Daily Papers

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.

Join discovery aims to identify tables from large data repositories that can augment a query table with complementary information, enabling downstream tasks such as data exploration, feature engineering, and business intelligence. Although numerous join discovery methods have been proposed, existing studies rely on method-specific benchmark construction, making reproducible and fair comparison difficult. We present TabJoinBench, a benchmark for evaluating join discovery methods across semantic, relational, and hybrid data lake scenarios. TabJoinBench constructs query-candidate pairs using source-specific validation strategies, systematically introduces structural, representation, and semantic changes through composable perturbations while preserving reliable ground truth. We evaluate representative join discovery methods spanning set-based, feature-based, and learned approaches, together with general-purpose language-model embedding baselines, and publicly release the processed datasets, ground-truth annotations, and generation pipeline to facilitate reproducible evaluation and future research.

Tabular data constitute a dominant form of information in modern data lakes and repositories, yet discovering the relevant tables to answer user questions remains challenging. Existing data discovery systems assume that each question can be answered by a single table and often rely on resource-intensive offline preprocessing, such as model training or large-scale content indexing. In practice, however, many questions require information spread across multiple tables -- either independently or through joins -- and users often seek specific cell values rather than entire tables. In this paper, we present Octopus, a lightweight, entity-aware, and training-free system for multi-table data discovery and cell-level value retrieval. Instead of embedding entire questions, Octopus identifies fine-grained entities (column mentions and value mentions) from natural-language queries using an LLM parser. It then matches these entities to table headers through a compact embedding index and scans table contents directly for value occurrences, eliminating the need for heavy content indexing or costly offline stages. The resulting fine-grained alignment not only improves table retrieval accuracy but also facilitates efficient downstream NL2SQL execution by reducing token usage and redundant LLM calls. To evaluate Octopus, we introduce a new benchmark covering both table- and cell-level discovery under multi-table settings, including five datasets for independent discovery and two for join-based discovery. Experimental results show that Octopus consistently outperforms existing systems while achieving substantially lower computational and token costs. Code is available at https://github.com/wenzhilics/octopus.

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.

Relational data augmentation is a powerful technique for enhancing data analytics and improving machine learning models by incorporating columns from external datasets. However, it is challenging to efficiently discover relevant external tables to join with a given input table. Existing approaches rely on data discovery systems to identify joinable tables from external sources, typically based on overlap or containment. However, the sheer number of tables obtained from these systems results in irrelevant joins that need to be performed; this can be computationally expensive or even infeasible in practice. We address this limitation by proposing the use of efficient mutual information (MI) estimation for finding relevant joinable tables. We introduce a new sketching method that enables efficient evaluation of relationship discovery queries by estimating MI without materializing the joins and returning a smaller set of tables that are more likely to be relevant. We also demonstrate the effectiveness of our approach at approximating MI in extensive experiments using synthetic and real-world datasets.

Public funding plays a central role in driving scientific discovery. To better understand the link between research inputs and outputs, we introduce FIND (Funding-Impact NSF Database), an open-access dataset that systematically links NSF grant proposals to their downstream research outputs, including publication metadata and abstracts. The primary contribution of this project is the creation of a large-scale, structured dataset that enables transparency, impact evaluation, and metascience research on the returns to public funding. To illustrate the potential of FIND, we present two proof-of-concept NLP applications. First, we analyze whether the language of grant proposals can predict the subsequent citation impact of funded research. Second, we leverage large language models to extract scientific claims from both proposals and resulting publications, allowing us to measure the extent to which funded projects deliver on their stated goals. Together, these applications highlight the utility of FIND for advancing metascience, informing funding policy, and enabling novel AI-driven analyses of the scientific process.

Large Language Models (LLMs) have been used for novel discovery of algorithms, theorems, drugs, and other tasks through the use of harnesses that prompt an LLM to iteratively optimize an objective. In this work, we study the relationship between the population of previous iterates and eventual discovery success. We generalize past work on harness design to develop a suite of 12 harnesses called 'Modular' and characterize their performance across 5 diverse discovery tasks, finding that discovery success is brittle and sensitive to harness design. We uncover mode collapse, characterized by a dramatic drop in the diversity of iterates, as a common failure mode. We find that popular state-of-the-art harnesses and diversity-inducing harness interventions, which aim to prolong this collapse, yield inconsistent gains. Our results instead uncover that the performance of early discoveries is predictive of eventual success. We therefore propose a universally applicable intervention that performs an initial stage of parallel exploration in order to initialize subsequent iterative optimization. Our method provides consistent gains across many harnesses and target applications, confirming the importance of initialization in LLM-driven discovery.

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.

Scientific progress depends on sequences of enabling contributions, yet existing AI4Science benchmarks largely focus on citation prediction, literature retrieval, or idea generation rather than the dependencies that make progress possible. In this paper, we introduce discovery pathway forecasting: given a target scientific contribution and the prior literature available at a specified time, the task is to (1) identify the enabling contributions required to realize it and (2) ground each in prior work when such prior work exists. We present SciPaths, a benchmark of 262 expert-annotated gold pathways and 2,444 silver pathways constructed from machine learning and natural language processing papers, where each pathway records enabling contributions, roles, rationales, and prior-work groundings or unmapped decisions. Evaluating frontier and open-weight language models, we find that the best model reaches only 0.189 F1 under strict semantic matching, with core methodological dependencies hardest to recover. Prior-work grounding improves substantially when gold enabling contributions are provided, showing that decomposition quality is a major bottleneck for end-to-end pathway recovery. SciPaths therefore shifts evaluation toward a missing capability in scientific forecasting: reasoning backward from a target contribution to the enabling scientific building blocks and prior-work dependencies that make it feasible.

Scientific discovery is a closed-loop process in which hypotheses guide data acquisition and observations refine the hypothesis space. Yet most approaches reduce discovery to supervised learning over fixed datasets, where limited observations can support multiple plausible mechanisms that fit locally but fail to generalize. Thus, the key challenge is selecting informative observations to resolve uncertainty, shifting the focus from static inference to adaptive data acquisition. To address this, we propose LLM-AutoSciLab, a closed-loop framework that couples hypothesis generation with hypothesis-conditioned experiment selection and mechanism refinement. Rather than fitting models to passively collected data, LLM-AutoSciLab iteratively proposes plausible hypotheses, selects informative experiments to distinguish or refine them, and updates its state using the resulting evidence. To evaluate dynamic, closed-loop scientific discovery with active data acquisition, we introduce ActiveSciBench, comprising two datasets: ActiveSciBench-Chem with 57 enzyme-kinetics tasks and ActiveSciBench-GRN with 45 gene-regulatory-network tasks. These datasets model discovery as a budget-constrained process requiring adaptive experiment design, variable selection, and recovery of true mechanisms. Across NewtonBench, ActiveSciBench-Chem, and ActiveSciBench-GRN, LLM-AutoSciLab outperforms prior methods, achieving 67.6% and 35.1% symbolic accuracy on NewtonBench and ActiveSciBench-Chem, respectively, and 31.1% exact graph recovery on ActiveSciBench-GRN. Moreover, hypothesis-guided experimentation is 2-5x more sample-efficient than the strongest competing baselines. Code and data are available at: https://github.com/scientific-discovery/LLM-AutoSciLab

Recent advances in LLMs have made automated scientific research the next frontline in the path to artificial superintelligence. However, these systems are bound either to tasks of narrow scope or the limited creative capabilities of LLMs. We propose Spacer, a scientific discovery system that develops creative and factually grounded concepts without external intervention. Spacer attempts to achieve this via 'deliberate decontextualization,' an approach that disassembles information into atomic units - keywords - and draws creativity from unexplored connections between them. Spacer consists of (i) Nuri, an inspiration engine that builds keyword sets, and (ii) the Manifesting Pipeline that refines these sets into elaborate scientific statements. Nuri extracts novel, high-potential keyword sets from a keyword graph built with 180,000 academic publications in biological fields. The Manifesting Pipeline finds links between keywords, analyzes their logical structure, validates their plausibility, and ultimately drafts original scientific concepts. According to our experiments, the evaluation metric of Nuri accurately classifies high-impact publications with an AUROC score of 0.737. Our Manifesting Pipeline also successfully reconstructs core concepts from the latest top-journal articles solely from their keyword sets. An LLM-based scoring system estimates that this reconstruction was sound for over 85% of the cases. Finally, our embedding space analysis shows that outputs from Spacer are significantly more similar to leading publications compared with those from SOTA LLMs.

We introduce InternAgent-1.5, a unified system designed for end-to-end scientific discovery across computational and empirical domains. The system is built on a structured architecture composed of three coordinated subsystems for generation, verification, and evolution. These subsystems are supported by foundational capabilities for deep research, solution optimization, and long horizon memory. The architecture allows InternAgent-1.5 to operate continuously across extended discovery cycles while maintaining coherent and improving behavior. It also enables the system to coordinate computational modeling and laboratory experimentation within a single unified system. We evaluate InternAgent-1.5 on scientific reasoning benchmarks such as GAIA, HLE, GPQA, and FrontierScience, and the system achieves leading performance that demonstrates strong foundational capabilities. Beyond these benchmarks, we further assess two categories of discovery tasks. In algorithm discovery tasks, InternAgent-1.5 autonomously designs competitive methods for core machine learning problems. In empirical discovery tasks, it executes complete computational or wet lab experiments and produces scientific findings in earth, life, biological, and physical domains. Overall, these results show that InternAgent-1.5 provides a general and scalable framework for autonomous scientific discovery.

Foundation models have progressed from learning and reasoning over existing knowledge, to increasingly learning through action, tool use, and outcome feedback. We argue that the next frontier is a further transition: from solving and acting within problems specified by humans to participating in the process by which new problems, representations, explanations, and knowledge are created. We refer to this capability as Discovery Intelligence. We formulate Discovery Foundation Models (DFMs) as general-purpose model systems for open-ended discovery. A DFM operates over a revisable research state and supports seven coupled capabilities spanning problem discovery, formulation, representation construction, hypothesis formation, intervention, evidence-grounded revision, and continual discovery improvement. We instantiate this framework with Zetema, which couples explicit research-state dynamics, verification and experimental gating, external grounding, and cross-task Discovery Skill evolution. We further ground the framework with GALILEO, a real therapeutic-discovery system in which Dry-Lab reasoning, robotic and hands-on Wet-Lab experimentation, external biological evidence, and iterative hypothesis and design revision form a closed physical discovery loop. We then formulate a unified approach to capability formation and process-centered evaluation, enabling discovery behavior to be trained, improved, and measured beyond final-answer performance. Together, these components establish discovery as a learnable, executable, and evaluable capability of foundation-model systems. We view this shift as a broader progression in intelligence scaling: from learning over existing knowledge, to learning from action outcomes, and ultimately to participating in the construction, testing, and revision of the structures through which new knowledge is discovered. Code: https://github.com/Gen-Verse/DFM-Plans

Data scientists today search large data lakes to discover and integrate datasets. In order to bring together disparate data sources, dataset discovery methods rely on some form of schema matching: the process of establishing correspondences between datasets. Traditionally, schema matching has been used to find matching pairs of columns between a source and a target schema. However, the use of schema matching in dataset discovery methods differs from its original use. Nowadays schema matching serves as a building block for indicating and ranking inter-dataset relationships. Surprisingly, although a discovery method's success relies highly on the quality of the underlying matching algorithms, the latest discovery methods employ existing schema matching algorithms in an ad-hoc fashion due to the lack of openly-available datasets with ground truth, reference method implementations, and evaluation metrics. In this paper, we aim to rectify the problem of evaluating the effectiveness and efficiency of schema matching methods for the specific needs of dataset discovery. To this end, we propose Valentine, an extensible open-source experiment suite to execute and organize large-scale automated matching experiments on tabular data. Valentine includes implementations of seminal schema matching methods that we either implemented from scratch (due to absence of open source code) or imported from open repositories. The contributions of Valentine are: i) the definition of four schema matching scenarios as encountered in dataset discovery methods, ii) a principled dataset fabrication process tailored to the scope of dataset discovery methods and iii) the most comprehensive evaluation of schema matching techniques to date, offering insight on the strengths and weaknesses of existing techniques, that can serve as a guide for employing schema matching in future dataset discovery methods.

Autonomous scientific discovery systems offer the potential to accelerate research by automating the process of hypothesis generation and validation. However, current systems operate within constrained search spaces or require predefined research questions, limiting their capacity for true open-ended inquiry. Furthermore, while they generate hypotheses iteratively, they largely lack the ability to explicitly synthesize their own accumulated findings to uncover complex, interconnected phenomena. We introduce DiscoPER, an autonomous large language model-powered framework that conducts open-ended research by dynamically generating and executing code to explore datasets without pre-specified research objectives. To ensure rigorous scientific validity, every proposed discovery must pass statistical testing. To overcome the limitations of isolated search, our framework introduces a second-order reasoning mechanism that periodically analyzes its own accumulated discoveries. By treating prior discoveries as empirical data, DiscoPER identifies structural patterns, confounds, and epistemic gaps, actively redirecting hypothesis exploration toward uncharted regions of the search space. The search space is further expanded by incorporating tool use, enabling the system to explore hypotheses beyond structured metadata by seamlessly processing and extracting useful information from multimodal sources like images. Evaluated on iNatDisco, a new multimodal ecological knowledge benchmark with pattern-level ground truth obtained from peer-reviewed literature, DiscoPER recovers 8 of 9 known patterns with a 72.7% hypothesis support rate, outperforming both classical causal discovery and LLM-guided baselines. Ablations show that DiscoPER scales with more data, and confirms the benefits of second-order meta-reflection.

Scientific discovery with language models requires finding the best valid solution within a finite computational budget. We study how feedback from this search can improve the procedure used to conduct it. We introduce HarnessTTT, a test-time learning framework that trains a harness proposer while keeping the executor frozen. The proposer generates executable harnesses comprising system prompts, reusable skills, tools, middleware, and execution controls. Each harness guides a budgeted discovery rollout, whose outcome provides feedback for updating the proposer. A discovery-oriented policy-gradient objective combines gap-normalized rewards, leave-one-out advantages (RLOO), and max-sharpening to favor high-performing proposals. Generated components are validated before execution, and the search retains the best valid solution and selected harnesses across rounds. Across fourteen discovery tasks in mathematics, systems, GPU kernels, heuristic programming, astrodynamics, and biology, HarnessTTT with a frozen 9B executor improves on OpenEvolve with the same executor on all eleven benchmark tasks (e.g., from 1.17 to 2.64 on circle packing), improves on the discovery-fine-tuned Finch-9B by up to 92%, holds the best open-weight sub-10B result on nine, and reaches 0.380919 on Erdős minimum overlap, better than the best human reference of 0.380927. Scaling the proposer and frozen executor to 27B improves on eleven of fourteen tasks, and transferring the learned harnesses to GPT-5.5 matches or exceeds the strongest reported system of any backbone on nine of fourteen tasks. Together, these results show that harness search can itself be learned at test time: a trained proposer lets a small frozen executor search effectively, and the harnesses it finds carry over to stronger executors.

