Daily Papers

Despite long-standing efforts in accelerating scientific discovery with AI, building AI co-scientists remains challenging due to limited high-quality data for training and evaluation. To tackle this data scarcity issue, we present AutoSDT, an automatic pipeline that collects high-quality coding tasks in real-world data-driven discovery workflows. AutoSDT leverages the coding capabilities and parametric knowledge of LLMs to search for diverse sources, select ecologically valid tasks, and synthesize accurate task instructions and code solutions. Using our pipeline, we construct AutoSDT-5K, a dataset of 5,404 coding tasks for data-driven discovery that covers four scientific disciplines and 756 unique Python packages. To the best of our knowledge, AutoSDT-5K is the only automatically collected and the largest open dataset for data-driven scientific discovery. Expert feedback on a subset of 256 tasks shows the effectiveness of AutoSDT: 93% of the collected tasks are ecologically valid, and 92.2% of the synthesized programs are functionally correct. Trained on AutoSDT-5K, the Qwen2.5-Coder-Instruct LLM series, dubbed AutoSDT-Coder, show substantial improvement on two challenging data-driven discovery benchmarks, ScienceAgentBench and DiscoveryBench. Most notably, AutoSDT-Coder-32B reaches the same level of performance as GPT-4o on ScienceAgentBench with a success rate of 7.8%, doubling the performance of its base model. On DiscoveryBench, it lifts the hypothesis matching score to 8.1, bringing a 17.4% relative improvement and closing the gap between open-weight models and GPT-4o.

Inferring causal structures from experimentation is a central task in many domains. For example, in biology, recent advances allow us to obtain single-cell expression data under multiple interventions such as drugs or gene knockouts. However, the targets of the interventions are often uncertain or unknown and the number of observations limited. As a result, standard causal discovery methods can no longer be reliably used. To fill this gap, we propose a Bayesian framework (BaCaDI) for discovering and reasoning about the causal structure that underlies data generated under various unknown experimental or interventional conditions. BaCaDI is fully differentiable, which allows us to infer the complex joint posterior over the intervention targets and the causal structure via efficient gradient-based variational inference. In experiments on synthetic causal discovery tasks and simulated gene-expression data, BaCaDI outperforms related methods in identifying causal structures and intervention targets.

The advancements of language language models (LLMs) have piqued growing interest in developing LLM-based language agents to automate scientific discovery end-to-end, which has sparked both excitement and skepticism about the true capabilities of such agents. In this work, we argue that for an agent to fully automate scientific discovery, it must be able to complete all essential tasks in the workflow. Thus, we call for rigorous assessment of agents on individual tasks in a scientific workflow before making bold claims on end-to-end automation. To this end, we present ScienceAgentBench, a new benchmark for evaluating language agents for data-driven scientific discovery. To ensure the scientific authenticity and real-world relevance of our benchmark, we extract 102 tasks from 44 peer-reviewed publications in four disciplines and engage nine subject matter experts to validate them. We unify the target output for every task to a self-contained Python program file and employ an array of evaluation metrics to examine the generated programs, execution results, and costs. Each task goes through multiple rounds of manual validation by annotators and subject matter experts to ensure its annotation quality and scientific plausibility. We also propose two effective strategies to mitigate data contamination concerns. Using our benchmark, we evaluate five open-weight and proprietary LLMs, each with three frameworks: direct prompting, OpenHands, and self-debug. Given three attempts for each task, the best-performing agent can only solve 32.4% of the tasks independently and 34.3% with expert-provided knowledge. These results underscore the limited capacities of current language agents in generating code for data-driven discovery, let alone end-to-end automation for scientific research.

Can the rapid advances in code generation, function calling, and data analysis using large language models (LLMs) help automate the search and verification of hypotheses purely from a set of provided datasets? To evaluate this question, we present DiscoveryBench, the first comprehensive benchmark that formalizes the multi-step process of data-driven discovery. The benchmark is designed to systematically assess current model capabilities in discovery tasks and provide a useful resource for improving them. Our benchmark contains 264 tasks collected across 6 diverse domains, such as sociology and engineering, by manually deriving discovery workflows from published papers to approximate the real-world challenges faced by researchers, where each task is defined by a dataset, its metadata, and a discovery goal in natural language. We additionally provide 903 synthetic tasks to conduct controlled evaluations across task complexity. Furthermore, our structured formalism of data-driven discovery enables a facet-based evaluation that provides useful insights into different failure modes. We evaluate several popular LLM-based reasoning frameworks using both open and closed LLMs as baselines on DiscoveryBench and find that even the best system scores only 25%. Our benchmark, thus, illustrates the challenges in autonomous data-driven discovery and serves as a valuable resource for the community to make progress.

Differential privacy is a widely adopted framework designed to safeguard the sensitive information of data providers within a data set. It is based on the application of controlled noise at the interface between the server that stores and processes the data, and the data consumers. Local differential privacy is a variant that allows data providers to apply the privatization mechanism themselves on their data individually. Therefore it provides protection also in contexts in which the server, or even the data collector, cannot be trusted. The introduction of noise, however, inevitably affects the utility of the data, particularly by distorting the correlations between individual data components. This distortion can prove detrimental to tasks such as causal discovery. In this paper, we consider various well-known locally differentially private mechanisms and compare the trade-off between the privacy they provide, and the accuracy of the causal structure produced by algorithms for causal learning when applied to data obfuscated by these mechanisms. Our analysis yields valuable insights for selecting appropriate local differentially private protocols for causal discovery tasks. We foresee that our findings will aid researchers and practitioners in conducting locally private causal discovery.

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.

Recent progress in Large Language Models (LLMs) has drawn attention to their potential for accelerating drug discovery. However, a central problem remains: translating theoretical ideas into robust implementations in the highly specialized context of pharmaceutical research. This limitation prevents practitioners from making full use of the latest AI developments in drug discovery. To address this challenge, we introduce DrugAgent, a multi-agent framework that automates machine learning (ML) programming for drug discovery tasks. DrugAgent employs an LLM Planner that formulates high-level ideas and an LLM Instructor that identifies and integrates domain knowledge when implementing those ideas. We present case studies on three representative drug discovery tasks. Our results show that DrugAgent consistently outperforms leading baselines, including a relative improvement of 4.92% in ROC-AUC compared to ReAct for drug-target interaction (DTI). DrugAgent is publicly available at https://anonymous.4open.science/r/drugagent-5C42/.

Concerns about hallucinations in Large Language Models (LLMs) have been raised by researchers, yet their potential in areas where creativity is vital, such as drug discovery, merits exploration. In this paper, we come up with the hypothesis that hallucinations can improve LLMs in drug discovery. To verify this hypothesis, we use LLMs to describe the SMILES string of molecules in natural language and then incorporate these descriptions as part of the prompt to address specific tasks in drug discovery. Evaluated on seven LLMs and five classification tasks, our findings confirm the hypothesis: LLMs can achieve better performance with text containing hallucinations. Notably, Llama-3.1-8B achieves an 18.35% gain in ROC-AUC compared to the baseline without hallucination. Furthermore, hallucinations generated by GPT-4o provide the most consistent improvements across models. Additionally, we conduct empirical analyses and a case study to investigate key factors affecting performance and the underlying reasons. Our research sheds light on the potential use of hallucinations for LLMs and offers new perspectives for future research leveraging LLMs in drug discovery.

We propose a novel framework that leverages LLMs for full causal graph discovery. While previous LLM-based methods have used a pairwise query approach, this requires a quadratic number of queries which quickly becomes impractical for larger causal graphs. In contrast, the proposed framework uses a breadth-first search (BFS) approach which allows it to use only a linear number of queries. We also show that the proposed method can easily incorporate observational data when available, to improve performance. In addition to being more time and data-efficient, the proposed framework achieves state-of-the-art results on real-world causal graphs of varying sizes. The results demonstrate the effectiveness and efficiency of the proposed method in discovering causal relationships, showcasing its potential for broad applicability in causal graph discovery tasks across different domains.

How can we discover join relationships among columns of tabular data in a data repository? Can this be done effectively when metadata is missing? Traditional column matching works mainly rely on similarity measures based on exact value overlaps, hence missing important semantics or failing to handle noise in the data. At the same time, recent dataset discovery methods focusing on deep table representation learning techniques, do not take into consideration the rich set of column similarity signals found in prior matching and discovery methods. Finally, existing methods heavily depend on user-provided similarity thresholds, hindering their deployability in real-world settings. In this paper, we propose OmniMatch, a novel join discovery technique that detects equi-joins and fuzzy-joins betwen columns by combining column-pair similarity measures with Graph Neural Networks (GNNs). OmniMatch's GNN can capture column relatedness leveraging graph transitivity, significantly improving the recall of join discovery tasks. At the same time, OmniMatch also increases the precision by augmenting its training data with negative column join examples through an automated negative example generation process. Most importantly, compared to the state-of-the-art matching and discovery methods, OmniMatch exhibits up to 14% higher effectiveness in F1 score and AUC without relying on metadata or user-provided thresholds for each similarity metric.

Large language models are emerging as powerful tools for scientific law discovery, a foundational challenge in AI-driven science. However, existing benchmarks for this task suffer from a fundamental methodological trilemma, forcing a trade-off between scientific relevance, scalability, and resistance to memorization. Furthermore, they oversimplify discovery as static function fitting, failing to capture the authentic scientific process of uncovering embedded laws through the interactive exploration of complex model systems. To address these critical gaps, we introduce NewtonBench, a benchmark comprising 324 scientific law discovery tasks across 12 physics domains. Our design mitigates the evaluation trilemma by using metaphysical shifts - systematic alterations of canonical laws - to generate a vast suite of problems that are scalable, scientifically relevant, and memorization-resistant. Moreover, we elevate the evaluation from static function fitting to interactive model discovery, requiring agents to experimentally probe simulated complex systems to uncover hidden principles. Our extensive experiment reveals a clear but fragile capability for discovery in frontier LLMs: this ability degrades precipitously with increasing system complexity and exhibits extreme sensitivity to observational noise. Notably, we uncover a paradoxical effect of tool assistance: providing a code interpreter can hinder more capable models by inducing a premature shift from exploration to exploitation, causing them to satisfice on suboptimal solutions. These results demonstrate that robust, generalizable discovery in complex, interactive environments remains the core challenge. By providing a scalable, robust, and scientifically authentic testbed, NewtonBench offers a crucial tool for measuring true progress and guiding the development of next-generation AI agents capable of genuine scientific discovery.

In drug-discovery-related tasks such as virtual screening, machine learning is emerging as a promising way to predict molecular properties. Conventionally, molecular fingerprints (numerical representations of molecules) are calculated through rule-based algorithms that map molecules to a sparse discrete space. However, these algorithms perform poorly for shallow prediction models or small datasets. To address this issue, we present SMILES Transformer. Inspired by Transformer and pre-trained language models from natural language processing, SMILES Transformer learns molecular fingerprints through unsupervised pre-training of the sequence-to-sequence language model using a huge corpus of SMILES, a text representation system for molecules. We performed benchmarks on 10 datasets against existing fingerprints and graph-based methods and demonstrated the superiority of the proposed algorithms in small-data settings where pre-training facilitated good generalization. Moreover, we define a novel metric to concurrently measure model accuracy and data efficiency.

We introduce InVirtuoGen, a discrete flow generative model for fragmented SMILES for de novo and fragment-constrained generation, and target-property/lead optimization of small molecules. The model learns to transform a uniform source over all possible tokens into the data distribution. Unlike masked models, its training loss accounts for predictions on all sequence positions at every denoising step, shifting the generation paradigm from completion to refinement, and decoupling the number of sampling steps from the sequence length. For de novo generation, InVirtuoGen achieves a stronger quality-diversity pareto frontier than prior fragment-based models and competitive performance on fragment-constrained tasks. For property and lead optimization, we propose a hybrid scheme that combines a genetic algorithm with a Proximal Property Optimization fine-tuning strategy adapted to discrete flows. Our approach sets a new state-of-the-art on the Practical Molecular Optimization benchmark, measured by top-10 AUC across tasks, and yields higher docking scores in lead optimization than previous baselines. InVirtuoGen thus establishes a versatile generative foundation for drug discovery, from early hit finding to multi-objective lead optimization. We further contribute to open science by releasing pretrained checkpoints and code, making our results fully reproduciblehttps://github.com/invirtuolabs/InVirtuoGen_results.

Autonomous agents have recently achieved remarkable progress across diverse domains, yet most evaluations focus on short-horizon, fully observable tasks. In contrast, many critical real-world tasks, such as large-scale software development, commercial investment, and scientific discovery, unfold in long-horizon and partially observable scenarios where success hinges on sustained reasoning, planning, memory management, and tool use. Existing benchmarks rarely capture these long-horizon challenges, leaving a gap in systematic evaluation. To bridge this gap, we introduce UltraHorizon a novel benchmark that measures the foundational capabilities essential for complex real-world challenges. We use exploration as a unifying task across three distinct environments to validate these core competencies. Agents are designed in long-horizon discovery tasks where they must iteratively uncover hidden rules through sustained reasoning, planning, memory and tools management, and interaction with environments. Under the heaviest scale setting, trajectories average 200k+ tokens and 400+ tool calls, whereas in standard configurations they still exceed 35k tokens and involve more than 60 tool calls on average. Our extensive experiments reveal that LLM-agents consistently underperform in these settings, whereas human participants achieve higher scores, underscoring a persistent gap in agents' long-horizon abilities. We also observe that simple scaling fails in our task. To better illustrate the failure of agents, we conduct an in-depth analysis of collected trajectories. We identify eight types of errors and attribute them to two primary causes: in-context locking and functional fundamental capability gaps. https://github.com/StarDewXXX/UltraHorizon{Our code will be available here.}

sec:abstract Large Language Models (LLMs) have shown promise in assisting scientific discovery. However, such applications are currently limited by LLMs' deficiencies in understanding intricate scientific concepts, deriving symbolic equations, and solving advanced numerical calculations. To bridge these gaps, we introduce SciGLM, a suite of scientific language models able to conduct college-level scientific reasoning. Central to our approach is a novel self-reflective instruction annotation framework to address the data scarcity challenge in the science domain. This framework leverages existing LLMs to generate step-by-step reasoning for unlabelled scientific questions, followed by a process of self-reflective critic-and-revise. Applying this framework, we curated SciInstruct, a diverse and high-quality dataset encompassing mathematics, physics, chemistry, and formal proofs. We fine-tuned the ChatGLM family of language models with SciInstruct, enhancing their capabilities in scientific and mathematical reasoning. Remarkably, SciGLM consistently improves both the base model (ChatGLM3-6B-Base) and larger-scale models (12B and 32B), without sacrificing the language understanding capabilities of the base model. This makes SciGLM a suitable foundational model to facilitate diverse scientific discovery tasks. For the benefit of the wider research community, we release SciInstruct, SciGLM, alongside a self-reflective framework and fine-tuning code at https://github.com/THUDM/SciGLM.

Large language models (LLMs) have recently demonstrated promising capabilities in chemistry tasks while still facing challenges due to outdated pretraining knowledge and the difficulty of incorporating specialized chemical expertise. To address these issues, we propose an LLM-based agent that synergistically integrates 137 external chemical tools created ranging from basic information retrieval to complex reaction predictions, and a dataset curation pipeline to generate the dataset ChemToolBench that facilitates both effective tool selection and precise parameter filling during fine-tuning and evaluation. We introduce a Hierarchical Evolutionary Monte Carlo Tree Search (HE-MCTS) framework, enabling independent optimization of tool planning and execution. By leveraging self-generated data, our approach supports step-level fine-tuning (FT) of the policy model and training task-adaptive PRM and ORM that surpass GPT-4o. Experimental evaluations demonstrate that our approach significantly improves performance in Chemistry QA and discovery tasks, offering a robust solution to integrate specialized tools with LLMs for advanced chemical applications. All datasets and code are available at https://github.com/AI4Chem/ChemistryAgent .

Generative Flow Networks (GFlowNets) are amortized samplers that learn stochastic policies to sequentially generate compositional objects from a given unnormalized reward distribution. They can generate diverse sets of high-reward objects, which is an important consideration in scientific discovery tasks. However, as they are typically trained from a given extrinsic reward function, it remains an important open challenge about how to leverage the power of pre-training and train GFlowNets in an unsupervised fashion for efficient adaptation to downstream tasks. Inspired by recent successes of unsupervised pre-training in various domains, we introduce a novel approach for reward-free pre-training of GFlowNets. By framing the training as a self-supervised problem, we propose an outcome-conditioned GFlowNet (OC-GFN) that learns to explore the candidate space. Specifically, OC-GFN learns to reach any targeted outcomes, akin to goal-conditioned policies in reinforcement learning. We show that the pre-trained OC-GFN model can allow for a direct extraction of a policy capable of sampling from any new reward functions in downstream tasks. Nonetheless, adapting OC-GFN on a downstream task-specific reward involves an intractable marginalization over possible outcomes. We propose a novel way to approximate this marginalization by learning an amortized predictor enabling efficient fine-tuning. Extensive experimental results validate the efficacy of our approach, demonstrating the effectiveness of pre-training the OC-GFN, and its ability to swiftly adapt to downstream tasks and discover modes more efficiently. This work may serve as a foundation for further exploration of pre-training strategies in the context of GFlowNets.

Developing therapeutics is a lengthy and expensive process that requires the satisfaction of many different criteria, and AI models capable of expediting the process would be invaluable. However, the majority of current AI approaches address only a narrowly defined set of tasks, often circumscribed within a particular domain. To bridge this gap, we introduce Tx-LLM, a generalist large language model (LLM) fine-tuned from PaLM-2 which encodes knowledge about diverse therapeutic modalities. Tx-LLM is trained using a collection of 709 datasets that target 66 tasks spanning various stages of the drug discovery pipeline. Using a single set of weights, Tx-LLM simultaneously processes a wide variety of chemical or biological entities(small molecules, proteins, nucleic acids, cell lines, diseases) interleaved with free-text, allowing it to predict a broad range of associated properties, achieving competitive with state-of-the-art (SOTA) performance on 43 out of 66 tasks and exceeding SOTA on 22. Among these, Tx-LLM is particularly powerful and exceeds best-in-class performance on average for tasks combining molecular SMILES representations with text such as cell line names or disease names, likely due to context learned during pretraining. We observe evidence of positive transfer between tasks with diverse drug types (e.g.,tasks involving small molecules and tasks involving proteins), and we study the impact of model size, domain finetuning, and prompting strategies on performance. We believe Tx-LLM represents an important step towards LLMs encoding biochemical knowledge and could have a future role as an end-to-end tool across the drug discovery development pipeline.

As the issue of global climate change becomes increasingly severe, the demand for research in climate science continues to grow. Natural language processing technologies, represented by Large Language Models (LLMs), have been widely applied to climate change-specific research, providing essential information support for decision-makers and the public. Some studies have improved model performance on relevant tasks by constructing climate change-related instruction data and instruction-tuning LLMs. However, current research remains inadequate in efficiently producing large volumes of high-precision instruction data for climate change, which limits further development of climate change LLMs. This study introduces an automated method for constructing instruction data. The method generates instructions using facts and background knowledge from documents and enhances the diversity of the instruction data through web scraping and the collection of seed instructions. Using this method, we constructed a climate change instruction dataset, named ClimateChat-Corpus, which was used to fine-tune open-source LLMs, resulting in an LLM named ClimateChat. Evaluation results show that ClimateChat significantly improves performance on climate change question-and-answer tasks. Additionally, we evaluated the impact of different base models and instruction data on LLM performance and demonstrated its capability to adapt to a wide range of climate change scientific discovery tasks, emphasizing the importance of selecting an appropriate base model for instruction tuning. This research provides valuable references and empirical support for constructing climate change instruction data and training climate change-specific LLMs.

