (protein sequences and fitness) and proposes candidates to explore next. These methods are challenged by sparsity of high-fitness samples in the training set, a problem that has been in the literature. A less recognized but equally important problem stems from the distribution of training samples in the design space: leading methods are not designed for scenarios where the desired optimum is in a region that is not only poorly represented in training data, but also relatively far from the highly represented low-fitness regions. We show that this problem of "separation" in the design space is a significant bottleneck in existing model-based optimization tools and propose a new approach that uses a novel VAE as its search model to overcome the problem. We demonstrate its advantage over prior methods in robustly finding improved samples, regardless of the imbalance and separation between low- and high-fitness training samples. Our comprehensive benchmark on real and semi-synthetic protein datasets as well as solution design for physics-informed neural networks, showcases the generality of our approach in discrete and continuous design spaces. Our implementation is available at https://github.com/sabagh1994/PGVAE.

Cis-regulatory elements (CREs), such as promoters and enhancers, are relatively short DNA sequences that directly regulate gene expression. The fitness of CREs, measured by their ability to modulate gene expression, highly depends on the nucleotide sequences, especially specific motifs known as transcription factor binding sites (TFBSs). Designing high-fitness CREs is crucial for therapeutic and bioengineering applications. Current CRE design methods are limited by two major drawbacks: (1) they typically rely on iterative optimization strategies that modify existing sequences and are prone to local optima, and (2) they lack the guidance of biological prior knowledge in sequence optimization. In this paper, we address these limitations by proposing a generative approach that leverages reinforcement learning (RL) to fine-tune a pre-trained autoregressive (AR) model. Our method incorporates data-driven biological priors by deriving computational inference-based rewards that simulate the addition of activator TFBSs and removal of repressor TFBSs, which are then integrated into the RL process. We evaluate our method on promoter design tasks in two yeast media conditions and enhancer design tasks for three human cell types, demonstrating its ability to generate high-fitness CREs while maintaining sequence diversity. The code is available at https://github.com/yangzhao1230/TACO.

Discovering novel drug candidate molecules is one of the most fundamental and critical steps in drug development. Generative deep learning models, which create synthetic data given a probability distribution, have been developed with the purpose of picking completely new samples from a partially known space. Generative models offer high potential for designing de novo molecules; however, in order for them to be useful in real-life drug development pipelines, these models should be able to design target-specific molecules, which is the next step in this field. In this study, we propose DrugGEN, for the de novo design of drug candidate molecules that interact with selected target proteins. The proposed system represents compounds and protein structures as graphs and processes them via serially connected two generative adversarial networks comprising graph transformers. DrugGEN is trained using a large dataset of compounds from ChEMBL and target-specific bioactive molecules, to design effective and specific inhibitory molecules against the AKT1 protein, which has critical importance for developing treatments against various types of cancer. On fundamental benchmarks, DrugGEN models have either competitive or better performance against other methods. To assess the target-specific generation performance, we conducted further in silico analysis with molecular docking and deep learning-based bioactivity prediction. Results indicate that de novo molecules have high potential for interacting with the AKT1 protein structure in the level of its native ligand. DrugGEN can be used to design completely novel and effective target-specific drug candidate molecules for any druggable protein, given target features and a dataset of experimental bioactivities. Code base, datasets, results and trained models of DrugGEN are available at https://github.com/HUBioDataLab/DrugGEN

This paper introduces diffusion protein language model (DPLM), a versatile protein language model that demonstrates strong generative and predictive capabilities for protein sequences. We first pre-train scalable DPLMs from evolutionary-scale protein sequences within a generative self-supervised discrete diffusion probabilistic framework, which generalizes language modeling for proteins in a principled way. After pre-training, DPLM exhibits the ability to generate structurally plausible, novel, and diverse protein sequences for unconditional generation. We further demonstrate the proposed diffusion generative pre-training makes DPLM possess a better understanding of proteins, making it a superior representation learner, which can be fine-tuned for various predictive tasks, comparing favorably to ESM2 (Lin et al., 2022). Moreover, DPLM can be tailored for various needs, which showcases its prowess of conditional generation in several ways: (1) conditioning on partial peptide sequences, e.g., generating scaffolds for functional motifs with high success rate; (2) incorporating other modalities as conditioner, e.g., structure-conditioned generation for inverse folding; and (3) steering sequence generation towards desired properties, e.g., satisfying specified secondary structures, through a plug-and-play classifier guidance. Code is released at https://github.com/bytedance/dplm.

We introduce a gradient-based approach for the problem of Bayesian optimal experimental design to learn causal models in a batch setting -- a critical component for causal discovery from finite data where interventions can be costly or risky. Existing methods rely on greedy approximations to construct a batch of experiments while using black-box methods to optimize over a single target-state pair to intervene with. In this work, we completely dispose of the black-box optimization techniques and greedy heuristics and instead propose a conceptually simple end-to-end gradient-based optimization procedure to acquire a set of optimal intervention target-state pairs. Such a procedure enables parameterization of the design space to efficiently optimize over a batch of multi-target-state interventions, a setting which has hitherto not been explored due to its complexity. We demonstrate that our proposed method outperforms baselines and existing acquisition strategies in both single-target and multi-target settings across a number of synthetic datasets.

Guidance in conditional diffusion generation is of great importance for sample quality and controllability. However, existing guidance schemes are to be desired. On one hand, mainstream methods such as classifier guidance and classifier-free guidance both require extra training with labeled data, which is time-consuming and unable to adapt to new conditions. On the other hand, training-free methods such as universal guidance, though more flexible, have yet to demonstrate comparable performance. In this work, through a comprehensive investigation into the design space, we show that it is possible to achieve significant performance improvements over existing guidance schemes by leveraging off-the-shelf classifiers in a training-free fashion, enjoying the best of both worlds. Employing calibration as a general guideline, we propose several pre-conditioning techniques to better exploit pretrained off-the-shelf classifiers for guiding diffusion generation. Extensive experiments on ImageNet validate our proposed method, showing that state-of-the-art diffusion models (DDPM, EDM, DiT) can be further improved (up to 20%) using off-the-shelf classifiers with barely any extra computational cost. With the proliferation of publicly available pretrained classifiers, our proposed approach has great potential and can be readily scaled up to text-to-image generation tasks. The code is available at https://github.com/AlexMaOLS/EluCD/tree/main.

Can we leverage LLMs to model the process of discovering novel language model (LM) architectures? Inspired by real research, we propose a multi-agent LLM approach that simulates the conventional stages of research, from ideation and literature search (proposal stage) to design implementation (code generation), generative pre-training, and downstream evaluation (verification). Using ideas from scaling laws, our system, Genesys, employs a Ladder of Scales approach; new designs are proposed, adversarially reviewed, implemented, and selectively verified at increasingly larger model scales (14Msim350M parameters) with a narrowing budget (the number of models we can train at each scale). To help make discovery efficient and factorizable, Genesys uses a novel genetic programming backbone, which we show has empirical advantages over commonly used direct prompt generation workflows (e.g., sim86\% percentage point improvement in successful design generation, a key bottleneck). We report experiments involving 1,162 newly discovered designs (1,062 fully verified through pre-training) and find the best designs to be highly competitive with known architectures (e.g., outperform GPT2, Mamba2, etc., on 6/9 common benchmarks). We couple these results with comprehensive system-level ablations and formal results, which give broader insights into the design of effective autonomous discovery systems.

Antibodies comprise the most versatile class of binding molecules, with numerous applications in biomedicine. Computational design of antibodies involves generating novel and diverse sequences, while maintaining structural consistency. Unique to antibodies, designing the complementarity-determining region (CDR), which determines the antigen binding affinity and specificity, creates its own unique challenges. Recent deep learning models have shown impressive results, however the limited number of known antibody sequence/structure pairs frequently leads to degraded performance, particularly lacking diversity in the generated sequences. In our work we address this challenge by leveraging Model Reprogramming (MR), which repurposes pretrained models on a source language to adapt to the tasks that are in a different language and have scarce data - where it may be difficult to train a high-performing model from scratch or effectively fine-tune an existing pre-trained model on the specific task. Specifically, we introduce ReprogBert in which a pretrained English language model is repurposed for protein sequence infilling - thus considers cross-language adaptation using less data. Results on antibody design benchmarks show that our model on low-resourced antibody sequence dataset provides highly diverse CDR sequences, up to more than a two-fold increase of diversity over the baselines, without losing structural integrity and naturalness. The generated sequences also demonstrate enhanced antigen binding specificity and virus neutralization ability. Code is available at https://github.com/IBM/ReprogBERT

Inverse design, where we seek to design input variables in order to optimize an underlying objective function, is an important problem that arises across fields such as mechanical engineering to aerospace engineering. Inverse design is typically formulated as an optimization problem, with recent works leveraging optimization across learned dynamics models. However, as models are optimized they tend to fall into adversarial modes, preventing effective sampling. We illustrate that by instead optimizing over the learned energy function captured by the diffusion model, we can avoid such adversarial examples and significantly improve design performance. We further illustrate how such a design system is compositional, enabling us to combine multiple different diffusion models representing subcomponents of our desired system to design systems with every specified component. In an N-body interaction task and a challenging 2D multi-airfoil design task, we demonstrate that by composing the learned diffusion model at test time, our method allows us to design initial states and boundary shapes that are more complex than those in the training data. Our method generalizes to more objects for N-body dataset and discovers formation flying to minimize drag in the multi-airfoil design task. Project website and code can be found at https://github.com/AI4Science-WestlakeU/cindm.

We report a mixture of expert strategy to create fine-tuned large language models using a deep layer-wise token-level approach based on low-rank adaptation (LoRA). Starting with a set of pre-trained LoRA adapters, we propose a gating strategy that uses the hidden states to dynamically mix adapted layers, allowing the resulting X-LoRA model to draw upon different capabilities and create never-before-used deep layer-wise combinations of adaptations are established to solve specific tasks. The design is inspired by the biological principles of universality and diversity, where neural network building blocks are reused in different hierarchical manifestations. Hence, the X-LoRA model can be easily implemented for any existing large language model (LLM) without a need for modifications of the underlying structure. We develop a tailored X-LoRA model that offers scientific capabilities including forward/inverse analysis tasks and enhanced reasoning capability, focused on biomaterial analysis, protein mechanics and design. The impact of this work include access to readily expandable, adaptable and changeable models with strong domain knowledge and the capability to integrate across areas of knowledge. With the X-LoRA model featuring experts in biology, mathematics, reasoning, bio-inspired materials, mechanics and materials, chemistry, and protein mechanics we conduct a series of physics-focused case studies. We examine knowledge recall, protein mechanics forward/inverse tasks, protein design, and adversarial agentic modeling including ontological knowledge graphs. The model is capable not only of making quantitative predictions of nanomechanical properties of proteins, but also reasons over the results and correctly predicts likely mechanisms that explain distinct molecular behaviors.

Given an unconditional diffusion model and a predictor for a target property of interest (e.g., a classifier), the goal of training-free guidance is to generate samples with desirable target properties without additional training. Existing methods, though effective in various individual applications, often lack theoretical grounding and rigorous testing on extensive benchmarks. As a result, they could even fail on simple tasks, and applying them to a new problem becomes unavoidably difficult. This paper introduces a novel algorithmic framework encompassing existing methods as special cases, unifying the study of training-free guidance into the analysis of an algorithm-agnostic design space. Via theoretical and empirical investigation, we propose an efficient and effective hyper-parameter searching strategy that can be readily applied to any downstream task. We systematically benchmark across 7 diffusion models on 16 tasks with 40 targets, and improve performance by 8.5% on average. Our framework and benchmark offer a solid foundation for conditional generation in a training-free manner.

Classifier-free guidance (CFG) has become the standard method for enhancing the quality of conditional diffusion models. However, employing CFG requires either training an unconditional model alongside the main diffusion model or modifying the training procedure by periodically inserting a null condition. There is also no clear extension of CFG to unconditional models. In this paper, we revisit the core principles of CFG and introduce a new method, independent condition guidance (ICG), which provides the benefits of CFG without the need for any special training procedures. Our approach streamlines the training process of conditional diffusion models and can also be applied during inference on any pre-trained conditional model. Additionally, by leveraging the time-step information encoded in all diffusion networks, we propose an extension of CFG, called time-step guidance (TSG), which can be applied to any diffusion model, including unconditional ones. Our guidance techniques are easy to implement and have the same sampling cost as CFG. Through extensive experiments, we demonstrate that ICG matches the performance of standard CFG across various conditional diffusion models. Moreover, we show that TSG improves generation quality in a manner similar to CFG, without relying on any conditional information.

The current advances in generative AI for learning large neural network models with the capability to produce essays, images, music and even 3D assets from text prompts create opportunities for a manifold of disciplines. In the present paper, we study the potential of deep text-to-3D models in the engineering domain, with focus on the chances and challenges when integrating and interacting with 3D assets in computational simulation-based design optimization. In contrast to traditional design optimization of 3D geometries that often searches for the optimum designs using numerical representations, such as B-Spline surface or deformation parameters in vehicle aerodynamic optimization, natural language challenges the optimization framework by requiring a different interpretation of variation operators while at the same time may ease and motivate the human user interaction. Here, we propose and realize a fully automated evolutionary design optimization framework using Shap-E, a recently published text-to-3D asset network by OpenAI, in the context of aerodynamic vehicle optimization. For representing text prompts in the evolutionary optimization, we evaluate (a) a bag-of-words approach based on prompt templates and Wordnet samples, and (b) a tokenisation approach based on prompt templates and the byte pair encoding method from GPT4. Our main findings from the optimizations indicate that, first, it is important to ensure that the designs generated from prompts are within the object class of application, i.e. diverse and novel designs need to be realistic, and, second, that more research is required to develop methods where the strength of text prompt variations and the resulting variations of the 3D designs share causal relations to some degree to improve the optimization.

This paper demonstrates that language models are strong structure-based protein designers. We present LM-Design, a generic approach to reprogramming sequence-based protein language models (pLMs), that have learned massive sequential evolutionary knowledge from the universe of natural protein sequences, to acquire an immediate capability to design preferable protein sequences for given folds. We conduct a structural surgery on pLMs, where a lightweight structural adapter is implanted into pLMs and endows it with structural awareness. During inference, iterative refinement is performed to effectively optimize the generated protein sequences. Experiments show that LM-Design improves the state-of-the-art results by a large margin, leading to up to 4% to 12% accuracy gains in sequence recovery (e.g., 55.65%/56.63% on CATH 4.2/4.3 single-chain benchmarks, and >60% when designing protein complexes). We provide extensive and in-depth analyses, which verify that LM-Design can (1) indeed leverage both structural and sequential knowledge to accurately handle structurally non-deterministic regions, (2) benefit from scaling data and model size, and (3) generalize to other proteins (e.g., antibodies and de novo proteins)

Existing methods, such as concept bottleneck models (CBMs), have been successful in providing concept-based interpretations for black-box deep learning models. They typically work by predicting concepts given the input and then predicting the final class label given the predicted concepts. However, (1) they often fail to capture the high-order, nonlinear interaction between concepts, e.g., correcting a predicted concept (e.g., "yellow breast") does not help correct highly correlated concepts (e.g., "yellow belly"), leading to suboptimal final accuracy; (2) they cannot naturally quantify the complex conditional dependencies between different concepts and class labels (e.g., for an image with the class label "Kentucky Warbler" and a concept "black bill", what is the probability that the model correctly predicts another concept "black crown"), therefore failing to provide deeper insight into how a black-box model works. In response to these limitations, we propose Energy-based Concept Bottleneck Models (ECBMs). Our ECBMs use a set of neural networks to define the joint energy of candidate (input, concept, class) tuples. With such a unified interface, prediction, concept correction, and conditional dependency quantification are then represented as conditional probabilities, which are generated by composing different energy functions. Our ECBMs address both limitations of existing CBMs, providing higher accuracy and richer concept interpretations. Empirical results show that our approach outperforms the state-of-the-art on real-world datasets.

The creation of manufacturable and editable 3D shapes through Computer-Aided Design (CAD) remains a highly manual and time-consuming task, hampered by the complex topology of boundary representations of 3D solids and unintuitive design tools. While most work in the 3D shape generation literature focuses on representations like meshes, voxels, or point clouds, practical engineering applications demand the modifiability and manufacturability of CAD models and the ability for multi-modal conditional CAD model generation. This paper introduces GenCAD, a generative model that employs autoregressive transformers with a contrastive learning framework and latent diffusion models to transform image inputs into parametric CAD command sequences, resulting in editable 3D shape representations. Extensive evaluations demonstrate that GenCAD significantly outperforms existing state-of-the-art methods in terms of the unconditional and conditional generations of CAD models. Additionally, the contrastive learning framework of GenCAD facilitates the retrieval of CAD models using image queries from large CAD databases, which is a critical challenge within the CAD community. Our results provide a significant step forward in highlighting the potential of generative models to expedite the entire design-to-production pipeline and seamlessly integrate different design modalities.

Recent improvements in conditional generative modeling have made it possible to generate high-quality images from language descriptions alone. We investigate whether these methods can directly address the problem of sequential decision-making. We view decision-making not through the lens of reinforcement learning (RL), but rather through conditional generative modeling. To our surprise, we find that our formulation leads to policies that can outperform existing offline RL approaches across standard benchmarks. By modeling a policy as a return-conditional diffusion model, we illustrate how we may circumvent the need for dynamic programming and subsequently eliminate many of the complexities that come with traditional offline RL. We further demonstrate the advantages of modeling policies as conditional diffusion models by considering two other conditioning variables: constraints and skills. Conditioning on a single constraint or skill during training leads to behaviors at test-time that can satisfy several constraints together or demonstrate a composition of skills. Our results illustrate that conditional generative modeling is a powerful tool for decision-making.

Creating graphic layouts is a fundamental step in graphic designs. In this work, we present a novel generative model named LayoutDiffusion for automatic layout generation. As layout is typically represented as a sequence of discrete tokens, LayoutDiffusion models layout generation as a discrete denoising diffusion process. It learns to reverse a mild forward process, in which layouts become increasingly chaotic with the growth of forward steps and layouts in the neighboring steps do not differ too much. Designing such a mild forward process is however very challenging as layout has both categorical attributes and ordinal attributes. To tackle the challenge, we summarize three critical factors for achieving a mild forward process for the layout, i.e., legality, coordinate proximity and type disruption. Based on the factors, we propose a block-wise transition matrix coupled with a piece-wise linear noise schedule. Experiments on RICO and PubLayNet datasets show that LayoutDiffusion outperforms state-of-the-art approaches significantly. Moreover, it enables two conditional layout generation tasks in a plug-and-play manner without re-training and achieves better performance than existing methods.

