AI Agents for Scientific Discovery

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26 papers in the last four weeks, up 44% on the four weeks before. 0.3% of all new papers.

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Latest papers 177

Oct 8, 2026cs.CL

SAIL: Scientific Agentic Intelligence via a Science-Aware Loop

We introduce SAIL, an open model with 35B total and 3B active parameters for literature research, scientific coding, and multi-step research workflows. SAIL is developed through a science-aware improvement loop: agents built on frontier AI models analyze its task failures and construct training tasks that address the underlying capability gaps. The diagnosis examines search and evidence selection in literature tasks, scientific assumptions and reasoning in coding, and planning and revision in longer investigations. The agents draw on paper collections and scientific code repositories to build problems, interaction trajectories, and executable tasks with the required environments and tools. We repeat this loop over multiple development cycles and train SAIL through supervised fine-tuning, specialist training, multi-teacher on-policy distillation, and agentic reinforcement learning. SAIL achieves competitive performance across scientific research tasks with substantially fewer parameters than leading open-weight models.

SAIL Model Team, Boyuan Sun, Bryan Dai +9

IQuest Research

Autonomous Research Agents AI Agents for Scientific Discovery LLM Agent Training Scientific Reasoning in Language Models

Oct 7, 2026cs.MA

A Society of Researchers: Designing Institutions for Populations of Autonomous Research Agents

Deployments of research agents are moving to populations of thousands that share one pool of compute, while most current systems organize one project at a time or leave the population unorganized. We argue that such a population will acquire an organization whether or not its designers provide one, so designers should provide it explicitly, and that the multi-agent systems community holds the tools to do so. We propose a society of agents, a population of persistent agents under explicit institutions, and develop it for science as a society of researchers built on six principles. Principal investigators compete for compute through requests for proposals, independent review, and grants; a human governor, the mayor, allocates resources and assigns no tasks. In a running society of ten thousand researchers, asked only to improve the pretraining of language models, one lab reported a way to reach the same quality with about 30% less compute, a result the labs that tested it do not yet agree on. We close with six open problems for the agents community.

Ali Asaria, Deep Gandhi, Tony Salomone

Transformer Lab Canada

Autonomous Research Agents Multi-Agent Systems AI Agent Governance AI Agents for Scientific Discovery

Oct 7, 2026physics.chem-ph

LLM-Assisted Generation of Transparent, Open-Source Multiphysics Models of Electrochemical Devices

Multiphysics continuum models are powerful tools for studying electrochemical devices, enabling in silico reactor design and resolution of local pH, potential, and concentration fields that govern device performance but are difficult to measure experimentally. However, constructing such models requires substantial numerical expertise or reliance on proprietary software. Here, we show that frontier large language model agents can remove this implementation burden while keeping the underlying physics under researcher control. Using one-dimensional electrochemical CO2 reduction to CO in a porous gas diffusion electrode as a test case, we develop a machine-readable, human-specified modeling harness containing governing equations, parameters, numerical methods, logical build stages, and human-verifiable checkpoints. From this specification, the agent reproducibly constructs complete multiphysics models in open-source Julia. Independently built models, including fully autonomous agent-built models, agree with an equivalent COMSOL implementation to within 0.7% of the peak CO partial current density, and with one another to within 0.04%. Systematically planted errors demonstrate the importance of explicit specifications for reproducibility and reveal the agent's capabilities and limitations in debugging model physics. This framework establishes a more transparent approach to multiphysics modeling in which physical descriptions and governing equations, rather than specialized code, become the primary inputs for computational model development.

Sebastian Castro, Maya F. Schuchert, Spencer A. McCluskey +2

Department of Chemical and Biomolecular Engineering, New York University, Brooklyn, NY, USA · Department of Chemical and Biological Engineering, University of British Columbia, Vancouver, BC, Canada

LLM Code Generation Physics-Based Simulation AI Agents for Scientific Discovery

Oct 7, 2026cs.AI

From Expert-Guided Proof Search to Automated Open-Problem Solving

Large language models are increasingly contributing to mathematical research, where progress often depends on efficient proof search, incremental improvements and careful verification. We describe Bolzano, a multi-agent open-source system that uses parallel prover agents with a verifier agent and maintains a human-readable research state. Initial manual use on expert-selected problems yielded 8 results whose proofs were checked by domain experts. Motivated by these case studies, we ran Bolzano without problem-specific human guidance on about 3,800 open problems extracted from four sets of papers, solving about 200 open problems. One experiment used papers accepted to STOC 2026, a top conference in theoretical computer science. There, we answered four questions raised in the papers, as confirmed by their authors.