Drug discovery typically consists of multiple steps, including identifying a target protein key to a disease's etiology, validating that interacting with this target could prevent symptoms or cure the disease, discovering a small molecule or biologic therapeutic to interact with it, and optimizing the candidate molecule through a complex landscape of required properties. Drug discovery related tasks often involve prediction and generation while considering multiple entities that potentially interact, which poses a challenge for typical AI models. For this purpose we present MAMMAL - Molecular Aligned Multi-Modal Architecture and Language - a method that we applied to create a versatile multi-task foundation model ibm/biomed.omics.bl.sm.ma-ted-458m that learns from large-scale biological datasets (2 billion samples) across diverse modalities, including proteins, small molecules, and genes. We introduce a prompt syntax that supports a wide range of classification, regression, and generation tasks. It allows combining different modalities and entity types as inputs and/or outputs. Our model handles combinations of tokens and scalars and enables the generation of small molecules and proteins, property prediction, and transcriptomic lab test predictions. We evaluated the model on 11 diverse downstream tasks spanning different steps within a typical drug discovery pipeline, where it reaches new SOTA in 9 tasks and is comparable to SOTA in 2 tasks. This performance is achieved while using a unified architecture serving all tasks, in contrast to the original SOTA performance achieved using tailored architectures. The model code and pretrained weights are publicly available at https://github.com/BiomedSciAI/biomed-multi-alignment and https://huggingface.co/ibm/biomed.omics.bl.sm.ma-ted-458m.

Discovering scaling laws for predicting model performance at scale is a fundamental and open-ended challenge, mostly reliant on slow, case specific human experimentation. To investigate the potential for LLMs to automate this process, we collect over 5,000 experiments from existing literature and curate seven diverse scaling law discovery tasks. While existing agents struggle to produce accurate law formulas, this paper introduces SLDAgent, an evolution-based agent that co-optimize the scaling law model and the parameters, enabling it to autonomously explore complex relationships between variables. For the first time, we demonstrates that SLDAgent can automatically discover laws that exhibit consistently more accurate extrapolation than their established, human-derived counterparts across all tasks. Through comprehensive analysis, we elucidate why these discovered laws are superior and verify their practical utility in both pretraining and finetuning applications. This work establishes a new paradigm for agentic scientific discovery, showing that AI systems can understand their own scaling behavior, and can contribute novel and practical knowledge back to the research community.

We present a simple self-supervised method to enhance the performance of ViT features for dense downstream tasks. Our Lightweight Feature Transform (LiFT) is a straightforward and compact postprocessing network that can be applied to enhance the features of any pre-trained ViT backbone. LiFT is fast and easy to train with a self-supervised objective, and it boosts the density of ViT features for minimal extra inference cost. Furthermore, we demonstrate that LiFT can be applied with approaches that use additional task-specific downstream modules, as we integrate LiFT with ViTDet for COCO detection and segmentation. Despite the simplicity of LiFT, we find that it is not simply learning a more complex version of bilinear interpolation. Instead, our LiFT training protocol leads to several desirable emergent properties that benefit ViT features in dense downstream tasks. This includes greater scale invariance for features, and better object boundary maps. By simply training LiFT for a few epochs, we show improved performance on keypoint correspondence, detection, segmentation, and object discovery tasks. Overall, LiFT provides an easy way to unlock the benefits of denser feature arrays for a fraction of the computational cost. For more details, refer to our project page at https://www.cs.umd.edu/~sakshams/LiFT/.

We present a comprehensive system for addressing Tasks A, B, and C of the LLMs4OL 2025 challenge, which together span the full ontology construction pipeline: term extraction, typing, and taxonomy discovery. Our approach combines retrieval-augmented prompting, zero-shot classification, and attention-based graph modeling -- each tailored to the demands of the respective task. For Task A, we jointly extract domain-specific terms and their ontological types using a retrieval-augmented generation (RAG) pipeline. Training data was reformulated into a document to terms and types correspondence, while test-time inference leverages semantically similar training examples. This single-pass method requires no model finetuning and improves overall performance through lexical augmentation Task B, which involves assigning types to given terms, is handled via a dual strategy. In the few-shot setting (for domains with labeled training data), we reuse the RAG scheme with few-shot prompting. In the zero-shot setting (for previously unseen domains), we use a zero-shot classifier that combines cosine similarity scores from multiple embedding models using confidence-based weighting. In Task C, we model taxonomy discovery as graph inference. Using embeddings of type labels, we train a lightweight cross-attention layer to predict is-a relations by approximating a soft adjacency matrix. These modular, task-specific solutions enabled us to achieve top-ranking results in the official leaderboard across all three tasks. Taken together these strategies showcase the scalability, adaptability, and robustness of LLM-based architectures for ontology learning across heterogeneous domains. Code is available at: https://github.com/BelyaevaAlex/LLMs4OL-Challenge-Alexbek

Crystal structure generation is a foundational challenge in materials discovery, particularly in designing functional inorganic crystalline materials with desired properties. Most existing diffusion-based generative models for crystals rely on complex, hand-crafted priors and modular architectures to separately model atom types, atomic positions, and lattice parameters. These methods often require customized diffusion processes and conditional denoising, which can introduce additional model complexities and inconsistencies. Here we introduce DiffCrysGen, a fully data-driven, score-based diffusion model that jointly learns the distribution of all structural components in crystalline materials. With crystal structure representation as unified 2D matrices, DiffCrysGen bypasses the need for task-specific priors or decoupled modules, enabling end-to-end generation of atom types, fractional coordinates, and lattice parameters within a single framework. Our model learns crystallographic symmetry and chemical validity directly from large-scale datasets, allowing it to scale to complex materials discovery tasks. As a demonstration, we applied DiffCrysGen to the design of rare-earth-free magnetic materials with high saturation magnetization, showing its effectiveness in generating stable, diverse, and property-aligned candidates for sustainable magnet applications.

The introduction of genome engineering technology has transformed biomedical research, making it possible to make precise changes to genetic information. However, creating an efficient gene-editing system requires a deep understanding of CRISPR technology, and the complex experimental systems under investigation. While Large Language Models (LLMs) have shown promise in various tasks, they often lack specific knowledge and struggle to accurately solve biological design problems. In this work, we introduce CRISPR-GPT, an LLM agent augmented with domain knowledge and external tools to automate and enhance the design process of CRISPR-based gene-editing experiments. CRISPR-GPT leverages the reasoning ability of LLMs to facilitate the process of selecting CRISPR systems, designing guide RNAs, recommending cellular delivery methods, drafting protocols, and designing validation experiments to confirm editing outcomes. We showcase the potential of CRISPR-GPT for assisting non-expert researchers with gene-editing experiments from scratch and validate the agent's effectiveness in a real-world use case. Furthermore, we explore the ethical and regulatory considerations associated with automated gene-editing design, highlighting the need for responsible and transparent use of these tools. Our work aims to bridge the gap between beginner biological researchers and CRISPR genome engineering techniques, and demonstrate the potential of LLM agents in facilitating complex biological discovery tasks.

The rapid evolution of artificial intelligence in drug discovery encounters challenges with generalization and extensive training, yet Large Language Models (LLMs) offer promise in reshaping interactions with complex molecular data. Our novel contribution, InstructMol, a multi-modal LLM, effectively aligns molecular structures with natural language via an instruction-tuning approach, utilizing a two-stage training strategy that adeptly combines limited domain-specific data with molecular and textual information. InstructMol showcases substantial performance improvements in drug discovery-related molecular tasks, surpassing leading LLMs and significantly reducing the gap with specialized models, thereby establishing a robust foundation for a versatile and dependable drug discovery assistant.

With the growing prominence of the Mixture of Experts (MoE) architecture in developing large-scale foundation models, we investigate the Hierarchical Mixture of Experts (HMoE), a specialized variant of MoE that excels in handling complex inputs and improving performance on targeted tasks. Our analysis highlights the advantages of using the Laplace gating function over the traditional Softmax gating within the HMoE frameworks. We theoretically demonstrate that applying the Laplace gating function at both levels of the HMoE model helps eliminate undesirable parameter interactions caused by the Softmax gating and, therefore, accelerates the expert convergence as well as enhances the expert specialization. Empirical validation across diverse scenarios supports these theoretical claims. This includes large-scale multimodal tasks, image classification, and latent domain discovery and prediction tasks, where our modified HMoE models show great performance improvements compared to the conventional HMoE models.

Foundation models (FMs), such as GPT-4 and AlphaFold, are reshaping the landscape of scientific research. Beyond accelerating tasks such as hypothesis generation, experimental design, and result interpretation, they prompt a more fundamental question: Are FMs merely enhancing existing scientific methodologies, or are they redefining the way science is conducted? In this paper, we argue that FMs are catalyzing a transition toward a new scientific paradigm. We introduce a three-stage framework to describe this evolution: (1) Meta-Scientific Integration, where FMs enhance workflows within traditional paradigms; (2) Hybrid Human-AI Co-Creation, where FMs become active collaborators in problem formulation, reasoning, and discovery; and (3) Autonomous Scientific Discovery, where FMs operate as independent agents capable of generating new scientific knowledge with minimal human intervention. Through this lens, we review current applications and emerging capabilities of FMs across existing scientific paradigms. We further identify risks and future directions for FM-enabled scientific discovery. This position paper aims to support the scientific community in understanding the transformative role of FMs and to foster reflection on the future of scientific discovery. Our project is available at https://github.com/usail-hkust/Awesome-Foundation-Models-for-Scientific-Discovery.

The tasks of out-of-domain (OOD) intent discovery and generalized intent discovery (GID) aim to extend a closed intent classifier to open-world intent sets, which is crucial to task-oriented dialogue (TOD) systems. Previous methods address them by fine-tuning discriminative models. Recently, although some studies have been exploring the application of large language models (LLMs) represented by ChatGPT to various downstream tasks, it is still unclear for the ability of ChatGPT to discover and incrementally extent OOD intents. In this paper, we comprehensively evaluate ChatGPT on OOD intent discovery and GID, and then outline the strengths and weaknesses of ChatGPT. Overall, ChatGPT exhibits consistent advantages under zero-shot settings, but is still at a disadvantage compared to fine-tuned models. More deeply, through a series of analytical experiments, we summarize and discuss the challenges faced by LLMs including clustering, domain-specific understanding, and cross-domain in-context learning scenarios. Finally, we provide empirical guidance for future directions to address these challenges.

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.

Materials synthesis is vital for innovations such as energy storage, catalysis, electronics, and biomedical devices. Yet, the process relies heavily on empirical, trial-and-error methods guided by expert intuition. Our work aims to support the materials science community by providing a practical, data-driven resource. We have curated a comprehensive dataset of 17K expert-verified synthesis recipes from open-access literature, which forms the basis of our newly developed benchmark, AlchemyBench. AlchemyBench offers an end-to-end framework that supports research in large language models applied to synthesis prediction. It encompasses key tasks, including raw materials and equipment prediction, synthesis procedure generation, and characterization outcome forecasting. We propose an LLM-as-a-Judge framework that leverages large language models for automated evaluation, demonstrating strong statistical agreement with expert assessments. Overall, our contributions offer a supportive foundation for exploring the capabilities of LLMs in predicting and guiding materials synthesis, ultimately paving the way for more efficient experimental design and accelerated innovation in materials science.

Scripting interfaces enable users to automate tasks and customize software workflows, but creating scripts traditionally requires programming expertise and familiarity with specific APIs, posing barriers for many users. While Large Language Models (LLMs) can generate code from natural language queries, runtime code generation is severely limited due to unverified code, security risks, longer response times, and higher computational costs. To bridge the gap, we propose an offline simulation framework to curate a software-specific skillset, a collection of verified scripts, by exploiting LLMs and publicly available scripting guides. Our framework comprises two components: (1) task creation, using top-down functionality guidance and bottom-up API synergy exploration to generate helpful tasks; and (2) skill generation with trials, refining and validating scripts based on execution feedback. To efficiently navigate the extensive API landscape, we introduce a Graph Neural Network (GNN)-based link prediction model to capture API synergy, enabling the generation of skills involving underutilized APIs and expanding the skillset's diversity. Experiments with Adobe Illustrator demonstrate that our framework significantly improves automation success rates, reduces response time, and saves runtime token costs compared to traditional runtime code generation. This is the first attempt to use software scripting interfaces as a testbed for LLM-based systems, highlighting the advantages of leveraging execution feedback in a controlled environment and offering valuable insights into aligning AI capabilities with user needs in specialized software domains.

Discovering efficient algorithms for solving complex problems has been an outstanding challenge in mathematics and computer science, requiring substantial human expertise over the years. Recent advancements in evolutionary search with large language models (LLMs) have shown promise in accelerating the discovery of algorithms across various domains, particularly in mathematics and optimization. However, existing approaches treat the LLM as a static generator, missing the opportunity to update the model with the signal obtained from evolutionary exploration. In this work, we propose to augment LLM-based evolutionary search by continuously refining the search operator - the LLM - through reinforcement learning (RL) fine-tuning. Our method leverages evolutionary search as an exploration strategy to discover improved algorithms, while RL optimizes the LLM policy based on these discoveries. Our experiments on three combinatorial optimization tasks - bin packing, traveling salesman, and the flatpack problem - show that combining RL and evolutionary search improves discovery efficiency of improved algorithms, showcasing the potential of RL-enhanced evolutionary strategies to assist computer scientists and mathematicians for more efficient algorithm design.

We present a method to formulate algorithm discovery as program search, and apply it to discover optimization algorithms for deep neural network training. We leverage efficient search techniques to explore an infinite and sparse program space. To bridge the large generalization gap between proxy and target tasks, we also introduce program selection and simplification strategies. Our method discovers a simple and effective optimization algorithm, Lion (Evo\textbf{Lved Sign Momentum}). It is more memory-efficient than Adam as it only keeps track of the momentum. Different from adaptive optimizers, its update has the same magnitude for each parameter calculated through the sign operation. We compare Lion with widely used optimizers, such as Adam and Adafactor, for training a variety of models on different tasks. On image classification, Lion boosts the accuracy of ViT by up to 2% on ImageNet and saves up to 5x the pre-training compute on JFT. On vision-language contrastive learning, we achieve 88.3% zero-shot and 91.1% fine-tuning accuracy on ImageNet, surpassing the previous best results by 2% and 0.1%, respectively. On diffusion models, Lion outperforms Adam by achieving a better FID score and reducing the training compute by up to 2.3x. For autoregressive, masked language modeling, and fine-tuning, Lion exhibits a similar or better performance compared to Adam. Our analysis of Lion reveals that its performance gain grows with the training batch size. It also requires a smaller learning rate than Adam due to the larger norm of the update produced by the sign function. Additionally, we examine the limitations of Lion and identify scenarios where its improvements are small or not statistically significant. The implementation of Lion is publicly available.

Deep generative models (DGMs) have been widely developed for graph data. However, much less investigation has been carried out on understanding the latent space of such pretrained graph DGMs. These understandings possess the potential to provide constructive guidelines for crucial tasks, such as graph controllable generation. Thus in this work, we are interested in studying this problem and propose GraphCG, a method for the unsupervised discovery of steerable factors in the latent space of pretrained graph DGMs. We first examine the representation space of three pretrained graph DGMs with six disentanglement metrics, and we observe that the pretrained representation space is entangled. Motivated by this observation, GraphCG learns the steerable factors via maximizing the mutual information between semantic-rich directions, where the controlled graph moving along the same direction will share the same steerable factors. We quantitatively verify that GraphCG outperforms four competitive baselines on two graph DGMs pretrained on two molecule datasets. Additionally, we qualitatively illustrate seven steerable factors learned by GraphCG on five pretrained DGMs over five graph datasets, including two for molecules and three for point clouds.

Visual similarities discovery (VSD) is an important task with broad e-commerce applications. Given an image of a certain object, the goal of VSD is to retrieve images of different objects with high perceptual visual similarity. Although being a highly addressed problem, the evaluation of proposed methods for VSD is often based on a proxy of an identification-retrieval task, evaluating the ability of a model to retrieve different images of the same object. We posit that evaluating VSD methods based on identification tasks is limited, and faithful evaluation must rely on expert annotations. In this paper, we introduce the first large-scale fashion visual similarity benchmark dataset, consisting of more than 110K expert-annotated image pairs. Besides this major contribution, we share insight from the challenges we faced while curating this dataset. Based on these insights, we propose a novel and efficient labeling procedure that can be applied to any dataset. Our analysis examines its limitations and inductive biases, and based on these findings, we propose metrics to mitigate those limitations. Though our primary focus lies on visual similarity, the methodologies we present have broader applications for discovering and evaluating perceptual similarity across various domains.

We tackle real-world long-horizon robot manipulation tasks through skill discovery. We present a bottom-up approach to learning a library of reusable skills from unsegmented demonstrations and use these skills to synthesize prolonged robot behaviors. Our method starts with constructing a hierarchical task structure from each demonstration through agglomerative clustering. From the task structures of multi-task demonstrations, we identify skills based on the recurring patterns and train goal-conditioned sensorimotor policies with hierarchical imitation learning. Finally, we train a meta controller to compose these skills to solve long-horizon manipulation tasks. The entire model can be trained on a small set of human demonstrations collected within 30 minutes without further annotations, making it amendable to real-world deployment. We systematically evaluated our method in simulation environments and on a real robot. Our method has shown superior performance over state-of-the-art imitation learning methods in multi-stage manipulation tasks. Furthermore, skills discovered from multi-task demonstrations boost the average task success by 8% compared to those discovered from individual tasks.

In recent years, groundbreaking advancements in natural language processing have culminated in the emergence of powerful large language models (LLMs), which have showcased remarkable capabilities across a vast array of domains, including the understanding, generation, and translation of natural language, and even tasks that extend beyond language processing. In this report, we delve into the performance of LLMs within the context of scientific discovery, focusing on GPT-4, the state-of-the-art language model. Our investigation spans a diverse range of scientific areas encompassing drug discovery, biology, computational chemistry (density functional theory (DFT) and molecular dynamics (MD)), materials design, and partial differential equations (PDE). Evaluating GPT-4 on scientific tasks is crucial for uncovering its potential across various research domains, validating its domain-specific expertise, accelerating scientific progress, optimizing resource allocation, guiding future model development, and fostering interdisciplinary research. Our exploration methodology primarily consists of expert-driven case assessments, which offer qualitative insights into the model's comprehension of intricate scientific concepts and relationships, and occasionally benchmark testing, which quantitatively evaluates the model's capacity to solve well-defined domain-specific problems. Our preliminary exploration indicates that GPT-4 exhibits promising potential for a variety of scientific applications, demonstrating its aptitude for handling complex problem-solving and knowledge integration tasks. Broadly speaking, we evaluate GPT-4's knowledge base, scientific understanding, scientific numerical calculation abilities, and various scientific prediction capabilities.

We present Denario, an AI multi-agent system designed to serve as a scientific research assistant. Denario can perform many different tasks, such as generating ideas, checking the literature, developing research plans, writing and executing code, making plots, and drafting and reviewing a scientific paper. The system has a modular architecture, allowing it to handle specific tasks, such as generating an idea, or carrying out end-to-end scientific analysis using Cmbagent as a deep-research backend. In this work, we describe in detail Denario and its modules, and illustrate its capabilities by presenting multiple AI-generated papers generated by it in many different scientific disciplines such as astrophysics, biology, biophysics, biomedical informatics, chemistry, material science, mathematical physics, medicine, neuroscience and planetary science. Denario also excels at combining ideas from different disciplines, and we illustrate this by showing a paper that applies methods from quantum physics and machine learning to astrophysical data. We report the evaluations performed on these papers by domain experts, who provided both numerical scores and review-like feedback. We then highlight the strengths, weaknesses, and limitations of the current system. Finally, we discuss the ethical implications of AI-driven research and reflect on how such technology relates to the philosophy of science. We publicly release the code at https://github.com/AstroPilot-AI/Denario. A Denario demo can also be run directly on the web at https://huggingface.co/spaces/astropilot-ai/Denario, and the full app will be deployed on the cloud.

