Daily Papers

Virtual Screening is an essential technique in the early phases of drug discovery, aimed at identifying promising drug candidates from vast molecular libraries. Recently, ligand-based virtual screening has garnered significant attention due to its efficacy in conducting extensive database screenings without relying on specific protein-binding site information. Obtaining binding affinity data for complexes is highly expensive, resulting in a limited amount of available data that covers a relatively small chemical space. Moreover, these datasets contain a significant amount of inconsistent noise. It is challenging to identify an inductive bias that consistently maintains the integrity of molecular activity during data augmentation. To tackle these challenges, we propose S-MolSearch, the first framework to our knowledge, that leverages molecular 3D information and affinity information in semi-supervised contrastive learning for ligand-based virtual screening. Drawing on the principles of inverse optimal transport, S-MolSearch efficiently processes both labeled and unlabeled data, training molecular structural encoders while generating soft labels for the unlabeled data. This design allows S-MolSearch to adaptively utilize unlabeled data within the learning process. Empirically, S-MolSearch demonstrates superior performance on widely-used benchmarks LIT-PCBA and DUD-E. It surpasses both structure-based and ligand-based virtual screening methods for AUROC, BEDROC and EF.

We call on the Document AI (DocAI) community to reevaluate current methodologies and embrace the challenge of creating more practically-oriented benchmarks. Document Understanding Dataset and Evaluation (DUDE) seeks to remediate the halted research progress in understanding visually-rich documents (VRDs). We present a new dataset with novelties related to types of questions, answers, and document layouts based on multi-industry, multi-domain, and multi-page VRDs of various origins, and dates. Moreover, we are pushing the boundaries of current methods by creating multi-task and multi-domain evaluation setups that more accurately simulate real-world situations where powerful generalization and adaptation under low-resource settings are desired. DUDE aims to set a new standard as a more practical, long-standing benchmark for the community, and we hope that it will lead to future extensions and contributions that address real-world challenges. Finally, our work illustrates the importance of finding more efficient ways to model language, images, and layout in DocAI.

Transformer-based text embedding models have improved their performance on benchmarks like MIRACL and BEIR by increasing their parameter counts. However, this scaling approach introduces significant deployment challenges, including increased inference latency and memory usage. These challenges are particularly severe in retrieval-augmented generation (RAG) applications, where large models' increased memory requirements constrain dataset ingestion capacity, and their higher latency directly impacts query-time performance. While causal language models have addressed similar efficiency challenges using Mixture of Experts (MoE) architectures, this approach hasn't been successfully adapted to the general text embedding setting. In this paper, we introduce Nomic Embed v2, the first general purpose MoE text embedding model. Our model outperforms models in the same parameter class on both monolingual and multilingual benchmarks while also maintaining competitive performance with models twice its size. We open-source all code, models, and evaluation data to ensure full reproducibility of our training pipeline.

This technical report describes the training of nomic-embed-vision, a highly performant, open-code, open-weights image embedding model that shares the same latent space as nomic-embed-text. Together, nomic-embed-vision and nomic-embed-text form the first unified latent space to achieve high performance across vision, language, and multimodal tasks.

This technical report describes the training of nomic-embed-text-v1, the first fully reproducible, open-source, open-weights, open-data, 8192 context length English text embedding model that outperforms both OpenAI Ada-002 and OpenAI text-embedding-3-small on short and long-context tasks. We release the training code and model weights under an Apache 2 license. In contrast with other open-source models, we release a training data loader with 235 million curated text pairs that allows for the full replication of nomic-embed-text-v1. You can find code and data to replicate the model at https://github.com/nomic-ai/contrastors

In this paper, hypernetworks are trained to generate behaviors across a range of unseen task conditions, via a novel TD-based training objective and data from a set of near-optimal RL solutions for training tasks. This work relates to meta RL, contextual RL, and transfer learning, with a particular focus on zero-shot performance at test time, enabled by knowledge of the task parameters (also known as context). Our technical approach is based upon viewing each RL algorithm as a mapping from the MDP specifics to the near-optimal value function and policy and seek to approximate it with a hypernetwork that can generate near-optimal value functions and policies, given the parameters of the MDP. We show that, under certain conditions, this mapping can be considered as a supervised learning problem. We empirically evaluate the effectiveness of our method for zero-shot transfer to new reward and transition dynamics on a series of continuous control tasks from DeepMind Control Suite. Our method demonstrates significant improvements over baselines from multitask and meta RL approaches.