Adrián Zámečník, Matěj Kripner, Martin Koutecký +5

Computer Science Institute, Charles University · Institute of Formal and Applied Linguistics, Charles University · Department of Applied Mathematics, Charles University +1

Automated Theorem Proving AI Agents for Scientific Discovery LLM Mathematical Reasoning Multi-Agent LLMs

Oct 7, 2026q-bio.QM

CircuitATLAS: Agentic reasoning over a systems neuroscience knowledge graph for target discovery in circuitopathies

Drug discovery for neurological disease has traditionally centered on the molecules altered by disease. But the molecules that cause pathology are not necessarily the best points from which to reverse it. Here, we ask which otherwise unaltered molecular control points can be engaged to restore pathological neural circuits toward functional states. We present CircuitATLAS, a provenance-grounded systems-neuroscience knowledge graph and agentic framework for target discovery in circuitopathies. It structures literature-derived relationships across diseases, phenotypes, electrophysiology, circuits, brain regions, cell types and molecular effectors, while deliberately excluding direct disease-gene and disease-protein edges to reduce shortcut reasoning. The graph contains 3.83 million nodes and 7.66 million edges, including 5.31 million LLM-extracted relations, and incorporates structured datasets such as the Human Cell Atlas and new multimodal in vivo measurements. We then introduce an agentic workflow that reasons from measurable disease phenotypes through their circuit and cellular substrates to molecular interventions, therapeutic feasibility and clinical constraints. Finally, we introduce a human-governed in vivo lab-in-the-loop linking hypothesis generation to experimental iteration. Within this framework an agent nominated ATP1A3, the neuronal alpha3 Na+/K+-ATPase, as a control point on cortical excitability; interneuron-restricted expression of ATP1A3 abolished the beta- and gamma-band response to a focal 4-aminopyridine challenge in vivo, and the validated target was then carried into a structure-guided small-molecule campaign terminating in a defined assay to resolve the direction of modulation. CircuitATLAS thus provides a framework for discovering therapeutics based not only on what is molecularly disrupted in disease, but on what can be controlled to restore circuit function.

Gabriel Ocana-Santero, Marko Tvrdic

Exin Therapeutics, Inc., 2261 Market Street STE 22614, San Francisco, California 94114, United States

Drug Discovery Biomedical KGs AI Agents for Scientific Discovery

Oct 7, 2026cs.AI

Ream: Unfolding Mutual Awareness in Human-Agent Workspaces

As AI agents work alongside humans in shared workspaces, a mutual awareness challenge arises: agents act at speeds that outpace human monitoring, and users' evolving interests are not always expressed in chat. This challenge is especially pressing in literature review, where both parties retrieve, read, and synthesize a growing body of papers. We present Ream, a literature review workspace that supports mutual awareness through structured artifacts, bidirectional engagement tracking, and localized visualizations. Users can see each party's activity within these documents, and agents can retrieve the same history to guide their work. In studies with eighteen researchers, participants used these traces to inspect evidence, steer agents, communicate through annotations, and reflect on their research focus. Shared histories also helped agents build on earlier work. These findings inform how engagement traces within shared documents can support transparency, personalized assistance, and coordination in human-agent knowledge work.

Peiling Jiang, Sangho Suh, Varsha Kishore +6

University of California San Diego La Jolla, California, USA · Allen Institute for AI (Ai2) · Allen Institute for AI Seattle, WA, USA +1

Human-AI Collaboration AI Agents for Scientific Discovery

Oct 6, 2026cond-mat.mtrl-sci

A self-learning scientific agent for X-ray diffraction

A central challenge for scientific agents is to turn analytical experience into reusable expertise grounded in physical evidence. Here we introduce Gan Jiang, a self-learning agent for powder X-ray diffraction built on a diffraction-analysis ecosystem we developed: XMatcher, XQueryer, XDecomposer and WPEM. Together, these engines span phase identification, multiphase decomposition and physics-constrained whole-pattern modelling. Gan Jiang converts analytical experience into executable skills by diagnosing failures, revising skill instructions and code, and validating revisions before reuse, without retraining the language model or changing the underlying physical models. Skills selected using development data and frozen before held-out evaluation achieve higher refinement scores than the original expert-designed skills across FullProf, GSAS-II and PyWPEM. The agent resolves strongly overlapping reflections, quantifies a five-phase ancient Egyptian cosmetic, tracks lattice evolution in an operating battery and compares atomic configurations in a disordered oxide catalyst. On DeltaXRDbench, it leads the evaluated methods in single- and multiphase identification across simulated and experimental data. Without supplied composition, single-phase top-1 accuracies reach 96.30%, 81.78% and 40.83% on MP500, RRUFF and opXRD, respectively, compared with 58.00%, 58.47% and 26.45% for the strongest comparator. These results demonstrate how an integrated scientific tool ecosystem can support agents that extract structural knowledge from measurements while accumulating validated analytical expertise that transfers to new samples.

Bin Cao, Huichi Zhou, Runyu Yang +7

The Hong Kong University of Science and Technology (Guangzhou), China · University College London, United Kingdom · AI Lab, The Yangtze River Delta, China +1

AI Agents for Scientific Discovery Materials Science Agent Skill Learning Self-Improving Agents

Oct 5, 2026cs.AI

From Benchmark to Bench: Can Agents Survive Real-World Drug Discovery?