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

Due to the usefulness in data enrichment for data analysis tasks, joinable table discovery has become an important operation in data lake management. Existing approaches target equi-joins, the most common way of combining tables for creating a unified view, or semantic joins, which tolerate misspellings and different formats to deliver more join results. They are either exact solutions whose running time is linear in the sizes of query column and target table repository or approximate solutions lacking precision. In this paper, we propose Deepjoin, a deep learning model for accurate and efficient joinable table discovery. Our solution is an embedding-based retrieval, which employs a pre-trained language model (PLM) and is designed as one framework serving both equi- and semantic joins. We propose a set of contextualization options to transform column contents to a text sequence. The PLM reads the sequence and is fine-tuned to embed columns to vectors such that columns are expected to be joinable if they are close to each other in the vector space. Since the output of the PLM is fixed in length, the subsequent search procedure becomes independent of the column size. With a state-of-the-art approximate nearest neighbor search algorithm, the search time is logarithmic in the repository size. To train the model, we devise the techniques for preparing training data as well as data augmentation. The experiments on real datasets demonstrate that by training on a small subset of a corpus, Deepjoin generalizes to large datasets and its precision consistently outperforms other approximate solutions'. Deepjoin is even more accurate than an exact solution to semantic joins when evaluated with labels from experts. Moreover, when equipped with a GPU, Deepjoin is up to two orders of magnitude faster than existing solutions.

We study the intriguing connection between visual data, deep networks, and the brain. Our method creates a universal channel alignment by using brain voxel fMRI response prediction as the training objective. We discover that deep networks, trained with different objectives, share common feature channels across various models. These channels can be clustered into recurring sets, corresponding to distinct brain regions, indicating the formation of visual concepts. Tracing the clusters of channel responses onto the images, we see semantically meaningful object segments emerge, even without any supervised decoder. Furthermore, the universal feature alignment and the clustering of channels produce a picture and quantification of how visual information is processed through the different network layers, which produces precise comparisons between the networks.

We propose a multitask pretraining approach ZeroPrompt for zero-shot generalization, focusing on task scaling and zero-shot prompting. While previous models are trained on only a few dozen tasks, we scale to 1,000 tasks for the first time using real-world data. This leads to a crucial discovery that task scaling can be an efficient alternative to model scaling; i.e., the model size has little impact on performance with an extremely large number of tasks. Our results show that task scaling can substantially improve training efficiency by 30 times in FLOPs. Moreover, we present a prompting method that incorporates a genetic algorithm to automatically search for the best prompt for unseen tasks, along with a few other improvements. Empirically, ZeroPrompt substantially improves both the efficiency and the performance of zero-shot learning across a variety of academic and production datasets.

Activation patching is a standard method in mechanistic interpretability for localizing the components of a model responsible for specific behaviors, but it is computationally expensive to apply at scale. Attribution patching offers a faster, gradient-based approximation, yet suffers from noise and reduced reliability in deep, highly non-linear networks. In this work, we introduce Relevance Patching (RelP), which replaces the local gradients in attribution patching with propagation coefficients derived from Layer-wise Relevance Propagation (LRP). LRP propagates the network's output backward through the layers, redistributing relevance to lower-level components according to local propagation rules that ensure properties such as relevance conservation or improved signal-to-noise ratio. Like attribution patching, RelP requires only two forward passes and one backward pass, maintaining computational efficiency while improving faithfulness. We validate RelP across a range of models and tasks, showing that it more accurately approximates activation patching than standard attribution patching, particularly when analyzing residual stream and MLP outputs in the Indirect Object Identification (IOI) task. For instance, for MLP outputs in GPT-2 Large, attribution patching achieves a Pearson correlation of 0.006, whereas RelP reaches 0.956, highlighting the improvement offered by RelP. Additionally, we compare the faithfulness of sparse feature circuits identified by RelP and Integrated Gradients (IG), showing that RelP achieves comparable faithfulness without the extra computational cost associated with IG.

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

Large language models are typically trained densely: all parameters are updated with respect to all inputs. This requires synchronization of billions of parameters across thousands of GPUs. We introduce a simple but effective method to asynchronously train large, sparse language models on arbitrary text corpora. Our method clusters a corpus into sets of related documents, trains a separate expert language model on each cluster, and combines them in a sparse ensemble for inference. This approach generalizes embarrassingly parallel training by automatically discovering the domains for each expert, and eliminates nearly all the communication overhead of existing sparse language models. Our technique outperforms dense baselines on multiple corpora and few-shot tasks, and our analysis shows that specializing experts to meaningful clusters is key to these gains. Performance also improves with the number of experts and size of training data, suggesting this is a highly efficient and accessible approach to training large language models.

The rapid advancement of large language models has fundamentally shifted the bottleneck in AI development from computational power to data availability-with countless valuable datasets remaining hidden across specialized repositories, research appendices, and domain platforms. As reasoning capabilities and deep research methodologies continue to evolve, a critical question emerges: can AI agents transcend conventional search to systematically discover any dataset that meets specific user requirements, enabling truly autonomous demand-driven data curation? We introduce DatasetResearch, the first comprehensive benchmark evaluating AI agents' ability to discover and synthesize datasets from 208 real-world demands across knowledge-intensive and reasoning-intensive tasks. Our tri-dimensional evaluation framework reveals a stark reality: even advanced deep research systems achieve only 22% score on our challenging DatasetResearch-pro subset, exposing the vast gap between current capabilities and perfect dataset discovery. Our analysis uncovers a fundamental dichotomy-search agents excel at knowledge tasks through retrieval breadth, while synthesis agents dominate reasoning challenges via structured generation-yet both catastrophically fail on "corner cases" outside existing distributions. These findings establish the first rigorous baseline for dataset discovery agents and illuminate the path toward AI systems capable of finding any dataset in the digital universe. Our benchmark and comprehensive analysis provide the foundation for the next generation of self-improving AI systems and are publicly available at https://github.com/GAIR-NLP/DatasetResearch.

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.

Scientific literature is growing exponentially, creating a critical bottleneck for researchers to efficiently synthesize knowledge. While general-purpose Large Language Models (LLMs) show potential in text processing, they often fail to capture scientific domain-specific nuances (e.g., technical jargon, methodological rigor) and struggle with complex scientific tasks, limiting their utility for interdisciplinary research. To address these gaps, this paper presents SciGPT, a domain-adapted foundation model for scientific literature understanding and ScienceBench, an open source benchmark tailored to evaluate scientific LLMs. Built on the Qwen3 architecture, SciGPT incorporates three key innovations: (1) low-cost domain distillation via a two-stage pipeline to balance performance and efficiency; (2) a Sparse Mixture-of-Experts (SMoE) attention mechanism that cuts memory consumption by 55\% for 32,000-token long-document reasoning; and (3) knowledge-aware adaptation integrating domain ontologies to bridge interdisciplinary knowledge gaps. Experimental results on ScienceBench show that SciGPT outperforms GPT-4o in core scientific tasks including sequence labeling, generation, and inference. It also exhibits strong robustness in unseen scientific tasks, validating its potential to facilitate AI-augmented scientific discovery.

Current AI-assisted skin image diagnosis has achieved dermatologist-level performance in classifying skin cancer, driven by rapid advancements in deep learning architectures. However, unlike traditional vision tasks, skin images in general present unique challenges due to the limited availability of well-annotated datasets, complex variations in conditions, and the necessity for detailed interpretations to ensure patient safety. Previous segmentation methods have sought to reduce image noise and enhance diagnostic performance, but these techniques require fine-grained, pixel-level ground truth masks for training. In contrast, with the rise of foundation models, the Segment Anything Model (SAM) has been introduced to facilitate promptable segmentation, enabling the automation of the segmentation process with simple yet effective prompts. Efforts applying SAM predominantly focus on dermatoscopy images, which present more easily identifiable lesion boundaries than clinical photos taken with smartphones. This limitation constrains the practicality of these approaches to real-world applications. To overcome the challenges posed by noisy clinical photos acquired via non-standardized protocols and to improve diagnostic accessibility, we propose a novel Cross-Attentive Fusion framework for interpretable skin lesion diagnosis. Our method leverages SAM to generate visual concepts for skin diseases using prompts, integrating local visual concepts with global image features to enhance model performance. Extensive evaluation on two skin disease datasets demonstrates our proposed method's effectiveness on lesion diagnosis and interpretability.

The distribution of subpopulations is an important property hidden within a dataset. Uncovering and analyzing the subpopulation distribution within datasets provides a comprehensive understanding of the datasets, standing as a powerful tool beneficial to various downstream tasks, including Dataset Subpopulation Organization, Subpopulation Shift, and Slice Discovery. Despite its importance, there has been no work that systematically explores the subpopulation distribution of datasets to our knowledge. To address the limitation and solve all the mentioned tasks in a unified way, we introduce a novel concept of subpopulation structures to represent, analyze, and utilize subpopulation distributions within datasets. To characterize the structures in an interpretable manner, we propose the Subpopulation Structure Discovery with Large Language Models (SSD-LLM) framework, which employs world knowledge and instruction-following capabilities of Large Language Models (LLMs) to linguistically analyze informative image captions and summarize the structures. Furthermore, we propose complete workflows to address downstream tasks, named Task-specific Tuning, showcasing the application of the discovered structure to a spectrum of subpopulation-related tasks, including dataset subpopulation organization, subpopulation shift, and slice discovery. Furthermore, we propose complete workflows to address downstream tasks, named Task-specific Tuning, showcasing the application of the discovered structure to a spectrum of subpopulation-related tasks, including dataset subpopulation organization, subpopulation shift, and slice discovery.

Machine learning has emerged as a powerful tool for scientific discovery, enabling researchers to extract meaningful insights from complex datasets. For instance, it has facilitated the identification of disease-predictive genes from gene expression data, significantly advancing healthcare. However, the traditional process for analyzing such datasets demands substantial human effort and expertise for the data selection, processing, and analysis. To address this challenge, we introduce a novel framework, a Team of AI-made Scientists (TAIS), designed to streamline the scientific discovery pipeline. TAIS comprises simulated roles, including a project manager, data engineer, and domain expert, each represented by a Large Language Model (LLM). These roles collaborate to replicate the tasks typically performed by data scientists, with a specific focus on identifying disease-predictive genes. Furthermore, we have curated a benchmark dataset to assess TAIS's effectiveness in gene identification, demonstrating our system's potential to significantly enhance the efficiency and scope of scientific exploration. Our findings represent a solid step towards automating scientific discovery through large language models.

Large Language Models (LLMs) have recently showcased remarkable reasoning abilities. However, larger models often surpass their smaller counterparts in reasoning tasks, posing the challenge of effectively transferring these capabilities from larger models. Existing approaches heavily rely on extensive fine-tuning data or continuous interactions with a superior teacher LLM during inference. We introduce a principle-based teacher-student framework called ``Teaching via Principle Discovery'' (TPD) to address these limitations. Inspired by human learning mechanisms, TPD mimics the interaction between a teacher and a student using a principle-based approach. The teacher LLM generates problem-solving instructions and corrective principles based on the student LLM's errors. These principles guide the refinement of instructions and the selection of instructive examples from a validation set. This enables the student model to learn from both the teacher's guidance and its own mistakes. Once the student model begins making inferences, TPD requires no further intervention from the teacher LLM or humans. Through extensive experiments across eight reasoning tasks, we demonstrate the effectiveness of TPD. Compared to standard chain-of-thought prompting, TPD significantly improves the student model's performance, achieving 6.2% improvement on average.

Finding new drugs is getting harder and harder. One of the hopes of drug discovery is to use machine learning models to predict molecular properties. That is why models for molecular property prediction are being developed and tested on benchmarks such as MoleculeNet. However, existing benchmarks are unrealistic and are too different from applying the models in practice. We have created a new practical Lo-Hi benchmark consisting of two tasks: Lead Optimization (Lo) and Hit Identification (Hi), corresponding to the real drug discovery process. For the Hi task, we designed a novel molecular splitting algorithm that solves the Balanced Vertex Minimum k-Cut problem. We tested state-of-the-art and classic ML models, revealing which works better under practical settings. We analyzed modern benchmarks and showed that they are unrealistic and overoptimistic. Review: https://openreview.net/forum?id=H2Yb28qGLV Lo-Hi benchmark: https://github.com/SteshinSS/lohi_neurips2023 Lo-Hi splitter library: https://github.com/SteshinSS/lohi_splitter

Novel Class Discovery (NCD) is a growing field where we are given during training a labeled set of known classes and an unlabeled set of different classes that must be discovered. In recent years, many methods have been proposed to address this problem, and the field has begun to mature. In this paper, we provide a comprehensive survey of the state-of-the-art NCD methods. We start by formally defining the NCD problem and introducing important notions. We then give an overview of the different families of approaches, organized by the way they transfer knowledge from the labeled set to the unlabeled set. We find that they either learn in two stages, by first extracting knowledge from the labeled data only and then applying it to the unlabeled data, or in one stage by conjointly learning on both sets. For each family, we describe their general principle and detail a few representative methods. Then, we briefly introduce some new related tasks inspired by the increasing number of NCD works. We also present some common tools and techniques used in NCD, such as pseudo labeling, self-supervised learning and contrastive learning. Finally, to help readers unfamiliar with the NCD problem differentiate it from other closely related domains, we summarize some of the closest areas of research and discuss their main differences.

Role-based learning holds the promise of achieving scalable multi-agent learning by decomposing complex tasks using roles. However, it is largely unclear how to efficiently discover such a set of roles. To solve this problem, we propose to first decompose joint action spaces into restricted role action spaces by clustering actions according to their effects on the environment and other agents. Learning a role selector based on action effects makes role discovery much easier because it forms a bi-level learning hierarchy -- the role selector searches in a smaller role space and at a lower temporal resolution, while role policies learn in significantly reduced primitive action-observation spaces. We further integrate information about action effects into the role policies to boost learning efficiency and policy generalization. By virtue of these advances, our method (1) outperforms the current state-of-the-art MARL algorithms on 10 of the 14 scenarios that comprise the challenging StarCraft II micromanagement benchmark and (2) achieves rapid transfer to new environments with three times the number of agents. Demonstrative videos are available at https://sites.google.com/view/rode-marl .

This paper studies the problem of concept-based interpretability of transformer representations for videos. Concretely, we seek to explain the decision-making process of video transformers based on high-level, spatiotemporal concepts that are automatically discovered. Prior research on concept-based interpretability has concentrated solely on image-level tasks. Comparatively, video models deal with the added temporal dimension, increasing complexity and posing challenges in identifying dynamic concepts over time. In this work, we systematically address these challenges by introducing the first Video Transformer Concept Discovery (VTCD) algorithm. To this end, we propose an efficient approach for unsupervised identification of units of video transformer representations - concepts, and ranking their importance to the output of a model. The resulting concepts are highly interpretable, revealing spatio-temporal reasoning mechanisms and object-centric representations in unstructured video models. Performing this analysis jointly over a diverse set of supervised and self-supervised representations, we discover that some of these mechanism are universal in video transformers. Finally, we demonstrate that VTCDcan be used to improve model performance for fine-grained tasks.

We consider enhancing large language models (LLMs) for complex planning tasks. While existing methods allow LLMs to explore intermediate steps to make plans, they either depend on unreliable self-verification or external verifiers to evaluate these steps, which demand significant data and computations. Here, we propose automated heuristics discovery (AutoHD), a novel approach that enables LLMs to explicitly generate heuristic functions to guide inference-time search, allowing accurate evaluation of intermediate states. These heuristic functions are further refined through a heuristic evolution process, improving their robustness and effectiveness. Our proposed method requires no additional model training or fine-tuning, and the explicit definition of heuristic functions generated by the LLMs provides interpretability and insights into the reasoning process. Extensive experiments across diverse benchmarks demonstrate significant gains over multiple baselines, including nearly twice the accuracy on some datasets, establishing our approach as a reliable and interpretable solution for complex planning tasks.

Keypoint-based representation has proven advantageous in various visual and robotic tasks. However, the existing 2D and 3D methods for detecting keypoints mainly rely on geometric consistency to achieve spatial alignment, neglecting temporal consistency. To address this issue, the Transporter method was introduced for 2D data, which reconstructs the target frame from the source frame to incorporate both spatial and temporal information. However, the direct application of the Transporter to 3D point clouds is infeasible due to their structural differences from 2D images. Thus, we propose the first 3D version of the Transporter, which leverages hybrid 3D representation, cross attention, and implicit reconstruction. We apply this new learning system on 3D articulated objects and nonrigid animals (humans and rodents) and show that learned keypoints are spatio-temporally consistent. Additionally, we propose a closed-loop control strategy that utilizes the learned keypoints for 3D object manipulation and demonstrate its superior performance. Codes are available at https://github.com/zhongcl-thu/3D-Implicit-Transporter.

In reinforcement learning, unsupervised skill discovery aims to learn diverse skills without extrinsic rewards. Previous methods discover skills by maximizing the mutual information (MI) between states and skills. However, such an MI objective tends to learn simple and static skills and may hinder exploration. In this paper, we propose a novel unsupervised skill discovery method through contrastive learning among behaviors, which makes the agent produce similar behaviors for the same skill and diverse behaviors for different skills. Under mild assumptions, our objective maximizes the MI between different behaviors based on the same skill, which serves as an upper bound of the previous MI objective. Meanwhile, our method implicitly increases the state entropy to obtain better state coverage. We evaluate our method on challenging mazes and continuous control tasks. The results show that our method generates diverse and far-reaching skills, and also obtains competitive performance in downstream tasks compared to the state-of-the-art methods.

Foundation models have revolutionized natural language processing and artificial intelligence, significantly enhancing how machines comprehend and generate human languages. Inspired by the success of these foundation models, researchers have developed foundation models for individual scientific domains, including small molecules, materials, proteins, DNA, and RNA. However, these models are typically trained in isolation, lacking the ability to integrate across different scientific domains. Recognizing that entities within these domains can all be represented as sequences, which together form the "language of nature", we introduce Nature Language Model (briefly, NatureLM), a sequence-based science foundation model designed for scientific discovery. Pre-trained with data from multiple scientific domains, NatureLM offers a unified, versatile model that enables various applications including: (i) generating and optimizing small molecules, proteins, RNA, and materials using text instructions; (ii) cross-domain generation/design, such as protein-to-molecule and protein-to-RNA generation; and (iii) achieving state-of-the-art performance in tasks like SMILES-to-IUPAC translation and retrosynthesis on USPTO-50k. NatureLM offers a promising generalist approach for various scientific tasks, including drug discovery (hit generation/optimization, ADMET optimization, synthesis), novel material design, and the development of therapeutic proteins or nucleotides. We have developed NatureLM models in different sizes (1 billion, 8 billion, and 46.7 billion parameters) and observed a clear improvement in performance as the model size increases.