Diffusion models excel at capturing the natural design spaces of images, molecules, DNA, RNA, and protein sequences. However, rather than merely generating designs that are natural, we often aim to optimize downstream reward functions while preserving the naturalness of these design spaces. Existing methods for achieving this goal often require ``differentiable'' proxy models (e.g., classifier guidance or DPS) or involve computationally expensive fine-tuning of diffusion models (e.g., classifier-free guidance, RL-based fine-tuning). In our work, we propose a new method to address these challenges. Our algorithm is an iterative sampling method that integrates soft value functions, which looks ahead to how intermediate noisy states lead to high rewards in the future, into the standard inference procedure of pre-trained diffusion models. Notably, our approach avoids fine-tuning generative models and eliminates the need to construct differentiable models. This enables us to (1) directly utilize non-differentiable features/reward feedback, commonly used in many scientific domains, and (2) apply our method to recent discrete diffusion models in a principled way. Finally, we demonstrate the effectiveness of our algorithm across several domains, including image generation, molecule generation, and DNA/RNA sequence generation. The code is available at https://github.com/masa-ue/SVDD{https://github.com/masa-ue/SVDD}.

The advancement of Large Language Models (LLMs) for domain applications in fields such as materials science and engineering depends on the development of fine-tuning strategies that adapt models for specialized, technical capabilities. In this work, we explore the effects of Continued Pretraining (CPT), Supervised Fine-Tuning (SFT), and various preference-based optimization approaches, including Direct Preference Optimization (DPO) and Odds Ratio Preference Optimization (ORPO), on fine-tuned LLM performance. Our analysis shows how these strategies influence model outcomes and reveals that the merging of multiple fine-tuned models can lead to the emergence of capabilities that surpass the individual contributions of the parent models. We find that model merging leads to new functionalities that neither parent model could achieve alone, leading to improved performance in domain-specific assessments. Experiments with different model architectures are presented, including Llama 3.1 8B and Mistral 7B models, where similar behaviors are observed. Exploring whether the results hold also for much smaller models, we use a tiny LLM with 1.7 billion parameters and show that very small LLMs do not necessarily feature emergent capabilities under model merging, suggesting that model scaling may be a key component. In open-ended yet consistent chat conversations between a human and AI models, our assessment reveals detailed insights into how different model variants perform and show that the smallest model achieves a high intelligence score across key criteria including reasoning depth, creativity, clarity, and quantitative precision. Other experiments include the development of image generation prompts based on disparate biological material design concepts, to create new microstructures, architectural concepts, and urban design based on biological materials-inspired construction principles.

Existing NAS methods suffer from either an excessive amount of time for repetitive sampling and training of many task-irrelevant architectures. To tackle such limitations of existing NAS methods, we propose a paradigm shift from NAS to a novel conditional Neural Architecture Generation (NAG) framework based on diffusion models, dubbed DiffusionNAG. Specifically, we consider the neural architectures as directed graphs and propose a graph diffusion model for generating them. Moreover, with the guidance of parameterized predictors, DiffusionNAG can flexibly generate task-optimal architectures with the desired properties for diverse tasks, by sampling from a region that is more likely to satisfy the properties. This conditional NAG scheme is significantly more efficient than previous NAS schemes which sample the architectures and filter them using the property predictors. We validate the effectiveness of DiffusionNAG through extensive experiments in two predictor-based NAS scenarios: Transferable NAS and Bayesian Optimization (BO)-based NAS. DiffusionNAG achieves superior performance with speedups of up to 35 times when compared to the baselines on Transferable NAS benchmarks. Furthermore, when integrated into a BO-based algorithm, DiffusionNAG outperforms existing BO-based NAS approaches, particularly in the large MobileNetV3 search space on the ImageNet 1K dataset. Code is available at https://github.com/CownowAn/DiffusionNAG.

Posterior sampling allows the exploitation of prior knowledge of the environment's transition dynamics to improve the sample efficiency of reinforcement learning. The prior is typically specified as a class of parametric distributions, a task that can be cumbersome in practice, often resulting in the choice of uninformative priors. In this work, we propose a novel posterior sampling approach in which the prior is given as a (partial) causal graph over the environment's variables. The latter is often more natural to design, such as listing known causal dependencies between biometric features in a medical treatment study. Specifically, we propose a hierarchical Bayesian procedure, called C-PSRL, simultaneously learning the full causal graph at the higher level and the parameters of the resulting factored dynamics at the lower level. For this procedure, we provide an analysis of its Bayesian regret, which explicitly connects the regret rate with the degree of prior knowledge. Our numerical evaluation conducted in illustrative domains confirms that C-PSRL strongly improves the efficiency of posterior sampling with an uninformative prior while performing close to posterior sampling with the full causal graph.

Designing biological sequences is an important challenge that requires satisfying complex constraints and thus is a natural problem to address with deep generative modeling. Diffusion generative models have achieved considerable success in many applications. Score-based generative stochastic differential equations (SDE) model is a continuous-time diffusion model framework that enjoys many benefits, but the originally proposed SDEs are not naturally designed for modeling discrete data. To develop generative SDE models for discrete data such as biological sequences, here we introduce a diffusion process defined in the probability simplex space with stationary distribution being the Dirichlet distribution. This makes diffusion in continuous space natural for modeling discrete data. We refer to this approach as Dirchlet diffusion score model. We demonstrate that this technique can generate samples that satisfy hard constraints using a Sudoku generation task. This generative model can also solve Sudoku, including hard puzzles, without additional training. Finally, we applied this approach to develop the first human promoter DNA sequence design model and showed that designed sequences share similar properties with natural promoter sequences.

Parametric Computer-Aided Design (CAD) is central to contemporary mechanical design. However, it encounters challenges in achieving precise parametric sketch modeling and lacks practical evaluation metrics suitable for mechanical design. We harness the capabilities of pre-trained foundation models, renowned for their successes in natural language processing and computer vision, to develop generative models specifically for CAD. These models are adept at understanding complex geometries and design reasoning, a crucial advancement in CAD technology. In this paper, we propose CadVLM, an end-to-end vision language model for CAD generation. Our approach involves adapting pre-trained foundation models to manipulate engineering sketches effectively, integrating both sketch primitive sequences and sketch images. Extensive experiments demonstrate superior performance on multiple CAD sketch generation tasks such as CAD autocompletion, CAD autoconstraint, and image conditional generation. To our knowledge, this is the first instance of a multimodal Large Language Model (LLM) being successfully applied to parametric CAD generation, representing a pioneering step in the field of computer-aided mechanical design.

Generating visual layouts is an essential ingredient of graphic design. The ability to condition layout generation on a partial subset of component attributes is critical to real-world applications that involve user interaction. Recently, diffusion models have demonstrated high-quality generative performances in various domains. However, it is unclear how to apply diffusion models to the natural representation of layouts which consists of a mix of discrete (class) and continuous (location, size) attributes. To address the conditioning layout generation problem, we introduce DLT, a joint discrete-continuous diffusion model. DLT is a transformer-based model which has a flexible conditioning mechanism that allows for conditioning on any given subset of all the layout component classes, locations, and sizes. Our method outperforms state-of-the-art generative models on various layout generation datasets with respect to different metrics and conditioning settings. Additionally, we validate the effectiveness of our proposed conditioning mechanism and the joint continuous-diffusion process. This joint process can be incorporated into a wide range of mixed discrete-continuous generative tasks.

Visual layout plays a critical role in graphic design fields such as advertising, posters, and web UI design. The recent trend towards content-aware layout generation through generative models has shown promise, yet it often overlooks the semantic intricacies of layout design by treating it as a simple numerical optimization. To bridge this gap, we introduce PosterLlama, a network designed for generating visually and textually coherent layouts by reformatting layout elements into HTML code and leveraging the rich design knowledge embedded within language models. Furthermore, we enhance the robustness of our model with a unique depth-based poster augmentation strategy. This ensures our generated layouts remain semantically rich but also visually appealing, even with limited data. Our extensive evaluations across several benchmarks demonstrate that PosterLlama outperforms existing methods in producing authentic and content-aware layouts. It supports an unparalleled range of conditions, including but not limited to unconditional layout generation, element conditional layout generation, layout completion, among others, serving as a highly versatile user manipulation tool.

Fragment-based drug discovery has been an effective paradigm in early-stage drug development. An open challenge in this area is designing linkers between disconnected molecular fragments of interest to obtain chemically-relevant candidate drug molecules. In this work, we propose DiffLinker, an E(3)-equivariant 3D-conditional diffusion model for molecular linker design. Given a set of disconnected fragments, our model places missing atoms in between and designs a molecule incorporating all the initial fragments. Unlike previous approaches that are only able to connect pairs of molecular fragments, our method can link an arbitrary number of fragments. Additionally, the model automatically determines the number of atoms in the linker and its attachment points to the input fragments. We demonstrate that DiffLinker outperforms other methods on the standard datasets generating more diverse and synthetically-accessible molecules. Besides, we experimentally test our method in real-world applications, showing that it can successfully generate valid linkers conditioned on target protein pockets.

Diffusion models have recently shown significant potential in solving decision-making problems, particularly in generating behavior plans -- also known as diffusion planning. While numerous studies have demonstrated the impressive performance of diffusion planning, the mechanisms behind the key components of a good diffusion planner remain unclear and the design choices are highly inconsistent in existing studies. In this work, we address this issue through systematic empirical experiments on diffusion planning in an offline reinforcement learning (RL) setting, providing practical insights into the essential components of diffusion planning. We trained and evaluated over 6,000 diffusion models, identifying the critical components such as guided sampling, network architecture, action generation and planning strategy. We revealed that some design choices opposite to the common practice in previous work in diffusion planning actually lead to better performance, e.g., unconditional sampling with selection can be better than guided sampling and Transformer outperforms U-Net as denoising network. Based on these insights, we suggest a simple yet strong diffusion planning baseline that achieves state-of-the-art results on standard offline RL benchmarks.

In 3D modeling, designers often use an existing 3D model as a reference to create new ones. This practice has inspired the development of Phidias, a novel generative model that uses diffusion for reference-augmented 3D generation. Given an image, our method leverages a retrieved or user-provided 3D reference model to guide the generation process, thereby enhancing the generation quality, generalization ability, and controllability. Our model integrates three key components: 1) meta-ControlNet that dynamically modulates the conditioning strength, 2) dynamic reference routing that mitigates misalignment between the input image and 3D reference, and 3) self-reference augmentations that enable self-supervised training with a progressive curriculum. Collectively, these designs result in a clear improvement over existing methods. Phidias establishes a unified framework for 3D generation using text, image, and 3D conditions with versatile applications.

In this work, we introduce ChemBFN, a language model that handles chemistry tasks based on Bayesian flow networks working on discrete data. A new accuracy schedule is proposed to improve the sampling quality by significantly reducing the reconstruction loss. We show evidence that our method is appropriate for generating molecules with satisfied diversity even when a smaller number of sampling steps is used. A classifier-free guidance method is adapted for conditional generation. It is also worthwhile to point out that after generative training, our model can be fine-tuned on regression and classification tasks with the state-of-the-art performance, which opens the gate of building all-in-one models in a single module style. Our model has been open sourced at https://github.com/Augus1999/bayesian-flow-network-for-chemistry.

Recent advances in Conditional Diffusion Models have led to substantial capabilities in various domains. However, understanding the impact of variations in the initial seed vector remains an underexplored area of concern. Particularly, latent-based diffusion models display inconsistencies in image generation under standard conditions when initialized with suboptimal initial seed vectors. To understand the impact of the initial seed vector on generated samples, we propose a reliability evaluation framework that evaluates the generated samples of a diffusion model when the initial seed vector is subjected to various synthetic shifts. Our results indicate that slight manipulations to the initial seed vector of the state-of-the-art Stable Diffusion (Rombach et al., 2022) can lead to significant disturbances in the generated samples, consequently creating images without the effect of conditioning variables. In contrast, GLIDE (Nichol et al., 2022) stands out in generating reliable samples even when the initial seed vector is transformed. Thus, our study sheds light on the importance of the selection and the impact of the initial seed vector in the latent-based diffusion model.

Offline model-based optimization aims to maximize a black-box objective function with a static dataset of designs and their scores. In this paper, we focus on biological sequence design to maximize some sequence score. A recent approach employs bidirectional learning, combining a forward mapping for exploitation and a backward mapping for constraint, and it relies on the neural tangent kernel (NTK) of an infinitely wide network to build a proxy model. Though effective, the NTK cannot learn features because of its parametrization, and its use prevents the incorporation of powerful pre-trained Language Models (LMs) that can capture the rich biophysical information in millions of biological sequences. We adopt an alternative proxy model, adding a linear head to a pre-trained LM, and propose a linearization scheme. This yields a closed-form loss and also takes into account the biophysical information in the pre-trained LM. In addition, the forward mapping and the backward mapping play different roles and thus deserve different weights during sequence optimization. To achieve this, we train an auxiliary model and leverage its weak supervision signal via a bi-level optimization framework to effectively learn how to balance the two mappings. Further, by extending the framework, we develop the first learning rate adaptation module Adaptive-eta, which is compatible with all gradient-based algorithms for offline model-based optimization. Experimental results on DNA/protein sequence design tasks verify the effectiveness of our algorithm. Our code is available~https://anonymous.4open.science/r/BIB-ICLR2023-Submission/README.md{here.}

Diffusion models have achieved remarkable success in text-to-image synthesis, largely attributed to the use of classifier-free guidance (CFG), which enables high-quality, condition-aligned image generation. CFG combines the conditional score (e.g., text-conditioned) with the unconditional score to control the output. However, the unconditional score is in charge of estimating the transition between manifolds of adjacent timesteps from x_t to x_{t-1}, which may inadvertently interfere with the trajectory toward the specific condition. In this work, we introduce a novel approach that leverages a geometric perspective on the unconditional score to enhance CFG performance when conditional scores are available. Specifically, we propose a method that filters the singular vectors of both conditional and unconditional scores using singular value decomposition. This filtering process aligns the unconditional score with the conditional score, thereby refining the sampling trajectory to stay closer to the manifold. Our approach improves image quality with negligible additional computation. We provide deeper insights into the score function behavior in diffusion models and present a practical technique for achieving more accurate and contextually coherent image synthesis.

In this work, we investigate automatic design composition from multimodal graphic elements. Although recent studies have developed various generative models for graphic design, they usually face the following limitations: they only focus on certain subtasks and are far from achieving the design composition task; they do not consider the hierarchical information of graphic designs during the generation process. To tackle these issues, we introduce the layered design principle into Large Multimodal Models (LMMs) and propose a novel approach, called LaDeCo, to accomplish this challenging task. Specifically, LaDeCo first performs layer planning for a given element set, dividing the input elements into different semantic layers according to their contents. Based on the planning results, it subsequently predicts element attributes that control the design composition in a layer-wise manner, and includes the rendered image of previously generated layers into the context. With this insightful design, LaDeCo decomposes the difficult task into smaller manageable steps, making the generation process smoother and clearer. The experimental results demonstrate the effectiveness of LaDeCo in design composition. Furthermore, we show that LaDeCo enables some interesting applications in graphic design, such as resolution adjustment, element filling, design variation, etc. In addition, it even outperforms the specialized models in some design subtasks without any task-specific training.

In this work, we present a new network design paradigm. Our goal is to help advance the understanding of network design and discover design principles that generalize across settings. Instead of focusing on designing individual network instances, we design network design spaces that parametrize populations of networks. The overall process is analogous to classic manual design of networks, but elevated to the design space level. Using our methodology we explore the structure aspect of network design and arrive at a low-dimensional design space consisting of simple, regular networks that we call RegNet. The core insight of the RegNet parametrization is surprisingly simple: widths and depths of good networks can be explained by a quantized linear function. We analyze the RegNet design space and arrive at interesting findings that do not match the current practice of network design. The RegNet design space provides simple and fast networks that work well across a wide range of flop regimes. Under comparable training settings and flops, the RegNet models outperform the popular EfficientNet models while being up to 5x faster on GPUs.

In this paper, we focus on the task of conditional image generation, where an image is synthesized according to user instructions. The critical challenge underpinning this task is ensuring both the fidelity of the generated images and their semantic alignment with the provided conditions. To tackle this issue, previous studies have employed supervised perceptual losses derived from pre-trained models, i.e., reward models, to enforce alignment between the condition and the generated result. However, we observe one inherent shortcoming: considering the diversity of synthesized images, the reward model usually provides inaccurate feedback when encountering newly generated data, which can undermine the training process. To address this limitation, we propose an uncertainty-aware reward modeling, called Ctrl-U, including uncertainty estimation and uncertainty-aware regularization, designed to reduce the adverse effects of imprecise feedback from the reward model. Given the inherent cognitive uncertainty within reward models, even images generated under identical conditions often result in a relatively large discrepancy in reward loss. Inspired by the observation, we explicitly leverage such prediction variance as an uncertainty indicator. Based on the uncertainty estimation, we regularize the model training by adaptively rectifying the reward. In particular, rewards with lower uncertainty receive higher loss weights, while those with higher uncertainty are given reduced weights to allow for larger variability. The proposed uncertainty regularization facilitates reward fine-tuning through consistency construction. Extensive experiments validate the effectiveness of our methodology in improving the controllability and generation quality, as well as its scalability across diverse conditional scenarios. Code will soon be available at https://grenoble-zhang.github.io/Ctrl-U-Page/.

Exploiting the recent advancements in artificial intelligence, showcased by ChatGPT and DALL-E, in real-world applications necessitates vast, domain-specific, and publicly accessible datasets. Unfortunately, the scarcity of such datasets poses a significant challenge for researchers aiming to apply these breakthroughs in engineering design. Synthetic datasets emerge as a viable alternative. However, practitioners are often uncertain about generating high-quality datasets that accurately represent real-world data and are suitable for the intended downstream applications. This study aims to fill this knowledge gap by proposing comprehensive guidelines for generating, annotating, and validating synthetic datasets. The trade-offs and methods associated with each of these aspects are elaborated upon. Further, the practical implications of these guidelines are illustrated through the creation of a turbo-compressors dataset. The study underscores the importance of thoughtful sampling methods to ensure the appropriate size, diversity, utility, and realism of a dataset. It also highlights that design diversity does not equate to performance diversity or realism. By employing test sets that represent uniform, real, or task-specific samples, the influence of sample size and sampling strategy is scrutinized. Overall, this paper offers valuable insights for researchers intending to create and publish synthetic datasets for engineering design, thereby paving the way for more effective applications of AI advancements in the field. The code and data for the dataset and methods are made publicly accessible at https://github.com/cyrilpic/radcomp .

Discrete diffusion or flow models could enable faster and more controllable sequence generation than autoregressive models. We show that na\"ive linear flow matching on the simplex is insufficient toward this goal since it suffers from discontinuities in the training target and further pathologies. To overcome this, we develop Dirichlet flow matching on the simplex based on mixtures of Dirichlet distributions as probability paths. In this framework, we derive a connection between the mixtures' scores and the flow's vector field that allows for classifier and classifier-free guidance. Further, we provide distilled Dirichlet flow matching, which enables one-step sequence generation with minimal performance hits, resulting in O(L) speedups compared to autoregressive models. On complex DNA sequence generation tasks, we demonstrate superior performance compared to all baselines in distributional metrics and in achieving desired design targets for generated sequences. Finally, we show that our classifier-free guidance approach improves unconditional generation and is effective for generating DNA that satisfies design targets. Code is available at https://github.com/HannesStark/dirichlet-flow-matching.