Agentic systems increasingly coordinate molecular-design tools, but it is unclear which layer of the stack limits outcomes on real projects. We developed MAGI, an open modular agent that authors objectives, launches and monitors optimization, interprets structure--activity relationships, and revises its strategy accordingly. MAGI generates molecules either directly through the LLM or by delegating to REINVENT 4, with scoring services interchangeable behind a common contract. We tested it across nine retrospective lead-optimization campaigns from three pharmaceutical companies, replayed under fixed temporal cutoffs. Both routes produced valid structures: LLM proposals stayed closer to local chemistry and reached comparable or higher primary activity in fewer operations, whereas REINVENT explored broader chemical space. Whether a campaign met its objective depended on the predictive models, not on the generation route: attainment followed model accuracy on the chemistry proposed, dropping once that chemistry moved outside the model's applicability domain. Separately, a blinded evaluation asked whether the MAGI's output could pass as expert work: chemists were not able to discriminate agentic proposals from held-out compounds, and judged the SAR reasoning broadly plausible yet incomplete. Together, these results position MAGI as a coordination layer pluggable into existing computational chemistry workflows. The ceiling on real projects, however, remains currently set by scorer applicability rather than by tool orchestration.

Pierre Llompart, Levent Guner, Helen Lai +2

AMD Silo AI, Stockholm, Sweden · Molecular AI, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK · Molecular AI, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden +1

AI Agents for Scientific Discovery LLM Agent Orchestration Molecular Generation Drug Discovery

Oct 5, 2026cs.AI

Bridging the Evidence-to-Execution Gap:A Reflective Agent for Multi-Objective Peptide Design

Large language models (LLMs) can reason over scientific literature to devise design strategies, yet fail to reliably implement them for biological sequences. While protein generative models learn sequence patterns, they lack the capacity to incorporate literature evidence for multi-step reflective reasoning, forming an evidence-to-execution gap between scientific reasoning and sequence manipulation. We present EASER (Evidence-Aware Sequence Engineering with Reflection), a reflective agent bridging reasoning and sequence generation via a learned property interface of offline-trained, fixed low-rank matrices. The agent steers a diffusion generator by combining these matrices, proposing intervention hypotheses (anchors, editable positions, control coefficients) grounded in retrieved evidence, sequence context and past results. A Probe-and-Steer mechanism validates interventions and allocates samples according to predicted property responses, with outcome reflection informing subsequent decisions. Evaluated on multi-objective antimicrobial peptide design (optimizing activity, non-hemolysis and non-toxicity), explicit hypothesis formulation delivers better multi-objective performance than direct action generation under identical decision conditions. Ablation studies verify the importance of evidence retrieval, episodic history, reflection and Probe-and-Steer. Over six repeated trials, EASER obtains the highest mean hypervolume and lowest mean IGD+ on screened candidates compared with competing baselines. Our work demonstrates how an executable property interface and iterative feedback link scientific reasoning to targeted peptide sequence generation.

Haosen Zhang, Yang Yang

School of Agriculture and Biology, Shanghai Jiao Tong University · School of Computer Science, Shanghai Jiao Tong University

AI Agents for Scientific Discovery Large Language Model-Guided Optimization Molecular Generation Protein Design Multi-Objective Optimization

Oct 4, 2026cs.AI

AgentDiscover: Autonomous Discovery with Minimal Search Scaffolding

Frameworks that use large language models for scientific discovery typically rely on a fixed, human-designed algorithm that decides what the model sees at each step, leaving the model only the role of proposer. The model knows nothing of the search beyond what it is shown. As models grow more capable, a question arises: does a search strategy chosen by a human before the run scale better than promoting the model from proposer to planner and letting it own the search? The Bitter Lesson suggests that choosing the strategy in advance is the kind of hand-designed structure that general methods eventually outscale. We introduce AgentDiscover, in which a coding agent plans the search using its context as working memory, runs experiments, and records every attempt in a database of ideas, candidates, and their relations. This database serves as the agent's long-term memory and is structured so that the selection rules of classical algorithms such as MAP-Elites and Monte Carlo tree search each reduce to a single query, which the agent is free to use, combine, or replace. A server maintains the database and steers the agent after every submission, keeping it on course over long runs. In our experiments, AgentDiscover is more cost-efficient than existing frameworks, reaching better scores at lower cost. On tasks in kernel engineering, biology, algorithm design, and mathematics, AgentDiscover outperforms prior discovery frameworks. Its programs would have placed first among human competitors in seven past AtCoder heuristic contests, and on eleven mathematical and systems optimization tasks it matches or exceeds every baseline that uses the same model. Our code is available at https://github.com/mhdfb/AgentDiscover.

Mahdi Farahbakhsh, Ilan Sela, Fatemeh Doudi +4

Texas A&M University

AI Agents for Scientific Discovery Automated Algorithm Discovery Automated Heuristic Design Autonomous Scientific Discovery LLM Agent Planning Memory-Augmented Language Model Agents

Oct 4, 2026cs.AI

From Scientific Observations to Mechanisms: Benchmarking Hypothesis Generation by AI Scientists

Data-driven mechanistic hypotheses are essential to scientific discovery because they explain how underlying processes produce observed phenomena. AI agents and AI scientists increasingly support scientific data analysis. However, their ability to turn empirical findings into mechanistic hypotheses remains insufficiently examined. To address this gap, we introduce MechHypoBench, the first benchmark for evaluating whether AI agents and AI scientists can generate such hypotheses from empirical data. It combines paper-derived mechanisms from 14 scientific fields with real-world datasets containing 17.98 million records. The construction retains the observational complexity of empirical data while providing a specified underlying mechanism. Agents analyze the observations and propose open-form hypotheses. We develop an evaluation framework that assesses open-form mechanistic hypotheses through their consequences under withheld conditions. Experiments with general agents and AI scientists reveal a substantial gap between generated hypotheses and the underlying mechanisms.