The vision of a broadly capable and goal-directed agent, such as an Internet-browsing agent in the digital world and a household humanoid in the physical world, has rapidly advanced, thanks to the generalization capability of foundation models. Such a generalist agent needs to have a large and diverse skill repertoire, such as finding directions between two travel locations and buying specific items from the Internet. If each skill needs to be specified manually through a fixed set of human-annotated instructions, the agent's skill repertoire will necessarily be limited due to the quantity and diversity of human-annotated instructions. In this work, we address this challenge by proposing Proposer-Agent-Evaluator, an effective learning system that enables foundation model agents to autonomously discover and practice skills in the wild. At the heart of PAE is a context-aware task proposer that autonomously proposes tasks for the agent to practice with context information of the environment such as user demos or even just the name of the website itself for Internet-browsing agents. Then, the agent policy attempts those tasks with thoughts and actual grounded operations in the real world with resulting trajectories evaluated by an autonomous VLM-based success evaluator. The success evaluation serves as the reward signal for the agent to refine its policies through RL. We validate PAE on challenging vision-based web navigation, using both real-world and self-hosted websites from WebVoyager and WebArena.To the best of our knowledge, this work represents the first effective learning system to apply autonomous task proposal with RL for agents that generalizes real-world human-annotated benchmarks with SOTA performances. Our open-source checkpoints and code can be found in https://yanqval.github.io/PAE/

Learning skills in open-world environments is essential for developing agents capable of handling a variety of tasks by combining basic skills. Online demonstration videos are typically long but unsegmented, making them difficult to segment and label with skill identifiers. Unlike existing methods that rely on sequence sampling or human labeling, we have developed a self-supervised learning-based approach to segment these long videos into a series of semantic-aware and skill-consistent segments. Drawing inspiration from human cognitive event segmentation theory, we introduce Skill Boundary Detection (SBD), an annotation-free temporal video segmentation algorithm. SBD detects skill boundaries in a video by leveraging prediction errors from a pretrained unconditional action-prediction model. This approach is based on the assumption that a significant increase in prediction error indicates a shift in the skill being executed. We evaluated our method in Minecraft, a rich open-world simulator with extensive gameplay videos available online. Our SBD-generated segments improved the average performance of conditioned policies by 63.7% and 52.1% on short-term atomic skill tasks, and their corresponding hierarchical agents by 11.3% and 20.8% on long-horizon tasks. Our method can leverage the diverse YouTube videos to train instruction-following agents. The project page can be found in https://craftjarvis.github.io/SkillDiscovery.

Multi-objective reinforcement learning (MORL) excels at handling rapidly changing preferences in tasks that involve multiple criteria, even for unseen preferences. However, previous dominating MORL methods typically generate a fixed policy set or preference-conditioned policy through multiple training iterations exclusively for sampled preference vectors, and cannot ensure the efficient discovery of the Pareto front. Furthermore, integrating preferences into the input of policy or value functions presents scalability challenges, in particular as the dimension of the state and preference space grow, which can complicate the learning process and hinder the algorithm's performance on more complex tasks. To address these issues, we propose a two-stage Pareto front discovery algorithm called Constrained MORL (C-MORL), which serves as a seamless bridge between constrained policy optimization and MORL. Concretely, a set of policies is trained in parallel in the initialization stage, with each optimized towards its individual preference over the multiple objectives. Then, to fill the remaining vacancies in the Pareto front, the constrained optimization steps are employed to maximize one objective while constraining the other objectives to exceed a predefined threshold. Empirically, compared to recent advancements in MORL methods, our algorithm achieves more consistent and superior performances in terms of hypervolume, expected utility, and sparsity on both discrete and continuous control tasks, especially with numerous objectives (up to nine objectives in our experiments).

Despite the success of equivariant neural networks in scientific applications, they require knowing the symmetry group a priori. However, it may be difficult to know which symmetry to use as an inductive bias in practice. Enforcing the wrong symmetry could even hurt the performance. In this paper, we propose a framework, LieGAN, to automatically discover equivariances from a dataset using a paradigm akin to generative adversarial training. Specifically, a generator learns a group of transformations applied to the data, which preserve the original distribution and fool the discriminator. LieGAN represents symmetry as interpretable Lie algebra basis and can discover various symmetries such as the rotation group SO(n), restricted Lorentz group SO(1,3)^+ in trajectory prediction and top-quark tagging tasks. The learned symmetry can also be readily used in several existing equivariant neural networks to improve accuracy and generalization in prediction.

Discovering causal structures with latent variables from observational data is a fundamental challenge in causal discovery. Existing methods often rely on constraint-based, iterative discrete searches, limiting their scalability to large numbers of variables. Moreover, these methods frequently assume linearity or invertibility, restricting their applicability to real-world scenarios. We present new theoretical results on the identifiability of nonlinear latent hierarchical causal models, relaxing previous assumptions in literature about the deterministic nature of latent variables and exogenous noise. Building on these insights, we develop a novel differentiable causal discovery algorithm that efficiently estimates the structure of such models. To the best of our knowledge, this is the first work to propose a differentiable causal discovery method for nonlinear latent hierarchical models. Our approach outperforms existing methods in both accuracy and scalability. We demonstrate its practical utility by learning interpretable hierarchical latent structures from high-dimensional image data and demonstrate its effectiveness on downstream tasks.

Robotic affordances, providing information about what actions can be taken in a given situation, can aid robotic manipulation. However, learning about affordances requires expensive large annotated datasets of interactions or demonstrations. In this work, we argue that well-directed interactions with the environment can mitigate this problem and propose an information-based measure to augment the agent's objective and accelerate the affordance discovery process. We provide a theoretical justification of our approach and we empirically validate the approach both in simulation and real-world tasks. Our method, which we dub IDA, enables the efficient discovery of visual affordances for several action primitives, such as grasping, stacking objects, or opening drawers, strongly improving data efficiency in simulation, and it allows us to learn grasping affordances in a small number of interactions, on a real-world setup with a UFACTORY XArm 6 robot arm.

We focus on the self-supervised discovery of manipulation concepts that can be adapted and reassembled to address various robotic tasks. We propose that the decision to conceptualize a physical procedure should not depend on how we name it (semantics) but rather on the significance of the informativeness in its representation regarding the low-level physical state and state changes. We model manipulation concepts (discrete symbols) as generative and discriminative goals and derive metrics that can autonomously link them to meaningful sub-trajectories from noisy, unlabeled demonstrations. Specifically, we employ a trainable codebook containing encodings (concepts) capable of synthesizing the end-state of a sub-trajectory given the current state (generative informativeness). Moreover, the encoding corresponding to a particular sub-trajectory should differentiate the state within and outside it and confidently predict the subsequent action based on the gradient of its discriminative score (discriminative informativeness). These metrics, which do not rely on human annotation, can be seamlessly integrated into a VQ-VAE framework, enabling the partitioning of demonstrations into semantically consistent sub-trajectories, fulfilling the purpose of discovering manipulation concepts and the corresponding sub-goal (key) states. We evaluate the effectiveness of the learned concepts by training policies that utilize them as guidance, demonstrating superior performance compared to other baselines. Additionally, our discovered manipulation concepts compare favorably to human-annotated ones while saving much manual effort.

Unsupervised domain adaptation (UDA) has proven to be highly effective in transferring knowledge from a label-rich source domain to a label-scarce target domain. However, the presence of additional novel categories in the target domain has led to the development of open-set domain adaptation (ODA) and universal domain adaptation (UNDA). Existing ODA and UNDA methods treat all novel categories as a single, unified unknown class and attempt to detect it during training. However, we found that domain variance can lead to more significant view-noise in unsupervised data augmentation, which affects the effectiveness of contrastive learning (CL) and causes the model to be overconfident in novel category discovery. To address these issues, a framework named Soft-contrastive All-in-one Network (SAN) is proposed for ODA and UNDA tasks. SAN includes a novel data-augmentation-based soft contrastive learning (SCL) loss to fine-tune the backbone for feature transfer and a more human-intuitive classifier to improve new class discovery capability. The SCL loss weakens the adverse effects of the data augmentation view-noise problem which is amplified in domain transfer tasks. The All-in-One (AIO) classifier overcomes the overconfidence problem of current mainstream closed-set and open-set classifiers. Visualization and ablation experiments demonstrate the effectiveness of the proposed innovations. Furthermore, extensive experiment results on ODA and UNDA show that SAN outperforms existing state-of-the-art methods.

Activity and property prediction models are the central workhorses in drug discovery and materials sciences, but currently they have to be trained or fine-tuned for new tasks. Without training or fine-tuning, scientific language models could be used for such low-data tasks through their announced zero- and few-shot capabilities. However, their predictive quality at activity prediction is lacking. In this work, we envision a novel type of activity prediction model that is able to adapt to new prediction tasks at inference time, via understanding textual information describing the task. To this end, we propose a new architecture with separate modules for chemical and natural language inputs, and a contrastive pre-training objective on data from large biochemical databases. In extensive experiments, we show that our method CLAMP yields improved predictive performance on few-shot learning benchmarks and zero-shot problems in drug discovery. We attribute the advances of our method to the modularized architecture and to our pre-training objective.

A widely used strategy to discover and understand language model mechanisms is circuit analysis. A circuit is a minimal subgraph of a model's computation graph that executes a specific task. We identify a gap in existing circuit discovery methods: they assume circuits are position-invariant, treating model components as equally relevant across input positions. This limits their ability to capture cross-positional interactions or mechanisms that vary across positions. To address this gap, we propose two improvements to incorporate positionality into circuits, even on tasks containing variable-length examples. First, we extend edge attribution patching, a gradient-based method for circuit discovery, to differentiate between token positions. Second, we introduce the concept of a dataset schema, which defines token spans with similar semantics across examples, enabling position-aware circuit discovery in datasets with variable length examples. We additionally develop an automated pipeline for schema generation and application using large language models. Our approach enables fully automated discovery of position-sensitive circuits, yielding better trade-offs between circuit size and faithfulness compared to prior work.

Open-vocabulary 3D Object Detection (OV-3DDet) addresses the detection of objects from an arbitrary list of novel categories in 3D scenes, which remains a very challenging problem. In this work, we propose CoDAv2, a unified framework designed to innovatively tackle both the localization and classification of novel 3D objects, under the condition of limited base categories. For localization, the proposed 3D Novel Object Discovery (3D-NOD) strategy utilizes 3D geometries and 2D open-vocabulary semantic priors to discover pseudo labels for novel objects during training. 3D-NOD is further extended with an Enrichment strategy that significantly enriches the novel object distribution in the training scenes, and then enhances the model's ability to localize more novel objects. The 3D-NOD with Enrichment is termed 3D-NODE. For classification, the Discovery-driven Cross-modal Alignment (DCMA) module aligns features from 3D point clouds and 2D/textual modalities, employing both class-agnostic and class-specific alignments that are iteratively refined to handle the expanding vocabulary of objects. Besides, 2D box guidance boosts the classification accuracy against complex background noises, which is coined as Box-DCMA. Extensive evaluation demonstrates the superiority of CoDAv2. CoDAv2 outperforms the best-performing method by a large margin (AP_Novel of 9.17 vs. 3.61 on SUN-RGBD and 9.12 vs. 3.74 on ScanNetv2). Source code and pre-trained models are available at the GitHub project page.

A fundamental bottleneck in human-AI collaboration is the "intention expression gap," the difficulty for humans to effectively convey complex, high-dimensional thoughts to AI. This challenge often traps users in inefficient trial-and-error loops and is exacerbated by the diverse expertise levels of users. We reframe this problem from passive instruction following to a Socratic collaboration paradigm, proposing an agent that actively probes for information to resolve its uncertainty about user intent. we name the proposed agent Nous, trained to acquire proficiency in this inquiry policy. The core mechanism of Nous is a training framework grounded in the first principles of information theory. Within this framework, we define the information gain from dialogue as an intrinsic reward signal, which is fundamentally equivalent to the reduction of Shannon entropy over a structured task space. This reward design enables us to avoid reliance on costly human preference annotations or external reward models. To validate our framework, we develop an automated simulation pipeline to generate a large-scale, preference-based dataset for the challenging task of scientific diagram generation. Comprehensive experiments, including ablations, subjective and objective evaluations, and tests across user expertise levels, demonstrate the effectiveness of our proposed framework. Nous achieves leading efficiency and output quality, while remaining robust to varying user expertise. Moreover, its design is domain-agnostic, and we show evidence of generalization beyond diagram generation. Experimental results prove that our work offers a principled, scalable, and adaptive paradigm for resolving uncertainty about user intent in complex human-AI collaboration.

Compound AI systems (CASs) that employ LLMs as agents to accomplish knowledge-intensive tasks via interactions with tools and data retrievers have garnered significant interest within database and AI communities. While these systems have the potential to supplement typical analysis workflows of data analysts in enterprise data platforms, unfortunately, CASs are subject to the same data discovery challenges that analysts have encountered over the years -- silos of multimodal data sources, created across teams and departments within an organization, make it difficult to identify appropriate data sources for accomplishing the task at hand. Existing data discovery benchmarks do not model such multimodality and multiplicity of data sources. Moreover, benchmarks of CASs prioritize only evaluating end-to-end task performance. To catalyze research on evaluating the data discovery performance of multimodal data retrievers in CASs within a real-world setting, we propose CMDBench, a benchmark modeling the complexity of enterprise data platforms. We adapt existing datasets and benchmarks in open-domain -- from question answering and complex reasoning tasks to natural language querying over structured data -- to evaluate coarse- and fine-grained data discovery and task execution performance. Our experiments reveal the impact of data retriever design on downstream task performance -- a 46% drop in task accuracy on average -- across various modalities, data sources, and task difficulty. The results indicate the need to develop optimization strategies to identify appropriate LLM agents and retrievers for efficient execution of CASs over enterprise data.

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.

Developing deep learning models that effectively learn object-centric representations, akin to human cognition, remains a challenging task. Existing approaches facilitate object discovery by representing objects as fixed-size vectors, called ``slots'' or ``object files''. While these approaches have shown promise in certain scenarios, they still exhibit certain limitations. First, they rely on architectural priors which can be unreliable and usually require meticulous engineering to identify the correct objects. Second, there has been a notable gap in investigating the practical utility of these representations in downstream tasks. To address the first limitation, we introduce a method that explicitly optimizes the constraint that each object in a scene should be associated with a distinct slot. We formalize this constraint by introducing consistency objectives which are cyclic in nature. By integrating these consistency objectives into various existing slot-based object-centric methods, we showcase substantial improvements in object-discovery performance. These enhancements consistently hold true across both synthetic and real-world scenes, underscoring the effectiveness and adaptability of the proposed approach. To tackle the second limitation, we apply the learned object-centric representations from the proposed method to two downstream reinforcement learning tasks, demonstrating considerable performance enhancements compared to conventional slot-based and monolithic representation learning methods. Our results suggest that the proposed approach not only improves object discovery, but also provides richer features for downstream tasks.

Learning from a large corpus of data, pre-trained models have achieved impressive progress nowadays. As popular generative pre-training, diffusion models capture both low-level visual knowledge and high-level semantic relations. In this paper, we propose to exploit such knowledgeable diffusion models for mainstream discriminative tasks, i.e., unsupervised object discovery: saliency segmentation and object localization. However, the challenges exist as there is one structural difference between generative and discriminative models, which limits the direct use. Besides, the lack of explicitly labeled data significantly limits performance in unsupervised settings. To tackle these issues, we introduce DiffusionSeg, one novel synthesis-exploitation framework containing two-stage strategies. To alleviate data insufficiency, we synthesize abundant images, and propose a novel training-free AttentionCut to obtain masks in the first synthesis stage. In the second exploitation stage, to bridge the structural gap, we use the inversion technique, to map the given image back to diffusion features. These features can be directly used by downstream architectures. Extensive experiments and ablation studies demonstrate the superiority of adapting diffusion for unsupervised object discovery.

To be capable of lifelong learning in a real-life environment, robots have to tackle multiple challenges. Being able to relate physical properties they may observe in their environment to possible interactions they may have is one of them. This skill, named affordance learning, is strongly related to embodiment and is mastered through each person's development: each individual learns affordances differently through their own interactions with their surroundings. Current methods for affordance learning usually use either fixed actions to learn these affordances or focus on static setups involving a robotic arm to be operated. In this article, we propose an algorithm using intrinsic motivation to guide the learning of affordances for a mobile robot. This algorithm is capable to autonomously discover, learn and adapt interrelated affordances without pre-programmed actions. Once learned, these affordances may be used by the algorithm to plan sequences of actions in order to perform tasks of various difficulties. We then present one experiment and analyse our system before comparing it with other approaches from reinforcement learning and affordance learning.

Large Language Models (LLMs) have greatly advanced knowledge graph question answering (KGQA), yet existing systems are typically optimized for returning highly relevant but predictable answers. A missing yet desired capacity is to exploit LLMs to suggest surprise and novel ("serendipitious") answers. In this paper, we formally define the serendipity-aware KGQA task and propose the SerenQA framework to evaluate LLMs' ability to uncover unexpected insights in scientific KGQA tasks. SerenQA includes a rigorous serendipity metric based on relevance, novelty, and surprise, along with an expert-annotated benchmark derived from the Clinical Knowledge Graph, focused on drug repurposing. Additionally, it features a structured evaluation pipeline encompassing three subtasks: knowledge retrieval, subgraph reasoning, and serendipity exploration. Our experiments reveal that while state-of-the-art LLMs perform well on retrieval, they still struggle to identify genuinely surprising and valuable discoveries, underscoring a significant room for future improvements. Our curated resources and extended version are released at: https://cwru-db-group.github.io/serenQA.

Long-form video understanding presents significant challenges due to extensive temporal-spatial complexity and the difficulty of question answering under such extended contexts. While Large Language Models (LLMs) have demonstrated considerable advancements in video analysis capabilities and long context handling, they continue to exhibit limitations when processing information-dense hour-long videos. To overcome such limitations, we propose the Deep Video Discovery agent to leverage an agentic search strategy over segmented video clips. Different from previous video agents manually designing a rigid workflow, our approach emphasizes the autonomous nature of agents. By providing a set of search-centric tools on multi-granular video database, our DVD agent leverages the advanced reasoning capability of LLM to plan on its current observation state, strategically selects tools, formulates appropriate parameters for actions, and iteratively refines its internal reasoning in light of the gathered information. We perform comprehensive evaluation on multiple long video understanding benchmarks that demonstrates the advantage of the entire system design. Our DVD agent achieves SOTA performance, significantly surpassing prior works by a large margin on the challenging LVBench dataset. Comprehensive ablation studies and in-depth tool analyses are also provided, yielding insights to further advance intelligent agents tailored for long-form video understanding tasks. The code will be released later.

Scientific discovery is a complex cognitive process that has driven human knowledge and technological progress for centuries. While artificial intelligence (AI) has made significant advances in automating aspects of scientific reasoning, simulation, and experimentation, we still lack integrated AI systems capable of performing autonomous long-term scientific research and discovery. This paper examines the current state of AI for scientific discovery, highlighting recent progress in large language models and other AI techniques applied to scientific tasks. We then outline key challenges and promising research directions toward developing more comprehensive AI systems for scientific discovery, including the need for science-focused AI agents, improved benchmarks and evaluation metrics, multimodal scientific representations, and unified frameworks combining reasoning, theorem proving, and data-driven modeling. Addressing these challenges could lead to transformative AI tools to accelerate progress across disciplines towards scientific discovery.

Text-to-image generative models have enabled high-resolution image synthesis across different domains, but require users to specify the content they wish to generate. In this paper, we consider the inverse problem -- given a collection of different images, can we discover the generative concepts that represent each image? We present an unsupervised approach to discover generative concepts from a collection of images, disentangling different art styles in paintings, objects, and lighting from kitchen scenes, and discovering image classes given ImageNet images. We show how such generative concepts can accurately represent the content of images, be recombined and composed to generate new artistic and hybrid images, and be further used as a representation for downstream classification tasks.

Self-supervised speech representation learning has become essential for extracting meaningful features from untranscribed audio. Recent advances highlight the potential of deriving discrete symbols from the features correlated with linguistic units, which enables text-less training across diverse tasks. In particular, sentence-level Self-Distillation of the pretrained HuBERT (SD-HuBERT) induces syllabic structures within latent speech frame representations extracted from an intermediate Transformer layer. In SD-HuBERT, sentence-level representation is accumulated from speech frame features through self-attention layers using a special CLS token. However, we observe that the information aggregated in the CLS token correlates more with speaker identity than with linguistic content. To address this, we propose a speech-only self-supervised fine-tuning approach that separates syllabic units from speaker information. Our method introduces speaker perturbation as data augmentation and adopts a frame-level training objective to prevent the CLS token from aggregating paralinguistic information. Experimental results show that our approach surpasses the current state-of-the-art method in most syllable segmentation and syllabic unit quality metrics on Librispeech, underscoring its effectiveness in promoting syllabic organization within speech-only models.