Recent studies have shown the impressive efficacy of counterfactually augmented data (CAD) for reducing NLU models' reliance on spurious features and improving their generalizability. However, current methods still heavily rely on human efforts or task-specific designs to generate counterfactuals, thereby impeding CAD's applicability to a broad range of NLU tasks. In this paper, we present AutoCAD, a fully automatic and task-agnostic CAD generation framework. AutoCAD first leverages a classifier to unsupervisedly identify rationales as spans to be intervened, which disentangles spurious and causal features. Then, AutoCAD performs controllable generation enhanced by unlikelihood training to produce diverse counterfactuals. Extensive evaluations on multiple out-of-domain and challenge benchmarks demonstrate that AutoCAD consistently and significantly boosts the out-of-distribution performance of powerful pre-trained models across different NLU tasks, which is comparable or even better than previous state-of-the-art human-in-the-loop or task-specific CAD methods. The code is publicly available at https://github.com/thu-coai/AutoCAD.

Designing high-quality presentation slides can be challenging for non-experts due to the complexity involved in navigating various design choices. Numerous automated tools can suggest layouts and color schemes, yet often lack the ability to refine their own output, which is a key aspect in real-world workflows. We propose DesignLab, which separates the design process into two roles, the design reviewer, who identifies design-related issues, and the design contributor who corrects them. This decomposition enables an iterative loop where the reviewer continuously detects issues and the contributor corrects them, allowing a draft to be further polished with each iteration, reaching qualities that were unattainable. We fine-tune large language models for these roles and simulate intermediate drafts by introducing controlled perturbations, enabling the design reviewer learn design errors and the contributor learn how to fix them. Our experiments show that DesignLab outperforms existing design-generation methods, including a commercial tool, by embracing the iterative nature of designing which can result in polished, professional slides.

Stable Diffusion and ControlNet have achieved excellent results in the field of image generation and synthesis. However, due to the granularity and method of its control, the efficiency improvement is limited for professional artistic creations such as comics and animation production whose main work is secondary painting. In the current workflow, fixing characters and image styles often need lengthy text prompts, and even requires further training through TextualInversion, DreamBooth or other methods, which is very complicated and expensive for painters. Therefore, we present a new method in this paper, Stable Diffusion Reference Only, a images-to-image self-supervised model that uses only two types of conditional images for precise control generation to accelerate secondary painting. The first type of conditional image serves as an image prompt, supplying the necessary conceptual and color information for generation. The second type is blueprint image, which controls the visual structure of the generated image. It is natively embedded into the original UNet, eliminating the need for ControlNet. We released all the code for the module and pipeline, and trained a controllable character line art coloring model at https://github.com/aihao2000/stable-diffusion-reference-only, that achieved state-of-the-art results in this field. This verifies the effectiveness of the structure and greatly improves the production efficiency of animations, comics, and fanworks.

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.

We study the problem of optimizing biological sequences, e.g., proteins, DNA, and RNA, to maximize a black-box score function that is only evaluated in an offline dataset. We propose a novel solution, bootstrapped training of score-conditioned generator (BootGen) algorithm. Our algorithm repeats a two-stage process. In the first stage, our algorithm trains the biological sequence generator with rank-based weights to enhance the accuracy of sequence generation based on high scores. The subsequent stage involves bootstrapping, which augments the training dataset with self-generated data labeled by a proxy score function. Our key idea is to align the score-based generation with a proxy score function, which distills the knowledge of the proxy score function to the generator. After training, we aggregate samples from multiple bootstrapped generators and proxies to produce a diverse design. Extensive experiments show that our method outperforms competitive baselines on biological sequential design tasks. We provide reproducible source code: https://github.com/kaist-silab/bootgen{https://github.com/kaist-silab/bootgen}.

Training multiple tasks jointly in one deep network yields reduced latency during inference and better performance over the single-task counterpart by sharing certain layers of a network. However, over-sharing a network could erroneously enforce over-generalization, causing negative knowledge transfer across tasks. Prior works rely on human intuition or pre-computed task relatedness scores for ad hoc branching structures. They provide sub-optimal end results and often require huge efforts for the trial-and-error process. In this work, we present an automated multi-task learning algorithm that learns where to share or branch within a network, designing an effective network topology that is directly optimized for multiple objectives across tasks. Specifically, we propose a novel tree-structured design space that casts a tree branching operation as a gumbel-softmax sampling procedure. This enables differentiable network splitting that is end-to-end trainable. We validate the proposed method on controlled synthetic data, CelebA, and Taskonomy.

Layout generation is a task to synthesize a harmonious layout with elements characterized by attributes such as category, position, and size. Human designers experiment with the placement and modification of elements to create aesthetic layouts, however, we observed that current discrete diffusion models (DDMs) struggle to correct inharmonious layouts after they have been generated. In this paper, we first provide novel insights into layout sticking phenomenon in DDMs and then propose a simple yet effective layout-assessment module Layout-Corrector, which works in conjunction with existing DDMs to address the layout sticking problem. We present a learning-based module capable of identifying inharmonious elements within layouts, considering overall layout harmony characterized by complex composition. During the generation process, Layout-Corrector evaluates the correctness of each token in the generated layout, reinitializing those with low scores to the ungenerated state. The DDM then uses the high-scored tokens as clues to regenerate the harmonized tokens. Layout-Corrector, tested on common benchmarks, consistently boosts layout-generation performance when in conjunction with various state-of-the-art DDMs. Furthermore, our extensive analysis demonstrates that the Layout-Corrector (1) successfully identifies erroneous tokens, (2) facilitates control over the fidelity-diversity trade-off, and (3) significantly mitigates the performance drop associated with fast sampling.

Recent progress in image generation has sparked research into controlling these models through condition signals, with various methods addressing specific challenges in conditional generation. Instead of proposing another specialized technique, we introduce a simple, unified framework to handle diverse conditional generation tasks involving a specific image-condition correlation. By learning a joint distribution over a correlated image pair (e.g. image and depth) with a diffusion model, our approach enables versatile capabilities via different inference-time sampling schemes, including controllable image generation (e.g. depth to image), estimation (e.g. image to depth), signal guidance, joint generation (image & depth), and coarse control. Previous attempts at unification often introduce significant complexity through multi-stage training, architectural modification, or increased parameter counts. In contrast, our simple formulation requires a single, computationally efficient training stage, maintains the standard model input, and adds minimal learned parameters (15% of the base model). Moreover, our model supports additional capabilities like non-spatially aligned and coarse conditioning. Extensive results show that our single model can produce comparable results with specialized methods and better results than prior unified methods. We also demonstrate that multiple models can be effectively combined for multi-signal conditional generation.

Generative molecular design has moved from proof-of-concept to real-world applicability, as marked by the surge in very recent papers reporting experimental validation. Key challenges in explainability and sample efficiency present opportunities to enhance generative design to directly optimize expensive high-fidelity oracles and provide actionable insights to domain experts. Here, we propose Beam Enumeration to exhaustively enumerate the most probable sub-sequences from language-based molecular generative models and show that molecular substructures can be extracted. When coupled with reinforcement learning, extracted substructures become meaningful, providing a source of explainability and improving sample efficiency through self-conditioned generation. Beam Enumeration is generally applicable to any language-based molecular generative model and notably further improves the performance of the recently reported Augmented Memory algorithm, which achieved the new state-of-the-art on the Practical Molecular Optimization benchmark for sample efficiency. The combined algorithm generates more high reward molecules and faster, given a fixed oracle budget. Beam Enumeration shows that improvements to explainability and sample efficiency for molecular design can be made synergistic.

Text-to-3D (T23D) generation has transformed digital content creation, yet remains bottlenecked by blind trial-and-error prompting processes that yield unpredictable results. While visual prompt engineering has advanced in text-to-image domains, its application to 3D generation presents unique challenges requiring multi-view consistency evaluation and spatial understanding. We present Sel3DCraft, a visual prompt engineering system for T23D that transforms unstructured exploration into a guided visual process. Our approach introduces three key innovations: a dual-branch structure combining retrieval and generation for diverse candidate exploration; a multi-view hybrid scoring approach that leverages MLLMs with innovative high-level metrics to assess 3D models with human-expert consistency; and a prompt-driven visual analytics suite that enables intuitive defect identification and refinement. Extensive testing and user studies demonstrate that Sel3DCraft surpasses other T23D systems in supporting creativity for designers.

In problem-solving, we humans can come up with multiple novel solutions to the same problem. However, reinforcement learning algorithms can only produce a set of monotonous policies that maximize the cumulative reward but lack diversity and novelty. In this work, we address the problem of generating novel policies in reinforcement learning tasks. Instead of following the multi-objective framework used in existing methods, we propose to rethink the problem under a novel perspective of constrained optimization. We first introduce a new metric to evaluate the difference between policies and then design two practical novel policy generation methods following the new perspective. The two proposed methods, namely the Constrained Task Novel Bisector (CTNB) and the Interior Policy Differentiation (IPD), are derived from the feasible direction method and the interior point method commonly known in the constrained optimization literature. Experimental comparisons on the MuJoCo control suite show our methods can achieve substantial improvement over previous novelty-seeking methods in terms of both the novelty of policies and their performances in the primal task.

Classifier-Free Guidance (CFG) is a fundamental technique in training conditional diffusion models. The common practice for CFG-based training is to use a single network to learn both conditional and unconditional noise prediction, with a small dropout rate for conditioning. However, we observe that the joint learning of unconditional noise with limited bandwidth in training results in poor priors for the unconditional case. More importantly, these poor unconditional noise predictions become a serious reason for degrading the quality of conditional generation. Inspired by the fact that most CFG-based conditional models are trained by fine-tuning a base model with better unconditional generation, we first show that simply replacing the unconditional noise in CFG with that predicted by the base model can significantly improve conditional generation. Furthermore, we show that a diffusion model other than the one the fine-tuned model was trained on can be used for unconditional noise replacement. We experimentally verify our claim with a range of CFG-based conditional models for both image and video generation, including Zero-1-to-3, Versatile Diffusion, DiT, DynamiCrafter, and InstructPix2Pix.

RNA design is the search for a sequence or set of sequences that will fold into predefined structures, also known as the inverse problem of RNA folding. While numerous RNA design methods have been invented to find sequences capable of folding into a target structure, little attention has been given to the identification of undesignable structures according to the minimum free energy (MFE) criterion under the Turner model. In this paper, we address this gap by first introducing mathematical theorems outlining sufficient conditions for recognizing undesignable structures, then proposing efficient algorithms, guided by these theorems, to verify the undesignability of RNA structures. Through the application of these theorems and algorithms to the Eterna100 puzzles, we demonstrate the ability to efficiently establish that 15 of the puzzles indeed fall within the category of undesignable structures. In addition, we provide specific insights from the study of undesignability, in the hope that it will enable more understanding of RNA folding and RNA design.

We introduce Zero-1-to-3, a framework for changing the camera viewpoint of an object given just a single RGB image. To perform novel view synthesis in this under-constrained setting, we capitalize on the geometric priors that large-scale diffusion models learn about natural images. Our conditional diffusion model uses a synthetic dataset to learn controls of the relative camera viewpoint, which allow new images to be generated of the same object under a specified camera transformation. Even though it is trained on a synthetic dataset, our model retains a strong zero-shot generalization ability to out-of-distribution datasets as well as in-the-wild images, including impressionist paintings. Our viewpoint-conditioned diffusion approach can further be used for the task of 3D reconstruction from a single image. Qualitative and quantitative experiments show that our method significantly outperforms state-of-the-art single-view 3D reconstruction and novel view synthesis models by leveraging Internet-scale pre-training.

To build effective therapeutics, biologists iteratively mutate antibody sequences to improve binding and stability. Proposed mutations can be informed by previous measurements or by learning from large antibody databases to predict only typical antibodies. Unfortunately, the space of typical antibodies is enormous to search, and experiments often fail to find suitable antibodies on a budget. We introduce Clone-informed Bayesian Optimization (CloneBO), a Bayesian optimization procedure that efficiently optimizes antibodies in the lab by teaching a generative model how our immune system optimizes antibodies. Our immune system makes antibodies by iteratively evolving specific portions of their sequences to bind their target strongly and stably, resulting in a set of related, evolving sequences known as a clonal family. We train a large language model, CloneLM, on hundreds of thousands of clonal families and use it to design sequences with mutations that are most likely to optimize an antibody within the human immune system. We propose to guide our designs to fit previous measurements with a twisted sequential Monte Carlo procedure. We show that CloneBO optimizes antibodies substantially more efficiently than previous methods in realistic in silico experiments and designs stronger and more stable binders in in vitro wet lab experiments.

AI powered code-recommendation systems, such as Copilot and CodeWhisperer, provide code suggestions inside a programmer's environment (e.g., an IDE) with the aim of improving productivity. We pursue mechanisms for leveraging signals about programmers' acceptance and rejection of code suggestions to guide recommendations. We harness data drawn from interactions with GitHub Copilot, a system used by millions of programmers, to develop interventions that can save time for programmers. We introduce a utility-theoretic framework to drive decisions about suggestions to display versus withhold. The approach, conditional suggestion display from human feedback (CDHF), relies on a cascade of models that provide the likelihood that recommended code will be accepted. These likelihoods are used to selectively hide suggestions, reducing both latency and programmer verification time. Using data from 535 programmers, we perform a retrospective evaluation of CDHF and show that we can avoid displaying a significant fraction of suggestions that would have been rejected. We further demonstrate the importance of incorporating the programmer's latent unobserved state in decisions about when to display suggestions through an ablation study. Finally, we showcase how using suggestion acceptance as a reward signal for guiding the display of suggestions can lead to suggestions of reduced quality, indicating an unexpected pitfall.

Graphic layout designs play an essential role in visual communication. Yet handcrafting layout designs is skill-demanding, time-consuming, and non-scalable to batch production. Generative models emerge to make design automation scalable but it remains non-trivial to produce designs that comply with designers' multimodal desires, i.e., constrained by background images and driven by foreground content. We propose LayoutDETR that inherits the high quality and realism from generative modeling, while reformulating content-aware requirements as a detection problem: we learn to detect in a background image the reasonable locations, scales, and spatial relations for multimodal foreground elements in a layout. Our solution sets a new state-of-the-art performance for layout generation on public benchmarks and on our newly-curated ad banner dataset. We integrate our solution into a graphical system that facilitates user studies, and show that users prefer our designs over baselines by significant margins. Our code, models, dataset, graphical system, and demos are available at https://github.com/salesforce/LayoutDETR.

Diffusion models are a class of probabilistic generative models that have been widely used as a prior for image processing tasks like text conditional generation and inpainting. We demonstrate that these models can be adapted to make predictions and provide uncertainty quantification for chaotic dynamical systems. In these applications, diffusion models can implicitly represent knowledge about outliers and extreme events; however, querying that knowledge through conditional sampling or measuring probabilities is surprisingly difficult. Existing methods for conditional sampling at inference time seek mainly to enforce the constraints, which is insufficient to match the statistics of the distribution or compute the probability of the chosen events. To achieve these ends, optimally one would use the conditional score function, but its computation is typically intractable. In this work, we develop a probabilistic approximation scheme for the conditional score function which provably converges to the true distribution as the noise level decreases. With this scheme we are able to sample conditionally on nonlinear userdefined events at inference time, and matches data statistics even when sampling from the tails of the distribution.

Motivation: The development of novel compounds targeting proteins of interest is one of the most important tasks in the pharmaceutical industry. Deep generative models have been applied to targeted molecular design and have shown promising results. Recently, target-specific molecule generation has been viewed as a translation between the protein language and the chemical language. However, such a model is limited by the availability of interacting protein-ligand pairs. On the other hand, large amounts of unlabeled protein sequences and chemical compounds are available and have been used to train language models that learn useful representations. In this study, we propose exploiting pretrained biochemical language models to initialize (i.e. warm start) targeted molecule generation models. We investigate two warm start strategies: (i) a one-stage strategy where the initialized model is trained on targeted molecule generation (ii) a two-stage strategy containing a pre-finetuning on molecular generation followed by target specific training. We also compare two decoding strategies to generate compounds: beam search and sampling. Results: The results show that the warm-started models perform better than a baseline model trained from scratch. The two proposed warm-start strategies achieve similar results to each other with respect to widely used metrics from benchmarks. However, docking evaluation of the generated compounds for a number of novel proteins suggests that the one-stage strategy generalizes better than the two-stage strategy. Additionally, we observe that beam search outperforms sampling in both docking evaluation and benchmark metrics for assessing compound quality. Availability and implementation: The source code is available at https://github.com/boun-tabi/biochemical-lms-for-drug-design and the materials are archived in Zenodo at https://doi.org/10.5281/zenodo.6832145

In this note we establish a 1-to-1 correspondence between the class of generalized quadrangles with ovoids and the class of balanced incomplete block designs that posses a non-triangular local resolution system and have the appropriate parameters. We present a non-triangular local resolution system for a difference family BIBD construction of Sprott.

For an artificial creative agent, an essential driver of the search for novelty is a value function which is often provided by the system designer or users. We argue that an important barrier for progress in creativity research is the inability of these systems to develop their own notion of value for novelty. We propose a notion of knowledge-driven creativity that circumvent the need for an externally imposed value function, allowing the system to explore based on what it has learned from a set of referential objects. The concept is illustrated by a specific knowledge model provided by a deep generative autoencoder. Using the described system, we train a knowledge model on a set of digit images and we use the same model to build coherent sets of new digits that do not belong to known digit types.

We introduce Diffusion World Model (DWM), a conditional diffusion model capable of predicting multistep future states and rewards concurrently. As opposed to traditional one-step dynamics models, DWM offers long-horizon predictions in a single forward pass, eliminating the need for recursive quires. We integrate DWM into model-based value estimation, where the short-term return is simulated by future trajectories sampled from DWM. In the context of offline reinforcement learning, DWM can be viewed as a conservative value regularization through generative modeling. Alternatively, it can be seen as a data source that enables offline Q-learning with synthetic data. Our experiments on the D4RL dataset confirm the robustness of DWM to long-horizon simulation. In terms of absolute performance, DWM significantly surpasses one-step dynamics models with a 44% performance gain, and achieves state-of-the-art performance.

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

In many applications of machine learning, like drug discovery and material design, the goal is to generate candidates that simultaneously maximize a set of objectives. As these objectives are often conflicting, there is no single candidate that simultaneously maximizes all objectives, but rather a set of Pareto-optimal candidates where one objective cannot be improved without worsening another. Moreover, in practice, these objectives are often under-specified, making the diversity of candidates a key consideration. The existing multi-objective optimization methods focus predominantly on covering the Pareto front, failing to capture diversity in the space of candidates. Motivated by the success of GFlowNets for generation of diverse candidates in a single objective setting, in this paper we consider Multi-Objective GFlowNets (MOGFNs). MOGFNs consist of a novel Conditional GFlowNet which models a family of single-objective sub-problems derived by decomposing the multi-objective optimization problem. Our work is the first to empirically demonstrate conditional GFlowNets. Through a series of experiments on synthetic and benchmark tasks, we empirically demonstrate that MOGFNs outperform existing methods in terms of Hypervolume, R2-distance and candidate diversity. We also demonstrate the effectiveness of MOGFNs over existing methods in active learning settings. Finally, we supplement our empirical results with a careful analysis of each component of MOGFNs.

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.