How can we use AI to discover a new state of the art for a scientific problem? Prior work in test-time scaling, such as AlphaEvolve, performs search by prompting a frozen LLM. We perform reinforcement learning at test time, so the LLM can continue to train, but now with experience specific to the test problem. This form of continual learning is quite special, because its goal is to produce one great solution rather than many good ones on average, and to solve this very problem rather than generalize to other problems. Therefore, our learning objective and search subroutine are designed to prioritize the most promising solutions. We call this method Test-Time Training to Discover (TTT-Discover). Following prior work, we focus on problems with continuous rewards. We report results for every problem we attempted, across mathematics, GPU kernel engineering, algorithm design, and biology. TTT-Discover sets the new state of the art in almost all of them: (i) Erdős' minimum overlap problem and an autocorrelation inequality; (ii) a GPUMode kernel competition (up to 2times faster than prior art); (iii) past AtCoder algorithm competitions; and (iv) denoising problem in single-cell analysis. Our solutions are reviewed by experts or the organizers. All our results are achieved with an open model, OpenAI gpt-oss-120b, and can be reproduced with our publicly available code, in contrast to previous best results that required closed frontier models. Our test-time training runs are performed using Tinker, an API by Thinking Machines, with a cost of only a few hundred dollars per problem.

Scientific discovery begins where known problems end. There, AI systems must engage in exploration: framing hypotheses, designing experiments, and iterating on the results. However, evaluating this ability is difficult: (1) how to verify whether a genuinely new hypothesis holds, and (2) how to determine whether a system has discovered it through exploration or merely recalled related knowledge from pre-training data. To this end, we introduce ExplorationBench, which turns the wicked problem of evaluating scientific exploration into a concrete and tractable framework built on verifiable Alien Worlds: their rules are executable, so every answer can be checked exactly, and they conflict with familiar knowledge, so recall alone cannot solve the tasks. The benchmark contains two sandboxes, AlienCode (31 discovery targets, 70 tasks) and AlienLogic (24 discovery targets, 70 tasks). Each sandbox provides a flawed manual, task-specific environmental feedback, and a dedicated tool-call schema. Systems use these resources to explore the sandbox, then solve held-out tasks. We evaluate 10 AI systems and find that the strongest systems can acquire and apply unfamiliar rules, while performance varies substantially across trajectories and continued exploration can stall or reverse earlier gains. ExplorationBench represents a step towards AI systems that can acquire and apply genuinely new knowledge through exploration in unknown environments.

Scientific discovery is a cumulative process and requires new ideas to be situated within an ever-expanding landscape of existing knowledge. An emerging and critical challenge is how to identify conceptually relevant prior work from rapidly growing literature, and assess how a new idea differentiates from existing research. Current embedding approaches typically conflate distinct conceptual aspects into single representations and cannot support fine-grained literature retrieval; meanwhile, LLM-based evaluators are subject to sycophancy biases, failing to provide discriminative novelty assessment. To tackle these challenges, we introduce the Ideation Space, a structured representation that decomposes scientific knowledge into three distinct dimensions, i.e., research problem, methodology, and core findings, each learned through contrastive training. This framework enables principled measurement of conceptual distance between ideas, and modeling of ideation transitions that capture the logical connections within a proposed idea. Building upon this representation, we propose a Hierarchical Sub-Space Retrieval framework for efficient, targeted literature retrieval, and a Decomposed Novelty Assessment algorithm that identifies which aspects of an idea are novel. Extensive experiments demonstrate substantial improvements, where our approach achieves Recall@30 of 0.329 (16.7% over baselines), our ideation transition retrieval reaches Hit Rate@30 of 0.643, and novelty assessment attains 0.37 correlation with expert judgments. In summary, our work provides a promising paradigm for future research on accelerating and evaluating scientific discovery.

Scientific discovery is not only answer generation but revision of the representational regime in which evidence, artifacts, operations, and verifiers are typed. We develop a category-theoretic account of agentic discovery for materials science. In a fixed regime b with schema category S_b, the system state is a copresheaf I_t: S_b -> Set, and provenance is the category of elements \int_{S_b} I_t. Fixed-regime operation is an update on such states, endofunctorial only when provenance-preserving refinements are specified and preserved. Discovery is instead a verified regime transition u: S_b -> S_b': old artifacts are preserved, transported by the left Kan extension Lan_u I_t, and compared with the post-transition state to identify residual content beyond functorial transport. This separates retrieval, search, and discovery without subjective novelty. We instantiate the framework in two systems. In Builder/Breaker, a protein-mechanics world model is revised under a Minimum Description Length gate; the accepted law expresses within-chain flexibility as all-mode elastic compliance conditioned by slow collective-mode participation, or mode-conditioned compliance. In CategoryScienceClaw, typed skills, artifacts, open needs, workflow mutation, gates, stress tests, and public discourse become a proof-carrying knowledge-computation graph. A fiber-network example records candidate models, rejected alternatives, an AIC gate, perturbation tests, and an accepted orientation-tensor anisotropic stiffness surrogate over an isotropic fiber-count descriptor. Together, the cases show how category theory can be both a mathematical language for discovery and an engineering specification for self-revising AI discovery systems.

Open-ended discovery requires learning from repeated attempts while continuing to explore directions whose value is not yet apparent. Search with a frozen large language model (LLM) can reuse previous solutions in context, but cannot update the model from its successes and failures on the test problem. Reinforcement learning (RL) enables such adaptation; however, strongly favoring high-reward trajectories may suppress low-reward yet potentially promising directions too early. We introduce CURIO, a curiosity-driven test-time learning framework that complements task feedback with an Intrinsic Curiosity World Model (ICWM). The ICWM learns transitions in the policy's hidden-state representation and supplies prediction-error bonuses at sampled tokens outside the policy's top-k choices. Epoch normalization and an annealed weight regulate their contribution to the policy update. On six mathematical discovery tasks and single-cell denoising with Qwen3 backbones from 8B to 235B, three-run means improve over a matched task-only RL control on five mathematical objectives, match the best reported performance on Circle Packing, and improve denoising Score and mean squared error (MSE) on both held-out corpora at every tested scale. Relative gains reach 18.3% on Hadamard and 10.8% on denoising Score. Code-diversity measurements show greater structural variation among generated programs, supporting curiosity as a complementary exploration signal for learning in open-ended discovery.

Open-ended scientific discovery with large language models (LLMs) increasingly operates as a long-horizon loop of hypothesis search and verification, where a reward signal guides which hypotheses to test next. A notable recent example is AutoDiscovery, which uses "Bayesian surprise" - the belief shift an LLM undergoes after observing evidence for a hypothesis - as both a discovery metric and a reward for search. We first observe that AutoDiscovery treats surprisal as a static quantity, while surprisal in human reasoning is non-stationary - it is defined relative to beliefs that evolve with experience, a prerequisite for continual scientific discovery. We address this mismatch with evidence-informed LLM beliefs: priors updated with evidence from previous hypotheses to compute non-stationary surprisal for new hypotheses. We compare in-context belief-updating mechanisms and find that embedding-based retrieval-augmented generation over prior discoveries best anticipates eventual posteriors, identifying 37.5% of static surprisals as spurious. We then modify search to avoid these spurious rewards and prioritize hypotheses that remain surprising under non-stationary beliefs. Concretely, we introduce two complementary changes to the original search procedure: belief-update filtering and diversity maximization. Across five discovery domains, our method increases accumulated non-stationary surprisal by 30.62% on average compared to the original search procedure, demonstrating that continual scientific discovery with LLMs requires not only better belief measurement but also search procedures that avoid redundancy and encourage diversity.

To handle ambiguous and open-ended requests, Large Language Models (LLMs) are increasingly trained to interact with users to surface intents they have not yet expressed (e.g., ask clarification questions). However, users are often ambiguous because they have not yet formed their intents: they must observe and explore outcomes to discover what they want. Simply asking "what kind of tone do you want?" fails when users themselves do not know. We introduce DiscoverLLM, a novel and generalizable framework that trains LLMs to help users form and discover their intents. Central to our approach is a novel user simulator that models cognitive state with a hierarchy of intents that progressively concretize as the model surfaces relevant options -- where the degree of concretization serves as a reward signal that models can be trained to optimize. Resulting models learn to collaborate with users by adaptively diverging (i.e., explore options) when intents are unclear, and converging (i.e., refine and implement) when intents concretize. Across proposed interactive benchmarks in creative writing, technical writing, and SVG drawing, DiscoverLLM achieves over 10% higher task performance while reducing conversation length by up to 40%. In a user study with 75 human participants, DiscoverLLM improved conversation satisfaction and efficiency compared to baselines.

Scientific equation discovery has long been central to scientific progress, proceeding through iterative cycles of hypothesis generation, observational testing, and refinement under scientific constraints. As LLM capabilities advance and their role in AI for Science expands, it remains an open problem whether they can genuinely discover scientific laws and how this ability should be evaluated. Existing evaluations, however, often either simplify discovery through synthetic settings or reuse published targets that may already be familiar to LLMs. We therefore introduce SCILAWS-BENCH, a benchmark for scientific law discovery built from published research and real scientific data. It comprises 118 problems drawn from 381 scientific papers, covering 291 candidate laws and roughly 8M real data points across six scientific disciplines. Each problem is instantiated in two complementary settings: (1) SCILAWS-REAL asks models to propose laws from fixed real observations and evaluates held-out predictive fit and scientific validity derived from the source literature, and (2) SCILAWS-PARALLEL asks models to actively query residual-calibrated worlds and recover synthesized hidden laws derived from published forms. This two-setting task design preserves each problem's scientific context while separately evaluating fixed-record law discovery and active recovery of a newly synthesized hidden law. We find that predictive fit can diverge from scientific validity, memorization shapes whether models reproduce or move beyond published formulas, and our best-of-N study reveals a selection bottleneck. Our work provides a paper-grounded benchmark and new empirical perspectives for evaluating AI for scientific discovery. Project page: https://yiyihum.github.io/SciLaws-Bench

Despite interdisciplinary research leading to larger and longer-term impact, most work remains confined to single-domain academic silos. Recent AI-based approaches to scientific discovery show promise for interdisciplinary research, but many prioritize rapidly designing experiments and solutions, bypassing the exploratory, collaborative reasoning processes that drive creative interdisciplinary breakthroughs. As a result, prior efforts largely prioritize automating scientific discovery rather than augmenting the reasoning processes that underlie scientific disruption. We present Idea-Catalyst, a novel framework that systematically identifies interdisciplinary insights to support creative reasoning in both humans and large language models. Starting from an abstract research goal, Idea-Catalyst is designed to assist the brainstorming stage, explicitly avoiding premature anchoring on specific solutions. The framework embodies key metacognitive features of interdisciplinary reasoning: (a) defining and assessing research goals, (b) awareness of a domain's opportunities and unresolved challenges, and (c) strategic exploration of interdisciplinary ideas based on impact potential. Concretely, Idea-Catalyst decomposes an abstract goal (e.g., improving human-AI collaboration) into core target-domain research questions that guide the analysis of progress and open challenges within that domain. These challenges are reformulated as domain-agnostic conceptual problems, enabling retrieval from external disciplines (e.g., Psychology, Sociology) that address analogous issues. By synthesizing and recontextualizing insights from these domains back into the target domain, Idea-Catalyst ranks source domains by their interdisciplinary potential. Empirically, this targeted integration improves average novelty by 21% and insightfulness by 16%, while remaining grounded in the original research problem.

Many organizations rely on data from government and third-party sources, and those sources rarely follow the same data formatting. This introduces challenges in integrating data from multiple sources or aligning external sources with internal databases. Commercial database systems do not offer adequate support for integrating data from heterogeneous sources, and manual integration is both time-consuming and inefficient. State-of-the-art data integration approaches that rely on similarity functions and textual transformations often fail to handle challenging cases where multiple mappings are required, or the mappings go beyond simple textual transformations. In this paper, we study the potentials of deep neural models for transforming tables for joinability. In particular, we cast the problem as a prediction task and develop a framework that leverages large deep-learning language models to transform tabular data from a source formatting to a desired target representation. Our framework can efficiently learn the patterns for mapping a source formatting into an expected target using just a few examples, which can then be used for tasks such as table joining, filling in missing values, and error detection. Compared to state-of-the-art mapping and joining approaches, our framework delivers noticeably more accurate and scalable performance on both real-world and synthetic datasets. Our experimental evaluation also shows that the performance of the proposed framework using our fine-tuned model is at par or better than large language models such as GPT-3, despite the significant difference in size, and that using large language models within our framework improves their performance.

Personalized discovery systems often train separate models for item ranking, carousel ranking, and search, even though these tasks expose complementary signals from the same viewer journey: watches shape carousel and item ranking, search queries reveal intent even when they do not lead to a catalog match, and watch history helps interpret search as rewatching, continuation, or new discovery. We introduce the user story, a serialized representation that turns a user's cross-surface history - attributes, sessions, watch events with surface and carousel context, and search events - into a single token sequence. By interleaving pretrained language tokens with domain-specific event tokens, user stories let heterogeneous recommendation and search tasks be expressed as prompted next-token prediction over a shared grammar. TubiFM is one instantiation of this approach: a Llama 3.2 1B-based model trained on user stories and prompted to rank items, carousels, or search results without task-specific architectures. In offline evaluation, this single model outperforms specialist baselines across item, carousel, and search ranking. In online A/B tests, TubiFM significantly improves search total viewing time (TVT) by +3.9% and carousel TVT by +0.30%. Item ranking is statistically neutral on TVT (+0.14%), but matches a mature production stack; across all three tasks, TubiFM serves on L40S GPUs and reduces p99 ranking latency from 500ms to 200ms. These results show that shared user stories can improve discovery while simplifying ranking systems.