Recent work in vision-and-language demonstrates that large-scale pretraining can learn generalizable models that are efficiently transferable to downstream tasks. While this may improve dataset-scale aggregate metrics, analyzing performance around hand-crafted subgroups targeting specific bias dimensions reveals systemic undesirable behaviors. However, this subgroup analysis is frequently stalled by annotation efforts, which require extensive time and resources to collect the necessary data. Prior art attempts to automatically discover subgroups to circumvent these constraints but typically leverages model behavior on existing task-specific annotations and rapidly degrades on more complex inputs beyond "tabular" data, none of which study vision-and-language models. This paper presents VLSlice, an interactive system enabling user-guided discovery of coherent representation-level subgroups with consistent visiolinguistic behavior, denoted as vision-and-language slices, from unlabeled image sets. We show that VLSlice enables users to quickly generate diverse high-coherency slices in a user study (n=22) and release the tool publicly.

One of the grand challenges of artificial general intelligence is developing agents capable of conducting scientific research and discovering new knowledge. While frontier models have already been used as aids to human scientists, e.g. for brainstorming ideas, writing code, or prediction tasks, they still conduct only a small part of the scientific process. This paper presents the first comprehensive framework for fully automatic scientific discovery, enabling frontier large language models to perform research independently and communicate their findings. We introduce The AI Scientist, which generates novel research ideas, writes code, executes experiments, visualizes results, describes its findings by writing a full scientific paper, and then runs a simulated review process for evaluation. In principle, this process can be repeated to iteratively develop ideas in an open-ended fashion, acting like the human scientific community. We demonstrate its versatility by applying it to three distinct subfields of machine learning: diffusion modeling, transformer-based language modeling, and learning dynamics. Each idea is implemented and developed into a full paper at a cost of less than $15 per paper. To evaluate the generated papers, we design and validate an automated reviewer, which we show achieves near-human performance in evaluating paper scores. The AI Scientist can produce papers that exceed the acceptance threshold at a top machine learning conference as judged by our automated reviewer. This approach signifies the beginning of a new era in scientific discovery in machine learning: bringing the transformative benefits of AI agents to the entire research process of AI itself, and taking us closer to a world where endless affordable creativity and innovation can be unleashed on the world's most challenging problems. Our code is open-sourced at https://github.com/SakanaAI/AI-Scientist

Retrieval-Augmented Generation (RAG) leverages retrieval tools to access external databases, thereby enhancing the generation quality of large language models (LLMs) through optimized context. However, the existing retrieval methods are constrained inherently, as they can only perform relevance matching between explicitly stated queries and well-formed knowledge, but unable to handle tasks involving ambiguous information needs or unstructured knowledge. Consequently, existing RAG systems are primarily effective for straightforward question-answering tasks. In this work, we propose MemoRAG, a novel retrieval-augmented generation paradigm empowered by long-term memory. MemoRAG adopts a dual-system architecture. On the one hand, it employs a light but long-range LLM to form the global memory of database. Once a task is presented, it generates draft answers, cluing the retrieval tools to locate useful information within the database. On the other hand, it leverages an expensive but expressive LLM, which generates the ultimate answer based on the retrieved information. Building on this general framework, we further optimize MemoRAG's performance by enhancing its cluing mechanism and memorization capacity. In our experiment, MemoRAG achieves superior performance across a variety of evaluation tasks, including both complex ones where conventional RAG fails and straightforward ones where RAG is commonly applied.

Large language models (LLMs) have demonstrated potential in assisting scientific research, yet their ability to discover high-quality research hypotheses remains unexamined due to the lack of a dedicated benchmark. To address this gap, we introduce the first large-scale benchmark for evaluating LLMs with a near-sufficient set of sub-tasks of scientific discovery: inspiration retrieval, hypothesis composition, and hypothesis ranking. We develop an automated framework that extracts critical components - research questions, background surveys, inspirations, and hypotheses - from scientific papers across 12 disciplines, with expert validation confirming its accuracy. To prevent data contamination, we focus exclusively on papers published in 2024, ensuring minimal overlap with LLM pretraining data. Our evaluation reveals that LLMs perform well in retrieving inspirations, an out-of-distribution task, suggesting their ability to surface novel knowledge associations. This positions LLMs as "research hypothesis mines", capable of facilitating automated scientific discovery by generating innovative hypotheses at scale with minimal human intervention.

Recent research in representation learning utilizes large databases of proteins or molecules to acquire knowledge of drug and protein structures through unsupervised learning techniques. These pre-trained representations have proven to significantly enhance the accuracy of subsequent tasks, such as predicting the affinity between drugs and target proteins. In this study, we demonstrate that by incorporating knowledge graphs from diverse sources and modalities into the sequences or SMILES representation, we can further enrich the representation and achieve state-of-the-art results on established benchmark datasets. We provide preprocessed and integrated data obtained from 7 public sources, which encompass over 30M triples. Additionally, we make available the pre-trained models based on this data, along with the reported outcomes of their performance on three widely-used benchmark datasets for drug-target binding affinity prediction found in the Therapeutic Data Commons (TDC) benchmarks. Additionally, we make the source code for training models on benchmark datasets publicly available. Our objective in releasing these pre-trained models, accompanied by clean data for model pretraining and benchmark results, is to encourage research in knowledge-enhanced representation learning.

Novel intent discovery automates the process of grouping similar messages (questions) to identify previously unknown intents. However, current research focuses on publicly available datasets which have only the question field and significantly differ from real-life datasets. This paper proposes methods to improve the intent discovery pipeline deployed in a large e-commerce platform. We show the benefit of pre-training language models on in-domain data: both self-supervised and with weak supervision. We also devise the best method to utilize the conversational structure (i.e., question and answer) of real-life datasets during fine-tuning for clustering tasks, which we call Conv. All our methods combined to fully utilize real-life datasets give up to 33pp performance boost over state-of-the-art Constrained Deep Adaptive Clustering (CDAC) model for question only. By comparison CDAC model for the question data only gives only up to 13pp performance boost over the naive baseline.

Modern science emerged from reasoning over repeatedly-observed planetary motions. We present Gravity-Bench-v1, an environment-based benchmark that challenges AI agents on tasks that parallel this historical development. Gravity-Bench-v1 evaluates agents on the discovery of physics concealed within a dynamic environment, using rigorous gravitational dynamics simulations. Gravity-Bench includes out-of-distribution cases, i.e. with physics that deviates from the real world, to evaluate true scientific generalization capabilities. Agents must plan to collect data within an experimental budget and must perform a dynamic form of data analysis and reasoning to solve tasks efficiently. Our benchmark admits an open-ended space of solutions. PhD-level solutions for each task are provided, to calibrate AI performance against human expertise. Technically at an upper-undergraduate level, our benchmark proves challenging to baseline AI agents. Gravity-Bench-v1 and planned extensions should help map out AI progress towards scientific discovery capabilities.

This paper studies the impact of artificial intelligence on innovation, exploiting the randomized introduction of a new materials discovery technology to 1,018 scientists in the R&D lab of a large U.S. firm. AI-assisted researchers discover 44% more materials, resulting in a 39% increase in patent filings and a 17% rise in downstream product innovation. These compounds possess more novel chemical structures and lead to more radical inventions. However, the technology has strikingly disparate effects across the productivity distribution: while the bottom third of scientists see little benefit, the output of top researchers nearly doubles. Investigating the mechanisms behind these results, I show that AI automates 57% of "idea-generation" tasks, reallocating researchers to the new task of evaluating model-produced candidate materials. Top scientists leverage their domain knowledge to prioritize promising AI suggestions, while others waste significant resources testing false positives. Together, these findings demonstrate the potential of AI-augmented research and highlight the complementarity between algorithms and expertise in the innovative process. Survey evidence reveals that these gains come at a cost, however, as 82% of scientists report reduced satisfaction with their work due to decreased creativity and skill underutilization.

Bumblebee is a foundation model for particle physics discovery, inspired by BERT. By removing positional encodings and embedding particle 4-vectors, Bumblebee captures both generator- and reconstruction-level information while ensuring sequence-order invariance. Pre-trained on a masked task, it improves dileptonic top quark reconstruction resolution by 10-20% and excels in downstream tasks, including toponium discrimination (AUROC 0.877) and initial state classification (AUROC 0.625). The flexibility of Bumblebee makes it suitable for a wide range of particle physics applications, especially the discovery of new particles.

The discovery and identification of molecules in biological and environmental samples is crucial for advancing biomedical and chemical sciences. Tandem mass spectrometry (MS/MS) is the leading technique for high-throughput elucidation of molecular structures. However, decoding a molecular structure from its mass spectrum is exceptionally challenging, even when performed by human experts. As a result, the vast majority of acquired MS/MS spectra remain uninterpreted, thereby limiting our understanding of the underlying (bio)chemical processes. Despite decades of progress in machine learning applications for predicting molecular structures from MS/MS spectra, the development of new methods is severely hindered by the lack of standard datasets and evaluation protocols. To address this problem, we propose MassSpecGym -- the first comprehensive benchmark for the discovery and identification of molecules from MS/MS data. Our benchmark comprises the largest publicly available collection of high-quality labeled MS/MS spectra and defines three MS/MS annotation challenges: de novo molecular structure generation, molecule retrieval, and spectrum simulation. It includes new evaluation metrics and a generalization-demanding data split, therefore standardizing the MS/MS annotation tasks and rendering the problem accessible to the broad machine learning community. MassSpecGym is publicly available at https://github.com/pluskal-lab/MassSpecGym.

Massively multitask neural architectures provide a learning framework for drug discovery that synthesizes information from many distinct biological sources. To train these architectures at scale, we gather large amounts of data from public sources to create a dataset of nearly 40 million measurements across more than 200 biological targets. We investigate several aspects of the multitask framework by performing a series of empirical studies and obtain some interesting results: (1) massively multitask networks obtain predictive accuracies significantly better than single-task methods, (2) the predictive power of multitask networks improves as additional tasks and data are added, (3) the total amount of data and the total number of tasks both contribute significantly to multitask improvement, and (4) multitask networks afford limited transferability to tasks not in the training set. Our results underscore the need for greater data sharing and further algorithmic innovation to accelerate the drug discovery process.

The exponential growth of astronomical literature poses significant challenges for researchers navigating and synthesizing general insights or even domain-specific knowledge. We present Pathfinder, a machine learning framework designed to enable literature review and knowledge discovery in astronomy, focusing on semantic searching with natural language instead of syntactic searches with keywords. Utilizing state-of-the-art large language models (LLMs) and a corpus of 350,000 peer-reviewed papers from the Astrophysics Data System (ADS), Pathfinder offers an innovative approach to scientific inquiry and literature exploration. Our framework couples advanced retrieval techniques with LLM-based synthesis to search astronomical literature by semantic context as a complement to currently existing methods that use keywords or citation graphs. It addresses complexities of jargon, named entities, and temporal aspects through time-based and citation-based weighting schemes. We demonstrate the tool's versatility through case studies, showcasing its application in various research scenarios. The system's performance is evaluated using custom benchmarks, including single-paper and multi-paper tasks. Beyond literature review, Pathfinder offers unique capabilities for reformatting answers in ways that are accessible to various audiences (e.g. in a different language or as simplified text), visualizing research landscapes, and tracking the impact of observatories and methodologies. This tool represents a significant advancement in applying AI to astronomical research, aiding researchers at all career stages in navigating modern astronomy literature.

With the development of computer-assisted techniques, research communities including biochemistry and deep learning have been devoted into the drug discovery field for over a decade. Various applications of deep learning have drawn great attention in drug discovery, such as molecule generation, molecular property prediction, retrosynthesis prediction, and reaction prediction. While most existing surveys only focus on one of the applications, limiting the view of researchers in the community. In this paper, we present a comprehensive review on the aforementioned four aspects, and discuss the relationships among different applications. The latest literature and classical benchmarks are presented for better understanding the development of variety of approaches. We commence by summarizing the molecule representation format in these works, followed by an introduction of recent proposed approaches for each of the four tasks. Furthermore, we review a variety of commonly used datasets and evaluation metrics and compare the performance of deep learning-based models. Finally, we conclude by identifying remaining challenges and discussing the future trend for deep learning methods in drug discovery.

We propose Deep Feature Factorization (DFF), a method capable of localizing similar semantic concepts within an image or a set of images. We use DFF to gain insight into a deep convolutional neural network's learned features, where we detect hierarchical cluster structures in feature space. This is visualized as heat maps, which highlight semantically matching regions across a set of images, revealing what the network `perceives' as similar. DFF can also be used to perform co-segmentation and co-localization, and we report state-of-the-art results on these tasks.

The discovery of novel Ionic Liquids (ILs) is hindered by critical challenges in property prediction, including limited data, poor model accuracy, and fragmented workflows. Leveraging the power of Large Language Models (LLMs), we introduce AIonopedia, to the best of our knowledge, the first LLM agent for IL discovery. Powered by an LLM-augmented multimodal domain foundation model for ILs, AIonopedia enables accurate property predictions and incorporates a hierarchical search architecture for molecular screening and design. Trained and evaluated on a newly curated and comprehensive IL dataset, our model delivers superior performance. Complementing these results, evaluations on literature-reported systems indicate that the agent can perform effective IL modification. Moving beyond offline tests, the practical efficacy was further confirmed through real-world wet-lab validation, in which the agent demonstrated exceptional generalization capabilities on challenging out-of-distribution tasks, underscoring its ability to accelerate real-world IL discovery.

In this paper, we explore the capabilities of LLMs in capturing lexical-semantic knowledge from WordNet on the example of the LLaMA-2-7b model and test it on multiple lexical semantic tasks. As the outcome of our experiments, we present TaxoLLaMA, the everything-in-one model, lightweight due to 4-bit quantization and LoRA. It achieves 11 SotA results, 4 top-2 results out of 16 tasks for the Taxonomy Enrichment, Hypernym Discovery, Taxonomy Construction, and Lexical Entailment tasks. Moreover, it demonstrates very strong zero-shot performance on Lexical Entailment and Taxonomy Construction with no fine-tuning. We also explore its hidden multilingual and domain adaptation capabilities with a little tuning or few-shot learning. All datasets, code, and model are available online at https://github.com/VityaVitalich/TaxoLLaMA

In this white paper, we present AlphaEvolve, an evolutionary coding agent that substantially enhances capabilities of state-of-the-art LLMs on highly challenging tasks such as tackling open scientific problems or optimizing critical pieces of computational infrastructure. AlphaEvolve orchestrates an autonomous pipeline of LLMs, whose task is to improve an algorithm by making direct changes to the code. Using an evolutionary approach, continuously receiving feedback from one or more evaluators, AlphaEvolve iteratively improves the algorithm, potentially leading to new scientific and practical discoveries. We demonstrate the broad applicability of this approach by applying it to a number of important computational problems. When applied to optimizing critical components of large-scale computational stacks at Google, AlphaEvolve developed a more efficient scheduling algorithm for data centers, found a functionally equivalent simplification in the circuit design of hardware accelerators, and accelerated the training of the LLM underpinning AlphaEvolve itself. Furthermore, AlphaEvolve discovered novel, provably correct algorithms that surpass state-of-the-art solutions on a spectrum of problems in mathematics and computer science, significantly expanding the scope of prior automated discovery methods (Romera-Paredes et al., 2023). Notably, AlphaEvolve developed a search algorithm that found a procedure to multiply two 4 times 4 complex-valued matrices using 48 scalar multiplications; offering the first improvement, after 56 years, over Strassen's algorithm in this setting. We believe AlphaEvolve and coding agents like it can have a significant impact in improving solutions of problems across many areas of science and computation.

Large language models (LLMs) are introducing a paradigm shift in molecular discovery by enabling text-guided interaction with chemical spaces through natural language, symbolic notations, with emerging extensions to incorporate multi-modal inputs. To advance the new field of LLM for molecular discovery, this survey provides an up-to-date and forward-looking review of the emerging use of LLMs for two central tasks: molecule generation and molecule optimization. Based on our proposed taxonomy for both problems, we analyze representative techniques in each category, highlighting how LLM capabilities are leveraged across different learning settings. In addition, we include the commonly used datasets and evaluation protocols. We conclude by discussing key challenges and future directions, positioning this survey as a resource for researchers working at the intersection of LLMs and molecular science. A continuously updated reading list is available at https://github.com/REAL-Lab-NU/Awesome-LLM-Centric-Molecular-Discovery.

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

In many scientific fields, large language models (LLMs) have revolutionized the way text and other modalities of data (e.g., molecules and proteins) are handled, achieving superior performance in various applications and augmenting the scientific discovery process. Nevertheless, previous surveys on scientific LLMs often concentrate on one or two fields or a single modality. In this paper, we aim to provide a more holistic view of the research landscape by unveiling cross-field and cross-modal connections between scientific LLMs regarding their architectures and pre-training techniques. To this end, we comprehensively survey over 260 scientific LLMs, discuss their commonalities and differences, as well as summarize pre-training datasets and evaluation tasks for each field and modality. Moreover, we investigate how LLMs have been deployed to benefit scientific discovery. Resources related to this survey are available at https://github.com/yuzhimanhua/Awesome-Scientific-Language-Models.

Images are increasingly becoming the currency for documenting biodiversity on the planet, providing novel opportunities for accelerating scientific discoveries in the field of organismal biology, especially with the advent of large vision-language models (VLMs). We ask if pre-trained VLMs can aid scientists in answering a range of biologically relevant questions without any additional fine-tuning. In this paper, we evaluate the effectiveness of 12 state-of-the-art (SOTA) VLMs in the field of organismal biology using a novel dataset, VLM4Bio, consisting of 469K question-answer pairs involving 30K images from three groups of organisms: fishes, birds, and butterflies, covering five biologically relevant tasks. We also explore the effects of applying prompting techniques and tests for reasoning hallucination on the performance of VLMs, shedding new light on the capabilities of current SOTA VLMs in answering biologically relevant questions using images. The code and datasets for running all the analyses reported in this paper can be found at https://github.com/sammarfy/VLM4Bio.

Novel Categories Discovery (NCD) facilitates learning from a partially annotated label space and enables deep learning (DL) models to operate in an open-world setting by identifying and differentiating instances of novel classes based on the labeled data notions. One of the primary assumptions of NCD is that the novel label space is perfectly disjoint and can be equipartitioned, but it is rarely realized by most NCD approaches in practice. To better align with this assumption, we propose a novel single-stage joint optimization-based NCD method, Negative learning, Entropy, and Variance regularization NCD (NEV-NCD). We demonstrate the efficacy of NEV-NCD in previously unexplored NCD applications of video action recognition (VAR) with the public UCF101 dataset and a curated in-house partial action-space annotated multi-view video dataset. We perform a thorough ablation study by varying the composition of final joint loss and associated hyper-parameters. During our experiments with UCF101 and multi-view action dataset, NEV-NCD achieves ~ 83% classification accuracy in test instances of labeled data. NEV-NCD achieves ~ 70% clustering accuracy over unlabeled data outperforming both naive baselines (by ~ 40%) and state-of-the-art pseudo-labeling-based approaches (by ~ 3.5%) over both datasets. Further, we propose to incorporate optional view-invariant feature learning with the multiview dataset to identify novel categories from novel viewpoints. Our additional view-invariance constraint improves the discriminative accuracy for both known and unknown categories by ~ 10% for novel viewpoints.

Work on scaling laws has found that large language models (LMs) show predictable improvements to overall loss with increased scale (model size, training data, and compute). Here, we present evidence for the claim that LMs may show inverse scaling, or worse task performance with increased scale, e.g., due to flaws in the training objective and data. We present empirical evidence of inverse scaling on 11 datasets collected by running a public contest, the Inverse Scaling Prize, with a substantial prize pool. Through analysis of the datasets, along with other examples found in the literature, we identify four potential causes of inverse scaling: (i) preference to repeat memorized sequences over following in-context instructions, (ii) imitation of undesirable patterns in the training data, (iii) tasks containing an easy distractor task which LMs could focus on, rather than the harder real task, and (iv) correct but misleading few-shot demonstrations of the task. We release the winning datasets at https://inversescaling.com/data to allow for further investigation of inverse scaling. Our tasks have helped drive the discovery of U-shaped and inverted-U scaling trends, where an initial trend reverses, suggesting that scaling trends are less reliable at predicting the behavior of larger-scale models than previously understood. Overall, our results suggest that there are tasks for which increased model scale alone may not lead to progress, and that more careful thought needs to go into the data and objectives for training language models.