Logic synthesis, a critical stage in electronic design automation (EDA), optimizes gate-level circuits to minimize power consumption and area occupancy in integrated circuits (ICs). Traditional logic synthesis tools rely on human-designed heuristics, often yielding suboptimal results. Although differentiable architecture search (DAS) has shown promise in generating circuits from truth tables, it faces challenges such as high computational complexity, convergence to local optima, and extensive hyperparameter tuning. Consequently, we propose a novel approach integrating conditional generative models with DAS for circuit generation. Our approach first introduces CircuitVQ, a circuit tokenizer trained based on our Circuit AutoEncoder We then develop CircuitAR, a masked autoregressive model leveraging CircuitVQ as the tokenizer. CircuitAR can generate preliminary circuit structures from truth tables, which guide DAS in producing functionally equivalent circuits. Notably, we observe the scalability and emergent capability in generating complex circuit structures of our CircuitAR models. Extensive experiments also show the superior performance of our method. This research bridges the gap between probabilistic generative models and precise circuit generation, offering a robust solution for logic synthesis.

Conditional computing processes an input using only part of the neural network's computational units. Learning to execute parts of a deep convolutional network by routing individual samples has several advantages: Reducing the computational burden is an obvious advantage. Furthermore, if similar classes are routed to the same path, that part of the network learns to discriminate between finer differences and better classification accuracies can be attained with fewer parameters. Recently, several papers have exploited this idea to take a particular child of a node in a tree-shaped network or to skip parts of a network. In this work, we follow a Trellis-based approach for generating specific execution paths in a deep convolutional neural network. We have designed routing mechanisms that use differentiable information gain-based cost functions to determine which subset of features in a convolutional layer will be executed. We call our method Conditional Information Gain Trellis (CIGT). We show that our conditional execution mechanism achieves comparable or better model performance compared to unconditional baselines, using only a fraction of the computational resources.

Event Causality Identification (ECI) aims at determining whether there is a causal relation between two event mentions. Conventional prompt learning designs a prompt template to first predict an answer word and then maps it to the final decision. Unlike conventional prompts, we argue that predicting an answer word may not be a necessary prerequisite for the ECI task. Instead, we can first make a deterministic assumption on the existence of causal relation between two events and then evaluate its rationality to either accept or reject the assumption. The design motivation is to try the most utilization of the encyclopedia-like knowledge embedded in a pre-trained language model. In light of such considerations, we propose a deterministic assumption prompt learning model, called DAPrompt, for the ECI task. In particular, we design a simple deterministic assumption template concatenating with the input event pair, which includes two masks as predicted events' tokens. We use the probabilities of predicted events to evaluate the assumption rationality for the final event causality decision. Experiments on the EventStoryLine corpus and Causal-TimeBank corpus validate our design objective in terms of significant performance improvements over the state-of-the-art algorithms.

Computational design of protein-binding proteins is a fundamental capability with broad utility in biomedical research and biotechnology. Recent methods have made strides against some target proteins, but on-demand creation of high-affinity binders without multiple rounds of experimental testing remains an unsolved challenge. This technical report introduces AlphaProteo, a family of machine learning models for protein design, and details its performance on the de novo binder design problem. With AlphaProteo, we achieve 3- to 300-fold better binding affinities and higher experimental success rates than the best existing methods on seven target proteins. Our results suggest that AlphaProteo can generate binders "ready-to-use" for many research applications using only one round of medium-throughput screening and no further optimization.

Recent advancements in prompt engineering strategies, such as Chain-of-Thought (CoT) and Self-Discover, have demonstrated significant potential in improving the reasoning abilities of Large Language Models (LLMs). However, these state-of-the-art (SOTA) prompting strategies rely on single or fixed set of static seed reasoning modules like "think step by step" or "break down this problem" intended to simulate human approach to problem-solving. This constraint limits the flexibility of models in tackling diverse problems effectively. In this paper, we introduce Auto-Evolve, a novel framework that enables LLMs to self-create dynamic reasoning modules and downstream action plan, resulting in significant improvements over current SOTA methods. We evaluate Auto-Evolve on the challenging BigBench-Hard (BBH) dataset with Claude 2.0, Claude 3 Sonnet, Mistral Large, and GPT 4, where it consistently outperforms the SOTA prompt strategies. Auto-Evolve outperforms CoT by up to 10.4% and on an average by 7% across these four models. Our framework introduces two innovations: a) Auto-Evolve dynamically generates reasoning modules for each task while aligning with human reasoning paradigm, thus eliminating the need for predefined templates. b) We introduce an iterative refinement component, that incrementally refines instruction guidance for LLMs and helps boost performance by average 2.8% compared to doing it in a single step.

In Novel Class Discovery (NCD), the goal is to find new classes in an unlabeled set given a labeled set of known but different classes. While NCD has recently gained attention from the community, no framework has yet been proposed for heterogeneous tabular data, despite being a very common representation of data. In this paper, we propose TabularNCD, a new method for discovering novel classes in tabular data. We show a way to extract knowledge from already known classes to guide the discovery process of novel classes in the context of tabular data which contains heterogeneous variables. A part of this process is done by a new method for defining pseudo labels, and we follow recent findings in Multi-Task Learning to optimize a joint objective function. Our method demonstrates that NCD is not only applicable to images but also to heterogeneous tabular data.

Logic synthesis, a pivotal stage in chip design, entails optimizing chip specifications encoded in hardware description languages like Verilog into highly efficient implementations using Boolean logic gates. The process involves a sequential application of logic minimization heuristics (``synthesis recipe"), with their arrangement significantly impacting crucial metrics such as area and delay. Addressing the challenge posed by the broad spectrum of design complexities - from variations of past designs (e.g., adders and multipliers) to entirely novel configurations (e.g., innovative processor instructions) - requires a nuanced `synthesis recipe` guided by human expertise and intuition. This study conducts a thorough examination of learning and search techniques for logic synthesis, unearthing a surprising revelation: pre-trained agents, when confronted with entirely novel designs, may veer off course, detrimentally affecting the search trajectory. We present ABC-RL, a meticulously tuned alpha parameter that adeptly adjusts recommendations from pre-trained agents during the search process. Computed based on similarity scores through nearest neighbor retrieval from the training dataset, ABC-RL yields superior synthesis recipes tailored for a wide array of hardware designs. Our findings showcase substantial enhancements in the Quality-of-result (QoR) of synthesized circuits, boasting improvements of up to 24.8% compared to state-of-the-art techniques. Furthermore, ABC-RL achieves an impressive up to 9x reduction in runtime (iso-QoR) when compared to current state-of-the-art methodologies.

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.

Diffusion models have made substantial advances in image generation, yet models trained on large, unfiltered datasets often yield outputs misaligned with human preferences. Numerous methods have been proposed to fine-tune pre-trained diffusion models, achieving notable improvements in aligning generated outputs with human preferences. However, we argue that existing preference alignment methods neglect the critical role of handling unconditional/negative-conditional outputs, leading to a diminished capacity to avoid generating undesirable outcomes. This oversight limits the efficacy of classifier-free guidance~(CFG), which relies on the contrast between conditional generation and unconditional/negative-conditional generation to optimize output quality. In response, we propose a straightforward but versatile effective approach that involves training a model specifically attuned to negative preferences. This method does not require new training strategies or datasets but rather involves minor modifications to existing techniques. Our approach integrates seamlessly with models such as SD1.5, SDXL, video diffusion models and models that have undergone preference optimization, consistently enhancing their alignment with human preferences.

AI-based design tools are proliferating in professional software to assist engineering and industrial designers in complex manufacturing and design tasks. These tools take on more agentic roles than traditional computer-aided design tools and are often portrayed as "co-creators." Yet, working effectively with such systems requires different skills than working with complex CAD tools alone. To date, we know little about how engineering designers learn to work with AI-based design tools. In this study, we observed trained designers as they learned to work with two AI-based tools on a realistic design task. We find that designers face many challenges in learning to effectively co-create with current systems, including challenges in understanding and adjusting AI outputs and in communicating their design goals. Based on our findings, we highlight several design opportunities to better support designer-AI co-creation.

Graphic design plays a crucial role in both commercial and personal contexts, yet creating high-quality, editable, and aesthetically pleasing graphic compositions remains a time-consuming and skill-intensive task, especially for beginners. Current AI tools automate parts of the workflow, but struggle to accurately incorporate user-supplied assets, maintain editability, and achieve professional visual appeal. Commercial systems, like Canva Magic Design, rely on vast template libraries, which are impractical for replicate. In this paper, we introduce CreatiPoster, a framework that generates editable, multi-layer compositions from optional natural-language instructions or assets. A protocol model, an RGBA large multimodal model, first produces a JSON specification detailing every layer (text or asset) with precise layout, hierarchy, content and style, plus a concise background prompt. A conditional background model then synthesizes a coherent background conditioned on this rendered foreground layers. We construct a benchmark with automated metrics for graphic-design generation and show that CreatiPoster surpasses leading open-source approaches and proprietary commercial systems. To catalyze further research, we release a copyright-free corpus of 100,000 multi-layer designs. CreatiPoster supports diverse applications such as canvas editing, text overlay, responsive resizing, multilingual adaptation, and animated posters, advancing the democratization of AI-assisted graphic design. Project homepage: https://github.com/graphic-design-ai/creatiposter

Recently, Stitchable Neural Networks (SN-Net) is proposed to stitch some pre-trained networks for quickly building numerous networks with different complexity and performance trade-offs. In this way, the burdens of designing or training the variable-sized networks, which can be used in application scenarios with diverse resource constraints, are alleviated. However, SN-Net still faces a few challenges. 1) Stitching from multiple independently pre-trained anchors introduces high storage resource consumption. 2) SN-Net faces challenges to build smaller models for low resource constraints. 3). SN-Net uses an unlearned initialization method for stitch layers, limiting the final performance. To overcome these challenges, motivated by the recently proposed Learngene framework, we propose a novel method called Learngene Pool. Briefly, Learngene distills the critical knowledge from a large pre-trained model into a small part (termed as learngene) and then expands this small part into a few variable-sized models. In our proposed method, we distill one pretrained large model into multiple small models whose network blocks are used as learngene instances to construct the learngene pool. Since only one large model is used, we do not need to store more large models as SN-Net and after distilling, smaller learngene instances can be created to build small models to satisfy low resource constraints. We also insert learnable transformation matrices between the instances to stitch them into variable-sized models to improve the performance of these models. Exhaustive experiments have been implemented and the results validate the effectiveness of the proposed Learngene Pool compared with SN-Net.

Spider webs are incredible biological structures, comprising thin but strong silk filament and arranged into complex hierarchical architectures with striking mechanical properties (e.g., lightweight but high strength, achieving diverse mechanical responses). While simple 2D orb webs can easily be mimicked, the modeling and synthesis of 3D-based web structures remain challenging, partly due to the rich set of design features. Here we provide a detailed analysis of the heterogenous graph structures of spider webs, and use deep learning as a way to model and then synthesize artificial, bio-inspired 3D web structures. The generative AI models are conditioned based on key geometric parameters (including average edge length, number of nodes, average node degree, and others). To identify graph construction principles, we use inductive representation sampling of large experimentally determined spider web graphs, to yield a dataset that is used to train three conditional generative models: 1) An analog diffusion model inspired by nonequilibrium thermodynamics, with sparse neighbor representation, 2) a discrete diffusion model with full neighbor representation, and 3) an autoregressive transformer architecture with full neighbor representation. All three models are scalable, produce complex, de novo bio-inspired spider web mimics, and successfully construct graphs that meet the design objectives. We further propose algorithm that assembles web samples produced by the generative models into larger-scale structures based on a series of geometric design targets, including helical and parametric shapes, mimicking, and extending natural design principles towards integration with diverging engineering objectives. Several webs are manufactured using 3D printing and tested to assess mechanical properties.

Artefact descriptions are the primary carriers of engineering design knowledge that is both an outcome and a driver of the design process. While an artefact could be described in different connotations, the design process requires a description to embody engineering design knowledge, which is expressed in the text through intricate placement of entities and relationships. As large-language models learn from all kinds of text merely as a sequence of characters/tokens, these are yet to generate text that embodies explicit engineering design facts. Existing ontological design theories are less likely to guide the large-language models whose applications are currently limited to ideation and learning purposes. In this article, we explicate engineering design knowledge as knowledge graphs from a large sample of 33,881 patent documents. We examine the constituents of these knowledge graphs to understand the linguistic and structural basis of engineering design knowledge. In terms of linguistic basis, we observe that entities and relationships could be generalised to 64 and 24 linguistic syntaxes. While relationships mainly capture attributes ('of'), structure ('in', 'with'), purpose ('to', 'for'), hierarchy ('include'), exemplification ('such as'), and behaviour ('to', 'from'), the hierarchical relationships could specifically be identified using 75 unique syntaxes. To understand the structural basis, we draw inspiration from various studies on biological/ecological networks and discover motifs from patent knowledge graphs. We identify four 3-node and four 4-node patterns that could further be converged and simplified into sequence [->...->], aggregation [->...<-], and hierarchy [<-...->]. Expected to guide large-language model based design tools, we propose few regulatory precepts for concretising abstract entities and relationships within subgraphs, while explicating hierarchical structures.

Machine learning is a prevalent approach to tame the complexity of design space exploration for domain-specific architectures. Using ML for design space exploration poses challenges. First, it's not straightforward to identify the suitable algorithm from an increasing pool of ML methods. Second, assessing the trade-offs between performance and sample efficiency across these methods is inconclusive. Finally, lack of a holistic framework for fair, reproducible, and objective comparison across these methods hinders progress of adopting ML-aided architecture design space exploration and impedes creating repeatable artifacts. To mitigate these challenges, we introduce ArchGym, an open-source gym and easy-to-extend framework that connects diverse search algorithms to architecture simulators. To demonstrate utility, we evaluate ArchGym across multiple vanilla and domain-specific search algorithms in designing custom memory controller, deep neural network accelerators, and custom SoC for AR/VR workloads, encompassing over 21K experiments. Results suggest that with unlimited samples, ML algorithms are equally favorable to meet user-defined target specification if hyperparameters are tuned; no solution is necessarily better than another (e.g., reinforcement learning vs. Bayesian methods). We coin the term hyperparameter lottery to describe the chance for a search algorithm to find an optimal design provided meticulously selected hyperparameters. The ease of data collection and aggregation in ArchGym facilitates research in ML-aided architecture design space exploration. As a case study, we show this advantage by developing a proxy cost model with an RMSE of 0.61% that offers a 2,000-fold reduction in simulation time. Code and data for ArchGym is available at https://bit.ly/ArchGym.

This work presents DAVINCI, a unified architecture for single-stage Computer-Aided Design (CAD) sketch parameterization and constraint inference directly from raster sketch images. By jointly learning both outputs, DAVINCI minimizes error accumulation and enhances the performance of constrained CAD sketch inference. Notably, DAVINCI achieves state-of-the-art results on the large-scale SketchGraphs dataset, demonstrating effectiveness on both precise and hand-drawn raster CAD sketches. To reduce DAVINCI's reliance on large-scale annotated datasets, we explore the efficacy of CAD sketch augmentations. We introduce Constraint-Preserving Transformations (CPTs), i.e. random permutations of the parametric primitives of a CAD sketch that preserve its constraints. This data augmentation strategy allows DAVINCI to achieve reasonable performance when trained with only 0.1% of the SketchGraphs dataset. Furthermore, this work contributes a new version of SketchGraphs, augmented with CPTs. The newly introduced CPTSketchGraphs dataset includes 80 million CPT-augmented sketches, thus providing a rich resource for future research in the CAD sketch domain.

The concept of negative prompts, emerging from conditional generation models like Stable Diffusion, allows users to specify what to exclude from the generated images.%, demonstrating significant practical efficacy. Despite the widespread use of negative prompts, their intrinsic mechanisms remain largely unexplored. This paper presents the first comprehensive study to uncover how and when negative prompts take effect. Our extensive empirical analysis identifies two primary behaviors of negative prompts. Delayed Effect: The impact of negative prompts is observed after positive prompts render corresponding content. Deletion Through Neutralization: Negative prompts delete concepts from the generated image through a mutual cancellation effect in latent space with positive prompts. These insights reveal significant potential real-world applications; for example, we demonstrate that negative prompts can facilitate object inpainting with minimal alterations to the background via a simple adaptive algorithm. We believe our findings will offer valuable insights for the community in capitalizing on the potential of negative prompts.

Robot design aims at learning to create robots that can be easily controlled and perform tasks efficiently. Previous works on robot design have proven its ability to generate robots for various tasks. However, these works searched the robots directly from the vast design space and ignored common structures, resulting in abnormal robots and poor performance. To tackle this problem, we propose a Symmetry-Aware Robot Design (SARD) framework that exploits the structure of the design space by incorporating symmetry searching into the robot design process. Specifically, we represent symmetries with the subgroups of the dihedral group and search for the optimal symmetry in structured subgroups. Then robots are designed under the searched symmetry. In this way, SARD can design efficient symmetric robots while covering the original design space, which is theoretically analyzed. We further empirically evaluate SARD on various tasks, and the results show its superior efficiency and generalizability.

Social computing prototypes probe the social behaviors that may arise in an envisioned system design. This prototyping practice is currently limited to recruiting small groups of people. Unfortunately, many challenges do not arise until a system is populated at a larger scale. Can a designer understand how a social system might behave when populated, and make adjustments to the design before the system falls prey to such challenges? We introduce social simulacra, a prototyping technique that generates a breadth of realistic social interactions that may emerge when a social computing system is populated. Social simulacra take as input the designer's description of a community's design -- goal, rules, and member personas -- and produce as output an instance of that design with simulated behavior, including posts, replies, and anti-social behaviors. We demonstrate that social simulacra shift the behaviors that they generate appropriately in response to design changes, and that they enable exploration of "what if?" scenarios where community members or moderators intervene. To power social simulacra, we contribute techniques for prompting a large language model to generate thousands of distinct community members and their social interactions with each other; these techniques are enabled by the observation that large language models' training data already includes a wide variety of positive and negative behavior on social media platforms. In evaluations, we show that participants are often unable to distinguish social simulacra from actual community behavior and that social computing designers successfully refine their social computing designs when using social simulacra.

Generative AI technologies are growing in power, utility, and use. As generative technologies are being incorporated into mainstream applications, there is a need for guidance on how to design those applications to foster productive and safe use. Based on recent research on human-AI co-creation within the HCI and AI communities, we present a set of seven principles for the design of generative AI applications. These principles are grounded in an environment of generative variability. Six principles are focused on designing for characteristics of generative AI: multiple outcomes & imperfection; exploration & control; and mental models & explanations. In addition, we urge designers to design against potential harms that may be caused by a generative model's hazardous output, misuse, or potential for human displacement. We anticipate these principles to usefully inform design decisions made in the creation of novel human-AI applications, and we invite the community to apply, revise, and extend these principles to their own work.