Xiaxun Xie, Qingqing Long, Meng Xiao +4

Computer Network Information Center, Chinese Academy of Sciences · National University of Singapore · Sichuan University

AI Agents for Scientific Discovery Scientific Hypothesis Generation AI Agent Benchmarks

Oct 1, 2026cs.AI

ScholarCatalyst: A Benchmark for Retrieving Papers That Inspire New Research

What makes great scientists great? Even as AI systems start to make progress on open problems, scientists remain far ahead of them at sensing which prior idea, buried in an ever-growing archive of research, a new problem needs. To study this skill, we draw on researchers who know firsthand which earlier work advanced their completed projects, with papers serving as pointers to the ideas within. Using our automated pipeline that makes author annotation scalable, we build ScholarCatalyst by having 184 lead authors of 207 recent computer science papers label which candidates did or could have advanced their project, each with a detailed rationale. We introduce a retrieval task with author-provided judgments: given an initial research question, retrieve these papers from only the literature available when the project began. Agentic search does no better than embedding retrieval (0.42 vs. 0.48 Recall@20) despite calling that same retriever as a tool. Even an agent built on Claude Fable 5.1, which may have seen the completed papers during training, reaches only 0.51 R@20. These results highlight the need for new training recipes that equip models with expert intuition for searching broad corpora. We envision ScholarCatalyst as a step toward scientific agents that can take a half-formed idea and point to the prior research it needs.

Sohyeon Kim, Yoonho Lee, Bo Liu +11

Stanford University · Seoul National University · University of Washington +3

AI Agents for Scientific Discovery Agentic Search AI Agent Benchmarks Information Retrieval IR Evaluation

Oct 1, 2026cs.AI

YouRA: A Persistent-State Architecture for Evidence-Traceable Autonomous Research Agents

End-to-end research agents can now produce complete scientific papers, yet manuscript claims often diverge from executed experiments. This gap is structural: research state, failure histories, and claim-evidence alignment are not maintained as persistent, verifiable state across long-horizon pipelines. We present YouRA (Your Research Agent), an architecture for stateful, evidence-traceable autonomous research. YouRA preserves research state, execution evidence, and failure history across the research trajectory by integrating three components: a Verification State Architecture (VSA) that tracks hypotheses, gates, and evidence pointers; an Independent Controller that turns state and reflection records into lifecycle, recovery, and debate/review control while separating control from execution; and Stateful Reflection that logs failures as structured lessons and routes recovery through bounded repair, redesign, or reset. On MLR-Bench's predefined ten-task end-to-end subset, YouRA improves over both MLR-Agent and AI Scientist V2 on scalar Overall across all three matched backbones. An automated diagnostic using MLR-Bench's hallucination taxonomy reports intersection/union counts for four fact-based failure types, and data-provenance diagnostic shows more real-data-based outputs. Ablating each of the four components (the VSA, the Independent Controller, MCP tool access, and reflection-guided recovery) supports their separable contributions. Removing either core-state component drops YouRA below the full system. Code: https://github.com/PrayPrey/Your-Research-Agent.

Yoonkyu Woo, Woojin Lee, Jin-Xia Huang

Electronics and Telecommunications Research Institute, Republic of Korea · Department of Artificial Intelligence, University of Science and Technology, Republic of Korea

AI Agent Reliability AI Agents for Scientific Discovery Memory-Augmented Agents Autonomous Research Agents

Oct 1, 2026cs.MA

Can AI Scientists Coordinate at Runtime?

Multi-agent AI scientists have shown improving performance across a diverse range of tasks. Yet a common approach is design-time agentic orchestration, which typically relies on fixed workflows. In contrast, human scientists coordinate and adjust their division of labor at runtime. We therefore ask: can AI scientists also coordinate at runtime? To this end, we introduce Runtime Agent Coordination (RAC), which selects agents from existing AI-scientist hosts during execution, assigns scoped work contracts, and provides artifact-grounded verification. Verification informs subsequent agents without blocking transitions or discarding artifacts. We conduct a single-seed exploratory evaluation across Agent Laboratory, EvoScientist, and ARK on ResearchClawBench, preserving host models, tools, and permissions under host-calibrated budgets. Four cumulative conditions separate native execution, runtime communication, runtime selection, and the combined addition of contracts and verification. Runtime selection yields the highest observed mean score for each host; adding contracts and verification reduces these means, with host-dependent outcomes relative to native execution. These results motivate runtime coordination while exposing the limits of additional coordination mechanisms under constrained budgets. Code is available at https://github.com/systemind-team/Runtime-AI-Scientist.