Knowledge discovery and collection are intelligence-intensive tasks that traditionally require significant human effort to ensure high-quality outputs. Recent research has explored multi-agent frameworks for automating Wikipedia-style article generation by retrieving and synthesizing information from the internet. However, these methods primarily focus on text-only generation, overlooking the importance of multimodal content in enhancing informativeness and engagement. In this work, we introduce WikiAutoGen, a novel system for automated multimodal Wikipedia-style article generation. Unlike prior approaches, WikiAutoGen retrieves and integrates relevant images alongside text, enriching both the depth and visual appeal of generated content. To further improve factual accuracy and comprehensiveness, we propose a multi-perspective self-reflection mechanism, which critically assesses retrieved content from diverse viewpoints to enhance reliability, breadth, and coherence, etc. Additionally, we introduce WikiSeek, a benchmark comprising Wikipedia articles with topics paired with both textual and image-based representations, designed to evaluate multimodal knowledge generation on more challenging topics. Experimental results show that WikiAutoGen outperforms previous methods by 8%-29% on our WikiSeek benchmark, producing more accurate, coherent, and visually enriched Wikipedia-style articles. We show some of our generated examples in https://wikiautogen.github.io/ .

Rationale discovery is defined as finding a subset of the input data that maximally supports the prediction of downstream tasks. In graph machine learning context, graph rationale is defined to locate the critical subgraph in the given graph topology, which fundamentally determines the prediction results. In contrast to the rationale subgraph, the remaining subgraph is named the environment subgraph. Graph rationalization can enhance the model performance as the mapping between the graph rationale and prediction label is viewed as invariant, by assumption. To ensure the discriminative power of the extracted rationale subgraphs, a key technique named "intervention" is applied. The core idea of intervention is that given any changing environment subgraphs, the semantics from the rationale subgraph is invariant, which guarantees the correct prediction result. However, most, if not all, of the existing rationalization works on graph data develop their intervention strategies on the graph level, which is coarse-grained. In this paper, we propose well-tailored intervention strategies on graph data. Our idea is driven by the development of Transformer models, whose self-attention module provides rich interactions between input nodes. Based on the self-attention module, our proposed invariant graph Transformer (IGT) can achieve fine-grained, more specifically, node-level and virtual node-level intervention. Our comprehensive experiments involve 7 real-world datasets, and the proposed IGT shows significant performance advantages compared to 13 baseline methods.

Retrieval over visually rich documents is essential for tasks such as legal discovery, scientific search, and enterprise knowledge management. Existing approaches fall into two paradigms: single-vector retrieval, which is efficient but coarse, and multi-vector retrieval, which is accurate but computationally expensive. To address this trade-off, we propose HEAVEN, a two-stage hybrid-vector framework. In the first stage, HEAVEN efficiently retrieves candidate pages using a single-vector method over Visually-Summarized Pages (VS-Pages), which assemble representative visual layouts from multiple pages. In the second stage, it reranks candidates with a multi-vector method while filtering query tokens by linguistic importance to reduce redundant computations. To evaluate retrieval systems under realistic conditions, we also introduce ViMDOC, the first benchmark for visually rich, multi-document, and long-document retrieval. Across four benchmarks, HEAVEN attains 99.87% of the Recall@1 performance of multi-vector models on average while reducing per-query computation by 99.82%, achieving efficiency and accuracy. Our code and datasets are available at: https://github.com/juyeonnn/HEAVEN

This paper presents an end-to-end neural architecture based on Diffusion Models for spatial puzzle solving, particularly jigsaw puzzle and room arrangement tasks. In the latter task, for instance, the proposed system "PuzzleFusion" takes a set of room layouts as polygonal curves in the top-down view and aligns the room layout pieces by estimating their 2D translations and rotations, akin to solving the jigsaw puzzle of room layouts. A surprising discovery of the paper is that the simple use of a Diffusion Model effectively solves these challenging spatial puzzle tasks as a conditional generation process. To enable learning of an end-to-end neural system, the paper introduces new datasets with ground-truth arrangements: 1) 2D Voronoi jigsaw dataset, a synthetic one where pieces are generated by Voronoi diagram of 2D pointset; and 2) MagicPlan dataset, a real one offered by MagicPlan from its production pipeline, where pieces are room layouts constructed by augmented reality App by real-estate consumers. The qualitative and quantitative evaluations demonstrate that our approach outperforms the competing methods by significant margins in all the tasks.

This work investigates the compatibility between label smoothing (LS) and knowledge distillation (KD). Contemporary findings addressing this thesis statement take dichotomous standpoints: Muller et al. (2019) and Shen et al. (2021b). Critically, there is no effort to understand and resolve these contradictory findings, leaving the primal question -- to smooth or not to smooth a teacher network? -- unanswered. The main contributions of our work are the discovery, analysis and validation of systematic diffusion as the missing concept which is instrumental in understanding and resolving these contradictory findings. This systematic diffusion essentially curtails the benefits of distilling from an LS-trained teacher, thereby rendering KD at increased temperatures ineffective. Our discovery is comprehensively supported by large-scale experiments, analyses and case studies including image classification, neural machine translation and compact student distillation tasks spanning across multiple datasets and teacher-student architectures. Based on our analysis, we suggest practitioners to use an LS-trained teacher with a low-temperature transfer to achieve high performance students. Code and models are available at https://keshik6.github.io/revisiting-ls-kd-compatibility/

Learning neural subset selection tasks, such as compound selection in AI-aided drug discovery, have become increasingly pivotal across diverse applications. The existing methodologies in the field primarily concentrate on constructing models that capture the relationship between utility function values and subsets within their respective supersets. However, these approaches tend to overlook the valuable information contained within the superset when utilizing neural networks to model set functions. In this work, we address this oversight by adopting a probabilistic perspective. Our theoretical findings demonstrate that when the target value is conditioned on both the input set and subset, it is essential to incorporate an invariant sufficient statistic of the superset into the subset of interest for effective learning. This ensures that the output value remains invariant to permutations of the subset and its corresponding superset, enabling identification of the specific superset from which the subset originated. Motivated by these insights, we propose a simple yet effective information aggregation module designed to merge the representations of subsets and supersets from a permutation invariance perspective. Comprehensive empirical evaluations across diverse tasks and datasets validate the enhanced efficacy of our approach over conventional methods, underscoring the practicality and potency of our proposed strategies in real-world contexts.

Preparing high-quality datasets required by various data-driven AI and machine learning models has become a cornerstone task in data-driven analysis. Conventional data discovery methods typically integrate datasets towards a single pre-defined quality measure that may lead to bias for downstream tasks. This paper introduces MODis, a framework that discovers datasets by optimizing multiple user-defined, model-performance measures. Given a set of data sources and a model, MODis selects and integrates data sources into a skyline dataset, over which the model is expected to have the desired performance in all the performance measures. We formulate MODis as a multi-goal finite state transducer, and derive three feasible algorithms to generate skyline datasets. Our first algorithm adopts a "reduce-from-universal" strategy, that starts with a universal schema and iteratively prunes unpromising data. Our second algorithm further reduces the cost with a bi-directional strategy that interleaves data augmentation and reduction. We also introduce a diversification algorithm to mitigate the bias in skyline datasets. We experimentally verify the efficiency and effectiveness of our skyline data discovery algorithms, and showcase their applications in optimizing data science pipelines.

Large language models (LLMs) have shown remarkable ability in various language tasks, especially with their emergent in-context learning capability. Extending LLMs to incorporate visual inputs, large vision-language models (LVLMs) have shown impressive performance in tasks such as recognition and visual question answering (VQA). Despite increasing interest in the utility of LLMs in causal reasoning tasks such as causal discovery and counterfactual reasoning, there has been relatively little work showcasing the abilities of LVLMs on visual causal reasoning tasks. We take this opportunity to formally introduce a comprehensive causal reasoning benchmark for multi-modal in-context learning from LVLMs. Our CausalVLBench encompasses three representative tasks: causal structure inference, intervention target prediction, and counterfactual prediction. We evaluate the ability of state-of-the-art open-source LVLMs on our causal reasoning tasks across three causal representation learning datasets and demonstrate their fundamental strengths and weaknesses. We hope that our benchmark elucidates the drawbacks of existing vision-language models and motivates new directions and paradigms in improving the visual causal reasoning abilities of LVLMs.

With the rise of Large Language Models(LLMs), it has become crucial to understand their capabilities and limitations in deciphering and explaining the complex web of causal relationships that language entails. Current methods use either explicit or implicit causal reasoning, yet there is a strong need for a unified approach combining both to tackle a wide array of causal relationships more effectively. This research proposes a novel architecture called Context Aware Reasoning Enhancement with Counterfactual Analysis(CARE CA) framework to enhance causal reasoning and explainability. The proposed framework incorporates an explicit causal detection module with ConceptNet and counterfactual statements, as well as implicit causal detection through LLMs. Our framework goes one step further with a layer of counterfactual explanations to accentuate LLMs understanding of causality. The knowledge from ConceptNet enhances the performance of multiple causal reasoning tasks such as causal discovery, causal identification and counterfactual reasoning. The counterfactual sentences add explicit knowledge of the not caused by scenarios. By combining these powerful modules, our model aims to provide a deeper understanding of causal relationships, enabling enhanced interpretability. Evaluation of benchmark datasets shows improved performance across all metrics, such as accuracy, precision, recall, and F1 scores. We also introduce CausalNet, a new dataset accompanied by our code, to facilitate further research in this domain.

In an era where symbolic mathematical equations are indispensable for modeling complex natural phenomena, scientific inquiry often involves collecting observations and translating them into mathematical expressions. Recently, deep learning has emerged as a powerful tool for extracting insights from data. However, existing models typically specialize in either numeric or symbolic domains, and are usually trained in a supervised manner tailored to specific tasks. This approach neglects the substantial benefits that could arise from a task-agnostic unified understanding between symbolic equations and their numeric counterparts. To bridge the gap, we introduce SNIP, a Symbolic-Numeric Integrated Pre-training, which employs joint contrastive learning between symbolic and numeric domains, enhancing their mutual similarities in the pre-trained embeddings. By performing latent space analysis, we observe that SNIP provides cross-domain insights into the representations, revealing that symbolic supervision enhances the embeddings of numeric data and vice versa. We evaluate SNIP across diverse tasks, including symbolic-to-numeric mathematical property prediction and numeric-to-symbolic equation discovery, commonly known as symbolic regression. Results show that SNIP effectively transfers to various tasks, consistently outperforming fully supervised baselines and competing strongly with established task-specific methods, especially in few-shot learning scenarios where available data is limited.

Open-ended learning benefits immensely from the use of symbolic methods for goal representation as they offer ways to structure knowledge for efficient and transferable learning. However, the existing Hierarchical Reinforcement Learning (HRL) approaches relying on symbolic reasoning are often limited as they require a manual goal representation. The challenge in autonomously discovering a symbolic goal representation is that it must preserve critical information, such as the environment dynamics. In this paper, we propose a developmental mechanism for goal discovery via an emergent representation that abstracts (i.e., groups together) sets of environment states that have similar roles in the task. We introduce a Feudal HRL algorithm that concurrently learns both the goal representation and a hierarchical policy. The algorithm uses symbolic reachability analysis for neural networks to approximate the transition relation among sets of states and to refine the goal representation. We evaluate our approach on complex navigation tasks, showing the learned representation is interpretable, transferrable and results in data efficient learning.

Deep Learning has revolutionized vision via convolutional neural networks (CNNs) and natural language processing via recurrent neural networks (RNNs). However, success stories of Deep Learning with standard feed-forward neural networks (FNNs) are rare. FNNs that perform well are typically shallow and, therefore cannot exploit many levels of abstract representations. We introduce self-normalizing neural networks (SNNs) to enable high-level abstract representations. While batch normalization requires explicit normalization, neuron activations of SNNs automatically converge towards zero mean and unit variance. The activation function of SNNs are "scaled exponential linear units" (SELUs), which induce self-normalizing properties. Using the Banach fixed-point theorem, we prove that activations close to zero mean and unit variance that are propagated through many network layers will converge towards zero mean and unit variance -- even under the presence of noise and perturbations. This convergence property of SNNs allows to (1) train deep networks with many layers, (2) employ strong regularization, and (3) to make learning highly robust. Furthermore, for activations not close to unit variance, we prove an upper and lower bound on the variance, thus, vanishing and exploding gradients are impossible. We compared SNNs on (a) 121 tasks from the UCI machine learning repository, on (b) drug discovery benchmarks, and on (c) astronomy tasks with standard FNNs and other machine learning methods such as random forests and support vector machines. SNNs significantly outperformed all competing FNN methods at 121 UCI tasks, outperformed all competing methods at the Tox21 dataset, and set a new record at an astronomy data set. The winning SNN architectures are often very deep. Implementations are available at: github.com/bioinf-jku/SNNs.

While previous AI Scientist systems can generate novel findings, they often lack the focus to produce scientifically valuable contributions that address pressing human-defined challenges. We introduce DeepScientist, a system designed to overcome this by conducting goal-oriented, fully autonomous scientific discovery over month-long timelines. It formalizes discovery as a Bayesian Optimization problem, operationalized through a hierarchical evaluation process consisting of "hypothesize, verify, and analyze". Leveraging a cumulative Findings Memory, this loop intelligently balances the exploration of novel hypotheses with exploitation, selectively promoting the most promising findings to higher-fidelity levels of validation. Consuming over 20,000 GPU hours, the system generated about 5,000 unique scientific ideas and experimentally validated approximately 1100 of them, ultimately surpassing human-designed state-of-the-art (SOTA) methods on three frontier AI tasks by 183.7\%, 1.9\%, and 7.9\%. This work provides the first large-scale evidence of an AI achieving discoveries that progressively surpass human SOTA on scientific tasks, producing valuable findings that genuinely push the frontier of scientific discovery. To facilitate further research into this process, we will open-source all experimental logs and system code at https://github.com/ResearAI/DeepScientist/.

Learning cooperative multi-agent policy from offline multi-task data that can generalize to unseen tasks with varying numbers of agents and targets is an attractive problem in many scenarios. Although aggregating general behavior patterns among multiple tasks as skills to improve policy transfer is a promising approach, two primary challenges hinder the further advancement of skill learning in offline multi-task MARL. Firstly, extracting general cooperative behaviors from various action sequences as common skills lacks bringing cooperative temporal knowledge into them. Secondly, existing works only involve common skills and can not adaptively choose independent knowledge as task-specific skills in each task for fine-grained action execution. To tackle these challenges, we propose Hierarchical and Separate Skill Discovery (HiSSD), a novel approach for generalizable offline multi-task MARL through skill learning. HiSSD leverages a hierarchical framework that jointly learns common and task-specific skills. The common skills learn cooperative temporal knowledge and enable in-sample exploitation for offline multi-task MARL. The task-specific skills represent the priors of each task and achieve a task-guided fine-grained action execution. To verify the advancement of our method, we conduct experiments on multi-agent MuJoCo and SMAC benchmarks. After training the policy using HiSSD on offline multi-task data, the empirical results show that HiSSD assigns effective cooperative behaviors and obtains superior performance in unseen tasks.

With the discovery of Wasserstein GANs, Optimal Transport (OT) has become a powerful tool for large-scale generative modeling tasks. In these tasks, OT cost is typically used as the loss for training GANs. In contrast to this approach, we show that the OT map itself can be used as a generative model, providing comparable performance. Previous analogous approaches consider OT maps as generative models only in the latent spaces due to their poor performance in the original high-dimensional ambient space. In contrast, we apply OT maps directly in the ambient space, e.g., a space of high-dimensional images. First, we derive a min-max optimization algorithm to efficiently compute OT maps for the quadratic cost (Wasserstein-2 distance). Next, we extend the approach to the case when the input and output distributions are located in the spaces of different dimensions and derive error bounds for the computed OT map. We evaluate the algorithm on image generation and unpaired image restoration tasks. In particular, we consider denoising, colorization, and inpainting, where the optimality of the restoration map is a desired attribute, since the output (restored) image is expected to be close to the input (degraded) one.

We propose the LLMs4OL approach, which utilizes Large Language Models (LLMs) for Ontology Learning (OL). LLMs have shown significant advancements in natural language processing, demonstrating their ability to capture complex language patterns in different knowledge domains. Our LLMs4OL paradigm investigates the following hypothesis: Can LLMs effectively apply their language pattern capturing capability to OL, which involves automatically extracting and structuring knowledge from natural language text? To test this hypothesis, we conduct a comprehensive evaluation using the zero-shot prompting method. We evaluate nine different LLM model families for three main OL tasks: term typing, taxonomy discovery, and extraction of non-taxonomic relations. Additionally, the evaluations encompass diverse genres of ontological knowledge, including lexicosemantic knowledge in WordNet, geographical knowledge in GeoNames, and medical knowledge in UMLS.

Puzzlehunts are a genre of complex, multi-step puzzles lacking well-defined problem definitions. In contrast to conventional reasoning benchmarks consisting of tasks with clear instructions, puzzlehunts require models to discover the underlying problem structure from multimodal evidence and iterative reasoning, mirroring real-world domains such as scientific discovery, exploratory data analysis, or investigative problem-solving. Despite recent progress in foundation models, their performance on such open-ended settings remains largely untested. In this paper, we introduce PuzzleWorld, a large-scale benchmark of 667 puzzlehunt-style problems designed to assess step-by-step, open-ended, and creative multimodal reasoning. Each puzzle is annotated with the final solution, detailed reasoning traces, and cognitive skill labels, enabling holistic benchmarking and fine-grained diagnostic analysis. Most state-of-the-art models achieve only 1-2% final answer accuracy, with the best model solving only 14% of puzzles and reaching 40% stepwise accuracy. To demonstrate the value of our reasoning annotations, we show that fine-tuning a small model on reasoning traces improves stepwise reasoning from 4% to 11%, while training on final answers alone degrades performance to near zero. Our error analysis reveals that current models exhibit myopic reasoning, are bottlenecked by the limitations of language-based inference, and lack sketching capabilities crucial for visual and spatial reasoning. We release PuzzleWorld at https://github.com/MIT-MI/PuzzleWorld to support future work on building more general, open-ended, and creative reasoning systems.

Predicting in-hospital mortality for intensive care unit (ICU) patients is key to final clinical outcomes. AI has shown advantaged accuracy but suffers from the lack of explainability. To address this issue, this paper proposes an eXplainable Multimodal Mortality Predictor (X-MMP) approaching an efficient, explainable AI solution for predicting in-hospital mortality via multimodal ICU data. We employ multimodal learning in our framework, which can receive heterogeneous inputs from clinical data and make decisions. Furthermore, we introduce an explainable method, namely Layer-Wise Propagation to Transformer, as a proper extension of the LRP method to Transformers, producing explanations over multimodal inputs and revealing the salient features attributed to prediction. Moreover, the contribution of each modality to clinical outcomes can be visualized, assisting clinicians in understanding the reasoning behind decision-making. We construct a multimodal dataset based on MIMIC-III and MIMIC-III Waveform Database Matched Subset. Comprehensive experiments on benchmark datasets demonstrate that our proposed framework can achieve reasonable interpretation with competitive prediction accuracy. In particular, our framework can be easily transferred to other clinical tasks, which facilitates the discovery of crucial factors in healthcare research.