Interior design allows us to be who we are and live how we want - each design is as unique as our distinct personality. However, it is not trivial for non-professionals to express and materialize this since it requires aligning functional and visual expectations with the constraints of physical space; this renders interior design a luxury. To make it more accessible, we present I-Design, a personalized interior designer that allows users to generate and visualize their design goals through natural language communication. I-Design starts with a team of large language model agents that engage in dialogues and logical reasoning with one another, transforming textual user input into feasible scene graph designs with relative object relationships. Subsequently, an effective placement algorithm determines optimal locations for each object within the scene. The final design is then constructed in 3D by retrieving and integrating assets from an existing object database. Additionally, we propose a new evaluation protocol that utilizes a vision-language model and complements the design pipeline. Extensive quantitative and qualitative experiments show that I-Design outperforms existing methods in delivering high-quality 3D design solutions and aligning with abstract concepts that match user input, showcasing its advantages across detailed 3D arrangement and conceptual fidelity.

We study the problem of extrapolative controlled generation, i.e., generating sequences with attribute values beyond the range seen in training. This task is of significant importance in automated design, especially drug discovery, where the goal is to design novel proteins that are better (e.g., more stable) than existing sequences. Thus, by definition, the target sequences and their attribute values are out of the training distribution, posing challenges to existing methods that aim to directly generate the target sequence. Instead, in this work, we propose Iterative Controlled Extrapolation (ICE) which iteratively makes local edits to a sequence to enable extrapolation. We train the model on synthetically generated sequence pairs that demonstrate small improvement in the attribute value. Results on one natural language task (sentiment analysis) and two protein engineering tasks (ACE2 stability and AAV fitness) show that ICE considerably outperforms state-of-the-art approaches despite its simplicity. Our code and models are available at: https://github.com/vishakhpk/iter-extrapolation.

The omnipresence of NP-hard combinatorial optimization problems (COPs) compels domain experts to engage in trial-and-error heuristic design. The long-standing endeavor of design automation has gained new momentum with the rise of large language models (LLMs). This paper introduces Language Hyper-Heuristics (LHHs), an emerging variant of Hyper-Heuristics that leverages LLMs for heuristic generation, featuring minimal manual intervention and open-ended heuristic spaces. To empower LHHs, we present Reflective Evolution (ReEvo), a novel integration of evolutionary search for efficiently exploring the heuristic space, and LLM reflections to provide verbal gradients within the space. Across five heterogeneous algorithmic types, six different COPs, and both white-box and black-box views of COPs, ReEvo yields state-of-the-art and competitive meta-heuristics, evolutionary algorithms, heuristics, and neural solvers, while being more sample-efficient than prior LHHs.

Modern front-end (FE) development, especially when leveraging the unique features of frameworks like React and Vue, presents distinctive challenges. These include managing modular architectures, ensuring synchronization between data and visual outputs for declarative rendering, and adapting reusable components to various scenarios. Such complexities make it particularly difficult for state-of-the-art large vision-language models (VLMs) to generate accurate and functional code directly from design images. To address these challenges, we propose a reflective agentic workflow that synthesizes high-quality image-text data to capture the diverse characteristics of FE development. This workflow automates the extraction of self-containedA \textbf{self-contained code snippet is one that encapsulates all necessary logic, styling, and dependencies, ensuring it functions independently without requiring external imports or context.} code snippets from real-world projects, renders the corresponding visual outputs, and generates detailed descriptions that link design elements to functional code. To further expand the scope and utility of the synthesis, we introduce three data synthesis strategies: Evolution-based synthesis, which enables scalable and diverse dataset expansion; Waterfall-Model-based synthesis, which generates logically coherent code derived from system requirements; and Additive Development synthesis, which iteratively increases the complexity of human-authored components. We build a large vision-language model, Flame, trained on the synthesized datasets and demonstrate its effectiveness in generating React code via the pass@k metric. Our results suggest that a code VLM trained to interpret images before code generation may achieve better performance.

We study the problem of adaptively identifying patient subpopulations that benefit from a given treatment during a confirmatory clinical trial. This type of adaptive clinical trial has been thoroughly studied in biostatistics, but has been allowed only limited adaptivity so far. Here, we aim to relax classical restrictions on such designs and investigate how to incorporate ideas from the recent machine learning literature on adaptive and online experimentation to make trials more flexible and efficient. We find that the unique characteristics of the subpopulation selection problem -- most importantly that (i) one is usually interested in finding subpopulations with any treatment benefit (and not necessarily the single subgroup with largest effect) given a limited budget and that (ii) effectiveness only has to be demonstrated across the subpopulation on average -- give rise to interesting challenges and new desiderata when designing algorithmic solutions. Building on these findings, we propose AdaGGI and AdaGCPI, two meta-algorithms for subpopulation construction. We empirically investigate their performance across a range of simulation scenarios and derive insights into their (dis)advantages across different settings.

Reasoning methods that adaptively allocate test-time compute have advanced LLM performance on easy to verify domains such as math and code. In this work, we study how to utilize this approach to train models that exhibit a degree of robustness to safety vulnerabilities, and show that doing so can provide benefits. We build a recipe called TARS (Training Adaptive Reasoners for Safety), a reinforcement learning (RL) approach that trains models to reason about safety using chain-of-thought traces and a reward signal that balances safety with task completion. To build TARS, we identify three critical design choices: (1) a "lightweight" warmstart SFT stage, (2) a mix of harmful, harmless, and ambiguous prompts to prevent shortcut behaviors such as too many refusals, and (3) a reward function to prevent degeneration of reasoning capabilities during training. Models trained with TARS exhibit adaptive behaviors by spending more compute on ambiguous queries, leading to better safety-refusal trade-offs. They also internally learn to better distinguish between safe and unsafe prompts and attain greater robustness to both white-box (e.g., GCG) and black-box attacks (e.g., PAIR). Overall, our work provides an effective, open recipe for training LLMs against jailbreaks and harmful requests by reasoning per prompt.

Recently, 3D generation methods have shown their powerful ability to automate 3D model creation. However, most 3D generation methods only rely on an input image or a text prompt to generate a 3D model, which lacks the control of each component of the generated 3D model. Any modifications of the input image lead to an entire regeneration of the 3D models. In this paper, we introduce a new method called CMD that generates a 3D model from an input image while enabling flexible local editing of each component of the 3D model. In CMD, we formulate the 3D generation as a conditional multiview diffusion model, which takes the existing or known parts as conditions and generates the edited or added components. This conditional multiview diffusion model not only allows the generation of 3D models part by part but also enables local editing of 3D models according to the local revision of the input image without changing other 3D parts. Extensive experiments are conducted to demonstrate that CMD decomposes a complex 3D generation task into multiple components, improving the generation quality. Meanwhile, CMD enables efficient and flexible local editing of a 3D model by just editing one rendered image.

Computer-aided design (CAD) tools are utilized in the manufacturing industry for modeling everything from cups to spacecraft. These programs are complex to use and typically require years of training and experience to master. Structured and well-constrained 2D sketches and 3D constructions are crucial components of CAD modeling. A well-executed CAD model can be seamlessly integrated into the manufacturing process, thereby enhancing production efficiency. Deep generative models of 3D shapes and 3D object reconstruction models have garnered significant research interest. However, most of these models produce discrete forms of 3D objects that are not editable. Moreover, the few models based on CAD operations often have substantial input restrictions. In this work, we fine-tuned pre-trained models to create OpenECAD models (0.55B, 0.89B, 2.4B and 3.1B), leveraging the visual, logical, coding, and general capabilities of visual language models. OpenECAD models can process images of 3D designs as input and generate highly structured 2D sketches and 3D construction commands, ensuring that the designs are editable. These outputs can be directly used with existing CAD tools' APIs to generate project files. To train our network, we created a series of OpenECAD datasets. These datasets are derived from existing public CAD datasets, adjusted and augmented to meet the specific requirements of vision language model (VLM) training. Additionally, we have introduced an approach that utilizes dependency relationships to define and generate sketches, further enriching the content and functionality of the datasets.

Neo-Darwinian evolutionary theory explains how the appearance of purposive design in the sophisticated adaptations of living organisms can have come about without their intentionally being designed. The explanation relies crucially on the possibility of certain physical processes: mainly, gene replication and natural selection. In this paper I show that for those processes to be possible without the design of biological adaptations being encoded in the laws of physics, those laws must have certain other properties. The theory of what these properties are is not part of evolution theory proper, and has not been developed, yet without it the neo-Darwinian theory does not fully achieve its purpose of explaining the appearance of design. To this end I apply Constructor Theory's new mode of explanation to provide an exact formulation of the appearance of design, of no-design laws, and of the logic of self-reproduction and natural selection, within fundamental physics. I conclude that self-reproduction, replication and natural selection are possible under no-design laws, the only non-trivial condition being that they allow digital information to be physically instantiated. This has an exact characterisation in the constructor theory of information. I also show that under no-design laws an accurate replicator requires the existence of a "vehicle" constituting, together with the replicator, a self-reproducer.

As LLMs become increasingly prevalent, it is interesting to consider how ``creative'' these models can be. From cognitive science, creativity consists of at least two key characteristics: convergent thinking (purposefulness to achieve a given goal) and divergent thinking (adaptability to new environments or constraints) runco2003critical. In this work, we introduce a framework for quantifying LLM creativity that incorporates the two characteristics. This is achieved by (1) Denial Prompting pushes LLMs to come up with more creative solutions to a given problem by incrementally imposing new constraints on the previous solution, compelling LLMs to adopt new strategies, and (2) defining and computing the NeoGauge metric which examines both convergent and divergent thinking in the generated creative responses by LLMs. We apply the proposed framework on Codeforces problems, a natural data source for collecting human coding solutions. We quantify NeoGauge for various proprietary and open-source models and find that even the most creative model, GPT-4, still falls short of demonstrating human-like creativity. We also experiment with advanced reasoning strategies (MCTS, self-correction, etc.) and observe no significant improvement in creativity. As a by-product of our analysis, we release NeoCoder dataset for reproducing our results on future models.

Evolvability is an important feature that impacts the ability of evolutionary processes to find interesting novel solutions and to deal with changing conditions of the problem to solve. The estimation of evolvability is not straightforward and is generally too expensive to be directly used as selective pressure in the evolutionary process. Indirectly promoting evolvability as a side effect of other easier and faster to compute selection pressures would thus be advantageous. In an unbounded behavior space, it has already been shown that evolvable individuals naturally appear and tend to be selected as they are more likely to invade empty behavior niches. Evolvability is thus a natural byproduct of the search in this context. However, practical agents and environments often impose limits on the reach-able behavior space. How do these boundaries impact evolvability? In this context, can evolvability still be promoted without explicitly rewarding it? We show that Novelty Search implicitly creates a pressure for high evolvability even in bounded behavior spaces, and explore the reasons for such a behavior. More precisely we show that, throughout the search, the dynamic evaluation of novelty rewards individuals which are very mobile in the behavior space, which in turn promotes evolvability.

Creating meaningful art is often viewed as a uniquely human endeavor. A human artist needs a combination of unique skills, understanding, and genuine intention to create artworks that evoke deep feelings and emotions. In this paper, we introduce a multi-conditional Generative Adversarial Network (GAN) approach trained on large amounts of human paintings to synthesize realistic-looking paintings that emulate human art. Our approach is based on the StyleGAN neural network architecture, but incorporates a custom multi-conditional control mechanism that provides fine-granular control over characteristics of the generated paintings, e.g., with regard to the perceived emotion evoked in a spectator. For better control, we introduce the conditional truncation trick, which adapts the standard truncation trick for the conditional setting and diverse datasets. Finally, we develop a diverse set of evaluation techniques tailored to multi-conditional generation.

We report a series of deep learning models to solve complex forward and inverse design problems in molecular modeling and design. Using both diffusion models inspired by nonequilibrium thermodynamics and attention-based transformer architectures, we demonstrate a flexible framework to capture complex chemical structures. First trained on the QM9 dataset and a series of quantum mechanical properties (e.g. homo, lumo, free energy, heat capacity, etc.), we then generalize the model to study and design key properties of deep eutectic solvents. In addition to separate forward and inverse models, we also report an integrated fully prompt-based multi-task generative pretrained transformer model that solves multiple forward, inverse design, and prediction tasks, flexibly and within one model. We show that the multi-task generative model has the overall best performance and allows for flexible integration of multiple objectives, within one model, and for distinct chemistries, suggesting that synergies emerge during training of this large language model. Trained jointly in tasks related to the QM9 dataset and deep eutectic solvents (DESs), the model can predict various quantum mechanical properties and critical properties to achieve deep eutectic solvent behavior. Several novel combinations of DESs are proposed based on this framework.

Recent text-to-image generative models have enabled us to transform our words into vibrant, captivating imagery. The surge of personalization techniques that has followed has also allowed us to imagine unique concepts in new scenes. However, an intriguing question remains: How can we generate a new, imaginary concept that has never been seen before? In this paper, we present the task of creative text-to-image generation, where we seek to generate new members of a broad category (e.g., generating a pet that differs from all existing pets). We leverage the under-studied Diffusion Prior models and show that the creative generation problem can be formulated as an optimization process over the output space of the diffusion prior, resulting in a set of "prior constraints". To keep our generated concept from converging into existing members, we incorporate a question-answering model that adaptively adds new constraints to the optimization problem, encouraging the model to discover increasingly more unique creations. Finally, we show that our prior constraints can also serve as a strong mixing mechanism allowing us to create hybrids between generated concepts, introducing even more flexibility into the creative process.

Test-Time Scaling (TTS) is a promising approach to progressively elicit the model's intelligence during inference. Recently, training-based TTS methods, such as continued reinforcement learning (RL), have further surged in popularity, while training-free TTS methods are gradually fading from prominence. However, the additional computation overhead of training amplifies the burden on test-time scaling. In this paper, we focus on training-free TTS methods for reasoning. We first design Conditional Step-level Self-refinement, a fine-grained sequential scaling method guided by process verification. On top of its effectiveness, we further combine it with other classical parallel scaling methods at the step level, to introduce a novel inference paradigm called Hybrid Test-Time Scaling. Extensive experiments on five instruction-tuned LLMs across different scales (3B-14B) and families demonstrate that hybrid strategy incorporating various training-free TTS methods at a fine granularity has considerable potential for expanding the reasoning performance boundaries of LLMs.

Pre-trained large language models demonstrate potential in extracting information from DNA sequences, yet adapting to a variety of tasks and data modalities remains a challenge. To address this, we propose DNAGPT, a generalized DNA pre-training model trained on over 200 billion base pairs from all mammals. By enhancing the classic GPT model with a binary classification task (DNA sequence order), a numerical regression task (guanine-cytosine content prediction), and a comprehensive token language, DNAGPT can handle versatile DNA analysis tasks while processing both sequence and numerical data. Our evaluation of genomic signal and region recognition, mRNA abundance regression, and artificial genomes generation tasks demonstrates DNAGPT's superior performance compared to existing models designed for specific downstream tasks, benefiting from pre-training using the newly designed model structure.

Deep generative models have various content creation applications such as graphic design, e-commerce, and virtual Try-on. However, current works mainly focus on synthesizing realistic visual outputs, often ignoring other sensory modalities, such as touch, which limits physical interaction with users. In this work, we leverage deep generative models to create a multi-sensory experience where users can touch and see the synthesized object when sliding their fingers on a haptic surface. The main challenges lie in the significant scale discrepancy between vision and touch sensing and the lack of explicit mapping from touch sensing data to a haptic rendering device. To bridge this gap, we collect high-resolution tactile data with a GelSight sensor and create a new visuotactile clothing dataset. We then develop a conditional generative model that synthesizes both visual and tactile outputs from a single sketch. We evaluate our method regarding image quality and tactile rendering accuracy. Finally, we introduce a pipeline to render high-quality visual and tactile outputs on an electroadhesion-based haptic device for an immersive experience, allowing for challenging materials and editable sketch inputs.

We target a 3D generative model for general natural scenes that are typically unique and intricate. Lacking the necessary volumes of training data, along with the difficulties of having ad hoc designs in presence of varying scene characteristics, renders existing setups intractable. Inspired by classical patch-based image models, we advocate for synthesizing 3D scenes at the patch level, given a single example. At the core of this work lies important algorithmic designs w.r.t the scene representation and generative patch nearest-neighbor module, that address unique challenges arising from lifting classical 2D patch-based framework to 3D generation. These design choices, on a collective level, contribute to a robust, effective, and efficient model that can generate high-quality general natural scenes with both realistic geometric structure and visual appearance, in large quantities and varieties, as demonstrated upon a variety of exemplar scenes.

Sketch colorization plays an important role in animation and digital illustration production tasks. However, existing methods still meet problems in that text-guided methods fail to provide accurate color and style reference, hint-guided methods still involve manual operation, and image-referenced methods are prone to cause artifacts. To address these limitations, we propose a diffusion-based framework inspired by real-world animation production workflows. Our approach leverages the sketch as the spatial guidance and an RGB image as the color reference, and separately extracts foreground and background from the reference image with spatial masks. Particularly, we introduce a split cross-attention mechanism with LoRA (Low-Rank Adaptation) modules. They are trained separately with foreground and background regions to control the corresponding embeddings for keys and values in cross-attention. This design allows the diffusion model to integrate information from foreground and background independently, preventing interference and eliminating the spatial artifacts. During inference, we design switchable inference modes for diverse use scenarios by changing modules activated in the framework. Extensive qualitative and quantitative experiments, along with user studies, demonstrate our advantages over existing methods in generating high-qualigy artifact-free results with geometric mismatched references. Ablation studies further confirm the effectiveness of each component. Codes are available at https://github.com/ tellurion-kanata/colorizeDiffusion.

Graphic design, which has been evolving since the 15th century, plays a crucial role in advertising. The creation of high-quality designs demands design-oriented planning, reasoning, and layer-wise generation. Unlike the recent CanvaGPT, which integrates GPT-4 with existing design templates to build a custom GPT, this paper introduces the COLE system - a hierarchical generation framework designed to comprehensively address these challenges. This COLE system can transform a vague intention prompt into a high-quality multi-layered graphic design, while also supporting flexible editing based on user input. Examples of such input might include directives like ``design a poster for Hisaishi's concert.'' The key insight is to dissect the complex task of text-to-design generation into a hierarchy of simpler sub-tasks, each addressed by specialized models working collaboratively. The results from these models are then consolidated to produce a cohesive final output. Our hierarchical task decomposition can streamline the complex process and significantly enhance generation reliability. Our COLE system comprises multiple fine-tuned Large Language Models (LLMs), Large Multimodal Models (LMMs), and Diffusion Models (DMs), each specifically tailored for design-aware layer-wise captioning, layout planning, reasoning, and the task of generating images and text. Furthermore, we construct the DESIGNINTENTION benchmark to demonstrate the superiority of our COLE system over existing methods in generating high-quality graphic designs from user intent. Last, we present a Canva-like multi-layered image editing tool to support flexible editing of the generated multi-layered graphic design images. We perceive our COLE system as an important step towards addressing more complex and multi-layered graphic design generation tasks in the future.