Large language models (LLMs) have recently achieved human-level performance on a range of professional and academic benchmarks. The accessibility of these models has lagged behind their performance. State-of-the-art LLMs require costly infrastructure; are only accessible via rate-limited, geo-locked, and censored web interfaces; and lack publicly available code and technical reports. In this paper, we tell the story of GPT4All, a popular open source repository that aims to democratize access to LLMs. We outline the technical details of the original GPT4All model family, as well as the evolution of the GPT4All project from a single model into a fully fledged open source ecosystem. It is our hope that this paper acts as both a technical overview of the original GPT4All models as well as a case study on the subsequent growth of the GPT4All open source ecosystem.

Leading vision-language models (VLMs) are trained on general Internet content, overlooking scientific journals' rich, domain-specific knowledge. Training on specialty-specific literature could yield high-performance, task-specific tools, enabling generative AI to match generalist models in specialty publishing, educational, and clinical tasks. We created NeuroPubs, a multimodal dataset of 23,000 Neurosurgery Publications articles (134M words, 78K image-caption pairs). Using NeuroPubs, VLMs generated publication-ready graphical abstracts (70% of 100 abstracts) and board-style questions indistinguishable from human-written ones (54% of 89,587 questions). We used these questions to train CNS-Obsidian, a 34B-parameter VLM. In a blinded, randomized controlled trial, our model demonstrated non-inferiority to then state-of-the-art GPT-4o in neurosurgical differential diagnosis (clinical utility, 40.62% upvotes vs. 57.89%, p=0.1150; accuracy, 59.38% vs. 65.79%, p=0.3797). Our pilot study demonstrates how training generative AI models on specialty-specific journal content - without large-scale internet data - results in high-performance academic and clinical tools, enabling domain-tailored AI across diverse fields.

Effective code retrieval plays a crucial role in advancing code generation, bug fixing, and software maintenance, particularly as software systems increase in complexity. While current code embedding models have demonstrated promise in retrieving code snippets for small-scale, well-defined tasks, they often underperform in more demanding real-world applications such as bug localization within GitHub repositories. We hypothesize that a key issue is their reliance on noisy and inconsistent datasets for training, which impedes their ability to generalize to more complex retrieval scenarios. To address these limitations, we introduce CoRNStack, a large-scale, high-quality contrastive training dataset for code that spans multiple programming languages. This dataset is curated using consistency filtering to eliminate noisy positives and is further enriched with mined hard negatives, thereby facilitating more effective learning. We demonstrate that contrastive training of embedding models using CoRNStack leads to state-of-the-art performance across a variety of code retrieval tasks. Furthermore, the dataset can be leveraged for training code reranking models, a largely underexplored area compared to text reranking. Our finetuned code reranking model significantly improves the ranking quality over the retrieved results. Finally, by employing our code retriever and reranker together, we demonstrate significant improvements in function localization for GitHub issues, an important component of real-world software development.

This work explores the capacity of large language models (LLMs) to address problems at the intersection of spatial planning and natural language interfaces for navigation.Our focus is on following relatively complex instructions that are more akin to natural conversation than traditional explicit procedural directives seen in robotics. Unlike most prior work, where navigation directives are provided as imperative commands (e.g., go to the fridge), we examine implicit directives within conversational interactions. We leverage the 3D simulator AI2Thor to create complex and repeatable scenarios at scale, and augment it by adding complex language queries for 40 object types. We demonstrate that a robot can better parse descriptive language queries than existing methods by using an LLM to interpret the user interaction in the context of a list of the objects in the scene.

Contribution from the USQCD Collaboration to the Proceedings of the US Community Study on the Future of Particle Physics (Snowmass 2021).

In this report, we introduce the Gemini 2.X model family: Gemini 2.5 Pro and Gemini 2.5 Flash, as well as our earlier Gemini 2.0 Flash and Flash-Lite models. Gemini 2.5 Pro is our most capable model yet, achieving SoTA performance on frontier coding and reasoning benchmarks. In addition to its incredible coding and reasoning skills, Gemini 2.5 Pro is a thinking model that excels at multimodal understanding and it is now able to process up to 3 hours of video content. Its unique combination of long context, multimodal and reasoning capabilities can be combined to unlock new agentic workflows. Gemini 2.5 Flash provides excellent reasoning abilities at a fraction of the compute and latency requirements and Gemini 2.0 Flash and Flash-Lite provide high performance at low latency and cost. Taken together, the Gemini 2.X model generation spans the full Pareto frontier of model capability vs cost, allowing users to explore the boundaries of what is possible with complex agentic problem solving.