Test-time scaling has enabled LLMs to solve increasingly complex reasoning, discovery, and optimization tasks. However, existing approaches often gather observations while seeking evidence for current hypotheses, then generate new hypotheses conditioned on those hypotheses and their associated evidence. This couples observation discovery to existing hypotheses, favoring local refinements over exploration of unknown hypotheses regions. Inspired by the hypothetico-deductive method (Hempel, 1945) and dual-space models of scientific discovery (Klahr & Dunbar, 1988), we introduce SHELDON, a scientific reasoning harness that separately represents and jointly explores hypothesis and observation spaces. By actively seeking new observations along with new hypotheses, SHELDON can discover observations that its current hypotheses do not explain. These unexplained observations expose gaps in its understanding, motivate new investigations, and guide the generation of hypotheses beyond refinements of existing ones. Across diagnosis, abstract reasoning, and optimization benchmarks, SHELDON outperforms evaluated baselines by up to 26.7 points. Additional analysis shows that SHELDON generates up to 4.5x more novel solutions.

This first release of Prior Labs in relational learning shows our continued commitment to open science. We open-source three pieces of software that we expect to accelerate research in the field towards meaningful real-world impact. We aim to steer further development based on feedback from, and in collaboration with, the community. Given the early stage of development, our α-release targets researchers and early-adopting practitioners. Over the past years, a variety of datasets and tasks for relational learning have emerged, but the community has not converged on a reliable, reproducible way to compare different methods on these tasks. Our α-release, RelArena-α, provides a unified framework for running and comparing baselines on RelBench v1 by standardizing data loading, evaluation protocols, tuning regimes, and support for systems with custom tuning, inspired by established tabular benchmarks such as TabArena. We plan to work with the research community to further develop RelArena-α into a catalyst for progress in the relational learning community. We release the initial version of TabPFN-Rel, a purpose-built relational harness for TabPFN-3. Currently ranked first among models on RelArena-α, TabPFN-Rel makes key improvements upon RDBLearn. Beyond its ranking, TabPFN-Rel serves as a strong baseline, adding to the growing evidence that flattening a relational database into a single table remains competitive with specialized relational architectures on real-world tasks. To facilitate adoption of relational learning methods in research and industry, we release an initial α-version of our Relational Predictive Interface, RPI, an open-source, model-agnostic interface that enables early adopters to easily define problems on new databases and apply any model implemented in RelArena-α, including TabPFN-Rel, to these problems.

Large Language Models (LLMs) are catalyzing a paradigm shift in scientific discovery, evolving from task-specific automation tools into increasingly autonomous agents and fundamentally redefining research processes and human-AI collaboration. This survey systematically charts this burgeoning field, placing a central focus on the changing roles and escalating capabilities of LLMs in science. Through the lens of the scientific method, we introduce a foundational three-level taxonomy-Tool, Analyst, and Scientist-to delineate their escalating autonomy and evolving responsibilities within the research lifecycle. We further identify pivotal challenges and future research trajectories such as robotic automation, self-improvement, and ethical governance. Overall, this survey provides a conceptual architecture and strategic foresight to navigate and shape the future of AI-driven scientific discovery, fostering both rapid innovation and responsible advancement. Github Repository: https://github.com/HKUST-KnowComp/Awesome-LLM-Scientific-Discovery.

Predicting the answer to interventional ``what if'' questions --- the outcome of an action never taken --- requires a mechanistic, causal model, not a curve fit; and learning such a model requires experiments, because passive data leaves its mechanisms unidentified. Experiments are expensive, so the central problem is data efficiency. We present the Model Discovery Agent (MDA), which couples a large language model (LLM), used as a proposer of candidate structures, with standard Bayesian machinery --- sequential Monte Carlo (SMC) for parameter and structure posteriors, simulation-based inference (SBI) for intractable likelihoods, and value-of-information (VoI) for experiment design --- to discover latent mechanistic world models from few interventions. MDA operates in the M-open setting: when the truth lies outside the current hypothesis class, a predictive check flags the inadequacy and the proposer expands the hypothesis space with a new model whose parameters are then identified by designed experiments. We show that discovery and design reinforce: the design step identifies the mechanism the discovery step proposes, and the identified mechanism improves predictions, enabling further discoveries from the remaining unexplained residuals. On three different benchmarks --- covering physics (\DPbench, wiemann2026discoverphysics), chemistry (\CHEMbench, kabra2026autoscilab) and biology (\HHbench, a new partially observed single-neuron electrophysiology benchmark we create) --- we show that MDA sets a new SOTA in terms of data-efficient model learning and reliable interventional prediction ability.

Progress in scientific discovery is rarely the result of a single "Eureka" moment, but is rather the product of hundreds of scientists incrementally working together toward a common goal. While existing agent workflows are capable of producing research autonomously, they do so in isolation, without the ability to continuously improve upon prior research results. To address these challenges, we introduce AgentRxiv-a framework that lets LLM agent laboratories upload and retrieve reports from a shared preprint server in order to collaborate, share insights, and iteratively build on each other's research. We task agent laboratories to develop new reasoning and prompting techniques and find that agents with access to their prior research achieve higher performance improvements compared to agents operating in isolation (11.4% relative improvement over baseline on MATH-500). We find that the best performing strategy generalizes to benchmarks in other domains (improving on average by 3.3%). Multiple agent laboratories sharing research through AgentRxiv are able to work together towards a common goal, progressing more rapidly than isolated laboratories, achieving higher overall accuracy (13.7% relative improvement over baseline on MATH-500). These findings suggest that autonomous agents may play a role in designing future AI systems alongside humans. We hope that AgentRxiv allows agents to collaborate toward research goals and enables researchers to accelerate discovery.

Large language models (LLMs) are increasingly applied to scientific research, yet prevailing science benchmarks probe decontextualized knowledge and overlook the iterative reasoning, hypothesis generation, and observation interpretation that drive scientific discovery. We introduce a scenario-grounded benchmark that evaluates LLMs across biology, chemistry, materials, and physics, where domain experts define research projects of genuine interest and decompose them into modular research scenarios from which vetted questions are sampled. The framework assesses models at two levels: (i) question-level accuracy on scenario-tied items and (ii) project-level performance, where models must propose testable hypotheses, design simulations or experiments, and interpret results. Applying this two-phase scientific discovery evaluation (SDE) framework to state-of-the-art LLMs reveals a consistent performance gap relative to general science benchmarks, diminishing return of scaling up model sizes and reasoning, and systematic weaknesses shared across top-tier models from different providers. Large performance variation in research scenarios leads to changing choices of the best performing model on scientific discovery projects evaluated, suggesting all current LLMs are distant to general scientific "superintelligence". Nevertheless, LLMs already demonstrate promise in a great variety of scientific discovery projects, including cases where constituent scenario scores are low, highlighting the role of guided exploration and serendipity in discovery. This SDE framework offers a reproducible benchmark for discovery-relevant evaluation of LLMs and charts practical paths to advance their development toward scientific discovery.

Scientific contributions rarely develop in isolation, but instead build upon prior discoveries. We formulate the task of automated technological roadmapping as extracting scientific contributions from scholarly articles and linking them to their prerequisites. We present the Scientific Contribution Graph, a large-scale resource containing 6 million detailed scientific contributions extracted from 655k open-access papers spanning computer science, medicine, biology, physics, chemistry, and other sciences, and connected by 36 million prerequisite edges. We further introduce scientific prerequisite prediction, a scientific discovery task in which models predict which existing technologies can enable future discoveries, and show that contemporary models are rapidly improving on this task, reaching 0.48 MAP when evaluated using temporally-filtered backtesting. We anticipate technological roadmapping resources such as this will support scientific impact assessment and automated scientific discovery.

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.

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.

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.

Recent AI systems have made rapid progress in scientific discovery when given well-defined metrics, but whether they can autonomously undertake open-ended scientific discovery remains unclear. We investigate AI's ability to tackle open-ended tasks in Station, an open-world environment in which multiple agents simulate a scientific ecosystem. To tackle challenges specific to open-ended tasks, we propose augmenting Station with two mechanisms: a Supervisor mechanism and periodic Meta Reflection, which encourage persistent exploration even when intermediate metrics are lacking. We construct open-ended tasks from three recent oral papers presented at ICLR. We give agents the main research question studied in each paper while withholding the paper's results and disabling web access. We then measure how many of the original findings-partitioned into individual criteria-agents rediscover. We find that Station rediscovers 62.7% of the criteria on average, compared with 15.4% for Codex Multiagent-v2 and 14.4-20.6% for AI Scientist-v2. Ablation and behavioral analyses indicate that adding the two mechanisms together improves research coverage and continuity. We further evaluate Station on two open-ended tasks without oracle papers and find that some of the discoveries made by the agents closely match discoveries reported by researchers after the knowledge cutoff date. Together, these results indicate that a suitable environment can enable agents to autonomously make meaningful progress in open-ended scientific discovery.

Scientific discovery contributes largely to human society's prosperity, and recent progress shows that LLMs could potentially catalyze this process. However, it is still unclear whether LLMs can discover novel and valid hypotheses in chemistry. In this work, we investigate this central research question: Can LLMs automatically discover novel and valid chemistry research hypotheses given only a chemistry research background (consisting of a research question and/or a background survey), without limitation on the domain of the research question? After extensive discussions with chemistry experts, we propose an assumption that a majority of chemistry hypotheses can be resulted from a research background and several inspirations. With this key insight, we break the central question into three smaller fundamental questions. In brief, they are: (1) given a background question, whether LLMs can retrieve good inspirations; (2) with background and inspirations, whether LLMs can lead to hypothesis; and (3) whether LLMs can identify good hypotheses to rank them higher. To investigate these questions, we construct a benchmark consisting of 51 chemistry papers published in Nature, Science, or a similar level in 2024 (all papers are only available online since 2024). Every paper is divided by chemistry PhD students into three components: background, inspirations, and hypothesis. The goal is to rediscover the hypothesis, given only the background and a large randomly selected chemistry literature corpus consisting the ground truth inspiration papers, with LLMs trained with data up to 2023. We also develop an LLM-based multi-agent framework that leverages the assumption, consisting of three stages reflecting the three smaller questions. The proposed method can rediscover many hypotheses with very high similarity with the ground truth ones, covering the main innovations.

Open-ended scientific discovery often requires repeatedly proposing and evaluating candidate solutions. LLM-based systems can support this process by generating and refining executable solutions from verifier feedback. Methods such as TTT-Discover use test-time training (TTT) to update the solution-generating LLM from verifier feedback, adapting its generation policy to improve subsequent proposals on the target problem. However, this becomes expensive when reliable execution requires a large model, since training must maintain gradients, optimizer states, and policy statistics while repeatedly generating long, structured outputs. It also complicates credit assignment: outcome-level verifier feedback must jointly evaluate the high-level strategy and its low-level implementation. In this work, we introduce Guidance-TTT, which separates these roles. A compact guidance model is trained at test time to propose high-level strategic changes, while a frozen execution model implements them as complete executable solutions. At each step, the system selects a promising previously discovered solution, proposes a change, executes and verifies it, and updates only the guidance model using an adaptive group-relative RL objective. This concentrates test-time learning on short strategic decisions while retaining the implementation capability of a substantially stronger model without adapting it. Without web access, Guidance-TTT produces strong solutions across four distinct domains: combinatorial optimization (Polyomino Packing), heuristic programming (AHC058), machine learning (Lasso), and GPU kernel optimization (TriMul). Across these tasks, it outperforms the best solutions reported in prior work while remaining competitive with state-of-the-art results on public online leaderboards. Code is available at https://github.com/Human-Agent-Society/reef/tree/guidance-ttt-support.

The exponential growth of scientific literature necessitates advanced tools for effective knowledge exploration. We present Knowledge Navigator, a system designed to enhance exploratory search abilities by organizing and structuring the retrieved documents from broad topical queries into a navigable, two-level hierarchy of named and descriptive scientific topics and subtopics. This structured organization provides an overall view of the research themes in a domain, while also enabling iterative search and deeper knowledge discovery within specific subtopics by allowing users to refine their focus and retrieve additional relevant documents. Knowledge Navigator combines LLM capabilities with cluster-based methods to enable an effective browsing method. We demonstrate our approach's effectiveness through automatic and manual evaluations on two novel benchmarks, CLUSTREC-COVID and SCITOC. Our code, prompts, and benchmarks are made publicly available.

Scientific discovery often involves optimising expensive-to-evaluate objectives over vast, structured, and open-ended hypothesis spaces, such as molecules, protein sequences, and computer programs. Generative models such as large language models (LLMs) provide expressive priors over such spaces, but their likelihoods and self-assessments are unreliable proxies for the objectives and calibrated epistemic uncertainty, especially for novel candidates outside the observed data distribution. We introduce the Large Discovery Model (LDM), an empirically grounded recurrent architecture that couples a generative model with a Bayesian non-parametric reward surrogate model. The generative model proposes and refines candidate designs, while the surrogate predicts their performance and quantifies uncertainty, yielding an uncertainty-aware value that guides candidate generation, refinement, and selection. The discovery memory and the surrogate model are continually updated as each new experimental observation arrives. We evaluate LDM on three scenarios spanning different design modalities and objectives, including neural-network training, antibody design, and molecular optimisation. Compared to LLM-only reflection or traditional statistical search across these domains, LDM achieves a 2.4times greater reduction in validation BPB, an 18.2% relative decrease in binding energy, and more than 60% relative gains in molecular multi-objective performance. These results suggests that LDM could serve as a general-purpose discovery engine for effective search over open-ended hypothesis spaces.

Keeping track of scientific challenges, advances and emerging directions is a fundamental part of research. However, researchers face a flood of papers that hinders discovery of important knowledge. In biomedicine, this directly impacts human lives. To address this problem, we present a novel task of extraction and search of scientific challenges and directions, to facilitate rapid knowledge discovery. We construct and release an expert-annotated corpus of texts sampled from full-length papers, labeled with novel semantic categories that generalize across many types of challenges and directions. We focus on a large corpus of interdisciplinary work relating to the COVID-19 pandemic, ranging from biomedicine to areas such as AI and economics. We apply a model trained on our data to identify challenges and directions across the corpus and build a dedicated search engine. In experiments with 19 researchers and clinicians using our system, we outperform a popular scientific search engine in assisting knowledge discovery. Finally, we show that models trained on our resource generalize to the wider biomedical domain and to AI papers, highlighting its broad utility. We make our data, model and search engine publicly available. https://challenges.apps.allenai.org/

Scientific discovery has advanced through successive transformations in the organization of knowledge. Observation and experimentation established the empirical foundations of science. Theory made it possible to derive general principles from particular phenomena. Computation extended inquiry into systems beyond direct observation, while data-intensive methods opened new spaces of pattern and prediction. Science now confronts a different frontier. The central challenge is no longer simply to produce more information, but to organize expanding knowledge, reasoning, and evidence into a coherent process of discovery. Here, we introduce Bridging Literature, Agents, and Zero-gap Experimentation (BLAZE), a paradigm of socialized scientific intelligence. BLAZE conceives AI not as an assistant for isolated research tasks, but as an organizational infrastructure for scientific discovery. It connects persistent knowledge, collective reasoning, empirical validation, and human judgment within a continuous research lifecycle, transforming fragmented activities into a cumulative process of inquiry, criticism, and revision. The central premise of BLAZE is that scientific intelligence does not arise from computation alone. It emerges from the sustained interaction among knowledge, hypotheses, experiments, and collective verification. By organizing humans and machines within a shared scientific process, BLAZE makes discovery more traceable, reproducible, and cumulative while preserving human creativity, judgment, and responsibility. Socialized scientific intelligence may provide a foundation for the next era of science. Its purpose is not to replace human discovery, but to extend the scale, depth, and continuity of collective scientific inquiry.