In the field of graphic design, automating the integration of design elements into a cohesive multi-layered artwork not only boosts productivity but also paves the way for the democratization of graphic design. One existing practice is Graphic Layout Generation (GLG), which aims to layout sequential design elements. It has been constrained by the necessity for a predefined correct sequence of layers, thus limiting creative potential and increasing user workload. In this paper, we present Hierarchical Layout Generation (HLG) as a more flexible and pragmatic setup, which creates graphic composition from unordered sets of design elements. To tackle the HLG task, we introduce Graphist, the first layout generation model based on large multimodal models. Graphist efficiently reframes the HLG as a sequence generation problem, utilizing RGB-A images as input, outputs a JSON draft protocol, indicating the coordinates, size, and order of each element. We develop new evaluation metrics for HLG. Graphist outperforms prior arts and establishes a strong baseline for this field. Project homepage: https://github.com/graphic-design-ai/graphist

In this paper, we present DesignDiffusion, a simple yet effective framework for the novel task of synthesizing design images from textual descriptions. A primary challenge lies in generating accurate and style-consistent textual and visual content. Existing works in a related task of visual text generation often focus on generating text within given specific regions, which limits the creativity of generation models, resulting in style or color inconsistencies between textual and visual elements if applied to design image generation. To address this issue, we propose an end-to-end, one-stage diffusion-based framework that avoids intricate components like position and layout modeling. Specifically, the proposed framework directly synthesizes textual and visual design elements from user prompts. It utilizes a distinctive character embedding derived from the visual text to enhance the input prompt, along with a character localization loss for enhanced supervision during text generation. Furthermore, we employ a self-play Direct Preference Optimization fine-tuning strategy to improve the quality and accuracy of the synthesized visual text. Extensive experiments demonstrate that DesignDiffusion achieves state-of-the-art performance in design image generation.

The past decade has seen vast progress in deep reinforcement learning (RL) on the back of algorithms manually designed by human researchers. Recently, it has been shown that it is possible to meta-learn update rules, with the hope of discovering algorithms that can perform well on a wide range of RL tasks. Despite impressive initial results from algorithms such as Learned Policy Gradient (LPG), there remains a generalization gap when these algorithms are applied to unseen environments. In this work, we examine how characteristics of the meta-training distribution impact the generalization performance of these algorithms. Motivated by this analysis and building on ideas from Unsupervised Environment Design (UED), we propose a novel approach for automatically generating curricula to maximize the regret of a meta-learned optimizer, in addition to a novel approximation of regret, which we name algorithmic regret (AR). The result is our method, General RL Optimizers Obtained Via Environment Design (GROOVE). In a series of experiments, we show that GROOVE achieves superior generalization to LPG, and evaluate AR against baseline metrics from UED, identifying it as a critical component of environment design in this setting. We believe this approach is a step towards the discovery of truly general RL algorithms, capable of solving a wide range of real-world environments.

Robot co-design, where the morphology of a robot is optimized jointly with a learned policy to solve a specific task, is an emerging area of research. It holds particular promise for soft robots, which are amenable to novel manufacturing techniques that can realize learned morphologies and actuators. Inspired by nature and recent novel robot designs, we propose to go a step further and explore the novel reconfigurable robots, defined as robots that can change their morphology within their lifetime. We formalize control of reconfigurable soft robots as a high-dimensional reinforcement learning (RL) problem. We unify morphology change, locomotion, and environment interaction in the same action space, and introduce an appropriate, coarse-to-fine curriculum that enables us to discover policies that accomplish fine-grained control of the resulting robots. We also introduce DittoGym, a comprehensive RL benchmark for reconfigurable soft robots that require fine-grained morphology changes to accomplish the tasks. Finally, we evaluate our proposed coarse-to-fine algorithm on DittoGym and demonstrate robots that learn to change their morphology several times within a sequence, uniquely enabled by our RL algorithm. More results are available at https://dittogym.github.io.

We investigate the theoretical foundations of classifier-free guidance (CFG). CFG is the dominant method of conditional sampling for text-to-image diffusion models, yet unlike other aspects of diffusion, it remains on shaky theoretical footing. In this paper, we disprove common misconceptions, by showing that CFG interacts differently with DDPM (Ho et al., 2020) and DDIM (Song et al., 2021), and neither sampler with CFG generates the gamma-powered distribution p(x|c)^gamma p(x)^{1-gamma}. Then, we clarify the behavior of CFG by showing that it is a kind of predictor-corrector method (Song et al., 2020) that alternates between denoising and sharpening, which we call predictor-corrector guidance (PCG). We prove that in the SDE limit, CFG is actually equivalent to combining a DDIM predictor for the conditional distribution together with a Langevin dynamics corrector for a gamma-powered distribution (with a carefully chosen gamma). Our work thus provides a lens to theoretically understand CFG by embedding it in a broader design space of principled sampling methods.

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.

It is common in graphic design humans visually arrange various elements according to their design intent and semantics. For example, a title text almost always appears on top of other elements in a document. In this work, we generate graphic layouts that can flexibly incorporate such design semantics, either specified implicitly or explicitly by a user. We optimize using the latent space of an off-the-shelf layout generation model, allowing our approach to be complementary to and used with existing layout generation models. Our approach builds on a generative layout model based on a Transformer architecture, and formulates the layout generation as a constrained optimization problem where design constraints are used for element alignment, overlap avoidance, or any other user-specified relationship. We show in the experiments that our approach is capable of generating realistic layouts in both constrained and unconstrained generation tasks with a single model. The code is available at https://github.com/ktrk115/const_layout .

We report a flexible language-model based deep learning strategy, applied here to solve complex forward and inverse problems in protein modeling, based on an attention neural network that integrates transformer and graph convolutional architectures in a causal multi-headed graph mechanism, to realize a generative pretrained model. The model is applied to predict secondary structure content (per-residue level and overall content), protein solubility, and sequencing tasks. Further trained on inverse tasks, the model is rendered capable of designing proteins with these properties as target features. The model is formulated as a general framework, completely prompt-based, and can be adapted for a variety of downstream tasks. We find that adding additional tasks yields emergent synergies that the model exploits in improving overall performance, beyond what would be possible by training a model on each dataset alone. Case studies are presented to validate the method, yielding protein designs specifically focused on structural proteins, but also exploring the applicability in the design of soluble, antimicrobial biomaterials. While our model is trained to ultimately perform 8 distinct tasks, with available datasets it can be extended to solve additional problems. In a broader sense, this work illustrates a form of multiscale modeling that relates a set of ultimate building blocks (here, byte-level utf8 characters) to complex output. This materiomic scheme captures complex emergent relationships between universal building block and resulting properties via a synergizing learning capacity to express a set of potentialities embedded in the knowledge used in training, via the interplay of universality and diversity.

Molecular dynamics (MD) is a powerful technique for studying microscopic phenomena, but its computational cost has driven significant interest in the development of deep learning-based surrogate models. We introduce generative modeling of molecular trajectories as a paradigm for learning flexible multi-task surrogate models of MD from data. By conditioning on appropriately chosen frames of the trajectory, we show such generative models can be adapted to diverse tasks such as forward simulation, transition path sampling, and trajectory upsampling. By alternatively conditioning on part of the molecular system and inpainting the rest, we also demonstrate the first steps towards dynamics-conditioned molecular design. We validate the full set of these capabilities on tetrapeptide simulations and show that our model can produce reasonable ensembles of protein monomers. Altogether, our work illustrates how generative modeling can unlock value from MD data towards diverse downstream tasks that are not straightforward to address with existing methods or even MD itself. Code is available at https://github.com/bjing2016/mdgen.

We introduce DEsignBench, a text-to-image (T2I) generation benchmark tailored for visual design scenarios. Recent T2I models like DALL-E 3 and others, have demonstrated remarkable capabilities in generating photorealistic images that align closely with textual inputs. While the allure of creating visually captivating images is undeniable, our emphasis extends beyond mere aesthetic pleasure. We aim to investigate the potential of using these powerful models in authentic design contexts. In pursuit of this goal, we develop DEsignBench, which incorporates test samples designed to assess T2I models on both "design technical capability" and "design application scenario." Each of these two dimensions is supported by a diverse set of specific design categories. We explore DALL-E 3 together with other leading T2I models on DEsignBench, resulting in a comprehensive visual gallery for side-by-side comparisons. For DEsignBench benchmarking, we perform human evaluations on generated images in DEsignBench gallery, against the criteria of image-text alignment, visual aesthetic, and design creativity. Our evaluation also considers other specialized design capabilities, including text rendering, layout composition, color harmony, 3D design, and medium style. In addition to human evaluations, we introduce the first automatic image generation evaluator powered by GPT-4V. This evaluator provides ratings that align well with human judgments, while being easily replicable and cost-efficient. A high-resolution version is available at https://github.com/design-bench/design-bench.github.io/raw/main/designbench.pdf?download=

Generative models for structure-based drug design (SBDD) have shown promising results in recent years. Existing works mainly focus on how to generate molecules with higher binding affinity, ignoring the feasibility prerequisites for generated 3D poses and resulting in false positives. We conduct thorough studies on key factors of ill-conformational problems when applying autoregressive methods and diffusion to SBDD, including mode collapse and hybrid continuous-discrete space. In this paper, we introduce MolCRAFT, the first SBDD model that operates in the continuous parameter space, together with a novel noise reduced sampling strategy. Empirical results show that our model consistently achieves superior performance in binding affinity with more stable 3D structure, demonstrating our ability to accurately model interatomic interactions. To our best knowledge, MolCRAFT is the first to achieve reference-level Vina Scores (-6.59 kcal/mol) with comparable molecular size, outperforming other strong baselines by a wide margin (-0.84 kcal/mol). Code is available at https://github.com/AlgoMole/MolCRAFT.

DeepSeek-R1 has shown that long chain-of-thought (CoT) reasoning can naturally emerge through a simple reinforcement learning (RL) framework with rule-based rewards, where the training may directly start from the base models-a paradigm referred to as zero RL training. Most recent efforts to reproduce zero RL training have primarily focused on the Qwen2.5 model series, which may not be representative as we find the base models already exhibit strong instruction-following and self-reflection abilities. In this work, we investigate zero RL training across 10 diverse base models, spanning different families and sizes including LLama3-8B, Mistral-7B/24B, DeepSeek-Math-7B, Qwen2.5-math-7B, and all Qwen2.5 models from 0.5B to 32B. Leveraging several key design strategies-such as adjusting format reward and controlling query difficulty-we achieve substantial improvements in both reasoning accuracy and response length across most settings. However, by carefully monitoring the training dynamics, we observe that different base models exhibit distinct patterns during training. For instance, the increased response length does not always correlate with the emergence of certain cognitive behaviors such as verification (i.e., the "aha moment"). Notably, we observe the "aha moment" for the first time in small models not from the Qwen family. We share the key designs that enable successful zero RL training, along with our findings and practices. To facilitate further research, we open-source the code, models, and analysis tools.

The discovery of novel materials and functional molecules can help to solve some of society's most urgent challenges, ranging from efficient energy harvesting and storage to uncovering novel pharmaceutical drug candidates. Traditionally matter engineering -- generally denoted as inverse design -- was based massively on human intuition and high-throughput virtual screening. The last few years have seen the emergence of significant interest in computer-inspired designs based on evolutionary or deep learning methods. The major challenge here is that the standard strings molecular representation SMILES shows substantial weaknesses in that task because large fractions of strings do not correspond to valid molecules. Here, we solve this problem at a fundamental level and introduce SELFIES (SELF-referencIng Embedded Strings), a string-based representation of molecules which is 100\% robust. Every SELFIES string corresponds to a valid molecule, and SELFIES can represent every molecule. SELFIES can be directly applied in arbitrary machine learning models without the adaptation of the models; each of the generated molecule candidates is valid. In our experiments, the model's internal memory stores two orders of magnitude more diverse molecules than a similar test with SMILES. Furthermore, as all molecules are valid, it allows for explanation and interpretation of the internal working of the generative models.

The rapid progress of foundation models has led to the prosperity of autonomous agents, which leverage the universal capabilities of foundation models to conduct reasoning, decision-making, and environmental interaction. However, the efficacy of agents remains limited when operating in intricate, realistic environments. In this work, we introduce the principles of Unified Alignment for Agents (UA^2), which advocate for the simultaneous alignment of agents with human intentions, environmental dynamics, and self-constraints such as the limitation of monetary budgets. From the perspective of UA^2, we review the current agent research and highlight the neglected factors in existing agent benchmarks and method candidates. We also conduct proof-of-concept studies by introducing realistic features to WebShop, including user profiles to demonstrate intentions, personalized reranking for complex environmental dynamics, and runtime cost statistics to reflect self-constraints. We then follow the principles of UA^2 to propose an initial design of our agent, and benchmark its performance with several candidate baselines in the retrofitted WebShop. The extensive experimental results further prove the importance of the principles of UA^2. Our research sheds light on the next steps of autonomous agent research with improved general problem-solving abilities.

The ability to generate 3D multiphase microstructures on-demand with targeted attributes can greatly accelerate the design of advanced materials. Here, we present a conditional latent diffusion model (LDM) framework that rapidly synthesizes high-fidelity 3D multiphase microstructures tailored to user specifications. Using this approach, we generate diverse two-phase and three-phase microstructures at high resolution (volumes of 128 times 128 times 64 voxels, representing >10^6 voxels each) within seconds, overcoming the scalability and time limitations of traditional simulation-based methods. Key design features, such as desired volume fractions and tortuosities, are incorporated as controllable inputs to guide the generative process, ensuring that the output structures meet prescribed statistical and topological targets. Moreover, the framework predicts corresponding manufacturing (processing) parameters for each generated microstructure, helping to bridge the gap between digital microstructure design and experimental fabrication. While demonstrated on organic photovoltaic (OPV) active-layer morphologies, the flexible architecture of our approach makes it readily adaptable to other material systems and microstructure datasets. By combining computational efficiency, adaptability, and experimental relevance, this framework addresses major limitations of existing methods and offers a powerful tool for accelerated materials discovery.

Minority samples are underrepresented instances located in low-density regions of a data manifold, and are valuable in many generative AI applications, such as data augmentation, creative content generation, etc. Unfortunately, existing diffusion-based minority generators often rely on computationally expensive guidance dedicated for minority generation. To address this, here we present a simple yet powerful guidance-free approach called Boost-and-Skip for generating minority samples using diffusion models. The key advantage of our framework requires only two minimal changes to standard generative processes: (i) variance-boosted initialization and (ii) timestep skipping. We highlight that these seemingly-trivial modifications are supported by solid theoretical and empirical evidence, thereby effectively promoting emergence of underrepresented minority features. Our comprehensive experiments demonstrate that Boost-and-Skip greatly enhances the capability of generating minority samples, even rivaling guidance-based state-of-the-art approaches while requiring significantly fewer computations. Code is available at https://github.com/soobin-um/BnS.

Recently, Large Language Models (LLMs) have achieved significant success, prompting increased interest in expanding their generative capabilities beyond general text into domain-specific areas. This study investigates the generation of parametric sequences for computer-aided design (CAD) models using LLMs. This endeavor represents an initial step towards creating parametric 3D shapes with LLMs, as CAD model parameters directly correlate with shapes in three-dimensional space. Despite the formidable generative capacities of LLMs, this task remains challenging, as these models neither encounter parametric sequences during their pretraining phase nor possess direct awareness of 3D structures. To address this, we present CAD-Llama, a framework designed to enhance pretrained LLMs for generating parametric 3D CAD models. Specifically, we develop a hierarchical annotation pipeline and a code-like format to translate parametric 3D CAD command sequences into Structured Parametric CAD Code (SPCC), incorporating hierarchical semantic descriptions. Furthermore, we propose an adaptive pretraining approach utilizing SPCC, followed by an instruction tuning process aligned with CAD-specific guidelines. This methodology aims to equip LLMs with the spatial knowledge inherent in parametric sequences. Experimental results demonstrate that our framework significantly outperforms prior autoregressive methods and existing LLM baselines.

Reinforcement learning (RL) over text representations can be effective for finding high-value policies that can search over graphs. However, RL requires careful structuring of the search space and algorithm design to be effective in this challenge. Through extensive experiments, we explore how different design choices for text grammar and algorithmic choices for training can affect an RL policy's ability to generate molecules with desired properties. We arrive at a new RL-based molecular design algorithm (ChemRLformer) and perform a thorough analysis using 25 molecule design tasks, including computationally complex protein docking simulations. From this analysis, we discover unique insights in this problem space and show that ChemRLformer achieves state-of-the-art performance while being more straightforward than prior work by demystifying which design choices are actually helpful for text-based molecule design.

Inspired by the principle of deliberate practice in human learning, we propose Deliberate Practice for Synthetic Data Generation (DP), a novel framework that improves sample efficiency through dynamic synthetic data generation. Prior work has shown that scaling synthetic data is inherently challenging, as naively adding new data leads to diminishing returns. To address this, pruning has been identified as a key mechanism for improving scaling, enabling models to focus on the most informative synthetic samples. Rather than generating a large dataset and pruning it afterward, DP efficiently approximates the direct generation of informative samples. We theoretically show how training on challenging, informative examples improves scaling laws and empirically validate that DP achieves better scaling performance with significantly fewer training samples and iterations. On ImageNet-100, DP generates 3.4x fewer samples and requires six times fewer iterations, while on ImageNet-1k, it generates 8x fewer samples with a 30 percent reduction in iterations, all while achieving superior performance compared to prior work.

Recent advancements in generative modeling have made it possible to generate high-quality content from context information, but a key question remains: how to teach models to know when to generate content? To answer this question, this study proposes a novel event generative model that draws its statistical intuition from marked temporal point processes, and offers a clean, flexible, and computationally efficient solution for a wide range of applications involving multi-dimensional marks. We aim to capture the distribution of the point process without explicitly specifying the conditional intensity or probability density. Instead, we use a conditional generator that takes the history of events as input and generates the high-quality subsequent event that is likely to occur given the prior observations. The proposed framework offers a host of benefits, including exceptional efficiency in learning the model and generating samples, as well as considerable representational power to capture intricate dynamics in multi- or even high-dimensional event space. Our numerical results demonstrate superior performance compared to other state-of-the-art baselines.

In computer-aided engineering design, the goal of a designer is to find an optimal design on a given requirement using the numerical simulator in loop with an optimization method. In this design optimization process, a good design optimization process is one that can reduce the time from inception to design. In this work, we take a class of design problem, that is computationally cheap to evaluate but has high dimensional design space. In such cases, traditional surrogate-based optimization does not offer any benefits. In this work, we propose an alternative way to use ML model to surrogate the design process that formulates the search problem as an inverse problem and can save time by finding the optimal design or at least a good initial seed design for optimization. By using this trained surrogate model with the traditional optimization method, we can get the best of both worlds. We call this as Surrogate Assisted Optimization (SAO)- a hybrid approach by mixing ML surrogate with the traditional optimization method. Empirical evaluations of propeller design problems show that a better efficient design can be found in fewer evaluations using SAO.

Conditional diffusion models are powerful generative models that can leverage various types of conditional information, such as class labels, segmentation masks, or text captions. However, in many real-world scenarios, conditional information may be noisy or unreliable due to human annotation errors or weak alignment. In this paper, we propose the Coherence-Aware Diffusion (CAD), a novel method that integrates coherence in conditional information into diffusion models, allowing them to learn from noisy annotations without discarding data. We assume that each data point has an associated coherence score that reflects the quality of the conditional information. We then condition the diffusion model on both the conditional information and the coherence score. In this way, the model learns to ignore or discount the conditioning when the coherence is low. We show that CAD is theoretically sound and empirically effective on various conditional generation tasks. Moreover, we show that leveraging coherence generates realistic and diverse samples that respect conditional information better than models trained on cleaned datasets where samples with low coherence have been discarded.