Zijian Liu, Yangzhixin Luo, Junyu Lu +6

University of Oxford · King Abdullah University of Science and Technology · University of Sydney +1

Multi-Agent Coordination Multi-Agent Orchestration AI Agents for Scientific Discovery

Sep 30, 2026cs.AI

CompMat-Bench: Benchmarking AI Agents for Computational Materials Science

Evaluating AI agents on scientific research tasks is constrained by the time and resources required for the underlying experiments or calculations. In computational materials research, repeating the same expensive simulations across agents and trials can make evaluation impractical. We introduce CompMat-Bench, a benchmark of 94 tasks derived from recently published computational materials studies, each asking agents to complete a step toward achieving the study's scientific goal. We reproduce the research steps in advance and assess agents on preparing inputs and analyzing outputs for expensive simulations, so expensive simulations can be avoided during evaluation. The reproduced inputs and results serve as ground truth for grading agents with fixed rules, without an LLM judge. The benchmark supports four evaluation conditions: single tasks and workflows composed of related tasks, each with full or reduced methodological guidance. With full guidance on single tasks, agents based on three LLMs demonstrate the ability to complete individual materials research steps, with pass rates of 66.0-90.4% across 94 tasks. Both longer workflows and reduced guidance can limit agent performance, but in different ways for different agents: they lower the pass rates of the weaker agents, whereas the strongest agent falls only when a long workflow is combined with reduced guidance. Failure analysis attributes most failures to scientific errors rather than to errors in software usage. CompMat-Bench provides a basis for comparing agents on the steps of real materials research and for analyzing agent failure modes.

Chenmu Zhang, Levi Felix, Jun-Jie Zhang +6

Department of Materials Science and NanoEngineering Rice University, Houston, TX 77005, USA

AI Agents for Scientific Discovery AI Agent Evaluation AI Agent Benchmarks Computational Materials Science

Sep 30, 2026cs.AI

Cogentic: Multi-Agent Orchestration for Automated Proof Discovery

We present Cogentic, a multi-agent harness for automated proof discovery on open research problems. While frontier language models can generate strong mathematical ideas in a single shot, single-shot generation is often insufficient for open problems that require exploring multiple competing conjectures, overcoming subtle technical obstructions, and retaining intermediate progress over a long horizon. Cogentic addresses these challenges through an iterative prove--verify loop in which an orchestrator allocates a population of independent provers across distinct proof directions, subjects their output to adversarial verification by several specialized components, and promotes confirmed intermediate results into a persistent verified ledger that later rounds build on. The harness is designed to be able to solve research-level math and theoretical computer science problems. Using Gemini as the base model, Cogentic produced novel results on five open problems across online learning, auction theory, and mechanism design. Each result was independently verified by domain experts and is developed in full in companion papers. We list these results, and new ones as they are verified, at https://sites.google.com/view/cogentic .

Yang Cai, Vineet Gupta, Yanchen Jiang +4

Google Research · Yale University · Google DeepMind

Multi-Agent LLM Systems AI Agents for Scientific Discovery Automated Theorem Proving Multi-Agent Collaboration

Sep 30, 2026hep-th

How AI Agents Discover Scientific Equations: From Hydrotope Rediscovery to New Water-Wave Amplitudes

We study how AI agents discover and validate scientific formulas using a controlled case study of the hydrotope, a recently discovered geometric formula that combines the different polynomial pieces of nonlinear surface-wave scattering into one global expression. This problem is deceptively difficult: simple formulas can hold within individual frequency regions, but the global result must identify their boundaries and combine exponentially many potentially active terms. We reconstruct how the formula was originally discovered through human--agent collaboration and analyze 18 single-prompt rediscovery runs under no hint and two forms of human guidance: a false hint representing an incorrect prior and a true hint representing domain-informed insight. Only four recover the formula across all kinematic chambers (i.e., regions in which a single polynomial form applies), while most unsuccessful runs find correct chamber polynomials but fail to combine them or test their full domain. Conventional and LLM-assisted symbolic regression and standard machine-learning regressors likewise fail to recover the global formula in our experiments. Guided by these failure modes, we test a PI

+

two-student workflow in which a coordinating lead agent assigns complementary analytic and numerical tasks to two research agents and independently evaluates their results. The PI

+

two-student team successfully rediscovers the complete hydrotope formula, while the same workflow applied to the harder three negative wavenumber problem discovers a new independent verified analytic expression for the six-point amplitude

A_6

.