Large Language Models (LLMs) have revolutionized natural language processing, excelling in handling longer sequences. However, the inefficiency and redundancy in processing extended in-context tokens remain a challenge. Many attempts to address this rely on compressing tokens with smaller text encoders, yet we question whether text encoders are truly indispensable. Our journey leads to an unexpected discovery-a much smaller vision encoder, applied directly to sequences of text tokens, can rival text encoders on text tasks. When pre-trained on large amounts of data and transferred to multiple mid-sized or small text understanding benchmarks, VIST leads to comparable results with 16% fewer FLOPs and 50% less memory usage. We further uncover significant token redundancy and devise a frequency-based masking strategy to guide the focus of the visual encoder toward the most critical tokens. Interestingly, we observe the trained visual encoder performs like a summarizer, selectively ignoring less important words such as prepositions and conjunctions. This approach delivers remarkable results, outperforming traditional text encoder-based methods by 5.7% on average over benchmarks like TriviaQA, NQ, PopQA, TREF, SST2, and SST5, setting a new standard for token efficiency in LLMs.

Foundation models (FMs) have exhibited remarkable performance across a wide range of downstream tasks in many domains. Nevertheless, general-purpose FMs often face challenges when confronted with domain-specific problems, due to their limited access to the proprietary training data in a particular domain. In biomedicine, there are various biological modalities, such as molecules, proteins, and cells, which are encoded by the language of life and exhibit significant modality gaps with human natural language. In this paper, we introduce BioMedGPT, an open multimodal generative pre-trained transformer (GPT) for biomedicine, to bridge the gap between the language of life and human natural language. BioMedGPT allows users to easily ``communicate'' with diverse biological modalities through free text, which is the first of its kind. BioMedGPT aligns different biological modalities with natural language via a large generative language model, namely, BioMedGPT-LM. We publish BioMedGPT-10B, which unifies the feature spaces of molecules, proteins, and natural language via encoding and alignment. Through fine-tuning, BioMedGPT-10B outperforms or is on par with human and significantly larger general-purpose foundation models on the biomedical QA task. It also demonstrates promising performance in the molecule QA and protein QA tasks, which could greatly accelerate the discovery of new drugs and therapeutic targets. In addition, BioMedGPT-LM-7B is the first large generative language model based on Llama2 in the biomedical domain, therefore is commercial friendly. Both BioMedGPT-10B and BioMedGPT-LM-7B are open-sourced to the research community. In addition, we publish the datasets that are meticulously curated for the alignment of multi-modalities, i.e., PubChemQA and UniProtQA. All the models, codes, and datasets are available at https://github.com/PharMolix/OpenBioMed.

Identifying recurring patterns and rare events in large-scale signals is a fundamental challenge in fields such as astronomy, physical simulations, and biomedical science. Convolutional Dictionary Learning (CDL) offers a powerful framework for modeling local structures in signals, but its use for detecting rare or anomalous events remains largely unexplored. In particular, CDL faces two key challenges in this setting: high computational cost and sensitivity to artifacts and outliers. In this paper, we introduce RoseCDL, a scalable and robust CDL algorithm designed for unsupervised rare event detection in long signals. RoseCDL combines stochastic windowing for efficient training on large datasets with inline outlier detection to enhance robustness and isolate anomalous patterns. This reframes CDL as a practical tool for event discovery and characterization in real-world signals, extending its role beyond traditional tasks like compression or denoising.

It has long been known in both neuroscience and AI that ``binding'' between neurons leads to a form of competitive learning where representations are compressed in order to represent more abstract concepts in deeper layers of the network. More recently, it was also hypothesized that dynamic (spatiotemporal) representations play an important role in both neuroscience and AI. Building on these ideas, we introduce Artificial Kuramoto Oscillatory Neurons (AKOrN) as a dynamical alternative to threshold units, which can be combined with arbitrary connectivity designs such as fully connected, convolutional, or attentive mechanisms. Our generalized Kuramoto updates bind neurons together through their synchronization dynamics. We show that this idea provides performance improvements across a wide spectrum of tasks such as unsupervised object discovery, adversarial robustness, calibrated uncertainty quantification, and reasoning. We believe that these empirical results show the importance of rethinking our assumptions at the most basic neuronal level of neural representation, and in particular show the importance of dynamical representations.

Self-supervised image backbones can be used to address complex 2D tasks (e.g., semantic segmentation, object discovery) very efficiently and with little or no downstream supervision. Ideally, 3D backbones for lidar should be able to inherit these properties after distillation of these powerful 2D features. The most recent methods for image-to-lidar distillation on autonomous driving data show promising results, obtained thanks to distillation methods that keep improving. Yet, we still notice a large performance gap when measuring the quality of distilled and fully supervised features by linear probing. In this work, instead of focusing only on the distillation method, we study the effect of three pillars for distillation: the 3D backbone, the pretrained 2D backbones, and the pretraining dataset. In particular, thanks to our scalable distillation method named ScaLR, we show that scaling the 2D and 3D backbones and pretraining on diverse datasets leads to a substantial improvement of the feature quality. This allows us to significantly reduce the gap between the quality of distilled and fully-supervised 3D features, and to improve the robustness of the pretrained backbones to domain gaps and perturbations.

The extraction of modular object-centric representations for downstream tasks is an emerging area of research. Learning grounded representations of objects that are guaranteed to be stable and invariant promises robust performance across different tasks and environments. Slot Attention (SA) learns object-centric representations by assigning objects to slots, but presupposes a single distribution from which all slots are randomly initialised. This results in an inability to learn specialized slots which bind to specific object types and remain invariant to identity-preserving changes in object appearance. To address this, we present \textsc{Conditional Slot Attention} (CoSA) using a novel concept of Grounded Slot Dictionary (GSD) inspired by vector quantization. Our proposed GSD comprises (i) canonical object-level property vectors and (ii) parametric Gaussian distributions, which define a prior over the slots. We demonstrate the benefits of our method in multiple downstream tasks such as scene generation, composition, and task adaptation, whilst remaining competitive with SA in popular object discovery benchmarks.

Although large language models (LLMs) have significant potential to advance chemical discovery, current LLMs lack core chemical knowledge, produce unreliable reasoning trajectories, and exhibit suboptimal performance across diverse chemical tasks. To address these challenges, we propose Chem-R, a generalizable Chemical Reasoning model designed to emulate the deliberative processes of chemists. Chem-R is trained through a three-phase framework that progressively builds advanced reasoning capabilities, including: 1) Chemical Foundation Training, which establishes core chemical knowledge. 2) Chemical Reasoning Protocol Distillation, incorporating structured, expert-like reasoning traces to guide systematic and reliable problem solving. 3) Multi-task Group Relative Policy Optimization that optimizes the model for balanced performance across diverse molecular- and reaction-level tasks. This structured pipeline enables Chem-R to achieve state-of-the-art performance on comprehensive benchmarks, surpassing leading large language models, including Gemini-2.5-Pro and DeepSeek-R1, by up to 46% on molecular tasks and 66% on reaction tasks. Meanwhile, Chem-R also consistently outperforms the existing chemical foundation models across both molecular and reaction level tasks. These results highlight Chem-R's robust generalization, interpretability, and potential as a foundation for next-generation AI-driven chemical discovery.

Self-supervised skill learning aims to acquire useful behaviors that leverage the underlying dynamics of the environment. Latent variable models, based on mutual information maximization, have been successful in this task but still struggle in the context of robotic manipulation. As it requires impacting a possibly large set of degrees of freedom composing the environment, mutual information maximization fails alone in producing useful and safe manipulation behaviors. Furthermore, tackling this by augmenting skill discovery rewards with additional rewards through a naive combination might fail to produce desired behaviors. To address this limitation, we introduce SLIM, a multi-critic learning approach for skill discovery with a particular focus on robotic manipulation. Our main insight is that utilizing multiple critics in an actor-critic framework to gracefully combine multiple reward functions leads to a significant improvement in latent-variable skill discovery for robotic manipulation while overcoming possible interference occurring among rewards which hinders convergence to useful skills. Furthermore, in the context of tabletop manipulation, we demonstrate the applicability of our novel skill discovery approach to acquire safe and efficient motor primitives in a hierarchical reinforcement learning fashion and leverage them through planning, significantly surpassing baseline approaches for skill discovery.

Cutting-edge Artificial Intelligence (AI) techniques keep reshaping our view of the world. For example, Large Language Models (LLMs) based applications such as ChatGPT have shown the capability of generating human-like conversation on extensive topics. Due to the impressive performance on a variety of language-related tasks (e.g., open-domain question answering, translation, and document summarization), one can envision the far-reaching impacts that can be brought by the LLMs with broader real-world applications (e.g., customer service, education and accessibility, and scientific discovery). Inspired by their success, this paper will offer an overview of state-of-the-art LLMs and their integration into a wide range of academic disciplines, including: (1) arts, letters, and law (e.g., history, philosophy, political science, arts and architecture, law), (2) economics and business (e.g., finance, economics, accounting, marketing), and (3) science and engineering (e.g., mathematics, physics and mechanical engineering, chemistry and chemical engineering, life sciences and bioengineering, earth sciences and civil engineering, computer science and electrical engineering). Integrating humanity and technology, in this paper, we will explore how LLMs are shaping research and practice in these fields, while also discussing key limitations, open challenges, and future directions in the era of generative AI. The review of how LLMs are engaged across disciplines-along with key observations and insights-can help researchers and practitioners interested in exploiting LLMs to advance their works in diverse real-world applications.

Chemical reasoning usually involves complex, multi-step processes that demand precise calculations, where even minor errors can lead to cascading failures. Furthermore, large language models (LLMs) encounter difficulties handling domain-specific formulas, executing reasoning steps accurately, and integrating code effectively when tackling chemical reasoning tasks. To address these challenges, we present ChemAgent, a novel framework designed to improve the performance of LLMs through a dynamic, self-updating library. This library is developed by decomposing chemical tasks into sub-tasks and compiling these sub-tasks into a structured collection that can be referenced for future queries. Then, when presented with a new problem, ChemAgent retrieves and refines pertinent information from the library, which we call memory, facilitating effective task decomposition and the generation of solutions. Our method designs three types of memory and a library-enhanced reasoning component, enabling LLMs to improve over time through experience. Experimental results on four chemical reasoning datasets from SciBench demonstrate that ChemAgent achieves performance gains of up to 46% (GPT-4), significantly outperforming existing methods. Our findings suggest substantial potential for future applications, including tasks such as drug discovery and materials science. Our code can be found at https://github.com/gersteinlab/chemagent

Over the last decades, excellent computational chemistry tools have been developed. Their full potential has not yet been reached as most are challenging to learn and exist in isolation. Recently, large-language models (LLMs) have shown strong performance in tasks across domains, but struggle with chemistry-related problems. Moreover, these models lack access to external knowledge sources, limiting their usefulness in scientific applications. In this study, we introduce ChemCrow, an LLM chemistry agent designed to accomplish tasks across organic synthesis, drug discovery, and materials design. By integrating 17 expert-designed tools, ChemCrow augments the LLM performance in chemistry, and new capabilities emerge. Our agent autonomously planned the syntheses of an insect repellent, three organocatalysts, as well as other relevant molecules. Our evaluation, including both LLM and expert assessments, demonstrates ChemCrow's effectiveness in automating a diverse set of chemical tasks. Surprisingly, we find that GPT-4 as an evaluator cannot distinguish between clearly wrong GPT-4 completions and Chemcrow's performance. There is a significant risk of misuse of tools like ChemCrow, and we discuss their potential harms. Employed responsibly, our work not only aids expert chemists and lowers barriers for non-experts, but also fosters scientific advancement by bridging the gap between experimental and computational chemistry. A subset of the code is publicly available at https://github.com/ur-whitelab/chemcrow-public.

Unsupervised learning methods based on contrastive learning have drawn increasing attention and achieved promising results. Most of them aim to learn representations invariant to instance-level variations, which are provided by different views of the same instance. In this paper, we propose Invariance Propagation to focus on learning representations invariant to category-level variations, which are provided by different instances from the same category. Our method recursively discovers semantically consistent samples residing in the same high-density regions in representation space. We demonstrate a hard sampling strategy to concentrate on maximizing the agreement between the anchor sample and its hard positive samples, which provide more intra-class variations to help capture more abstract invariance. As a result, with a ResNet-50 as the backbone, our method achieves 71.3% top-1 accuracy on ImageNet linear classification and 78.2% top-5 accuracy fine-tuning on only 1% labels, surpassing previous results. We also achieve state-of-the-art performance on other downstream tasks, including linear classification on Places205 and Pascal VOC, and transfer learning on small scale datasets.

Curiosity-based reward schemes can present powerful exploration mechanisms which facilitate the discovery of solutions for complex, sparse or long-horizon tasks. However, as the agent learns to reach previously unexplored spaces and the objective adapts to reward new areas, many behaviours emerge only to disappear due to being overwritten by the constantly shifting objective. We argue that merely using curiosity for fast environment exploration or as a bonus reward for a specific task does not harness the full potential of this technique and misses useful skills. Instead, we propose to shift the focus towards retaining the behaviours which emerge during curiosity-based learning. We posit that these self-discovered behaviours serve as valuable skills in an agent's repertoire to solve related tasks. Our experiments demonstrate the continuous shift in behaviour throughout training and the benefits of a simple policy snapshot method to reuse discovered behaviour for transfer tasks.

Despite recent breakthroughs in reasoning-enhanced large language models (LLMs) like DeepSeek-R1, incorporating inference-time reasoning into machine translation (MT), where human translators naturally employ structured, multi-layered reasoning chain-of-thoughts (CoTs), is yet underexplored. Existing methods either design a fixed CoT tailored for a specific MT sub-task (e.g., literature translation), or rely on synthesizing CoTs unaligned with humans and supervised fine-tuning (SFT) prone to catastrophic forgetting, limiting their adaptability to diverse translation scenarios. This paper introduces R1-Translator (R1-T1), a novel framework to achieve inference-time reasoning for general MT via reinforcement learning (RL) with human-aligned CoTs comprising six common patterns. Our approach pioneers three innovations: (1) extending reasoning-based translation beyond MT sub-tasks to six languages and diverse tasks (e.g., legal/medical domain adaptation, idiom resolution); (2) formalizing six expert-curated CoT templates that mirror hybrid human strategies like context-aware paraphrasing and back translation; and (3) enabling self-evolving CoT discovery and anti-forgetting adaptation through RL with KL-constrained rewards. Experimental results indicate a steady translation performance improvement in 21 languages and 80 translation directions on Flores-101 test set, especially on the 15 languages unseen from training, with its general multilingual abilities preserved compared with plain SFT.

Playlists have become a significant part of our listening experience because of the digital cloud-based services such as Spotify, Pandora, Apple Music. Owing to the meteoric rise in the usage of playlists, recommending playlists is crucial to music services today. Although there has been a lot of work done in playlist prediction, the area of playlist representation hasn't received that level of attention. Over the last few years, sequence-to-sequence models, especially in the field of natural language processing, have shown the effectiveness of learned embeddings in capturing the semantic characteristics of sequences. We can apply similar concepts to music to learn fixed length representations for playlists and use those representations for downstream tasks such as playlist discovery, browsing, and recommendation. In this work, we formulate the problem of learning a fixed-length playlist representation in an unsupervised manner, using Sequence-to-sequence (Seq2seq) models, interpreting playlists as sentences and songs as words. We compare our model with two other encoding architectures for baseline comparison. We evaluate our work using the suite of tasks commonly used for assessing sentence embeddings, along with a few additional tasks pertaining to music, and a recommendation task to study the traits captured by the playlist embeddings and their effectiveness for the purpose of music recommendation.

Scientific innovation is undergoing a paradigm shift driven by the rapid advancement of Large Language Models (LLMs). As science faces mounting challenges including information overload, disciplinary silos, and diminishing returns on conventional research methods, LLMs are emerging as powerful agents capable not only of enhancing scientific workflows but also of participating in and potentially leading the innovation process. Existing surveys mainly focus on different perspectives, phrases, and tasks in scientific research and discovery, while they have limitations in understanding the transformative potential and role differentiation of LLM. This survey proposes a comprehensive framework to categorize the evolving roles of LLMs in scientific innovation across three hierarchical levels: Evaluator, Collaborator, and Scientist. We distinguish between LLMs' contributions to structured scientific research processes and open-ended scientific discovery, thereby offering a unified taxonomy that clarifies capability boundaries, evaluation criteria, and human-AI interaction patterns at each level. Through an extensive analysis of current methodologies, benchmarks, systems, and evaluation metrics, this survey delivers an in-depth and systematic synthesis on LLM-driven scientific innovation. We present LLMs not only as tools for automating existing processes, but also as catalysts capable of reshaping the epistemological foundations of science itself. This survey offers conceptual clarity, practical guidance, and theoretical foundations for future research, while also highlighting open challenges and ethical considerations in the pursuit of increasingly autonomous AI-driven science. Resources related to this survey can be accessed on GitHub at: https://github.com/haoxuan-unt2024/llm4innovation.

Neural architecture search (NAS), the study of automating the discovery of optimal deep neural network architectures for tasks in domains such as computer vision and natural language processing, has seen rapid growth in the machine learning research community. While there have been many recent advancements in NAS, there is still a significant focus on reducing the computational cost incurred when validating discovered architectures by making search more efficient. Evolutionary algorithms, specifically genetic algorithms, have a history of usage in NAS and continue to gain popularity versus other optimization approaches as a highly efficient way to explore the architecture objective space. Most NAS research efforts have centered around computer vision tasks and only recently have other modalities, such as the rapidly growing field of natural language processing, been investigated in depth. In this work, we show how genetic algorithms can be paired with lightly trained objective predictors in an iterative cycle to accelerate multi-objective architectural exploration in a way that works in the modalities of both machine translation and image classification.

This paper describes the ARIEL-CMU submissions to the Low Resource Human Language Technologies (LoReHLT) 2018 evaluations for the tasks Machine Translation (MT), Entity Discovery and Linking (EDL), and detection of Situation Frames in Text and Speech (SF Text and Speech).

Training generally capable agents that thoroughly explore their environment and learn new and diverse skills is a long-term goal of robot learning. Quality Diversity Reinforcement Learning (QD-RL) is an emerging research area that blends the best aspects of both fields -- Quality Diversity (QD) provides a principled form of exploration and produces collections of behaviorally diverse agents, while Reinforcement Learning (RL) provides a powerful performance improvement operator enabling generalization across tasks and dynamic environments. Existing QD-RL approaches have been constrained to sample efficient, deterministic off-policy RL algorithms and/or evolution strategies, and struggle with highly stochastic environments. In this work, we, for the first time, adapt on-policy RL, specifically Proximal Policy Optimization (PPO), to the Differentiable Quality Diversity (DQD) framework and propose additional improvements over prior work that enable efficient optimization and discovery of novel skills on challenging locomotion tasks. Our new algorithm, Proximal Policy Gradient Arborescence (PPGA), achieves state-of-the-art results, including a 4x improvement in best reward over baselines on the challenging humanoid domain.

Many patterns in nature exhibit self-similarity: they can be compactly described via self-referential transformations. Said patterns commonly appear in natural and artificial objects, such as molecules, shorelines, galaxies and even images. In this work, we investigate the role of learning in the automated discovery of self-similarity and in its utilization for downstream tasks. To this end, we design a novel class of implicit operators, Neural Collages, which (1) represent data as the parameters of a self-referential, structured transformation, and (2) employ hypernetworks to amortize the cost of finding these parameters to a single forward pass. We investigate how to leverage the representations produced by Neural Collages in various tasks, including data compression and generation. Neural Collages image compressors are orders of magnitude faster than other self-similarity-based algorithms during encoding and offer compression rates competitive with implicit methods. Finally, we showcase applications of Neural Collages for fractal art and as deep generative models.

Learning object-centric representations of complex scenes is a promising step towards enabling efficient abstract reasoning from low-level perceptual features. Yet, most deep learning approaches learn distributed representations that do not capture the compositional properties of natural scenes. In this paper, we present the Slot Attention module, an architectural component that interfaces with perceptual representations such as the output of a convolutional neural network and produces a set of task-dependent abstract representations which we call slots. These slots are exchangeable and can bind to any object in the input by specializing through a competitive procedure over multiple rounds of attention. We empirically demonstrate that Slot Attention can extract object-centric representations that enable generalization to unseen compositions when trained on unsupervised object discovery and supervised property prediction tasks.