Generating realistic simulations is critical for autonomous system applications such as self-driving and human-robot interactions. However, driving simulators nowadays still have difficulty in generating controllable, diverse, and rule-compliant behaviors for road participants: Rule-based models cannot produce diverse behaviors and require careful tuning, whereas learning-based methods imitate the policy from data but are not designed to follow the rules explicitly. Besides, the real-world datasets are by nature "single-outcome", making the learning method hard to generate diverse behaviors. In this paper, we leverage Signal Temporal Logic (STL) and Diffusion Models to learn controllable, diverse, and rule-aware policy. We first calibrate the STL on the real-world data, then generate diverse synthetic data using trajectory optimization, and finally learn the rectified diffusion policy on the augmented dataset. We test on the NuScenes dataset and our approach can achieve the most diverse rule-compliant trajectories compared to other baselines, with a runtime 1/17X to the second-best approach. In the closed-loop testing, our approach reaches the highest diversity, rule satisfaction rate, and the least collision rate. Our method can generate varied characteristics conditional on different STL parameters in testing. A case study on human-robot encounter scenarios shows our approach can generate diverse and closed-to-oracle trajectories. The annotation tool, augmented dataset, and code are available at https://github.com/mengyuest/pSTL-diffusion-policy.

Generative models inspired by dynamical transport of measure -- such as flows and diffusions -- construct a continuous-time map between two probability densities. Conventionally, one of these is the target density, only accessible through samples, while the other is taken as a simple base density that is data-agnostic. In this work, using the framework of stochastic interpolants, we formalize how to couple the base and the target densities. This enables us to incorporate information about class labels or continuous embeddings to construct dynamical transport maps that serve as conditional generative models. We show that these transport maps can be learned by solving a simple square loss regression problem analogous to the standard independent setting. We demonstrate the usefulness of constructing dependent couplings in practice through experiments in super-resolution and in-painting.

Embodiment co-design aims to optimize a robot's morphology and control policy simultaneously. While prior work has demonstrated its potential for generating environment-adaptive robots, this field still faces persistent challenges in optimization efficiency due to the (i) combinatorial nature of morphological search spaces and (ii) intricate dependencies between morphology and control. We prove that the ineffective morphology representation and unbalanced reward signals between the design and control stages are key obstacles to efficiency. To advance towards efficient embodiment co-design, we propose BodyGen, which utilizes (1) topology-aware self-attention for both design and control, enabling efficient morphology representation with lightweight model sizes; (2) a temporal credit assignment mechanism that ensures balanced reward signals for optimization. With our findings, Body achieves an average 60.03% performance improvement against state-of-the-art baselines. We provide codes and more results on the website: https://genesisorigin.github.io.

Large language models (LLMs) can perform complex reasoning by generating intermediate reasoning steps. Providing these steps for prompting demonstrations is called chain-of-thought (CoT) prompting. CoT prompting has two major paradigms. One leverages a simple prompt like "Let's think step by step" to facilitate step-by-step thinking before answering a question. The other uses a few manual demonstrations one by one, each composed of a question and a reasoning chain that leads to an answer. The superior performance of the second paradigm hinges on the hand-crafting of task-specific demonstrations one by one. We show that such manual efforts may be eliminated by leveraging LLMs with the "Let's think step by step" prompt to generate reasoning chains for demonstrations one by one, i.e., let's think not just step by step, but also one by one. However, these generated chains often come with mistakes. To mitigate the effect of such mistakes, we find that diversity matters for automatically constructing demonstrations. We propose an automatic CoT prompting method: Auto-CoT. It samples questions with diversity and generates reasoning chains to construct demonstrations. On ten public benchmark reasoning tasks with GPT-3, Auto-CoT consistently matches or exceeds the performance of the CoT paradigm that requires manual designs of demonstrations. Code is available at https://github.com/amazon-research/auto-cot

Reliable machine learning and statistical analysis rely on diverse, well-distributed training data. However, real-world datasets are often limited in size and exhibit underrepresentation across key subpopulations, leading to biased predictions and reduced performance, particularly in supervised tasks such as classification. To address these challenges, we propose Conditional Data Synthesis Augmentation (CoDSA), a novel framework that leverages generative models, such as diffusion models, to synthesize high-fidelity data for improving model performance across multimodal domains including tabular, textual, and image data. CoDSA generates synthetic samples that faithfully capture the conditional distributions of the original data, with a focus on under-sampled or high-interest regions. Through transfer learning, CoDSA fine-tunes pre-trained generative models to enhance the realism of synthetic data and increase sample density in sparse areas. This process preserves inter-modal relationships, mitigates data imbalance, improves domain adaptation, and boosts generalization. We also introduce a theoretical framework that quantifies the statistical accuracy improvements enabled by CoDSA as a function of synthetic sample volume and targeted region allocation, providing formal guarantees of its effectiveness. Extensive experiments demonstrate that CoDSA consistently outperforms non-adaptive augmentation strategies and state-of-the-art baselines in both supervised and unsupervised settings.

Artificial Intelligence (AI) advancement is heavily dependent on access to large-scale, high-quality training data. However, in specialized domains such as healthcare, data acquisition faces significant constraints due to privacy regulations, ethical considerations, and limited availability. While synthetic data generation offers a promising solution, conventional approaches typically require substantial real data for training generative models. The emergence of large-scale prompt-based models presents new opportunities for synthetic data generation without direct access to protected data. However, crafting effective prompts for domain-specific data generation remains challenging, and manual prompt engineering proves insufficient for achieving output with sufficient precision and authenticity. We review recent developments in automatic prompt optimization, following PRISMA guidelines. We analyze six peer-reviewed studies published between 2020 and 2024 that focus on automatic data-free prompt optimization methods. Our analysis reveals three approaches: feedback-driven, error-based, and control-theoretic. Although all approaches demonstrate promising capabilities in prompt refinement and adaptation, our findings suggest the need for an integrated framework that combines complementary optimization techniques to enhance synthetic data generation while minimizing manual intervention. We propose future research directions toward developing robust, iterative prompt optimization frameworks capable of improving the quality of synthetic data. This advancement can be particularly crucial for sensitive fields and in specialized domains where data access is restricted, potentially transforming how we approach synthetic data generation for AI development.

Multi-cellular robot design aims to create robots comprised of numerous cells that can be efficiently controlled to perform diverse tasks. Previous research has demonstrated the ability to generate robots for various tasks, but these approaches often optimize robots directly in the vast design space, resulting in robots with complicated morphologies that are hard to control. In response, this paper presents a novel coarse-to-fine method for designing multi-cellular robots. Initially, this strategy seeks optimal coarse-grained robots and progressively refines them. To mitigate the challenge of determining the precise refinement juncture during the coarse-to-fine transition, we introduce the Hyperbolic Embeddings for Robot Design (HERD) framework. HERD unifies robots of various granularity within a shared hyperbolic space and leverages a refined Cross-Entropy Method for optimization. This framework enables our method to autonomously identify areas of exploration in hyperbolic space and concentrate on regions demonstrating promise. Finally, the extensive empirical studies on various challenging tasks sourced from EvoGym show our approach's superior efficiency and generalization capability.

In engineering design, navigating complex decision-making landscapes demands a thorough exploration of the design, performance, and constraint spaces, often impeded by resource-intensive simulations. Data-driven methods can mitigate this challenge by harnessing historical data to delineate feasible domains, accelerate optimization, or evaluate designs. However, the implementation of these methods usually demands machine-learning expertise and multiple trials to choose the right method and hyperparameters. This makes them less accessible for numerous engineering situations. Additionally, there is an inherent trade-off between training speed and accuracy, with faster methods sometimes compromising precision. In our paper, we demonstrate that a recently released general-purpose transformer-based classification model, TabPFN, is both fast and accurate. Notably, it requires no dataset-specific training to assess new tabular data. TabPFN is a Prior-Data Fitted Network, which undergoes a one-time offline training across a broad spectrum of synthetic datasets and performs in-context learning. We evaluated TabPFN's efficacy across eight engineering design classification problems, contrasting it with seven other algorithms, including a state-of-the-art AutoML method. For these classification challenges, TabPFN consistently outperforms in speed and accuracy. It is also the most data-efficient and provides the added advantage of being differentiable and giving uncertainty estimates. Our findings advocate for the potential of pre-trained models that learn from synthetic data and require no domain-specific tuning to make data-driven engineering design accessible to a broader community and open ways to efficient general-purpose models valid across applications. Furthermore, we share a benchmark problem set for evaluating new classification algorithms in engineering design.

Layout generation is the keystone in achieving automated graphic design, requiring arranging the position and size of various multi-modal design elements in a visually pleasing and constraint-following manner. Previous approaches are either inefficient for large-scale applications or lack flexibility for varying design requirements. Our research introduces a unified framework for automated graphic layout generation, leveraging the multi-modal large language model (MLLM) to accommodate diverse design tasks. In contrast, our data-driven method employs structured text (JSON format) and visual instruction tuning to generate layouts under specific visual and textual constraints, including user-defined natural language specifications. We conducted extensive experiments and achieved state-of-the-art (SOTA) performance on public multi-modal layout generation benchmarks, demonstrating the effectiveness of our method. Moreover, recognizing existing datasets' limitations in capturing the complexity of real-world graphic designs, we propose two new datasets for much more challenging tasks (user-constrained generation and complicated poster), further validating our model's utility in real-life settings. Marking by its superior accessibility and adaptability, this approach further automates large-scale graphic design tasks. The code and datasets will be publicly available on https://github.com/posterllava/PosterLLaVA.

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.

Graphic designers often get inspiration through the recombination of references. Our formative study (N=6) reveals that graphic designers focus on conceptual keywords during this process, and want support for discovering the keywords, expanding them, and exploring diverse recombination options of them, while still having room for designers' creativity. We propose CreativeConnect, a system with generative AI pipelines that helps users discover useful elements from the reference image using keywords, recommends relevant keywords, generates diverse recombination options with user-selected keywords, and shows recombinations as sketches with text descriptions. Our user study (N=16) showed that CreativeConnect helped users discover keywords from the reference and generate multiple ideas based on them, ultimately helping users produce more design ideas with higher self-reported creativity compared to the baseline system without generative pipelines. While CreativeConnect was shown effective in ideation, we discussed how CreativeConnect can be extended to support other types of tasks in creativity support.

We present sketch-rnn, a recurrent neural network (RNN) able to construct stroke-based drawings of common objects. The model is trained on thousands of crude human-drawn images representing hundreds of classes. We outline a framework for conditional and unconditional sketch generation, and describe new robust training methods for generating coherent sketch drawings in a vector format.

Scientific discovery relies on scientists generating novel hypotheses that undergo rigorous experimental validation. To augment this process, we introduce an AI co-scientist, a multi-agent system built on Gemini 2.0. The AI co-scientist is intended to help uncover new, original knowledge and to formulate demonstrably novel research hypotheses and proposals, building upon prior evidence and aligned to scientist-provided research objectives and guidance. The system's design incorporates a generate, debate, and evolve approach to hypothesis generation, inspired by the scientific method and accelerated by scaling test-time compute. Key contributions include: (1) a multi-agent architecture with an asynchronous task execution framework for flexible compute scaling; (2) a tournament evolution process for self-improving hypotheses generation. Automated evaluations show continued benefits of test-time compute, improving hypothesis quality. While general purpose, we focus development and validation in three biomedical areas: drug repurposing, novel target discovery, and explaining mechanisms of bacterial evolution and anti-microbial resistance. For drug repurposing, the system proposes candidates with promising validation findings, including candidates for acute myeloid leukemia that show tumor inhibition in vitro at clinically applicable concentrations. For novel target discovery, the AI co-scientist proposed new epigenetic targets for liver fibrosis, validated by anti-fibrotic activity and liver cell regeneration in human hepatic organoids. Finally, the AI co-scientist recapitulated unpublished experimental results via a parallel in silico discovery of a novel gene transfer mechanism in bacterial evolution. These results, detailed in separate, co-timed reports, demonstrate the potential to augment biomedical and scientific discovery and usher an era of AI empowered scientists.

LLMs have demonstrated commendable performance across diverse domains. Nevertheless, formulating high-quality prompts to instruct LLMs proficiently poses a challenge for non-AI experts. Existing research in prompt engineering suggests somewhat scattered optimization principles and designs empirically dependent prompt optimizers. Unfortunately, these endeavors lack a structured design template, incurring high learning costs and resulting in low reusability. In addition, it is not conducive to the iterative updating of prompts. Inspired by structured reusable programming languages, we propose LangGPT, a dual-layer prompt design framework as the programming language for LLMs. LangGPT has an easy-to-learn normative structure and provides an extended structure for migration and reuse. Experiments illustrate that LangGPT significantly enhances the performance of LLMs. Moreover, the case study shows that LangGPT leads LLMs to generate higher-quality responses. Furthermore, we analyzed the ease of use and reusability of LangGPT through a user survey in our online community.

Inverse molecular design with diffusion models holds great potential for advancements in material and drug discovery. Despite success in unconditional molecular generation, integrating multiple properties such as synthetic score and gas permeability as condition constraints into diffusion models remains unexplored. We present the Graph Diffusion Transformer (Graph DiT) for multi-conditional molecular generation. Graph DiT integrates an encoder to learn numerical and categorical property representations with the Transformer-based denoiser. Unlike previous graph diffusion models that add noise separately on the atoms and bonds in the forward diffusion process, Graph DiT is trained with a novel graph-dependent noise model for accurate estimation of graph-related noise in molecules. We extensively validate Graph DiT for multi-conditional polymer and small molecule generation. Results demonstrate the superiority of Graph DiT across nine metrics from distribution learning to condition control for molecular properties. A polymer inverse design task for gas separation with feedback from domain experts further demonstrates its practical utility.

The black-box nature of deep neural networks (DNN) has brought to attention the issues of transparency and fairness. Deep Reinforcement Learning (Deep RL or DRL), which uses DNN to learn its policy, value functions etc, is thus also subject to similar concerns. This paper proposes a way to circumvent the issues through the bottom-up design of neural networks with detailed interpretability, where each neuron or layer has its own meaning and utility that corresponds to humanly understandable concept. The framework introduced in this paper is called the Self Reward Design (SRD), inspired by the Inverse Reward Design, and this interpretable design can (1) solve the problem by pure design (although imperfectly) and (2) be optimized like a standard DNN. With deliberate human designs, we show that some RL problems such as lavaland and MuJoCo can be solved using a model constructed with standard NN components with few parameters. Furthermore, with our fish sale auction example, we demonstrate how SRD is used to address situations that will not make sense if black-box models are used, where humanly-understandable semantic-based decision is required.

This work breaks through the Base-New Tradeoff (BNT)dilemma in prompt tuning, i.e., the better the tuned model generalizes to the base (or target) task, the worse it generalizes to new tasks, and vice versa. Specifically, through an in-depth analysis of the learned features of the base and new tasks, we observe that the BNT stems from a channel bias issue, i.e., the vast majority of feature channels are occupied by base-specific knowledge, resulting in the collapse of taskshared knowledge important to new tasks. To address this, we propose the Decoupled Prompt Tuning (DePT) framework, which decouples base-specific knowledge from feature channels into an isolated feature space during prompt tuning, so as to maximally preserve task-shared knowledge in the original feature space for achieving better zero-shot generalization on new tasks. Importantly, our DePT is orthogonal to existing prompt tuning methods, hence it can improve all of them. Extensive experiments on 11 datasets show the strong flexibility and effectiveness of DePT. Our code and pretrained models are available at https://github.com/Koorye/DePT.

Recently, there is a growing interest in creating computer-aided design (CAD) models based on user intent, known as controllable CAD generation. Existing work offers limited controllability and needs separate models for different types of control, reducing efficiency and practicality. To achieve controllable generation across all CAD construction hierarchies, such as sketch-extrusion, extrusion, sketch, face, loop and curve, we propose FlexCAD, a unified model by fine-tuning large language models (LLMs). First, to enhance comprehension by LLMs, we represent a CAD model as a structured text by abstracting each hierarchy as a sequence of text tokens. Second, to address various controllable generation tasks in a unified model, we introduce a hierarchy-aware masking strategy. Specifically, during training, we mask a hierarchy-aware field in the CAD text with a mask token. This field, composed of a sequence of tokens, can be set flexibly to represent various hierarchies. Subsequently, we ask LLMs to predict this masked field. During inference, the user intent is converted into a CAD text with a mask token replacing the part the user wants to modify, which is then fed into FlexCAD to generate new CAD models. Comprehensive experiments on public dataset demonstrate the effectiveness of FlexCAD in both generation quality and controllability. Code will be available at https://github.com/microsoft/FlexCAD.

Ensuring sufficient exploration is a central challenge when training meta-reinforcement learning (meta-RL) agents to solve novel environments. Conventional solutions to the exploration-exploitation dilemma inject explicit incentives such as randomization, uncertainty bonuses, or intrinsic rewards to encourage exploration. In this work, we hypothesize that an agent trained solely to maximize a greedy (exploitation-only) objective can nonetheless exhibit emergent exploratory behavior, provided three conditions are met: (1) Recurring Environmental Structure, where the environment features repeatable regularities that allow past experience to inform future choices; (2) Agent Memory, enabling the agent to retain and utilize historical interaction data; and (3) Long-Horizon Credit Assignment, where learning propagates returns over a time frame sufficient for the delayed benefits of exploration to inform current decisions. Through experiments in stochastic multi-armed bandits and temporally extended gridworlds, we observe that, when both structure and memory are present, a policy trained on a strictly greedy objective exhibits information-seeking exploratory behavior. We further demonstrate, through controlled ablations, that emergent exploration vanishes if either environmental structure or agent memory is absent (Conditions 1 & 2). Surprisingly, removing long-horizon credit assignment (Condition 3) does not always prevent emergent exploration-a result we attribute to the pseudo-Thompson Sampling effect. These findings suggest that, under the right prerequisites, exploration and exploitation need not be treated as orthogonal objectives but can emerge from a unified reward-maximization process.

Protein family design emerges as a promising alternative by combining the advantages of de novo protein design and mutation-based directed evolution.In this paper, we propose ProfileBFN, the Profile Bayesian Flow Networks, for specifically generative modeling of protein families. ProfileBFN extends the discrete Bayesian Flow Network from an MSA profile perspective, which can be trained on single protein sequences by regarding it as a degenerate profile, thereby achieving efficient protein family design by avoiding large-scale MSA data construction and training. Empirical results show that ProfileBFN has a profound understanding of proteins. When generating diverse and novel family proteins, it can accurately capture the structural characteristics of the family. The enzyme produced by this method is more likely than the previous approach to have the corresponding function, offering better odds of generating diverse proteins with the desired functionality.

Finding a suitable layout represents a crucial task for diverse applications in graphic design. Motivated by simpler and smoother sampling trajectories, we explore the use of Flow Matching as an alternative to current diffusion-based layout generation models. Specifically, we propose LayoutFlow, an efficient flow-based model capable of generating high-quality layouts. Instead of progressively denoising the elements of a noisy layout, our method learns to gradually move, or flow, the elements of an initial sample until it reaches its final prediction. In addition, we employ a conditioning scheme that allows us to handle various generation tasks with varying degrees of conditioning with a single model. Empirically, LayoutFlow performs on par with state-of-the-art models while being significantly faster.