Zihan Zhou, Digvijay Wadekar, Matias Zaldarriaga

Department of Physics, Princeton University, Princeton, NJ 08540, USA · Center for Gravitational Physics, University of Texas at Austin, Austin, TX 78712, USA · School of Natural Sciences, Institute for Advanced Study, 1 Einstein Drive, Princeton, NJ 08540, USA

AI Agents for Scientific Discovery Scientific Discovery LLM Agent Orchestration Human-AI Collaboration Symbolic Regression

Sep 30, 2026cs.AI

Experimental Experience Modeling for Autonomous Research

Autonomous research agents can generate hypotheses and conduct experiments, but experimentation remains a major source of computational cost. A fundamental challenge is deciding which experiments are worth running, particularly when prior evidence is insufficient to resolve uncertainty. Yet current research agents lack a systematic way to leverage experimental experience when making such decisions. We introduce Experimental Experience Modeling (EEM), a framework for making informed experimental decisions by acquiring, reusing, and accumulating experimental experience. EEM extracts decision-relevant records from earlier experimental trajectories, distills them into reusable experience, and organizes them in an experience library. For a new experimental decision, EEM retrieves relevant historical experience and assesses whether it provides sufficient support for deciding whether a candidate direction warrants further investment. When historical experience is insufficient, EEM conducts a targeted, low-cost pilot experiment to acquire the missing decision-relevant experience on demand. It then combines this newly acquired experience with retrieved historical experience to determine whether the direction warrants full-scale evaluation, which requires substantial resources. The resulting experimental outcomes are further distilled into reusable experience, allowing the library to continually grow through iterative accumulation. Experiments on autonomous research benchmarks show that EEM improves research performance while reducing model interaction overhead, demonstrating the value of reusing accumulated experience and acquiring additional experience only when needed.

Wenda Wei, Yingchen Zhang, Ruqing Zhang +3

State Key Laboratory of AI Safety · Institute of Computing Technology, Chinese Academy of Sciences · University of Chinese Academy of Sciences +1

AI Agents for Scientific Discovery Autonomous Experimentation Autonomous Research Agents

Sep 29, 2026cs.AI

Can an AI Agent Rediscover a Blaschke-Curve Invariant?

We study generalized Blaschke curves as a controlled environment for AI-assisted mathematical rediscovery. For one fixed degree-four Blaschke product, an agent receives numerical coordinates of the six pair-lines determined by each of 80 boundary configurations. The target theorem is withheld from the task instructions. The saved research log reports rejected geometric hypotheses and a homogeneous cubic fitted to polygon sides. Its frozen coefficients predict 480 lines from 80 unseen parameter values, with a recorded RMS scale-free residual of

8.88\times10^{-17}

. Discovery-set diagonals provide an out-of-fit consistency check, not a fully held-out test. A separate one-configuration run reports insufficient evidence for invariance. A post-review deterministic degree-search baseline also recovers the cubic, so the experiment does not establish an advantage over polynomial fitting. We present this single-instance case study as a protocol for separating conjecture, numerical validation, and proof, with explicit limitations concerning agent metadata, prior knowledge, and reproducibility.

Yunus E. Zeytuncu

University of Michigan-Dearborn

AI Agents for Scientific Discovery AI Agent Evaluation Autonomous Scientific Discovery Scientific Reproducibility

Sep 28, 2026hep-th

Solver Agent: an Agentic AI Framework for Theoretical Physics Computations Applied to F-theory Uplifts of O3-planes and S-folds

We introduce Solver Agent, an AI framework based on large language models for calculations and proofs in mathematics and theoretical physics. The solution process is tracked through a persistent ledger that records assumptions, derivations, and computations. A central agent delegates tasks to specialized sub-agents, while independent agents verify both intermediate steps and the final result. This setup improves the traceability, reproducibility, and verification of computer-assisted calculations. Applying Solver Agent, we study global F-theory uplifts of Type IIB orientifolds and their S-fold generalizations. We establish sufficient conditions for Weierstrass models over projective threefolds with terminal

\mathbb{Z}_k

quotient singularities (

k\in\{2,3,4,6\}

) to give

\mathbb{Q}

-factorial projective elliptically fibered Calabi-Yau fourfolds with isolated Gorenstein terminal quotient singularities. These geometries realize O3-planes and S-folds, where local D3-brane probes of the latter yield four-dimensional

\mathcal{N}=3

superconformal field theories. Using stringy invariants, we derive fixed-point contributions to Hodge data and Euler characteristics, and show that these Euler corrections determine the localized D3-brane charges required for tadpole cancellation. We illustrate these results using toric hypersurface constructions, where a single three-dimensional polytope determines both the Type IIB Calabi-Yau threefold and the F-theory base; here, the orientifold double cover naturally forms a bisection of an alternative genus-one-fibered uplift with discrete

\mathbb{Z}_2

gauge symmetry. Finally, we provide methods for toric computations and four-form flux analysis in four-dimensional

\mathcal{N}=1

compactifications with non-abelian gauge sectors.