Transformers have recently emerged as a powerful tool for learning visual representations. In this paper, we identify and characterize artifacts in feature maps of both supervised and self-supervised ViT networks. The artifacts correspond to high-norm tokens appearing during inference primarily in low-informative background areas of images, that are repurposed for internal computations. We propose a simple yet effective solution based on providing additional tokens to the input sequence of the Vision Transformer to fill that role. We show that this solution fixes that problem entirely for both supervised and self-supervised models, sets a new state of the art for self-supervised visual models on dense visual prediction tasks, enables object discovery methods with larger models, and most importantly leads to smoother feature maps and attention maps for downstream visual processing.

Information tasks such as writing surveys or analytical reports require complex search and reasoning, and have recently been grouped under the umbrella of deep research -- a term also adopted by recent models targeting these capabilities. Despite growing interest, the scope of the deep research task remains underdefined and its distinction from other reasoning-intensive problems is poorly understood. In this paper, we propose a formal characterization of the deep research (DR) task and introduce a benchmark to evaluate the performance of DR systems. We argue that the core defining feature of deep research is not the production of lengthy report-style outputs, but rather the high fan-out over concepts required during the search process, i.e., broad and reasoning-intensive exploration. To enable objective evaluation, we define DR using an intermediate output representation that encodes key claims uncovered during search-separating the reasoning challenge from surface-level report generation. Based on this formulation, we propose a diverse, challenging benchmark LiveDRBench with 100 challenging tasks over scientific topics (e.g., datasets, materials discovery, prior art search) and public interest events (e.g., flight incidents, movie awards). Across state-of-the-art DR systems, F1 score ranges between 0.02 and 0.72 for any sub-category. OpenAI's model performs the best with an overall F1 score of 0.55. Analysis of reasoning traces reveals the distribution over the number of referenced sources, branching, and backtracking events executed by current DR systems, motivating future directions for improving their search mechanisms and grounding capabilities. The benchmark is available at https://github.com/microsoft/LiveDRBench.

Data of sequential nature arise in many application domains in forms of, e.g. textual data, DNA sequences, and software execution traces. Different research disciplines have developed methods to learn sequence models from such datasets: (i) in the machine learning field methods such as (hidden) Markov models and recurrent neural networks have been developed and successfully applied to a wide-range of tasks, (ii) in process mining process discovery techniques aim to generate human-interpretable descriptive models, and (iii) in the grammar inference field the focus is on finding descriptive models in the form of formal grammars. Despite their different focuses, these fields share a common goal - learning a model that accurately describes the behavior in the underlying data. Those sequence models are generative, i.e, they can predict what elements are likely to occur after a given unfinished sequence. So far, these fields have developed mainly in isolation from each other and no comparison exists. This paper presents an interdisciplinary experimental evaluation that compares sequence modeling techniques on the task of next-element prediction on four real-life sequence datasets. The results indicate that machine learning techniques that generally have no aim at interpretability in terms of accuracy outperform techniques from the process mining and grammar inference fields that aim to yield interpretable models.

Accurately classifying chemical structures is essential for cheminformatics and bioinformatics, including tasks such as identifying bioactive compounds of interest, screening molecules for toxicity to humans, finding non-organic compounds with desirable material properties, or organizing large chemical libraries for drug discovery or environmental monitoring. However, manual classification is labor-intensive and difficult to scale to large chemical databases. Existing automated approaches either rely on manually constructed classification rules, or the use of deep learning methods that lack explainability. This work presents an approach that uses generative artificial intelligence to automatically write chemical classifier programs for classes in the Chemical Entities of Biological Interest (ChEBI) database. These programs can be used for efficient deterministic run-time classification of SMILES structures, with natural language explanations. The programs themselves constitute an explainable computable ontological model of chemical class nomenclature, which we call the ChEBI Chemical Class Program Ontology (C3PO). We validated our approach against the ChEBI database, and compared our results against state of the art deep learning models. We also demonstrate the use of C3PO to classify out-of-distribution examples taken from metabolomics repositories and natural product databases. We also demonstrate the potential use of our approach to find systematic classification errors in existing chemical databases, and show how an ensemble artificial intelligence approach combining generated ontologies, automated literature search, and multimodal vision models can be used to pinpoint potential errors requiring expert validation

We revisit the well-studied problem of approximating a matrix product, A^TB, based on small space sketches S(A) and S(B) of A in R^{n times d} and Bin R^{n times m}. We are interested in the setting where the sketches must be computed independently of each other, except for the use of a shared random seed. We prove that, when A and B are sparse, methods based on coordinated random sampling can outperform classical linear sketching approaches, like Johnson-Lindenstrauss Projection or CountSketch. For example, to obtain Frobenius norm error epsilon|A|_F|B|_F, coordinated sampling requires sketches of size O(s/epsilon^2) when A and B have at most s leq d,m non-zeros per row. In contrast, linear sketching leads to sketches of size O(d/epsilon^2) and O(m/epsilon^2) for A and B. We empirically evaluate our approach on two applications: 1) distributed linear regression in databases, a problem motivated by tasks like dataset discovery and augmentation, and 2) approximating attention matrices in transformer-based language models. In both cases, our sampling algorithms yield an order of magnitude improvement over linear sketching.

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

Recent breakthroughs in large language models (LLMs) offer unprecedented natural language understanding and generation capabilities. However, existing surveys on LLMs in biomedicine often focus on specific applications or model architectures, lacking a comprehensive analysis that integrates the latest advancements across various biomedical domains. This review, based on an analysis of 484 publications sourced from databases including PubMed, Web of Science, and arXiv, provides an in-depth examination of the current landscape, applications, challenges, and prospects of LLMs in biomedicine, distinguishing itself by focusing on the practical implications of these models in real-world biomedical contexts. Firstly, we explore the capabilities of LLMs in zero-shot learning across a broad spectrum of biomedical tasks, including diagnostic assistance, drug discovery, and personalized medicine, among others, with insights drawn from 137 key studies. Then, we discuss adaptation strategies of LLMs, including fine-tuning methods for both uni-modal and multi-modal LLMs to enhance their performance in specialized biomedical contexts where zero-shot fails to achieve, such as medical question answering and efficient processing of biomedical literature. Finally, we discuss the challenges that LLMs face in the biomedicine domain including data privacy concerns, limited model interpretability, issues with dataset quality, and ethics due to the sensitive nature of biomedical data, the need for highly reliable model outputs, and the ethical implications of deploying AI in healthcare. To address these challenges, we also identify future research directions of LLM in biomedicine including federated learning methods to preserve data privacy and integrating explainable AI methodologies to enhance the transparency of LLMs.

High-quality data is crucial for accurate machine learning and actionable analytics, however, mislabeled or noisy data is a common problem in many domains. Distinguishing low- from high-quality data can be challenging, often requiring expert knowledge and considerable manual intervention. Data Valuation algorithms are a class of methods that seek to quantify the value of each sample in a dataset based on its contribution or importance to a given predictive task. These data values have shown an impressive ability to identify mislabeled observations, and filtering low-value data can boost machine learning performance. In this work, we present a simple alternative to existing methods, termed Data Valuation with Gradient Similarity (DVGS). This approach can be easily applied to any gradient descent learning algorithm, scales well to large datasets, and performs comparably or better than baseline valuation methods for tasks such as corrupted label discovery and noise quantification. We evaluate the DVGS method on tabular, image and RNA expression datasets to show the effectiveness of the method across domains. Our approach has the ability to rapidly and accurately identify low-quality data, which can reduce the need for expert knowledge and manual intervention in data cleaning tasks.

Artificial intelligence is transforming computational materials science, improving the prediction of material properties, and accelerating the discovery of novel materials. Recently, publicly available material data repositories have grown rapidly. This growth encompasses not only more materials, but also a greater variety and quantity of their associated properties. Existing machine learning efforts in materials science focus primarily on single-modality tasks, i.e., relationships between materials and a single physical property, thus not taking advantage of the rich and multimodal set of material properties. Here, we introduce Multimodal Learning for Materials (MultiMat), which enables self-supervised multi-modality training of foundation models for materials. We demonstrate our framework's potential using data from the Materials Project database on multiple axes: (i) MultiMat achieves state-of-the-art performance for challenging material property prediction tasks; (ii) MultiMat enables novel and accurate material discovery via latent space similarity, enabling screening for stable materials with desired properties; and (iii) MultiMat encodes interpretable emergent features that may provide novel scientific insights.

We introduce ShinkaEvolve: a new open-source framework leveraging large language models (LLMs) to advance scientific discovery with state-of-the-art performance and unprecedented efficiency. Recent advances in scaling inference time compute of LLMs have enabled significant progress in generalized scientific discovery. These approaches rely on evolutionary agentic harnesses that leverage LLMs as mutation operators to generate candidate solutions. However, current code evolution methods suffer from critical limitations: they are sample inefficient, requiring thousands of samples to identify effective solutions, and remain closed-source, hindering broad adoption and extension. ShinkaEvolve addresses these limitations, introducing three key innovations: a parent sampling technique balancing exploration and exploitation, code novelty rejection-sampling for efficient search space exploration, and a bandit-based LLM ensemble selection strategy. We evaluate ShinkaEvolve across diverse tasks, demonstrating consistent improvements in sample efficiency and solution quality. ShinkaEvolve discovers a new state-of-the-art circle packing solution using only 150 samples, designs high-performing agentic harnesses for AIME mathematical reasoning tasks, identifies improvements to ALE-Bench competitive programming solutions, and discovers novel mixture-of-expert load balancing loss functions that illuminate the space of optimization strategies. Our results demonstrate that ShinkaEvolve achieves broad applicability with exceptional sample efficiency. By providing open-source accessibility and cost-efficiency, this work democratizes open-ended discovery across diverse computational problems.

Localizing objects in an unsupervised manner poses significant challenges due to the absence of key visual information such as the appearance, type and number of objects, as well as the lack of labeled object classes typically available in supervised settings. While recent approaches to unsupervised object localization have demonstrated significant progress by leveraging self-supervised visual representations, they often require computationally intensive training processes, resulting in high resource demands in terms of computation, learnable parameters, and data. They also lack explicit modeling of visual context, potentially limiting their accuracy in object localization. To tackle these challenges, we propose a single-stage learning framework, dubbed PEEKABOO, for unsupervised object localization by learning context-based representations at both the pixel- and shape-level of the localized objects through image masking. The key idea is to selectively hide parts of an image and leverage the remaining image information to infer the location of objects without explicit supervision. The experimental results, both quantitative and qualitative, across various benchmark datasets, demonstrate the simplicity, effectiveness and competitive performance of our approach compared to state-of-the-art methods in both single object discovery and unsupervised salient object detection tasks. Code and pre-trained models are available at: https://github.com/hasibzunair/peekaboo

Large Vision-Language Models (LVLMs) show significant strides in general-purpose multimodal applications such as visual dialogue and embodied navigation. However, existing multimodal evaluation benchmarks cover a limited number of multimodal tasks testing rudimentary capabilities, falling short in tracking LVLM development. In this study, we present MMT-Bench, a comprehensive benchmark designed to assess LVLMs across massive multimodal tasks requiring expert knowledge and deliberate visual recognition, localization, reasoning, and planning. MMT-Bench comprises 31,325 meticulously curated multi-choice visual questions from various multimodal scenarios such as vehicle driving and embodied navigation, covering 32 core meta-tasks and 162 subtasks in multimodal understanding. Due to its extensive task coverage, MMT-Bench enables the evaluation of LVLMs using a task map, facilitating the discovery of in- and out-of-domain tasks. Evaluation results involving 30 LVLMs such as the proprietary GPT-4V, GeminiProVision, and open-sourced InternVL-Chat, underscore the significant challenges posed by MMT-Bench. We anticipate that MMT-Bench will inspire the community to develop next-generation multimodal foundation models aimed at achieving general-purpose multimodal intelligence.

In this paper, we investigate the challenge of integrating tables from data lakes, focusing on three core tasks: 1) pairwise integrability judgment, which determines whether a tuple pair in a table is integrable, accounting for any occurrences of semantic equivalence or typographical errors; 2) integrable set discovery, which aims to identify all integrable sets in a table based on pairwise integrability judgments established in the first task; 3) multi-tuple conflict resolution, which resolves conflicts among multiple tuples during integration. We train a binary classifier to address the task of pairwise integrability judgment. Given the scarcity of labeled data, we propose a self-supervised adversarial contrastive learning algorithm to perform classification, which incorporates data augmentation methods and adversarial examples to autonomously generate new training data. Upon the output of pairwise integrability judgment, each integrable set is considered as a community, a densely connected sub-graph where nodes and edges correspond to tuples in the table and their pairwise integrability, respectively. We proceed to investigate various community detection algorithms to address the integrable set discovery objective. Moving forward to tackle multi-tuple conflict resolution, we introduce an novel in-context learning methodology. This approach capitalizes on the knowledge embedded within pretrained large language models to effectively resolve conflicts that arise when integrating multiple tuples. Notably, our method minimizes the need for annotated data. Since no suitable test collections are available for our tasks, we develop our own benchmarks using two real-word dataset repositories: Real and Join. We conduct extensive experiments on these benchmarks to validate the robustness and applicability of our methodologies in the context of integrating tables within data lakes.

Large reasoning models have demonstrated strong problem-solving abilities, yet real-world tasks often require external tools and long-horizon interactions. Existing agent frameworks typically follow predefined workflows, which limit autonomous and global task completion. In this paper, we introduce DeepAgent, an end-to-end deep reasoning agent that performs autonomous thinking, tool discovery, and action execution within a single, coherent reasoning process. To address the challenges of long-horizon interactions, particularly the context length explosion from multiple tool calls and the accumulation of interaction history, we introduce an autonomous memory folding mechanism that compresses past interactions into structured episodic, working, and tool memories, reducing error accumulation while preserving critical information. To teach general-purpose tool use efficiently and stably, we develop an end-to-end reinforcement learning strategy, namely ToolPO, that leverages LLM-simulated APIs and applies tool-call advantage attribution to assign fine-grained credit to the tool invocation tokens. Extensive experiments on eight benchmarks, including general tool-use tasks (ToolBench, API-Bank, TMDB, Spotify, ToolHop) and downstream applications (ALFWorld, WebShop, GAIA, HLE), demonstrate that DeepAgent consistently outperforms baselines across both labeled-tool and open-set tool retrieval scenarios. This work takes a step toward more general and capable agents for real-world applications. The code and demo are available at https://github.com/RUC-NLPIR/DeepAgent.

Large Language Models (LLMs) have extended their impact beyond Natural Language Processing, substantially fostering the development of interdisciplinary research. Recently, various LLM-based agents have been developed to assist scientific discovery progress across multiple aspects and domains. Among these, computer-using agents, capable of interacting with operating systems as humans do, are paving the way to automated scientific problem-solving and addressing routines in researchers' workflows. Recognizing the transformative potential of these agents, we introduce ScienceBoard, which encompasses two complementary contributions: (i) a realistic, multi-domain environment featuring dynamic and visually rich scientific workflows with integrated professional software, where agents can autonomously interact via different interfaces to accelerate complex research tasks and experiments; and (ii) a challenging benchmark of 169 high-quality, rigorously validated real-world tasks curated by humans, spanning scientific-discovery workflows in domains such as biochemistry, astronomy, and geoinformatics. Extensive evaluations of agents with state-of-the-art backbones (e.g., GPT-4o, Claude 3.7, UI-TARS) show that, despite some promising results, they still fall short of reliably assisting scientists in complex workflows, achieving only a 15% overall success rate. In-depth analysis further provides valuable insights for addressing current agent limitations and more effective design principles, paving the way to build more capable agents for scientific discovery. Our code, environment, and benchmark are at https://qiushisun.github.io/ScienceBoard-Home/.

The causal capabilities of large language models (LLMs) are a matter of significant debate, with critical implications for the use of LLMs in societally impactful domains such as medicine, science, law, and policy. We conduct a "behavorial" study of LLMs to benchmark their capability in generating causal arguments. Across a wide range of tasks, we find that LLMs can generate text corresponding to correct causal arguments with high probability, surpassing the best-performing existing methods. Algorithms based on GPT-3.5 and 4 outperform existing algorithms on a pairwise causal discovery task (97%, 13 points gain), counterfactual reasoning task (92%, 20 points gain) and event causality (86% accuracy in determining necessary and sufficient causes in vignettes). We perform robustness checks across tasks and show that the capabilities cannot be explained by dataset memorization alone, especially since LLMs generalize to novel datasets that were created after the training cutoff date. That said, LLMs exhibit unpredictable failure modes, and we discuss the kinds of errors that may be improved and what are the fundamental limits of LLM-based answers. Overall, by operating on the text metadata, LLMs bring capabilities so far understood to be restricted to humans, such as using collected knowledge to generate causal graphs or identifying background causal context from natural language. As a result, LLMs may be used by human domain experts to save effort in setting up a causal analysis, one of the biggest impediments to the widespread adoption of causal methods. Given that LLMs ignore the actual data, our results also point to a fruitful research direction of developing algorithms that combine LLMs with existing causal techniques. Code and datasets are available at https://github.com/py-why/pywhy-llm.

Localizing objects in image collections without supervision can help to avoid expensive annotation campaigns. We propose a simple approach to this problem, that leverages the activation features of a vision transformer pre-trained in a self-supervised manner. Our method, LOST, does not require any external object proposal nor any exploration of the image collection; it operates on a single image. Yet, we outperform state-of-the-art object discovery methods by up to 8 CorLoc points on PASCAL VOC 2012. We also show that training a class-agnostic detector on the discovered objects boosts results by another 7 points. Moreover, we show promising results on the unsupervised object discovery task. The code to reproduce our results can be found at https://github.com/valeoai/LOST.

Learning causal graphs from multivariate time series is a ubiquitous challenge in all application domains dealing with time-dependent systems, such as in Earth sciences, biology, or engineering, to name a few. Recent developments for this causal discovery learning task have shown considerable skill, notably the specific time-series adaptations of the popular conditional independence-based learning framework. However, uncertainty estimation is challenging for conditional independence-based methods. Here, we introduce a novel bootstrap approach designed for time series causal discovery that preserves the temporal dependencies and lag structure. It can be combined with a range of time series causal discovery methods and provides a measure of confidence for the links of the time series graphs. Furthermore, next to confidence estimation, an aggregation, also called bagging, of the bootstrapped graphs by majority voting results in bagged causal discovery methods. In this work, we combine this approach with the state-of-the-art conditional-independence-based algorithm PCMCI+. With extensive numerical experiments we empirically demonstrate that, in addition to providing confidence measures for links, Bagged-PCMCI+ improves in precision and recall as compared to its base algorithm PCMCI+, at the cost of higher computational demands. These statistical performance improvements are especially pronounced in the more challenging settings (short time sample size, large number of variables, high autocorrelation). Our bootstrap approach can also be combined with other time series causal discovery algorithms and can be of considerable use in many real-world applications.

We consider the problem of predicting gene expressions from DNA sequences. A key challenge of this task is to find the regulatory elements that control gene expressions. Here, we introduce Seq2Exp, a Sequence to Expression network explicitly designed to discover and extract regulatory elements that drive target gene expression, enhancing the accuracy of the gene expression prediction. Our approach captures the causal relationship between epigenomic signals, DNA sequences and their associated regulatory elements. Specifically, we propose to decompose the epigenomic signals and the DNA sequence conditioned on the causal active regulatory elements, and apply an information bottleneck with the Beta distribution to combine their effects while filtering out non-causal components. Our experiments demonstrate that Seq2Exp outperforms existing baselines in gene expression prediction tasks and discovers influential regions compared to commonly used statistical methods for peak detection such as MACS3. The source code is released as part of the AIRS library (https://github.com/divelab/AIRS/).