Training a high-quality deep neural network requires choosing suitable hyperparameters, which is a non-trivial and expensive process. Current works try to automatically optimize or design principles of hyperparameters, such that they can generalize to diverse unseen scenarios. However, most designs or optimization methods are agnostic to the choice of network structures, and thus largely ignore the impact of neural architectures on hyperparameters. In this work, we precisely characterize the dependence of initializations and maximal learning rates on the network architecture, which includes the network depth, width, convolutional kernel size, and connectivity patterns. By pursuing every parameter to be maximally updated with the same mean squared change in pre-activations, we can generalize our initialization and learning rates across MLPs (multi-layer perception) and CNNs (convolutional neural network) with sophisticated graph topologies. We verify our principles with comprehensive experiments. More importantly, our strategy further sheds light on advancing current benchmarks for architecture design. A fair comparison of AutoML algorithms requires accurate network rankings. However, we demonstrate that network rankings can be easily changed by better training networks in benchmarks with our architecture-aware learning rates and initialization.

Drug discovery is a complex process that involves multiple scenarios and stages, such as fragment-constrained molecule generation, hit generation and lead optimization. However, existing molecular generative models can only tackle one or two of these scenarios and lack the flexibility to address various aspects of the drug discovery pipeline. In this paper, we present Generalist Molecular generative model (GenMol), a versatile framework that addresses these limitations by applying discrete diffusion to the Sequential Attachment-based Fragment Embedding (SAFE) molecular representation. GenMol generates SAFE sequences through non-autoregressive bidirectional parallel decoding, thereby allowing utilization of a molecular context that does not rely on the specific token ordering and enhanced computational efficiency. Moreover, under the discrete diffusion framework, we introduce fragment remasking, a strategy that optimizes molecules by replacing fragments with masked tokens and regenerating them, enabling effective exploration of chemical space. GenMol significantly outperforms the previous GPT-based model trained on SAFE representations in de novo generation and fragment-constrained generation, and achieves state-of-the-art performance in goal-directed hit generation and lead optimization. These experimental results demonstrate that GenMol can tackle a wide range of drug discovery tasks, providing a unified and versatile approach for molecular design.

Retrosynthesis, which aims to find a route to synthesize a target molecule from commercially available starting materials, is a critical task in drug discovery and materials design. Recently, the combination of ML-based single-step reaction predictors with multi-step planners has led to promising results. However, the single-step predictors are mostly trained offline to optimize the single-step accuracy, without considering complete routes. Here, we leverage reinforcement learning (RL) to improve the single-step predictor, by using a tree-shaped MDP to optimize complete routes. Specifically, we propose a novel online training algorithm, called Planning with Dual Value Networks (PDVN), which alternates between the planning phase and updating phase. In PDVN, we construct two separate value networks to predict the synthesizability and cost of molecules, respectively. To maintain the single-step accuracy, we design a two-branch network structure for the single-step predictor. On the widely-used USPTO dataset, our PDVN algorithm improves the search success rate of existing multi-step planners (e.g., increasing the success rate from 85.79% to 98.95% for Retro*, and reducing the number of model calls by half while solving 99.47% molecules for RetroGraph). Additionally, PDVN helps find shorter synthesis routes (e.g., reducing the average route length from 5.76 to 4.83 for Retro*, and from 5.63 to 4.78 for RetroGraph).

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

An essential and challenging problem in causal inference is causal effect estimation from observational data. The problem becomes more difficult with the presence of unobserved confounding variables. The front-door adjustment is a practical approach for dealing with unobserved confounding variables. However, the restriction for the standard front-door adjustment is difficult to satisfy in practice. In this paper, we relax some of the restrictions by proposing the concept of conditional front-door (CFD) adjustment and develop the theorem that guarantees the causal effect identifiability of CFD adjustment. Furthermore, as it is often impossible for a CFD variable to be given in practice, it is desirable to learn it from data. By leveraging the ability of deep generative models, we propose CFDiVAE to learn the representation of the CFD adjustment variable directly from data with the identifiable Variational AutoEncoder and formally prove the model identifiability. Extensive experiments on synthetic datasets validate the effectiveness of CFDiVAE and its superiority over existing methods. The experiments also show that the performance of CFDiVAE is less sensitive to the causal strength of unobserved confounding variables. We further apply CFDiVAE to a real-world dataset to demonstrate its potential application.

We tackle the problem disentangling the latent space of an autoencoder in order to separate labelled attribute information from other characteristic information. This then allows us to change selected attributes while preserving other information. Our method, matrix subspace projection, is much simpler than previous approaches to latent space factorisation, for example not requiring multiple discriminators or a careful weighting among their loss functions. Furthermore our new model can be applied to autoencoders as a plugin, and works across diverse domains such as images or text. We demonstrate the utility of our method for attribute manipulation in autoencoders trained across varied domains, using both human evaluation and automated methods. The quality of generation of our new model (e.g. reconstruction, conditional generation) is highly competitive to a number of strong baselines.

Real-world design tasks - such as picture book creation, film storyboard development using character sets, photo retouching, visual effects, and font transfer - are highly diverse and complex, requiring deep interpretation and extraction of various elements from instructions, descriptions, and reference images. The resulting images often implicitly capture key features from references or user inputs, making it challenging to develop models that can effectively address such varied tasks. While existing visual generative models can produce high-quality images based on prompts, they face significant limitations in professional design scenarios that involve varied forms and multiple inputs and outputs, even when enhanced with adapters like ControlNets and LoRAs. To address this, we introduce IDEA-Bench, a comprehensive benchmark encompassing 100 real-world design tasks, including rendering, visual effects, storyboarding, picture books, fonts, style-based, and identity-preserving generation, with 275 test cases to thoroughly evaluate a model's general-purpose generation capabilities. Notably, even the best-performing model only achieves 22.48 on IDEA-Bench, while the best general-purpose model only achieves 6.81. We provide a detailed analysis of these results, highlighting the inherent challenges and providing actionable directions for improvement. Additionally, we provide a subset of 18 representative tasks equipped with multimodal large language model (MLLM)-based auto-evaluation techniques to facilitate rapid model development and comparison. We releases the benchmark data, evaluation toolkits, and an online leaderboard at https://github.com/ali-vilab/IDEA-Bench, aiming to drive the advancement of generative models toward more versatile and applicable intelligent design systems.

Reinforcement Learning (RL) algorithms are often known for sample inefficiency and difficult generalization. Recently, Unsupervised Environment Design (UED) emerged as a new paradigm for zero-shot generalization by simultaneously learning a task distribution and agent policies on the generated tasks. This is a non-stationary process where the task distribution evolves along with agent policies; creating an instability over time. While past works demonstrated the potential of such approaches, sampling effectively from the task space remains an open challenge, bottlenecking these approaches. To this end, we introduce CLUTR: a novel unsupervised curriculum learning algorithm that decouples task representation and curriculum learning into a two-stage optimization. It first trains a recurrent variational autoencoder on randomly generated tasks to learn a latent task manifold. Next, a teacher agent creates a curriculum by maximizing a minimax REGRET-based objective on a set of latent tasks sampled from this manifold. Using the fixed-pretrained task manifold, we show that CLUTR successfully overcomes the non-stationarity problem and improves stability. Our experimental results show CLUTR outperforms PAIRED, a principled and popular UED method, in the challenging CarRacing and navigation environments: achieving 10.6X and 45\% improvement in zero-shot generalization, respectively. CLUTR also performs comparably to the non-UED state-of-the-art for CarRacing, while requiring 500X fewer environment interactions.

The sharp increase in data-related expenses has motivated research into condensing datasets while retaining the most informative features. Dataset distillation has thus recently come to the fore. This paradigm generates synthetic datasets that are representative enough to replace the original dataset in training a neural network. To avoid redundancy in these synthetic datasets, it is crucial that each element contains unique features and remains diverse from others during the synthesis stage. In this paper, we provide a thorough theoretical and empirical analysis of diversity within synthesized datasets. We argue that enhancing diversity can improve the parallelizable yet isolated synthesizing approach. Specifically, we introduce a novel method that employs dynamic and directed weight adjustment techniques to modulate the synthesis process, thereby maximizing the representativeness and diversity of each synthetic instance. Our method ensures that each batch of synthetic data mirrors the characteristics of a large, varying subset of the original dataset. Extensive experiments across multiple datasets, including CIFAR, Tiny-ImageNet, and ImageNet-1K, demonstrate the superior performance of our method, highlighting its effectiveness in producing diverse and representative synthetic datasets with minimal computational expense. Our code is available at https://github.com/AngusDujw/Diversity-Driven-Synthesis.https://github.com/AngusDujw/Diversity-Driven-Synthesis.

Curriculum design is a fundamental component of education. For example, when we learn mathematics at school, we build upon our knowledge of addition to learn multiplication. These and other concepts must be mastered before our first algebra lesson, which also reinforces our addition and multiplication skills. Designing a curriculum for teaching either a human or a machine shares the underlying goal of maximizing knowledge transfer from earlier to later tasks, while also minimizing forgetting of learned tasks. Prior research on curriculum design for image classification focuses on the ordering of training examples during a single offline task. Here, we investigate the effect of the order in which multiple distinct tasks are learned in a sequence. We focus on the online class-incremental continual learning setting, where algorithms or humans must learn image classes one at a time during a single pass through a dataset. We find that curriculum consistently influences learning outcomes for humans and for multiple continual machine learning algorithms across several benchmark datasets. We introduce a novel-object recognition dataset for human curriculum learning experiments and observe that curricula that are effective for humans are highly correlated with those that are effective for machines. As an initial step towards automated curriculum design for online class-incremental learning, we propose a novel algorithm, dubbed Curriculum Designer (CD), that designs and ranks curricula based on inter-class feature similarities. We find significant overlap between curricula that are empirically highly effective and those that are highly ranked by our CD. Our study establishes a framework for further research on teaching humans and machines to learn continuously using optimized curricula.

Designing biological sequences that satisfy multiple, often conflicting, functional and biophysical criteria remains a central challenge in biomolecule engineering. While discrete flow matching models have recently shown promise for efficient sampling in high-dimensional sequence spaces, existing approaches address only single objectives or require continuous embeddings that can distort discrete distributions. We present Multi-Objective-Guided Discrete Flow Matching (MOG-DFM), a general framework to steer any pretrained discrete-time flow matching generator toward Pareto-efficient trade-offs across multiple scalar objectives. At each sampling step, MOG-DFM computes a hybrid rank-directional score for candidate transitions and applies an adaptive hypercone filter to enforce consistent multi-objective progression. We also trained two unconditional discrete flow matching models, PepDFM for diverse peptide generation and EnhancerDFM for functional enhancer DNA generation, as base generation models for MOG-DFM. We demonstrate MOG-DFM's effectiveness in generating peptide binders optimized across five properties (hemolysis, non-fouling, solubility, half-life, and binding affinity), and in designing DNA sequences with specific enhancer classes and DNA shapes. In total, MOG-DFM proves to be a powerful tool for multi-property-guided biomolecule sequence design.

In recent years, large language models have achieved breakthroughs on a wide range of benchmarks in natural language processing and continue to increase in performance. Recently, the advances of large language models have raised interest outside the natural language processing community and could have a large impact on daily life. In this paper, we pose the question: How will large language models and other foundation models shape the future product development process? We provide the reader with an overview of the subject by summarizing both recent advances in natural language processing and the use of information technology in the engineering design process. We argue that discourse should be regarded as the core of engineering design processes, and therefore should be represented in a digital artifact. On this basis, we describe how foundation models such as large language models could contribute to the design discourse by automating parts thereof that involve creativity and reasoning, and were previously reserved for humans. We describe how simulations, experiments, topology optimizations, and other process steps can be integrated into a machine-actionable, discourse-centric design process. Finally, we outline the future research that will be necessary for the implementation of the conceptualized framework.

The primary axes of interest in image-generating diffusion models are image quality, the amount of variation in the results, and how well the results align with a given condition, e.g., a class label or a text prompt. The popular classifier-free guidance approach uses an unconditional model to guide a conditional model, leading to simultaneously better prompt alignment and higher-quality images at the cost of reduced variation. These effects seem inherently entangled, and thus hard to control. We make the surprising observation that it is possible to obtain disentangled control over image quality without compromising the amount of variation by guiding generation using a smaller, less-trained version of the model itself rather than an unconditional model. This leads to significant improvements in ImageNet generation, setting record FIDs of 1.01 for 64x64 and 1.25 for 512x512, using publicly available networks. Furthermore, the method is also applicable to unconditional diffusion models, drastically improving their quality.

AI technologies are moving rapidly from research to production. With the popularity of Foundation Models (FMs) that generate text, images, and video, AI-based systems are increasing their complexity. Compared to traditional AI-based software, systems employing FMs, or GenAI-based systems, are more difficult to design due to their scale and versatility. This makes it necessary to document best practices, known as design patterns in software engineering, that can be used across GenAI applications. Our first contribution is to formalize two techniques, Task Decomposition and Retrieval-Augmented Generation (RAG), as design patterns for GenAI-based systems. We discuss their trade-offs in terms of software quality attributes and comment on alternative approaches. We recommend to AI practitioners to consider these techniques not only from a scientific perspective but also from the standpoint of desired engineering properties such as flexibility, maintainability, safety, and security. As a second contribution, we describe our industry experience applying Task Decomposition and RAG to build a complex real-world GenAI application for enterprise users: Workflow Generation. The task of generating workflows entails generating a specific plan using data from the system environment, taking as input a user requirement. As these two patterns affect the entire AI development cycle, we explain how they impacted the dataset creation, model training, model evaluation, and deployment phases.

To deduce new facts on a knowledge graph (KG), a link predictor learns from the graph structure and collects local evidence to find the answer to a given query. However, existing methods suffer from a severe scalability problem due to the utilization of the whole KG for prediction, which hinders their promise on large scale KGs and cannot be directly addressed by vanilla sampling methods. In this work, we propose the one-shot-subgraph link prediction to achieve efficient and adaptive prediction. The design principle is that, instead of directly acting on the whole KG, the prediction procedure is decoupled into two steps, i.e., (i) extracting only one subgraph according to the query and (ii) predicting on this single, query dependent subgraph. We reveal that the non-parametric and computation-efficient heuristics Personalized PageRank (PPR) can effectively identify the potential answers and supporting evidence. With efficient subgraph-based prediction, we further introduce the automated searching of the optimal configurations in both data and model spaces. Empirically, we achieve promoted efficiency and leading performances on five large-scale benchmarks. The code is publicly available at: https://github.com/tmlr-group/one-shot-subgraph.

In computational social science (CSS), researchers analyze documents to explain social and political phenomena. In most scenarios, CSS researchers first obtain labels for documents and then explain labels using interpretable regression analyses in the second step. One increasingly common way to annotate documents cheaply at scale is through large language models (LLMs). However, like other scalable ways of producing annotations, such surrogate labels are often imperfect and biased. We present a new algorithm for using imperfect annotation surrogates for downstream statistical analyses while guaranteeing statistical properties -- like asymptotic unbiasedness and proper uncertainty quantification -- which are fundamental to CSS research. We show that direct use of surrogate labels in downstream statistical analyses leads to substantial bias and invalid confidence intervals, even with high surrogate accuracy of 80-90%. To address this, we build on debiased machine learning to propose the design-based supervised learning (DSL) estimator. DSL employs a doubly-robust procedure to combine surrogate labels with a smaller number of high-quality, gold-standard labels. Our approach guarantees valid inference for downstream statistical analyses, even when surrogates are arbitrarily biased and without requiring stringent assumptions, by controlling the probability of sampling documents for gold-standard labeling. Both our theoretical analysis and experimental results show that DSL provides valid statistical inference while achieving root mean squared errors comparable to existing alternatives that focus only on prediction without inferential guarantees.

Virtual Try-On (VTON) has become a transformative technology, empowering users to experiment with fashion without ever having to physically try on clothing. However, existing methods often struggle with generating high-fidelity and detail-consistent results. While diffusion models, such as Stable Diffusion series, have shown their capability in creating high-quality and photorealistic images, they encounter formidable challenges in conditional generation scenarios like VTON. Specifically, these models struggle to maintain a balance between control and consistency when generating images for virtual clothing trials. OutfitAnyone addresses these limitations by leveraging a two-stream conditional diffusion model, enabling it to adeptly handle garment deformation for more lifelike results. It distinguishes itself with scalability-modulating factors such as pose, body shape and broad applicability, extending from anime to in-the-wild images. OutfitAnyone's performance in diverse scenarios underscores its utility and readiness for real-world deployment. For more details and animated results, please see https://humanaigc.github.io/outfit-anyone/.

We propose an end-to-end variational generative model for scene layout synthesis conditioned on scene graphs. Unlike unconditional scene layout generation, we use scene graphs as an abstract but general representation to guide the synthesis of diverse scene layouts that satisfy relationships included in the scene graph. This gives rise to more flexible control over the synthesis process, allowing various forms of inputs such as scene layouts extracted from sentences or inferred from a single color image. Using our conditional layout synthesizer, we can generate various layouts that share the same structure of the input example. In addition to this conditional generation design, we also integrate a differentiable rendering module that enables layout refinement using only 2D projections of the scene. Given a depth and a semantics map, the differentiable rendering module enables optimizing over the synthesized layout to fit the given input in an analysis-by-synthesis fashion. Experiments suggest that our model achieves higher accuracy and diversity in conditional scene synthesis and allows exemplar-based scene generation from various input forms.

In the field of antibody engineering, an essential task is to design a novel antibody whose paratopes bind to a specific antigen with correct epitopes. Understanding antibody structure and its paratope can facilitate a mechanistic understanding of its function. Therefore, antibody structure prediction from its sequence alone has always been a highly valuable problem for de novo antibody design. AlphaFold2, a breakthrough in the field of structural biology, provides a solution to predict protein structure based on protein sequences and computationally expensive coevolutionary multiple sequence alignments (MSAs). However, the computational efficiency and undesirable prediction accuracy of antibodies, especially on the complementarity-determining regions (CDRs) of antibodies limit their applications in the industrially high-throughput drug design. To learn an informative representation of antibodies, we employed a deep antibody language model (ALM) on curated sequences from the observed antibody space database via a transformer model. We also developed a novel model named xTrimoABFold to predict antibody structure from antibody sequence based on the pretrained ALM as well as efficient evoformers and structural modules. The model was trained end-to-end on the antibody structures in PDB by minimizing the ensemble loss of domain-specific focal loss on CDR and the frame-aligned point loss. xTrimoABFold outperforms AlphaFold2 and other protein language model based SOTAs, e.g., OmegaFold, HelixFold-Single, and IgFold with a large significant margin (30+\% improvement on RMSD) while performing 151 times faster than AlphaFold2. To the best of our knowledge, xTrimoABFold achieved state-of-the-art antibody structure prediction. Its improvement in both accuracy and efficiency makes it a valuable tool for de novo antibody design and could make further improvements in immuno-theory.