Eliott Morgensztern, Cesar Fierro Cota, Alessandro Mininno

Sorbonne Université, CNRS, Laboratoire de Physique Théorique et Hautes Energies, Campus Pierre et Marie Curie, 4 place Jussieu, F-75005, Paris, France · Department of Physics, University of Wisconsin–Madison, 1150 University Avenue, Madison, WI 53706, USA

AI Agents for Scientific Discovery LLM Agent Verification High-Energy Physics Multi-Agent Reasoning

Sep 28, 2026cs.AI

Reinforcing Agentic Creativity in Scientific Ideation with Night Science

Large language models (LLMs) excel at structured, verifiable tasks, but their low-entropy bias can produce homogeneous and predictable outputs, limiting their utility for open-ended scientific ideation. Effective discovery, however, spans a broader creative spectrum: from structured day science to loosely structured, serendipitous night science that reaches ideas beyond those typically considered. We introduce AI Night-Scientist, an agentic framework that uses reinforcement learning to teach models when and how to depart from predictable reasoning. Grounded in cognitive science, we model creativity along three axes: action (what to do and how creatively), process (when to explore versus exploit), and outcome (the novelty and usefulness of the resulting idea). We use these axes to train models with GRPO, exposing them to varying degrees and forms of creativity throughout training. This produces substantially more diverse scientific proposals, expanding the range of research directions by 27.8% and contribution types by 14.9% over the base model. It also improves predicted citation impact by up to 32.0 percentage points and originality by 66.2 points. These gains cannot be reproduced by simply increasing decoding temperature; instead, we find that semantic guidance specifying what kind of creativity to pursue is critical. Overall, our results suggest that creativity is a learnable, multi-level ability that can be shaped to help researchers reach ideas beyond those typically explored by LLMs.

Priyanka Kargupta, Silviu Cucerzan, Shweti Mahajan +4

University of Illinois Urbana-Champaign · Microsoft · Microsoft Research

AI Agents for Scientific Discovery Scientific Hypothesis Generation Computational Creativity RL for LLM Agents

Sep 28, 2026cs.LG

NeuronDiscover: Agent-in-Twin for Mechanistic Discovery in Neuronal Microenvironments with World Action Models

Mechanistic discovery in neuronal microenvironments requires interventions and measurements that separate competing explanations of solute transport and neuronal response. Predictive accuracy cannot settle the question: a real mechanistic change and an error in the computational twin leave the same signature in sparse observations. We formalize this twin confounding and reason over a joint mechanism--discrepancy belief, designing experiments that separate the two. NeuronDiscover is an Agent-in-Twin framework whose shared, mechanism-grounded World Action Model (WAM) couples prediction, intervention proposals, and observation design; independently adjudicated outcomes revise a scoped Mechanism--Intervention--Observation--Outcome (MIOY) graph, whose supported relations compile into executable programs carrying discrepancy-adjusted acceptance bounds. We evaluate on simulated brain-fluid tracer-transport worlds adjudicated by an independently frozen finer-mesh reference solver, and on donor-disjoint public current-clamp recordings of cortical neurons. Counting only relations that reach a certified terminal status, and scoring abstentions as unresolved for every method, at a matched budget of 16 experiments over 32 source units NeuronDiscover resolves 4.0 relations per assigned world against 3.4 for the strongest baseline and 3.2 without graph revision, at 5% false support and 82% scope accuracy. Joint mechanism--discrepancy acquisition resolves 3.8 relations versus 2.9 for plug-in expected information gain; discrepancy-adjusted verification lowers accepted-program failure from 15% to 9% at 60% acceptance coverage; and transfer to the recordings yields 1.94 versus 1.53 relations per assigned world. Correctness is adjudicated within declared model worlds and archival recordings.

Haowei Xu, Wanyi Fu, Hongbin Han +1

Institute of Medical Technology, Peking University Health Science Center, Beijing, China · Beijing Key Laboratory of Intelligent Neuromodulation and Brain Disorder Treatment, Beijing, China · Department of Radiology, Peking University Third Hospital, Beijing, China +1

AI Agents for Scientific Discovery Scientific Discovery Action-Conditioned World Models Bayesian Experimental Design

Sep 24, 2026cs.AI

Advancing Model Research in AgentX: Long-Horizon Autonomy for Industrial Recommender Systems

Sustaining industrial recommendation research requires using the results of one experiment to decide what to investigate next. We present AgentX-Model, the next generation of AgentX's model research framework, which connects proposal development and model experimentation within sandboxes defined by business inputs and prediction tasks. AgentX-Model adopts a dual-agent architecture comprising a Research Agent and a Model Agent. The Research Agent develops independently reviewed proposals from papers and experimental findings, while the Model Agent conducts multi-round investigations and returns code, measurements, and unresolved questions. Using the returned results, the Research Agent selects a starting implementation and formulates the next research question, allowing subsequent experiments to build on earlier findings. We organize this continuing research around four actions: Reproduce, Follow-up, Composition, and Diagnose. The first three actions drive routine research, while Diagnose acquires the evidence needed to choose a repair, including for issues raised by business feedback and online evaluation, such as prediction bias measured by PCOC. Across the production evaluation, 560 of 636 completed model-changing experiments recorded AUC above their business baselines. As research continued, some experiments recorded AUC above every comparable ancestor in their lineages. The five latest online A/B evaluations across different business settings reported gains including 10-15% in acquisition efficiency, 15-20% in target-segment advertising spend, and 0.3-0.8% in watch time; the watch-time model used approximately 10% fewer FLOPs and parameters. A dependency-aware historical-replay benchmark further evaluates research allocation, with initial results showing no consistent efficiency gain from more complex scheduling when agents already analyze and select concrete candidates.