Scientific knowledge is growing rapidly, making it challenging to track progress and high-level conceptual links across broad disciplines. While existing tools like citation networks and search engines make it easy to access a few related papers, they fundamentally lack the flexible abstraction needed to represent the density of activity in various scientific subfields. We motivate SCIENCE HIERARCHOGRAPHY, the goal of organizing scientific literature into a high-quality hierarchical structure that allows for the categorization of scientific work across varying levels of abstraction, from very broad fields to very specific studies. Such a representation can provide insights into which fields are well-explored and which are under-explored. To achieve the goals of SCIENCE HIERARCHOGRAPHY, we develop a range of algorithms. Our primary approach combines fast embedding-based clustering with LLM-based prompting to balance the computational efficiency of embedding methods with the semantic precision offered by LLM prompting. We demonstrate that this approach offers the best trade-off between quality and speed compared to methods that heavily rely on LLM prompting, such as iterative tree construction with LLMs. To better reflect the interdisciplinary and multifaceted nature of research papers, our hierarchy captures multiple dimensions of categorization beyond simple topic labels. We evaluate the utility of our framework by assessing how effectively an LLM-based agent can locate target papers using the hierarchy. Results show that this structured approach enhances interpretability, supports trend discovery, and offers an alternative pathway for exploring scientific literature beyond traditional search methods. Code, data and demo: https://github.com/JHU-CLSP/science-hierarchography{https://github.com/JHU-CLSP/science-hierarchography}

The cycle of scientific discovery is frequently bottlenecked by the slow, manual creation of software to support computational experiments. To address this, we present an AI system that creates expert-level scientific software whose goal is to maximize a quality metric. The system uses a Large Language Model (LLM) and Tree Search (TS) to systematically improve the quality metric and intelligently navigate the large space of possible solutions. The system achieves expert-level results when it explores and integrates complex research ideas from external sources. The effectiveness of tree search is demonstrated across a wide range of benchmarks. In bioinformatics, it discovered 40 novel methods for single-cell data analysis that outperformed the top human-developed methods on a public leaderboard. In epidemiology, it generated 14 models that outperformed the CDC ensemble and all other individual models for forecasting COVID-19 hospitalizations. Our method also produced state-of-the-art software for geospatial analysis, neural activity prediction in zebrafish, time series forecasting and numerical solution of integrals. By devising and implementing novel solutions to diverse tasks, the system represents a significant step towards accelerating scientific progress.

This paper introduces a pioneering approach to artificial intelligence research, embodied in our O1 Replication Journey. In response to the announcement of OpenAI's groundbreaking O1 model, we embark on a transparent, real-time exploration to replicate its capabilities while reimagining the process of conducting and communicating AI research. Our methodology addresses critical challenges in modern AI research, including the insularity of prolonged team-based projects, delayed information sharing, and the lack of recognition for diverse contributions. By providing comprehensive, real-time documentation of our replication efforts, including both successes and failures, we aim to foster open science, accelerate collective advancement, and lay the groundwork for AI-driven scientific discovery. Our research progress report diverges significantly from traditional research papers, offering continuous updates, full process transparency, and active community engagement throughout the research journey. Technologically, we proposed the journey learning paradigm, which encourages models to learn not just shortcuts, but the complete exploration process, including trial and error, reflection, and backtracking. With only 327 training samples and without any additional tricks, journey learning outperformed conventional supervised learning by over 8\% on the MATH dataset, demonstrating its extremely powerful potential. We believe this to be the most crucial component of O1 technology that we have successfully decoded. We share valuable resources including technical hypotheses and insights, cognitive exploration maps, custom-developed tools, etc at https://github.com/GAIR-NLP/O1-Journey.

AI systems are increasingly capable of contributing to mathematical research. In research practice, frontier-model reasoning is a limited resource, and expert mathematical review is even more sharply constrained. Allocating these scarce resources well is therefore central to making AI-assisted mathematical discovery efficient. In most current AI-for-math workflows, human effort is concentrated at the beginning and end, in selecting suitable research problems and later reviewing the resulting artifacts. These two stages are becoming bottlenecks for research-level mathematics. We address them by proposing a new human-AI discovery paradigm. The human input is no longer a single problem selected in advance, but a research direction in which the experts have interest and expertise. The system then searches a broad literature corpus for candidate problems in that direction. Inspired by search and recommender systems, we build Find, Attempt, and Recommend (FAR), a literature-to-review cascade that automates the search for suitable problems and focuses human attention on artifacts that have passed several stages of filtering. In a combinatorics pilot, the pipeline starts from 5,245 combinatorics papers, recovers 6,453 candidate conjectures or open problems, and filters them to 4,717 apparently well-posed and still-open conjectures. Subsequent reasoning and automated triage stages surface 598 potential resolutions and select 77 items for author-team review. Among them, we identify many interesting discoveries, including results on conjectures and questions of Davies--Jenssen--Perkins--Roberts, Erdős--Straus, Ikenmeyer--Pak--Panova, and Lund--Saraf--Wolf. These results demonstrate the effectiveness of this new mode of human-AI collaboration for mathematical discovery.

Finding relevant tables among databases, lakes, and repositories is the first step in extracting value from data. Such a task remains difficult because assessing whether a table is relevant to a problem does not always depend only on its content but also on the context, which is usually tribal knowledge known to the individual or team. While tools like data catalogs and academic data discovery systems target this problem, they rely on keyword search or more complex interfaces, limiting non-technical users' ability to find relevant data. The advent of large language models (LLMs) offers a unique opportunity for users to ask questions directly in natural language, making dataset discovery more intuitive, accessible, and efficient. In this paper, we introduce Pneuma, a retrieval-augmented generation (RAG) system designed to efficiently and effectively discover tabular data. Pneuma leverages large language models (LLMs) for both table representation and table retrieval. For table representation, Pneuma preserves schema and row-level information to ensure comprehensive data understanding. For table retrieval, Pneuma augments LLMs with traditional information retrieval techniques, such as full-text and vector search, harnessing the strengths of both to improve retrieval performance. To evaluate Pneuma, we generate comprehensive benchmarks that simulate table discovery workload on six real-world datasets including enterprise data, scientific databases, warehousing data, and open data. Our results demonstrate that Pneuma outperforms widely used table search systems (such as full-text search and state-of-the-art RAG systems) in accuracy and resource efficiency.

Recent advances in Tool-Integrated Large Language Models have made web search a core capability of information-seeking agents. However, as interaction histories grow, agents increasingly struggle to track task progress. When search attempts fail to yield useful evidence, current single- and multi-agent systems can become trapped in repetitive loops, wasting search budgets and ultimately compromising the quality and completeness of the final output. We introduce SearchOS, a system-level multi-agent framework that turns fragile, implicit search progress into explicit, persistent, and shared state. First, we formulate open-domain information seeking as relational schema completion with grounded citations, where agents discover entities, populate attributes across linked tables, and anchor each value to source evidence. Then we design Search-Oriented Context Management (SOCM), which externalizes the evolving state into Frontier Task, an Evidence Graph, a Coverage Map, and Failure Memory. Built on SOCM, SearchOS applies a pipeline-parallel scheduling mechanism that overlaps the execution of sub-agents and continuously refills freed slots with tasks targeting unresolved coverage gaps to improve utilization and throughput. To schedule and control the execution of search agents, SearchOS introduces a Search Tool Middleware Harness that intercepts model and tool interactions to record grounded evidence and react to stalls or budget exhaustion, and provides a reusable hierarchical skill system comprising strategy and access skills to augment the agents' search process and avoid repeating failed search patterns across runs. On WideSearch and GISA, SearchOS leads all metrics among the evaluated single- and multi-agent baselines, paving the way toward robust information-seeking collaboration.

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.

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.

Large language models are increasingly deployed as tool-augmented agents to acquire information beyond parametric knowledge. While recent work has improved long-horizon tool-use reasoning, most approaches focus on tasks with a single correct answer. In contrast, many real-world queries require discovering a comprehensive set of valid answers, a setting known as Multi-Answer QA. This setting raises two challenges: fine-grained credit assignment over long search trajectories and reward alignment for sustained exploration beyond easy high-frequency entities. We propose SPADER, a reinforcement learning framework for long-horizon tool use in Multi-Answer QA. SPADER includes Step-wise Peer Advantage (SPA), a critic-free step-level credit assignment mechanism that aligns parallel trajectories by decision step and estimates advantages from peer returns. It also includes a diversity-aware exploration reward that promotes long-tail entity discovery by upweighting rare findings and downweighting redundant ones. Experiments on QAMPARI, Mintaka, WebQSP, and QUEST show that SPADER generally improves recall and overall F1 over prompting-based agents, outcome-supervised RL methods, and recent step-level supervision approaches. Our code and model weights are available at https://github.com/KhanCold/spader.

Large Language Model (LLM)-based multi-agent systems (MAS) demonstrate remarkable potential for scientific discovery. Existing approaches, however, often automate scientific discovery using predefined workflows that lack rationality constraints. This often leads to aimless hypothesizing and a failure to consistently link hypotheses with evidence, thereby hindering systematic uncertainty reduction. Overcoming these limitations fundamentally requires systematic uncertainty reduction. We introduce PiFlow, an information-theoretical framework, treating automated scientific discovery as a structured uncertainty reduction problem guided by principles (e.g., scientific laws). In evaluations across three distinct scientific domains -- discovering nanomaterial structures, bio-molecules, and superconductor candidates with targeted properties -- our method significantly improves discovery efficiency, reflected by a 73.55\% increase in the Area Under the Curve (AUC) of property values versus exploration steps, and enhances solution quality by 94.06\% compared to a vanilla agent system. Overall, PiFlow serves as a Plug-and-Play method, establishing a novel paradigm shift in highly efficient automated scientific discovery, paving the way for more robust and accelerated AI-driven research. Code is publicly available at our https://github.com/amair-lab/PiFlow{GitHub}.

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/.

We propose a federated learning-like framework, Federation over Text (FoT), that enables multiple clients solving different tasks to collectively generate a shared library of metacognitive insights by iteratively federating their local reasoning processes without sharing actual problem instances or task instructions. Instead of federation over gradients (e.g., as in distributed training), FoT operates at the semantic level without any gradient optimization or supervision signal. Iteratively, each client runs an LLM agent that does local thinking and self-improvement on their specific tasks independently, and shares reasoning traces with a central server, which aggregates and distills them into a cross-task (and cross-domain) insight library that existing and future agents can leverage to improve performance on related tasks. Experiments show that FoT improves reasoning effectiveness and efficiency across a wide range of challenging applications, including mathematical problem solving, cross-domain collaboration, real-world daily tasks, and machine learning research insight discovery. Specifically, it improves average performance scores by 25% while reducing the reasoning tokens by 4% across the first three applications. In the research insight discovery application, FoT is able to generate insights that cover over 80% of the major contributions in the subsequent papers.

The rapid growth of biomedical literature and curated databases has made it increasingly difficult for researchers to systematically connect biomarker mechanisms to actionable drug combination hypotheses. We present AI Co-Scientist (CoDHy), an interactive, human-in-the-loop system for biomarker-guided drug combination hypothesis generation in cancer research. CoDHy integrates structured biomedical databases and unstructured literature evidence into a task-specific knowledge graph, which serves as the basis for graph-based reasoning and hypothesis construction. The system combines knowledge graph embeddings with agent-based reasoning to generate, validate, and rank candidate drug combinations, while explicitly grounding each hypothesis in retrievable evidence. Through a web-based interface, users can configure the scientific context, inspect intermediate results, and iteratively refine hypotheses, enabling transparent and researcher-steerable exploration rather than automated decision-making. We demonstrate CoDHy as a system for exploratory hypothesis generation and decision support in translational oncology, highlighting its design, interaction workflow, and practical use cases.

Large Language Models (LLMs) are transforming scientific hypothesis generation and validation by enabling information synthesis, latent relationship discovery, and reasoning augmentation. This survey provides a structured overview of LLM-driven approaches, including symbolic frameworks, generative models, hybrid systems, and multi-agent architectures. We examine techniques such as retrieval-augmented generation, knowledge-graph completion, simulation, causal inference, and tool-assisted reasoning, highlighting trade-offs in interpretability, novelty, and domain alignment. We contrast early symbolic discovery systems (e.g., BACON, KEKADA) with modern LLM pipelines that leverage in-context learning and domain adaptation via fine-tuning, retrieval, and symbolic grounding. For validation, we review simulation, human-AI collaboration, causal modeling, and uncertainty quantification, emphasizing iterative assessment in open-world contexts. The survey maps datasets across biomedicine, materials science, environmental science, and social science, introducing new resources like AHTech and CSKG-600. Finally, we outline a roadmap emphasizing novelty-aware generation, multimodal-symbolic integration, human-in-the-loop systems, and ethical safeguards, positioning LLMs as agents for principled, scalable scientific discovery.

The rapid advancement of scientific progress requires innovative tools that can accelerate discovery. While recent AI methods, particularly large language models (LLMs), have shown promise in tasks such as hypothesis generation and experimental design, they fall short in replicating the collaborative nature of real-world scientific practices, where diverse teams of experts work together to tackle complex problems. To address the limitation, we propose an LLM-based multi-agent system, i.e., Virtual Scientists (VirSci), designed to mimic the teamwork inherent in scientific research. VirSci organizes a team of agents to collaboratively generate, evaluate, and refine research ideas. Through comprehensive experiments, we demonstrate that this multi-agent approach outperforms the state-of-the-art method in producing novel and impactful scientific ideas, showing potential in aligning with key insights in the Science of Science field. Our findings suggest that integrating collaborative agents can lead to more innovative scientific outputs, offering a robust system for autonomous scientific discovery.