An amplitude analysis of B^-rightarrow D^- D^0 K_S^0 decays is performed using proton-proton collision data, corresponding to an integrated luminosity of 9,fb^{-1}, collected with the LHCb detector at center-of-mass energies of 7, 8, and 13,Tekern -0.1em V. A resonant structure of spin-parity 0^+ is observed in the D^0 K_S^0 invariant-mass spectrum with a significance of 5.3,sigma. The mass and width of the state, modeled with a Breit-Wigner lineshape, are determined to be 2883pm11pm6,Mekern -0.1em V!/c^2 and 87_{-47}^{+22}pm6,Mekern -0.1em V respectively, where the first uncertainties are statistical and the second systematic. These properties and the quark content are consistent with those of the open-charm tetraquark state T_{cs 0}^{*}(2870)^0 observed previously in the D^+ K^- final state of the B^-rightarrow D^- D^+ K^- decay. This result confirms the existence of the T_{cs 0}^{*}(2870)^0 state in a new decay mode. The T_{cs1}^{*}(2900)^0 state, reported in the B^-rightarrow D^- D^+ K^- decay, is also searched for in the D^0 K_S^0 invariant-mass spectrum of the B^- rightarrow D^- D^0 K_S^0 decay, without finding evidence for it.

Document Visual Question Answering (Document VQA) must cope with documents that span dozens of pages, yet leading systems still concatenate every page or rely on very large vision-language models, both of which are memory-hungry. Retrieval-Augmented Generation (RAG) offers an attractive alternative, first retrieving a concise set of relevant segments before generating answers from this selected evidence. In this paper, we systematically evaluate the impact of incorporating RAG into Document VQA through different retrieval variants - text-based retrieval using OCR tokens and purely visual retrieval without OCR - across multiple models and benchmarks. Evaluated on the multi-page datasets MP-DocVQA, DUDE, and InfographicVQA, the text-centric variant improves the "concatenate-all-pages" baseline by up to +22.5 ANLS, while the visual variant achieves +5.0 ANLS improvement without requiring any text extraction. An ablation confirms that retrieval and reranking components drive most of the gain, whereas the layout-guided chunking strategy - proposed in several recent works to leverage page structure - fails to help on these datasets. Our experiments demonstrate that careful evidence selection consistently boosts accuracy across multiple model sizes and multi-page benchmarks, underscoring its practical value for real-world Document VQA.

Question answering over visually rich documents (VRDs) requires reasoning not only over isolated content but also over documents' structural organization and cross-page dependencies. However, conventional retrieval-augmented generation (RAG) methods encode content in isolated chunks during ingestion, losing structural and cross-page dependencies, and retrieve a fixed number of pages at inference, regardless of the specific demands of the question or context. This often results in incomplete evidence retrieval and degraded answer quality for multi-page reasoning tasks. To address these limitations, we propose LAD-RAG, a novel Layout-Aware Dynamic RAG framework. During ingestion, LAD-RAG constructs a symbolic document graph that captures layout structure and cross-page dependencies, adding it alongside standard neural embeddings to yield a more holistic representation of the document. During inference, an LLM agent dynamically interacts with the neural and symbolic indices to adaptively retrieve the necessary evidence based on the query. Experiments on MMLongBench-Doc, LongDocURL, DUDE, and MP-DocVQA demonstrate that LAD-RAG improves retrieval, achieving over 90% perfect recall on average without any top-k tuning, and outperforming baseline retrievers by up to 20% in recall at comparable noise levels, yielding higher QA accuracy with minimal latency.

Vision-Language Models (VLMs) excel in diverse visual tasks but face challenges in document understanding, which requires fine-grained text processing. While typical visual tasks perform well with low-resolution inputs, reading-intensive applications demand high-resolution, resulting in significant computational overhead. Using OCR-extracted text in VLM prompts partially addresses this issue but underperforms compared to full-resolution counterpart, as it lacks the complete visual context needed for optimal performance. We introduce DocVLM, a method that integrates an OCR-based modality into VLMs to enhance document processing while preserving original weights. Our approach employs an OCR encoder to capture textual content and layout, compressing these into a compact set of learned queries incorporated into the VLM. Comprehensive evaluations across leading VLMs show that DocVLM significantly reduces reliance on high-resolution images for document understanding. In limited-token regimes (448times448), DocVLM with 64 learned queries improves DocVQA results from 56.0% to 86.6% when integrated with InternVL2 and from 84.4% to 91.2% with Qwen2-VL. In LLaVA-OneVision, DocVLM achieves improved results while using 80% less image tokens. The reduced token usage allows processing multiple pages effectively, showing impressive zero-shot results on DUDE and state-of-the-art performance on MP-DocVQA, highlighting DocVLM's potential for applications requiring high-performance and efficiency.