Public repositories host millions of fine-tuned models, yet community usage remains disproportionately concentrated on a small number of foundation checkpoints. We investigate whether this concentration reflects efficient market selection or if superior models are systematically overlooked. Through an extensive evaluation of over 2,000 models, we show the prevalence of "hidden gems", unpopular fine-tunes that significantly outperform their popular counterparts. Notably, within the Llama-3.1-8B family, we find rarely downloaded checkpoints that improve math performance from 83.2% to 96.0% without increasing inference costs. However, discovering these models through exhaustive evaluation of every uploaded model is computationally infeasible. We therefore formulate model discovery as a Multi-Armed Bandit problem and accelerate the Sequential Halving search algorithm by using shared query sets and aggressive elimination schedules. Our method retrieves top models with as few as 50 queries per candidate, accelerating discovery by over 50x.

The success of language models, especially transformer-based architectures, has trickled into other domains giving rise to "scientific language models" that operate on small molecules, proteins or polymers. In chemistry, language models contribute to accelerating the molecule discovery cycle as evidenced by promising recent findings in early-stage drug discovery. Here, we review the role of language models in molecular discovery, underlining their strength in de novo drug design, property prediction and reaction chemistry. We highlight valuable open-source software assets thus lowering the entry barrier to the field of scientific language modeling. Last, we sketch a vision for future molecular design that combines a chatbot interface with access to computational chemistry tools. Our contribution serves as a valuable resource for researchers, chemists, and AI enthusiasts interested in understanding how language models can and will be used to accelerate chemical discovery.

We introduce and release ScienceBuddy, an interactive scientific research workspace that brings continually improving scientific agents into researchers' everyday workflows. ScienceBuddy supports researchers in carrying out scientific tasks while transforming their requests, feedback, and execution evidence into tasks and evaluation rubrics for continual learning. At its core is recursive-in-recursive self-improvement, a paradigm that couples harness evolution with model reinforcement learning: the inner recursion improves the harness with the model fixed, while the outer recursion trains the model under the improved harness. Harness evolution shapes training experience, and model learning creates new opportunities for harness adaptation. We present case studies of researcher interaction, harness refinement, and model learning, with the benchmark cases spanning four scientific task families. By releasing ScienceBuddy as a research product, we make this paradigm available to the scientific community and take a step toward discovery intelligence: scientific AI that advances through sustained collaboration with researchers and evolves alongside the research it supports. Website: http://science-buddy.io

In collaborative data sharing and machine learning, multiple parties aggregate their data resources to train a machine learning model with better model performance. However, as the parties incur data collection costs, they are only willing to do so when guaranteed incentives, such as fairness and individual rationality. Existing frameworks assume that all parties join the collaboration simultaneously, which does not hold in many real-world scenarios. Due to the long processing time for data cleaning, difficulty in overcoming legal barriers, or unawareness, the parties may join the collaboration at different times. In this work, we propose the following perspective: As a party who joins earlier incurs higher risk and encourages the contribution from other wait-and-see parties, that party should receive a reward of higher value for sharing data earlier. To this end, we propose a fair and time-aware data sharing framework, including novel time-aware incentives. We develop new methods for deciding reward values to satisfy these incentives. We further illustrate how to generate model rewards that realize the reward values and empirically demonstrate the properties of our methods on synthetic and real-world datasets.

Scientific discovery is defined by the ability to identify the boundaries of existing knowledge and venture into unexplored territory. The ultimate vision for AI in science is problem-driven autonomous research: given a fundamental challenge by a human expert, the AI independently navigates the scientific landscape, uncovers theoretical and empirical bottlenecks, and systematically expands the frontier of knowledge. In this paper, we introduce ScientistTwo, a fully autonomous multi-agent framework designed to realize this vision. Specifically, ScientistTwo takes an initial problem as input, establishes state-of-the-art baselines, formulates novel hypotheses, and coordinates specialized agents to orchestrate an end-to-end discovery cycle without human intervention. Moreover, the framework rigorously conducts experiments using diverse datasets and metrics, refines methodologies through automated ablation studies, and validates research findings via a closed-loop simulated peer-review rebuttal engine. To evaluate ScientistTwo's capabilities against the highest standards of human scientific achievement, we benchmark it across papers accepted at top-tier conferences such as ICLR, ICML, and NeurIPS. As a result, ScientistTwo autonomously generates expert-level, publishable papers and fully verified, executable codebases. Its solutions consistently outperform human state-of-the-art models, and achieve higher average review ratings than human-authored papers under automated AI review agents. These results show that ScientistTwo is not merely an assistive tool but an autonomous scientific pioneer capable of pushing the frontiers of human discovery. Project website: https://scientist-two.github.io/

Literature-Based Discovery (LBD) aims to discover new scientific knowledge by mining papers and generating hypotheses. Standard LBD is limited to predicting pairwise relations between discrete concepts (e.g., drug-disease links), and ignores critical contexts like experimental settings (e.g., a specific patient population where a drug is evaluated) and background motivations (e.g., to find drugs without specific side effects). We address these limitations with a novel formulation of contextualized-LBD (C-LBD): generating scientific hypotheses in natural language, while grounding them in a context that controls the hypothesis search space. We present a modeling framework using retrieval of ``inspirations'' from past scientific papers. Our evaluations reveal that GPT-4 tends to generate ideas with overall low technical depth and novelty, while our inspiration prompting approaches partially mitigate this issue. Our work represents a first step toward building language models that generate new ideas derived from scientific literature.

Scientific discovery increasingly requires AI systems that can reason over scientific evidence of heterogeneous modalities, interact with scientific tools and environments, and sustain progress across long task horizons. We present Intern-S2-Preview, a series of scientific agentic foundation models designed to support multimodal scientific understanding, reasoning, generation, and long-horizon tasks. The training pipeline begins with scientific multimodal pre-training over rendered scientific documents, interleaved image-text data, and diverse scientific corpora. Starting from the pretrained checkpoint, we apply a unified post-training pipeline consisting of supervised fine-tuning, scalable multi-task reinforcement learning (RL), black- and white-box agentic RL, and on-policy distillation. This pipeline is supported by practical techniques that improve rollout and training stability and efficiency, including partial rollout with off-policy correction, adaptive length regularization, online speculative decoding, robust multi-task optimization, and trace-aware experience assembly for agentic tasks. At the architecture level, Intern-S2-Preview-397B extends time series modelling from efficient long-sequence understanding to numerical forecasting, while Memory Decoder is studied as a separate memory-augmented path for rapid scientific specialization without modifying the frozen 397B backbone. Evaluations across scientific, multimodal, agentic, and general-purpose benchmarks show that Intern-S2-Preview-397B achieves competitive or leading results in multiple settings. The time series modules improve scientific signal understanding and forecasting on SciTS, while the separate Intern-MemDec-4B extension improves the Biology-Instructions average score from 56.92 to 60.32 without modifying the frozen 397B backbone.

Autonomous discovery systems such as OpenEvolve and TTT-Discover are often used as general-purpose harnesses. However, in practice these are composite systems combining several design choices about archives, parent selection, exploration, and budget allocation into a single recipe. Because discovery runs are expensive and inherently stochastic, existing harnesses are often compared using too few independent trials to distinguish key methodological improvements from run-to-run variance. We systematically decompose OpenEvolve-style evolutionary search and the TTT-Discover search harness into its constituent components and systematically evaluate 30 budget-matched harnesses across 12 model-problem pairs using more than 3.1 million LLM rollouts and repeated-trial statistical analysis. Our results show that discovery harnesses have a generalization problem: No fixed harness is reliably superior across the evaluated model-problem pairs, and variants of OpenEvolve generally underperform simpler alternatives. Thus, harness choice is better viewed as a hyperparameter rather than as a universal recipe, and should be tailored to the specific problem and underlying model. We also find that early discovery progress predicts final performance, and use this property to present a budget-matched adaptive-allocation experiment that starts multiple harnesses, prunes weak partial runs, and reallocates compute to stronger survivors, outperforming both commitment to a randomly sampled fixed harness and a non-adaptive harness ensemble. Together, these results motivate shifting from fixed harness selection to online adaptation guided by early performance. We release all run pools including baseline null distributions for every model-problem pair as reusable statistical infrastructure against for future harness proposals.

The rapid advancement of Large Language Models (LLMs) has opened new opportunities in data science, yet their practical deployment is often constrained by the challenge of discovering relevant data within large heterogeneous data lakes. Existing methods struggle with this: single-agent systems are quickly overwhelmed by large, heterogeneous files in the large data lakes, while multi-agent systems designed based on a master-slave paradigm depend on a rigid central controller for task allocation that requires precise knowledge of each sub-agent's capabilities. To address these limitations, we propose a novel multi-agent communication paradigm inspired by the blackboard architecture for traditional AI models. In this framework, a central agent posts requests to a shared blackboard, and autonomous subordinate agents -- either responsible for a partition of the data lake or general information retrieval -- volunteer to respond based on their capabilities. This design improves scalability and flexibility by eliminating the need for a central coordinator to have prior knowledge of all sub-agents' expertise. We evaluate our method on three benchmarks that require explicit data discovery: KramaBench and modified versions of DS-Bench and DA-Code to incorporate data discovery. Experimental results demonstrate that the blackboard architecture substantially outperforms baselines, including RAG and the master-slave multi-agent paradigm, achieving between 13% to 57% relative improvement in end-to-end task success and up to a 9% relative gain in F1 score for data discovery over the best-performing baselines across both proprietary and open-source LLMs. Our findings establish the blackboard paradigm as a scalable and generalizable communication framework for multi-agent systems.

Large language models (LLMs) excel at answering pre-specified questions, yet their ability to navigate the open-ended, pre-conclusion stage of discovery remains largely unmeasured. We introduce Prospective Hypothesis Discovery (PHD), which asks models to autonomously construct grounded, discriminative, and testable hypothesis spaces from inconclusive evidence, including anomalous observations and fragmented records, to guide subsequent investigation. To evaluate this capability, we introduce HypoArena, comprising HypoData, a benchmark of 988 cases across six scientific and analytical domains, and HypoEval, an evaluation framework for open-ended hypothesis sets. To construct HypoData at scale, we propose Retrospective Context Regression, a Forge--Audit pipeline that reconstructs pre-conclusion contexts from completed expert documents by removing explicit conclusions, target hypotheses, and retrospective causal attributions while preserving the factual substrate. Because PHD admits multiple valid outputs, HypoEval combines bidirectional pairwise judgments with Bradley--Terry--Davidson aggregation for ranking and six-dimensional rubric scoring for diagnosis. Experiments on 15 frontier LLMs reveal clear capability stratification and model-dependent effects of structured analytical skills, with gains for several lower-performing models on HypoArena but regressions for other systems, including a top-performing model. Compared with absolute rubric scoring, arena evaluation resolves finer-grained differences among models, with aggregated rankings showing strong agreement with human experts and an independent judge. Together, these results support treating PHD as a distinct target for evaluating how LLMs formulate investigative directions when final conclusions are withheld. Our code and data are publicly available at github.com/SKYLENAGE-AI/HypoArena and github.com/SKYLENAGE-AI/HypoArena.

Realistic text-to-SQL workflows often require joining multiple tables. As a result, accurately retrieving the relevant set of tables becomes a key bottleneck for end-to-end performance. We study an open-book setting where queries must be answered over large, heterogeneous table collections pooled from many sources, without clean scoping signals such as database identifiers. Here, dense retrieval (DR) achieves high recall but returns many distractors, while join-aware alternatives often rely on extra assumptions and/or incur high inference overhead. We propose CORE-T, a scalable, training-free framework that enriches tables with LLM-generated purpose metadata and pre-computes a lightweight table-compatibility cache. At inference time, DR returns top-K candidates; a single LLM call selects a coherent, joinable subset, and a two-step additive adjustment stage restores strongly compatible tables. Across Bird, Spider, MMQA, and Beaver, CORE-T improves over DR by up to 22.7 points in table-selection F1 while returning up to 40% fewer tables, and by up to 24.4 points in multi-table execution accuracy, and uses 1.64-4.20x fewer total selection tokens than LLM-intensive baselines.

With recent Nobel Prizes recognising AI contributions to science, Large Language Models (LLMs) are transforming scientific research by enhancing productivity and reshaping the scientific method. LLMs are now involved in experimental design, data analysis, and workflows, particularly in chemistry and biology. However, challenges such as hallucinations and reliability persist. In this contribution, we review how Large Language Models (LLMs) are redefining the scientific method and explore their potential applications across different stages of the scientific cycle, from hypothesis testing to discovery. We conclude that, for LLMs to serve as relevant and effective creative engines and productivity enhancers, their deep integration into all steps of the scientific process should be pursued in collaboration and alignment with human scientific goals, with clear evaluation metrics. The transition to AI-driven science raises ethical questions about creativity, oversight, and responsibility. With careful guidance, LLMs could evolve into creative engines, driving transformative breakthroughs across scientific disciplines responsibly and effectively. However, the scientific community must also decide how much it leaves to LLMs to drive science, even when associations with 'reasoning', mostly currently undeserved, are made in exchange for the potential to explore hypothesis and solution regions that might otherwise remain unexplored by human exploration alone.

Scientific equation discovery is a fundamental task in the history of scientific progress, enabling the derivation of laws governing natural phenomena. Recently, Large Language Models (LLMs) have gained interest for this task due to their potential to leverage embedded scientific knowledge for hypothesis generation. However, evaluating the true discovery capabilities of these methods remains challenging, as existing benchmarks often rely on common equations that are susceptible to memorization by LLMs, leading to inflated performance metrics that do not reflect discovery. In this paper, we introduce LLM-SRBench, a comprehensive benchmark with 239 challenging problems across four scientific domains specifically designed to evaluate LLM-based scientific equation discovery methods while preventing trivial memorization. Our benchmark comprises two main categories: LSR-Transform, which transforms common physical models into less common mathematical representations to test reasoning beyond memorized forms, and LSR-Synth, which introduces synthetic, discovery-driven problems requiring data-driven reasoning. Through extensive evaluation of several state-of-the-art methods, using both open and closed LLMs, we find that the best-performing system so far achieves only 31.5% symbolic accuracy. These findings highlight the challenges of scientific equation discovery, positioning LLM-SRBench as a valuable resource for future research.

Recruiting patients to participate in clinical trials can be challenging and time-consuming. Usually, participation in a clinical trial is initiated by a healthcare professional and proposed to the patient. Promoting clinical trials directly to patients via online recruitment might help to reach them more efficiently. In this study, we address the case where a patient is initiating their own recruitment process and wants to determine whether they are eligible for a given clinical trial, using their own language to describe their medical profile. To study whether this creates difficulties in the patient trial matching process, we design a new dataset and task, Natural Language Inference for Patient Recruitment (NLI4PR), in which patient language profiles must be matched to clinical trials. We create it by adapting the TREC 2022 Clinical Trial Track dataset, which provides patients' medical profiles, and rephrasing them manually using patient language. We also use the associated clinical trial reports where the patients are either eligible or excluded. We prompt several open-source Large Language Models on our task and achieve from 56.5 to 71.8 of F1 score using patient language, against 64.7 to 73.1 for the same task using medical language. When using patient language, we observe only a small loss in performance for the best model, suggesting that having the patient as a starting point could be adopted to help recruit patients for clinical trials. The corpus and code bases are all freely available on our Github and HuggingFace repositories.

Autonomous scientific discovery with large language model (LLM)-based agents has recently made substantial progress, demonstrating the ability to automate end-to-end research workflows. However, existing systems largely rely on runtime-centric execution paradigms, repeatedly reading, summarizing, and reasoning over large volumes of scientific literature online. This on-the-spot computation strategy incurs high computational cost, suffers from context window limitations, and often leads to brittle reasoning and hallucination. We propose Idea2Story, a pre-computation-driven framework for autonomous scientific discovery that shifts literature understanding from online reasoning to offline knowledge construction. Idea2Story continuously collects peer-reviewed papers together with their review feedback, extracts core methodological units, composes reusable research patterns, and organizes them into a structured methodological knowledge graph. At runtime, underspecified user research intents are aligned to established research paradigms, enabling efficient retrieval and reuse of high-quality research patterns instead of open-ended generation and trial-and-error. By grounding research planning and execution in a pre-built knowledge graph, Idea2Story alleviates the context window bottleneck of LLMs and substantially reduces repeated runtime reasoning over literature. We conduct qualitative analyses and preliminary empirical studies demonstrating that Idea2Story can generate coherent, methodologically grounded, and novel research patterns, and can produce several high-quality research demonstrations in an end-to-end setting. These results suggest that offline knowledge construction provides a practical and scalable foundation for reliable autonomous scientific discovery.

There has been a surge of interest in harnessing the reasoning capabilities of Large Language Models (LLMs) to accelerate scientific discovery. While existing approaches rely on grounding the discovery process within the relevant literature, effectiveness varies significantly with the quality and nature of the retrieved literature. We address the challenge of retrieving prior work whose concepts can inspire solutions for a given research problem, a task we define as Methodology Inspiration Retrieval (MIR). We construct a novel dataset tailored for training and evaluating retrievers on MIR, and establish baselines. To address MIR, we build the Methodology Adjacency Graph (MAG); capturing methodological lineage through citation relationships. We leverage MAG to embed an "intuitive prior" into dense retrievers for identifying patterns of methodological inspiration beyond superficial semantic similarity. This achieves significant gains of +5.4 in Recall@3 and +7.8 in Mean Average Precision (mAP) over strong baselines. Further, we adapt LLM-based re-ranking strategies to MIR, yielding additional improvements of +4.5 in Recall@3 and +4.8 in mAP. Through extensive ablation studies and qualitative analyses, we exhibit the promise of MIR in enhancing automated scientific discovery and outline avenues for advancing inspiration-driven retrieval.

The rapid advancement of large language models (LLMs) has opened new boundaries in the extraction and synthesis of medical knowledge, particularly within evidence synthesis. This paper reviews the state-of-the-art applications of LLMs in the biomedical domain, exploring their effectiveness in automating complex tasks such as evidence synthesis and data extraction from a biomedical corpus of documents. While LLMs demonstrate remarkable potential, significant challenges remain, including issues related to hallucinations, contextual understanding, and the ability to generalize across diverse medical tasks. We highlight critical gaps in the current research literature, particularly the need for unified benchmarks to standardize evaluations and ensure reliability in real-world applications. In addition, we propose directions for future research, emphasizing the integration of state-of-the-art techniques such as retrieval-augmented generation (RAG) to enhance LLM performance in evidence synthesis. By addressing these challenges and utilizing the strengths of LLMs, we aim to improve access to medical literature and facilitate meaningful discoveries in healthcare.

Autonomous discovery systems couple a resource that answers queries (a simulator, instrument, or analytic model) to an algorithm that selects what to query next. Most software frameworks for this loop inherit the control structure of numerical optimization: campaigns run for a fixed number of iterations, query costs are absent from the programming interface, and decision-making is treated as free. In practice, queries may differ in cost by orders of magnitude, and planners built on large language models or expensive surrogates consume resources of their own. Here we present CADAQUES, an open-source Python framework built on one architectural principle: cost is a first-class primitive of the discovery loop. CADAQUES separates the loop into two structural protocols, an Oracle that answers queries and a Driver that proposes them, and charges both evaluations and decisions against a common vector-valued budget spanning wall time, CPU hours, monetary cost, and language model tokens. An append-only ledger records, for each transaction, the cost declared before execution and the cost settled afterwards, making their discrepancy an observable property of the campaign. We evaluate the architecture by locating the critical temperature of the two-dimensional Ising model from noisy finite-size estimates against the exact thermodynamic-limit reference. In this noisy setting, strategies that concentrate around the best observed result can be misled by noise-induced peaks, whereas a schedule that explores with cheap low-fidelity queries and refines with higher-fidelity ones yields lower and less variable errors than high fidelity throughout, at the studied budget scale. Metering adds tens of microseconds per iteration, three orders of magnitude below the cheapest oracle query. The framework is MIT-licensed and archived at Zenodo (doi:10.5281/zenodo.21293589).

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.

Language models are increasingly used in scientific discovery to generate hypotheses, propose candidate solutions, implement systems, and iteratively refine them. At the core of these trial-and-error loops lies evaluation: the process of obtaining feedback on candidate solutions via verifiers, simulators, or task-specific scoring functions. While prior work has highlighted the importance of evaluation, it has not explicitly formulated the problem of how evaluation-driven discovery loops can be scaled up in a principled and effective manner to push the boundaries of scientific discovery, a problem this paper seeks to address. We introduce Simple Test-time Evaluation-driven Scaling (SimpleTES), a general framework that strategically combines parallel exploration, feedback-driven refinement, and local selection, revealing substantial gains unlocked by scaling evaluation-driven discovery loops along the right dimensions. Across 21 scientific problems spanning six domains, SimpleTES discovers state-of-the-art solutions using gpt-oss models, consistently outperforming both frontier-model baselines and sophisticated optimization pipelines. Particularly, we sped up the widely used LASSO algorithm by over 2x, designed quantum circuit routing policies that reduce gate overhead by 24.5%, and discovered new Erdos minimum overlap constructions that surpass the best-known results. Beyond novel discoveries, SimpleTES produces trajectory-level histories that naturally supervise feedback-driven learning. When post-trained on successful trajectories, models not only improve efficiency on seen problems but also generalize to unseen problems, discovering solutions that base models fail to uncover. Together, our results establish effective evaluation-driven loop scaling as a central axis for advancing LLM-driven scientific discovery, and provide a simple yet practical framework for realizing these gains.

The rapid acceleration of scientific publishing has created substantial challenges for researchers attempting to discover, contextualize, and interpret relevant literature. Traditional keyword-based search systems provide limited semantic understanding, while existing AI-driven tools typically focus on isolated tasks such as retrieval, clustering, or bibliometric visualization. This paper presents an integrated system for scientific literature exploration that combines large-scale data acquisition, hybrid retrieval, semantic topic modeling, and heterogeneous knowledge graph construction. The system builds a comprehensive corpus by merging full-text data from arXiv with structured metadata from OpenAlex. A hybrid retrieval architecture fuses BM25 lexical search with embedding-based semantic search using Reciprocal Rank Fusion. Topic modeling is performed on retrieved results using BERTopic or non-negative matrix factorization depending on computational resources. A knowledge graph unifies papers, authors, institutions, countries, and extracted topics into an interpretable structure. The system provides a multi-layered exploration environment that reveals not only relevant publications but also the conceptual and relational landscape surrounding a query. Evaluation across multiple queries demonstrates improvements in retrieval relevance, topic coherence, and interpretability. The proposed framework contributes an extensible foundation for AI-assisted scientific 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.

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.

Causal discovery is an imperative foundation for decision-making across domains, such as smart health, AI for drug discovery and AIOps. Traditional statistical causal discovery methods, while well-established, predominantly rely on observational data and often overlook the semantic cues inherent in cause-and-effect relationships. The advent of Large Language Models (LLMs) has ushered in an affordable way of leveraging the semantic cues for knowledge-driven causal discovery, but the development of LLMs for causal discovery lags behind other areas, particularly in the exploration of multi-modal data. To bridge the gap, we introduce MATMCD, a multi-agent system powered by tool-augmented LLMs. MATMCD has two key agents: a Data Augmentation agent that retrieves and processes modality-augmented data, and a Causal Constraint agent that integrates multi-modal data for knowledge-driven reasoning. The proposed design of the inner-workings ensures successful cooperation of the agents. Our empirical study across seven datasets suggests the significant potential of multi-modality enhanced causal discovery.

Scholars studying organizations often work with multiple datasets lacking shared unique identifiers or covariates. In such situations, researchers may turn to approximate string matching methods to combine datasets. String matching, although useful, faces fundamental challenges. Even when two strings appear similar to humans, fuzzy matching often does not work because it fails to adapt to the informativeness of the character combinations presented. Worse, many entities have multiple names that are dissimilar (e.g., "Fannie Mae" and "Federal National Mortgage Association"), a case where string matching has little hope of succeeding. This paper introduces data from a prominent employment-related networking site (LinkedIn) as a tool to address these problems. We propose interconnected approaches to leveraging the massive amount of information from LinkedIn regarding organizational name-to-name links. The first approach builds a machine learning model for predicting matches from character strings, treating the trillions of user-contributed organizational name pairs as a training corpus: this approach constructs a string matching metric that explicitly maximizes match probabilities. A second approach identifies relationships between organization names using network representations of the LinkedIn data. A third approach combines the first and second. We document substantial improvements over fuzzy matching in applications, making all methods accessible in open-source software ("LinkOrgs").

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.

Clinical trials drive improvements in cancer treatments and outcomes. However, most adults with cancer do not participate in trials, and trials often fail to enroll enough patients to answer their scientific questions. Artificial intelligence could accelerate matching of patients to appropriate clinical trials. Here, we describe the development and evaluation of the MatchMiner-AI pipeline for clinical trial searching and ranking. MatchMiner-AI focuses on matching patients to potential trials based on core criteria describing clinical "spaces," or disease contexts, targeted by a trial. It aims to accelerate the human work of identifying potential matches, not to fully automate trial screening. The pipeline includes modules for extraction of key information from a patient's longitudinal electronic health record; rapid ranking of candidate trial-patient matches based on embeddings in vector space; and classification of whether a candidate match represents a reasonable clinical consideration. Code and synthetic data are available at https://huggingface.co/ksg-dfci/MatchMiner-AI . Model weights based on synthetic data are available at https://huggingface.co/ksg-dfci/TrialSpace and https://huggingface.co/ksg-dfci/TrialChecker . A simple cancer clinical trial search engine to demonstrate pipeline components is available at https://huggingface.co/spaces/ksg-dfci/trial_search_alpha .

WANDR (Wide ANd Deep Research) is a benchmark of 500 realistic, challenging data-collection tasks for research agents. Each task requires a system to discover a large set of entities that satisfy specified criteria (breadth), investigate each entity through multiple coordinated web searches (depth), and return independently verifiable records with supporting sources and excerpts. Tasks are represented as qualification key hierarchies that specify the entities, relationships, evidence, and required count at each level; a hierarchy with n companies, m employees per company, and k sources per employee requires n x m x k records. This structure supports diverse workflows such as market mapping, due diligence, literature review, product comparison, and talent sourcing, with targets ranging from dozens to thousands of records. WANDR replaces static gold answer sets with task-specific judges that refetch cited pages and verify each record against its evidence, allowing evaluation of current and changing facts. Record verdicts are aggregated into soft and hard precision, recall, and F1 scores that distinguish factual quality, coverage, and hierarchical completeness. The tasks are derived from de-identified product-usage logs and produced through a semi-automated pipeline with automated checks, empirical audits, and human review where needed. We evaluate six production research systems and find that the benchmark is far from saturated: at high effort, the strongest system reaches only 0.363 soft F1 and 0.133 hard F1. Performance degrades as target volume and hierarchy depth increase, with incomplete discovery, missing enrichment, and incomplete evidence construction remaining major bottlenecks. The benchmark and evaluation harness are available at https://github.com/perplexityai/wandr.

The way in which data are shared can affect their utility and reusability. Here, we demonstrate how data that we had previously shared in bulk can be mobilized further through a knowledge graph that allows for much more granular exploration and interrogation. The original dataset is about the computational reproducibility of GitHub-hosted Jupyter notebooks associated with biomedical publications. It contains rich metadata about the publications, associated GitHub repositories and Jupyter notebooks, and the notebooks' reproducibility. We took this dataset, converted it into semantic triples and loaded these into a triple store to create a knowledge graph, FAIR Jupyter, that we made accessible via a web service. This enables granular data exploration and analysis through queries that can be tailored to specific use cases. Such queries may provide details about any of the variables from the original dataset, highlight relationships between them or combine some of the graph's content with materials from corresponding external resources. We provide a collection of example queries addressing a range of use cases in research and education. We also outline how sets of such queries can be used to profile specific content types, either individually or by class. We conclude by discussing how such a semantically enhanced sharing of complex datasets can both enhance their FAIRness, i.e., their findability, accessibility, interoperability, and reusability, and help identify and communicate best practices, particularly with regards to data quality, standardization, automation and reproducibility.

Scientific breakthroughs often emerge from synthesizing prior ideas into novel contributions. While language models (LMs) show promise in scientific discovery, their ability to perform this targeted, literature-grounded synthesis remains underexplored. We introduce insight anticipation, a generation task in which a model predicts a downstream paper's core insight from its foundational parent papers. To evaluate this capability, we develop GiantsBench, a benchmark of 17k examples across eight scientific domains, where each example consists of a set of parent papers paired with the core insight of a downstream paper. We evaluate models using an LM judge that scores similarity between generated and ground-truth insights, and show that these similarity scores correlate with expert human ratings. Finally, we present GIANTS-4B, an LM trained via reinforcement learning (RL) to optimize insight anticipation using these similarity scores as a proxy reward. Despite its smaller open-source architecture, GIANTS-4B outperforms proprietary baselines and generalizes to unseen domains, achieving a 34% relative improvement in similarity score over gemini-3-pro. Human evaluations further show that GIANTS-4B produces insights that are more conceptually clear than those of the base model. In addition, SciJudge-30B, a third-party model trained to compare research abstracts by likely citation impact, predicts that insights generated by GIANTS-4B are more likely to lead to higher citations, preferring them over the base model in 68% of pairwise comparisons. We release our code, benchmark, and model to support future research in automated scientific discovery.

New Intent Discovery (NID) aims to recognize known and infer new intent categories with the help of limited labeled and large-scale unlabeled data. The task is addressed as a feature-clustering problem and recent studies augment instance representation. However, existing methods fail to capture cluster-friendly representations, since they show less capability to effectively control and coordinate within-cluster and between-cluster distances. Tailored to the NID problem, we propose a Robust and Adaptive Prototypical learning (RAP) framework for globally distinct decision boundaries for both known and new intent categories. Specifically, a robust prototypical attracting learning (RPAL) method is designed to compel instances to gravitate toward their corresponding prototype, achieving greater within-cluster compactness. To attain larger between-cluster separation, another adaptive prototypical dispersing learning (APDL) method is devised to maximize the between-cluster distance from the prototype-to-prototype perspective. Experimental results evaluated on three challenging benchmarks (CLINC, BANKING, and StackOverflow) of our method with better cluster-friendly representation demonstrate that RAP brings in substantial improvements over the current state-of-the-art methods (even large language model) by a large margin (average +5.5% improvement).

Large language models (LLMs) are on the rise for accelerating scientific discovery, most recently in advanced tasks such as generating valid scientific hypotheses. Yet in many discovery settings, the goal is not to identify a single best hypothesis since validation can be noisy and expensive, and scientists benefit from a set of high-quality alternative hypotheses that hedge against downstream uncertainty for the best solutions. Nevertheless, commonly used evolutionary search recipes tend to prioritize optimization over exploration in hypothesis generation, and the resulting selection pressure during the search process leads to diversity collapse. Motivated by these limitations, we formulate hypothesis search as a sampling problem, where the objective is to efficiently produce diverse, high-quality hypotheses under a fixed validation budget. Building on this perspective, we propose \ours, an evolutionary framework inspired by the classical parallel tempering algorithm that searches hypotheses at multiple temperature levels and enables principled information exchange across temperatures to improve exploration without disrupting convergence. Across domains including molecular discovery, equation discovery, and algorithm discovery, our approach consistently improves both hypothesis quality and diversity under the same validation budget, and produces candidates that remain robust under more expensive downstream computational validations.

Scientific archives now contain hundreds of petabytes of data across genomics, ecology, climate, and molecular biology that could reveal undiscovered patterns if systematically analyzed at scale. Large-scale, weakly-supervised datasets in language and vision have driven the development of foundation models whose internal representations encode structure (patterns, co-occurrences and statistical regularities) beyond their training objectives. Most existing methods extract structure only for pre-specified targets; they excel at confirmation but do not support open-ended discovery of unknown patterns. We ask whether sparse autoencoders (SAEs) can enable open-ended feature discovery from foundation model representations. We evaluate this question in controlled rediscovery studies, where the learned SAE features are tested for alignment with semantic concepts on a standard segmentation benchmark and compared against strong label-free alternatives on concept-alignment metrics. Applied to ecological imagery, the same procedure surfaces fine-grained anatomical structure without access to segmentation or part labels, providing a scientific case study with ground-truth validation. While our experiments focus on vision with an ecology case study, the method is domain-agnostic and applicable to models in other sciences (e.g., proteins, genomics, weather). Our results indicate that sparse decomposition provides a practical instrument for exploring what scientific foundation models have learned, an important prerequisite for moving from confirmation to genuine discovery.

Evaluating novelty is critical yet challenging in peer review, as reviewers must assess submissions against a vast, rapidly evolving literature. This report presents OpenNovelty, an LLM-powered agentic system for transparent, evidence-based novelty analysis. The system operates through four phases: (1) extracting the core task and contribution claims to generate retrieval queries; (2) retrieving relevant prior work based on extracted queries via semantic search engine; (3) constructing a hierarchical taxonomy of core-task-related work and performing contribution-level full-text comparisons against each contribution; and (4) synthesizing all analyses into a structured novelty report with explicit citations and evidence snippets. Unlike naive LLM-based approaches, OpenNovelty grounds all assessments in retrieved real papers, ensuring verifiable judgments. We deploy our system on 500+ ICLR 2026 submissions with all reports publicly available on our website, and preliminary analysis suggests it can identify relevant prior work, including closely related papers that authors may overlook. OpenNovelty aims to empower the research community with a scalable tool that promotes fair, consistent, and evidence-backed peer review.

Retrieval module can be plugged into many downstream NLP tasks to improve their performance, such as open-domain question answering and retrieval-augmented generation. The key to a retrieval system is to calculate relevance scores to query and passage pairs. However, the definition of relevance is often ambiguous. We observed that a major class of relevance aligns with the concept of entailment in NLI tasks. Based on this observation, we designed a method called entailment tuning to improve the embedding of dense retrievers. Specifically, we unify the form of retrieval data and NLI data using existence claim as a bridge. Then, we train retrievers to predict the claims entailed in a passage with a variant task of masked prediction. Our method can be efficiently plugged into current dense retrieval methods, and experiments show the effectiveness of our method.

The rapid growth of biomedical knowledge has outpaced our ability to efficiently extract insights and generate novel hypotheses. Large language models (LLMs) have emerged as a promising tool to revolutionize knowledge interaction and potentially accelerate biomedical discovery. In this paper, we present a comprehensive evaluation of LLMs as biomedical hypothesis generators. We construct a dataset of background-hypothesis pairs from biomedical literature, carefully partitioned into training, seen, and unseen test sets based on publication date to mitigate data contamination. Using this dataset, we assess the hypothesis generation capabilities of top-tier instructed models in zero-shot, few-shot, and fine-tuning settings. To enhance the exploration of uncertainty, a crucial aspect of scientific discovery, we incorporate tool use and multi-agent interactions in our evaluation framework. Furthermore, we propose four novel metrics grounded in extensive literature review to evaluate the quality of generated hypotheses, considering both LLM-based and human assessments. Our experiments yield two key findings: 1) LLMs can generate novel and validated hypotheses, even when tested on literature unseen during training, and 2) Increasing uncertainty through multi-agent interactions and tool use can facilitate diverse candidate generation and improve zero-shot hypothesis generation performance. However, we also observe that the integration of additional knowledge through few-shot learning and tool use may not always lead to performance gains, highlighting the need for careful consideration of the type and scope of external knowledge incorporated. These findings underscore the potential of LLMs as powerful aids in biomedical hypothesis generation and provide valuable insights to guide further research in this area.

The convergence of artificial intelligence and materials science presents a transformative opportunity, but achieving true acceleration in discovery requires moving beyond task-isolated, fine-tuned models toward agentic systems that plan, act, and learn across the full discovery loop. This survey advances a unique pipeline-centric view that spans from corpus curation and pretraining, through domain adaptation and instruction tuning, to goal-conditioned agents interfacing with simulation and experimental platforms. Unlike prior reviews, we treat the entire process as an end-to-end system to be optimized for tangible discovery outcomes rather than proxy benchmarks. This perspective allows us to trace how upstream design choices-such as data curation and training objectives-can be aligned with downstream experimental success through effective credit assignment. To bridge communities and establish a shared frame of reference, we first present an integrated lens that aligns terminology, evaluation, and workflow stages across AI and materials science. We then analyze the field through two focused lenses: From the AI perspective, the survey details LLM strengths in pattern recognition, predictive analytics, and natural language processing for literature mining, materials characterization, and property prediction; from the materials science perspective, it highlights applications in materials design, process optimization, and the acceleration of computational workflows via integration with external tools (e.g., DFT, robotic labs). Finally, we contrast passive, reactive approaches with agentic design, cataloging current contributions while motivating systems that pursue long-horizon goals with autonomy, memory, and tool use. This survey charts a practical roadmap towards autonomous, safety-aware LLM agents aimed at discovering novel and useful materials.

Scientific discovery is an inherently creative and uncertain process, requiring reasoning beyond the recall of known knowledge. While many benchmarks have been proposed to evaluate large language model (LLM) performance on deep research tasks via multi-hop retrieval, their innovative reasoning abilities essential for true scientific discovery remain largely untested. We introduce a benchmark framework for evaluating model performance in scientific discovery and reasoning, building up from a raw problem to the classical null hypothesis test. In our framework, models initially receive only the topic and research question from a recent paper, with technical details progressively revealed. At each stage of information disclosure, the model is tasked with generating hypotheses that address the research question, which is compared with the conclusions from the original paper and evaluated via automated semantic similarity of constituent atomic claims. This progressive evaluation of semantic divergence from ground-truth conclusions enables assessment of a model's innovativeness (under minimal information) to grounded reasoning capabilities (under full experimental details), both critical for using LLMs for scientific discovery purposes. Our framework provides a foundation for systematically evaluating scientific reasoning and discovery capabilities in LLMs, crucial for advancing the development of next-generation AI scientist/co-scientist systems. Specifically, here we evaluate GPT-5, GPT-5.4, Gemini 2.5 pro, and Gemini 3.1 pro preview across 45 papers spanning bioactive materials, mechanical materials, and nanomaterials. We find that GPT-5.4 and Gemini 3.1 pro outperform their previous generation counterparts as expected, and GPT-5.4 in particular maintains 0.7 F1 score alignment with ground truth conclusions even under minimal context.

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/.

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.

Data products are reusable, self-contained assets designed for specific business use cases. Automating their discovery and generation is of great industry interest, as it enables discovery in large data lakes and supports analytical Data Product Requests (DPRs). Currently, there is no benchmark established specifically for data product discovery. Existing datasets focus on answering single factoid questions over individual tables rather than collecting multiple data assets for broader, coherent products. To address this gap, we introduce DPBench, the first user-request-driven data product benchmark over hybrid table-text corpora. Our framework systematically repurposes existing table-text QA datasets by clustering related tables and passages into coherent data products, generating professional-level analytical requests that span both data sources, and validating benchmark quality through multi-LLM evaluation. DPBench preserves full provenance while producing actionable, analyst-like data product requests. Baseline experiments with hybrid retrieval methods establish the feasibility of DPR evaluation, reveal current limitations, and point to new opportunities for automatic data product discovery research. Code and datasets are available at: https://anonymous.4open.science/r/data-product-benchmark-BBA7/

Hypothesis ranking is a crucial component of automated scientific discovery, particularly in natural sciences where wet-lab experiments are costly and throughput-limited. Existing approaches focus on pre-experiment ranking, relying solely on large language model's internal reasoning without incorporating empirical outcomes from experiments. We introduce the task of experiment-guided ranking, which aims to prioritize candidate hypotheses based on the results of previously tested ones. However, developing such strategies is challenging due to the impracticality of repeatedly conducting real experiments in natural science domains. To address this, we propose a simulator grounded in three domain-informed assumptions, modeling hypothesis performance as a function of similarity to a known ground truth hypothesis, perturbed by noise. We curate a dataset of 124 chemistry hypotheses with experimentally reported outcomes to validate the simulator. Building on this simulator, we develop a pseudo experiment-guided ranking method that clusters hypotheses by shared functional characteristics and prioritizes candidates based on insights derived from simulated experimental feedback. Experiments show that our method outperforms pre-experiment baselines and strong ablations.

Mentions of new concepts appear regularly in texts and require automated approaches to harvest and place them into Knowledge Bases (KB), e.g., ontologies and taxonomies. Existing datasets suffer from three issues, (i) mostly assuming that a new concept is pre-discovered and cannot support out-of-KB mention discovery; (ii) only using the concept label as the input along with the KB and thus lacking the contexts of a concept label; and (iii) mostly focusing on concept placement w.r.t a taxonomy of atomic concepts, instead of complex concepts, i.e., with logical operators. To address these issues, we propose a new benchmark, adapting MedMentions dataset (PubMed abstracts) with SNOMED CT versions in 2014 and 2017 under the Diseases sub-category and the broader categories of Clinical finding, Procedure, and Pharmaceutical / biologic product. We provide usage on the evaluation with the dataset for out-of-KB mention discovery and concept placement, adapting recent Large Language Model based methods.

A promising application of AI to healthcare is the retrieval of information from electronic health records (EHRs), e.g. to aid clinicians in finding relevant information for a consultation or to recruit suitable patients for a study. This requires search capabilities far beyond simple string matching, including the retrieval of concepts (diagnoses, symptoms, medications, etc.) related to the one in question. The suitability of AI methods for such applications is tested by predicting the relatedness of concepts with known relatedness scores. However, all existing biomedical concept relatedness datasets are notoriously small and consist of hand-picked concept pairs. We open-source a novel concept relatedness benchmark overcoming these issues: it is six times larger than existing datasets and concept pairs are chosen based on co-occurrence in EHRs, ensuring their relevance for the application of interest. We present an in-depth analysis of our new dataset and compare it to existing ones, highlighting that it is not only larger but also complements existing datasets in terms of the types of concepts included. Initial experiments with state-of-the-art embedding methods show that our dataset is a challenging new benchmark for testing concept relatedness models.

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

Motivation: Biomedical question answering often requires evidence beyond topically retrieved literature, including gene alias resolution, database identifier normalization, and atlas-derived biological measurements. However, existing retrieval-augmented generation (RAG) systems typically follow a fixed workflow and lack an explicit mechanism for deciding when retrieved text is sufficient, when curated biomedical knowledge is required, or when executable evidence assembly over structured measurements should be invoked. This motivates a substrate-aware large language model (LLM) harness that selectively assembles sufficient evidence across literature, knowledge bases, and biological atlases. Results: We introduce BioHarness, an LLM harness for staged biomedical evidence assembly across literature retrieval, curated biomedical knowledge resources, and atlas-derived structured measurements. BioHarness first attempts to answer from reranked literature evidence and escalates through grounded cascade control to REPL-style evidence assembly only when the current evidence is uncertain, weakly grounded, or substrate-mismatched. Across 19,302 biomedical QA items spanning seven answer formats, BioHarness improves the pooled score from 65.9 to 71.0 over the strongest non-oracle baseline. Ablations, case studies, and backbone-scaling analyses show that these gains arise from repairing evidence-substrate mismatches through reranking, entity grounding, and structured measurement access, rather than from indiscriminately invoking more reasoning steps, retrieving additional literature, or relying on a particular answer-model scale.

This paper presents UMASS_BioNLP team participation in the MEDIQA-Chat 2023 shared task for Task-A and Task-C. We focus especially on Task-C and propose a novel LLMs cooperation system named a doctor-patient loop to generate high-quality conversation data sets. The experiment results demonstrate that our approaches yield reasonable performance as evaluated by automatic metrics such as ROUGE, medical concept recall, BLEU, and Self-BLEU. Furthermore, we conducted a comparative analysis between our proposed method and ChatGPT and GPT-4. This analysis also investigates the potential of utilizing cooperation LLMs to generate high-quality datasets.

Background. In the last decades, several life science resources have structured data using the same framework and made these accessible using the same query language to facilitate interoperability. Knowledge graphs have seen increased adoption in bioinformatics due to their advantages for representing data in a generic graph format. For example, yummydata.org catalogs more than 60 knowledge graphs accessible through SPARQL, a technical query language. Although SPARQL allows powerful, expressive queries, even across physically distributed knowledge graphs, formulating such queries is a challenge for most users. Therefore, to guide users in retrieving the relevant data, many of these resources provide representative examples. These examples can also be an important source of information for machine learning, if a sufficiently large number of examples are provided and published in a common, machine-readable and standardized format across different resources. Findings. We introduce a large collection of human-written natural language questions and their corresponding SPARQL queries over federated bioinformatics knowledge graphs (KGs) collected for several years across different research groups at the SIB Swiss Institute of Bioinformatics. The collection comprises more than 1000 example questions and queries, including 65 federated queries. We propose a methodology to uniformly represent the examples with minimal metadata, based on existing standards. Furthermore, we introduce an extensive set of open-source applications, including query graph visualizations and smart query editors, easily reusable by KG maintainers who adopt the proposed methodology. Conclusions. We encourage the community to adopt and extend the proposed methodology, towards richer KG metadata and improved Semantic Web services.

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

Artificial intelligence has advanced scientific discovery, but most AI4Science systems remain fragmented tools that rely on humans to coordinate problem formulation, literature grounding, model use, simulation, validation, and knowledge reuse. This paper presents SCION (Scientific Collaborative Innovation with Agentic Organizational Nexus), an agentic scientific operating system that acts as an organizational nexus. Through a Science Agent serving as a Meta-Harness, SCION connects scientific tasks, tools, agents, artifacts, and memory, transforming research into an executable, auditable, and reusable operational process. At its core is the Research Execution Plan (REP), which compiles high-level scientific intent into staged objectives, dependencies, verification checkpoints, tool requirements, expected artifacts, and fallback conditions. SCION further integrates hierarchical multi-agent execution, profile-driven specialization, selective context construction, governed delegation, and layered epistemic memory to support long-horizon scientific work. We formulate discovery under SCION as Target-conditioned Inverse Search and extend it to hidden-target settings through batch active search under finite experimental budgets. Applications in materials analysis, molecule design, and protein or antibody screening, together with experiments on scientific reading, idea generation, molecule generation, and antibody screening, show that SCION outperforms existing autonomous research-agent baselines, especially in decomposition, verification, refinement, and memory reuse. Overall, SCION shifts AI from isolated tools toward a coordinated operational layer for traceable and reusable scientific innovation.

Autonomous research loops such as AutoResearch show that one coding agent can improve a training setup unattended. Run several of them and each session starts from scratch, so more agents tend to mean more duplicated search rather than more discovery. Agora is a shared memory for such agents: research is recorded as an append-only directed acyclic graph (DAG) stored in Git, so that every claim is a commit anyone can check out and rerun. Each result, insight, hypothesis, verification, and report is an immutable commit whose parent edges say what it builds on; a derived index exposes the frontier, the neglected branches, and the verification status of each claim, and a diversity-aware selection rule keeps the community from collapsing onto one leader. We describe the system and report its first sustained use: a run of nearly 12 days in which 13 language-model workers, with no assigned tasks and no central planner, worked on a weight-transfer problem. Given 141 pretrained donor models and a frozen 119.6M-parameter attention-SSM hybrid whose dimensions match no donor, the workers had to initialize the target without training data or gradient updates. They published 1,703 contributions and drove the evaluator from 3.39 to 1.899 bits per byte, closing 62% of the gap to a trained GPT-2 124M. The winning recipe compresses donor next-token statistics into the target's embedding and output head, then adds a short-range context signal through sparse edits to attention, feed-forward, and state-space blocks. Its 145-commit ancestry spans 15 accounts, and 165 independent reproductions were posted, none of which failed. We describe the single mid-run human intervention that pulled the community out of a monoculture, what the trace does and does not establish, and the controlled comparison that would settle whether shared research state improves discovery per unit of compute.

Large Language Models (LLMs) are increasingly deployed in discovery domains such as math and science. The usual approach is to present the problem to the model and use its answer as the proposed solution. However, beyond this best guess, discovery can be enhanced by increasing test-time compute. In a process called pass@k, the model is allowed to explore the solution space and generate diverse candidate solutions. Unfortunately, the standard approach to post-training LLMs through Reinforcement Learning (RL) may limit pass@k: the model's output distribution narrows around high-reward outputs, causing the solution coverage to collapse. The alternative is to use Evolution Strategies (ES), a population-based, gradient-free post-training method that optimizes directly in weight space through random perturbations. As this paper shows, ES achieves consistently higher pass@k than RL and produces a broader output distribution with greater solution coverage. This coverage in turn makes it possible to achieve better results in e.g. standard math benchmarks. Thus, ES provides a better foundation for post-training in discovery problems and other domains where diverse solution coverage is critical.

In collaborative learning with streaming data, nodes (e.g., organizations) jointly and continuously learn a machine learning (ML) model by sharing the latest model updates computed from their latest streaming data. For the more resourceful nodes to be willing to share their model updates, they need to be fairly incentivized. This paper explores an incentive design that guarantees fairness so that nodes receive rewards commensurate to their contributions. Our approach leverages an explore-then-exploit formulation to estimate the nodes' contributions (i.e., exploration) for realizing our theoretically guaranteed fair incentives (i.e., exploitation). However, we observe a "rich get richer" phenomenon arising from the existing approaches to guarantee fairness and it discourages the participation of the less resourceful nodes. To remedy this, we additionally preserve asymptotic equality, i.e., less resourceful nodes achieve equal performance eventually to the more resourceful/"rich" nodes. We empirically demonstrate in two settings with real-world streaming data: federated online incremental learning and federated reinforcement learning, that our proposed approach outperforms existing baselines in fairness and learning performance while remaining competitive in preserving equality.

Social and collaborative platforms emit multivariate time-series traces in which early interactions-such as views, likes, or downloads-are followed, sometimes months or years later, by higher impact like citations, sales, or reviews. We formalize this setting as Lead-Lag Forecasting (LLF): given an early usage channel (the lead), predict a correlated but temporally shifted outcome channel (the lag). Despite the ubiquity of such patterns, LLF has not been treated as a unified forecasting problem within the time-series community, largely due to the absence of standardized datasets. To anchor research in LLF, here we present two high-volume benchmark datasets-arXiv (accesses -> citations of 2.3M papers) and GitHub (pushes/stars -> forks of 3M repositories)-and outline additional domains with analogous lead-lag dynamics, including Wikipedia (page views -> edits), Spotify (streams -> concert attendance), e-commerce (click-throughs -> purchases), and LinkedIn profile (views -> messages). Our datasets provide ideal testbeds for lead-lag forecasting, by capturing long-horizon dynamics across years, spanning the full spectrum of outcomes, and avoiding survivorship bias in sampling. We documented all technical details of data curation and cleaning, verified the presence of lead-lag dynamics through statistical and classification tests, and benchmarked parametric and non-parametric baselines for regression. Our study establishes LLF as a novel forecasting paradigm and lays an empirical foundation for its systematic exploration in social and usage data. Our data portal with downloads and documentation is available at https://lead-lag-forecasting.github.io/.

Open Artificial Intelligence (Open source AI) collaboratives offer alternative pathways for how AI can be developed beyond well-resourced technology companies and who can be a part of the process. To understand how and why they work and what additionality they bring to the landscape, we focus on three such communities, each focused on a different kind of activity around AI: building models (BigScience workshop), tools and ways of working (The Turing Way), and ecosystems (Mozilla Festival's Building Trustworthy AI Working Group). First, we document the community structures that facilitate these distributed, volunteer-led teams, comparing the collaboration styles that drive each group towards their specific goals. Through interviews with community leaders, we map user journeys for how members discover, join, contribute, and participate. Ultimately, this paper aims to highlight the diversity of AI work and workers that have come forth through these collaborations and how they offer a broader practice of openness to the AI space.

Open data repositories hold potential for evidence-based decision-making, yet are inaccessible to non-experts lacking expertise in dataset discovery, schema mapping, and statistical analysis. Large language models show promise for individual tasks, but end-to-end analytical workflows expose fundamental limitations: attention dilutes across growing contexts, specialized reasoning patterns interfere, and errors propagate undetected. We present PublicAgent, a multi-agent framework that addresses these limitations through decomposition into specialized agents for intent clarification, dataset discovery, analysis, and reporting. This architecture maintains focused attention within agent contexts and enables validation at each stage. Evaluation across five models and 50 queries derives five design principles for multi-agent LLM systems. First, specialization provides value independent of model strength--even the strongest model shows 97.5% agent win rates, with benefits orthogonal to model scale. Second, agents divide into universal (discovery, analysis) and conditional (report, intent) categories. Universal agents show consistent effectiveness (std dev 12.4%) while conditional agents vary by model (std dev 20.5%). Third, agents mitigate distinct failure modes--removing discovery or analysis causes catastrophic failures (243-280 instances), while removing report or intent causes quality degradation. Fourth, architectural benefits persist across task complexity with stable win rates (86-92% analysis, 84-94% discovery), indicating workflow management value rather than reasoning enhancement. Fifth, wide variance in agent effectiveness across models (42-96% for analysis) requires model-aware architecture design. These principles guide when and why specialization is necessary for complex analytical workflows while enabling broader access to public data through natural language interfaces.

Materials discovery and design are essential for advancing technology across various industries by enabling the development of application-specific materials. Recent research has leveraged Large Language Models (LLMs) to accelerate this process. We explore the potential of LLMs to generate viable hypotheses that, once validated, can expedite materials discovery. Collaborating with materials science experts, we curated a novel dataset from recent journal publications, featuring real-world goals, constraints, and methods for designing real-world applications. Using this dataset, we test LLM-based agents that generate hypotheses for achieving given goals under specific constraints. To assess the relevance and quality of these hypotheses, we propose a novel scalable evaluation metric that emulates the process a materials scientist would use to evaluate a hypothesis critically. Our curated dataset, proposed method, and evaluation framework aim to advance future research in accelerating materials discovery and design with LLMs.

Scientific discovery is driven by the iterative process of background research, hypothesis generation, experimentation, and data analysis. Despite recent advancements in applying artificial intelligence to scientific discovery, no system has yet automated all of these stages in a single workflow. Here, we introduce Robin, the first multi-agent system capable of fully automating the key intellectual steps of the scientific process. By integrating literature search agents with data analysis agents, Robin can generate hypotheses, propose experiments, interpret experimental results, and generate updated hypotheses, achieving a semi-autonomous approach to scientific discovery. By applying this system, we were able to identify a novel treatment for dry age-related macular degeneration (dAMD), the major cause of blindness in the developed world. Robin proposed enhancing retinal pigment epithelium phagocytosis as a therapeutic strategy, and identified and validated a promising therapeutic candidate, ripasudil. Ripasudil is a clinically-used rho kinase (ROCK) inhibitor that has never previously been proposed for treating dAMD. To elucidate the mechanism of ripasudil-induced upregulation of phagocytosis, Robin then proposed and analyzed a follow-up RNA-seq experiment, which revealed upregulation of ABCA1, a critical lipid efflux pump and possible novel target. All hypotheses, experimental plans, data analyses, and data figures in the main text of this report were produced by Robin. As the first AI system to autonomously discover and validate a novel therapeutic candidate within an iterative lab-in-the-loop framework, Robin establishes a new paradigm for AI-driven scientific discovery.

Systematic literature review is essential for evidence-based medicine, requiring comprehensive analysis of clinical trial publications. However, the application of artificial intelligence (AI) models for medical literature mining has been limited by insufficient training and evaluation across broad therapeutic areas and diverse tasks. Here, we present LEADS, an AI foundation model for study search, screening, and data extraction from medical literature. The model is trained on 633,759 instruction data points in LEADSInstruct, curated from 21,335 systematic reviews, 453,625 clinical trial publications, and 27,015 clinical trial registries. We showed that LEADS demonstrates consistent improvements over four cutting-edge generic large language models (LLMs) on six tasks. Furthermore, LEADS enhances expert workflows by providing supportive references following expert requests, streamlining processes while maintaining high-quality results. A study with 16 clinicians and medical researchers from 14 different institutions revealed that experts collaborating with LEADS achieved a recall of 0.81 compared to 0.77 experts working alone in study selection, with a time savings of 22.6%. In data extraction tasks, experts using LEADS achieved an accuracy of 0.85 versus 0.80 without using LEADS, alongside a 26.9% time savings. These findings highlight the potential of specialized medical literature foundation models to outperform generic models, delivering significant quality and efficiency benefits when integrated into expert workflows for medical literature mining.

Modern machine learning relies on datasets to develop and validate research ideas. Given the growth of publicly available data, finding the right dataset to use is increasingly difficult. Any research question imposes explicit and implicit constraints on how well a given dataset will enable researchers to answer this question, such as dataset size, modality, and domain. We operationalize the task of recommending datasets given a short natural language description of a research idea, to help people find relevant datasets for their needs. Dataset recommendation poses unique challenges as an information retrieval problem; datasets are hard to directly index for search and there are no corpora readily available for this task. To facilitate this task, we build the DataFinder Dataset which consists of a larger automatically-constructed training set (17.5K queries) and a smaller expert-annotated evaluation set (392 queries). Using this data, we compare various information retrieval algorithms on our test set and present a superior bi-encoder retriever for text-based dataset recommendation. This system, trained on the DataFinder Dataset, finds more relevant search results than existing third-party dataset search engines. To encourage progress on dataset recommendation, we release our dataset and models to the public.

Clinical trial matching is a key process in health delivery and discovery. In practice, it is plagued by overwhelming unstructured data and unscalable manual processing. In this paper, we conduct a systematic study on scaling clinical trial matching using large language models (LLMs), with oncology as the focus area. Our study is grounded in a clinical trial matching system currently in test deployment at a large U.S. health network. Initial findings are promising: out of box, cutting-edge LLMs, such as GPT-4, can already structure elaborate eligibility criteria of clinical trials and extract complex matching logic (e.g., nested AND/OR/NOT). While still far from perfect, LLMs substantially outperform prior strong baselines and may serve as a preliminary solution to help triage patient-trial candidates with humans in the loop. Our study also reveals a few significant growth areas for applying LLMs to end-to-end clinical trial matching, such as context limitation and accuracy, especially in structuring patient information from longitudinal medical records.