Shuang Yang, Zijie Zhuang, Changxin Lao +20

AI Agents for Scientific Discovery Long-Horizon Agent Evaluation Recommender Systems Autonomous Experimentation Autonomous Research Agents

Sep 23, 2026cs.AI

Driving Epidemic Models with AI Agents: the Epydemix Agent Framework

Artificial Intelligence agents based on large language models provide convenient natural language interfaces to scientific software, but reliability is not automatic. Here we introduce the Epydemix Agent Framework, an additive layer over Epydemix, an open-source Python library for stochastic compartmental epidemic modeling. The framework extends the library with four capabilities to facilitate interaction with an AI agent: discovery of available models and parameters, preventive validation of a declarative scenario specification, execution through tested library code, and inspectability of results. These capabilities let an agent handle the entire modeling process, from the natural-language description of the scenario to quantitative results, figures, and interpretation of findings without writing custom code. Each step reads input files and saves results in a separate output bundle, making the process auditable and reproducible. First, we show the end-to-end workflow with a case study comparing vaccination strategies for a novel respiratory virus. Second, we assessed the framework across 50 agent sessions and five modeling tasks by comparing the agent use of the framework against the direct use of the Python interface. The framework reduced turns, output tokens, and cost on most tasks, unless it trades resources for per-point reproducibility.

Nicolò Gozzi, Ciro Cattuto, Alessandro Vespignani

ISI Foundation, Turin, Italy · Network Science Institute, Northeastern University, Boston, MA, USA

AI Agents for Scientific Discovery LLM Agent Harnesses LLM Agent Reliability

Sep 23, 2026cs.AI

Large Knowledge Model: A Knowledge Foundation for Agentic Science at Scale

Agentic science envisions many autonomous agents investigating concurrently while building on a shared, evolving body of scientific knowledge. This requires a knowledge foundation that supports high-concurrency access, preserves traceable and reusable reasoning, and grows incrementally. We propose the Large Knowledge Model (LKM), a growing, agent-native knowledge foundation that provides a general representation of scientific knowledge across disciplines. LKM organizes the scientific literature into reasoning graphs, with claims as the core nodes and associated reasoning chains that make explicit how premises and evidence support conclusions. These source-grounded objects are persistent and addressable; cross-paper links organize them into aligned question, workflow, and evidence views. Newly extracted papers extend the foundation incrementally while preserving existing object identities. Building on this foundation, we develop an agent-native, reasoning-aware scientific retrieval system that retrieves claims together with their reasoning chains and sources, enabling agents to inspect and reuse the evidence underlying scientific conclusions. Across benchmarks, agents using LKM retrieve more evidence, cite more faithfully, and answer scientific questions more accurately: LKM nearly doubles the known supporting and contradicting evidence retrieved on SciFact-Open (818 versus 443 claim-paper pairs), reasoning graphs raise citation F1 on ScholarQABench by more than 5 points over the same retrieved papers, and LKM retrieval improves a fixed answering model by 9.3, 4.2, and 14.7 points over no retrieval on ChemBench, PubMedQA, and SciBench. LKM lays the foundation for a scientific ecosystem in which AI scientists not only recall accumulated knowledge but also extend it, returning new questions, workflows, and evidence to a memory that every subsequent investigation can build on.

Yuan Huang, Sihan Hu, Hongyu Gu +18

DP Technology, Beijing, China · Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing, China · International Center for Quantum Materials, School of Physics, Peking University, Beijing, China +4

KG Construction AI Agents for Scientific Discovery Scientific QA Knowledge Representation Evidence Retrieval

Sep 23, 2026cs.LG

Discover, Falsify, Revise: Auditing Input-Use Claims from Source Code to Predictive Contribution in Agent-Discovered Cell Models

AI virtual cells aim to predict cellular responses to specified interventions, yet held-out predictive performance alone does not establish use of the supplied perturbation information. This prediction-claim gap matters in agentic model discovery, where language-model agents generate and revise predictors using score-based feedback. We introduce CELLAUDIT, which audits input-use claims by asking whether an input can enter the cited computation, whether fitted predictions depend on it, and whether that dependence improves prediction of observed response. On a paired morphology-transcriptomics perturbation benchmark (BBBC047), an agent-selected predictor attains a mean held-out Global Pearson correlation coefficient (PCC) of 0.3153 but remains invariant to compound replacement; a control-profile-only predictor reaches 0.3142. Source inspection identifies a compound-query pathway blocked by singleton key-value attention, and the invariance persists after refitting with disjoint control wells. In a stratified audit of 48 candidates across two linked tasks, 47 change predictions under compound replacement on both held-out folds, but only 20 show target-loss gains with intervals above zero on both folds. On BBBC047, falsification-guided revisions recover positive mean compound contributions while retaining gains over the control-profile-only baseline. In matched sci-Plex searches, audit-enriched feedback yields higher held-out performance and larger mean compound and dose contributions across five trajectories, although paired intervals span zero. Refitting fixed designs on an independently acquired cohort shows predictive generalization need not imply generalization of input-use claims: dose contribution persists, whereas support for compound identity does not. CELLAUDIT adds a falsification layer to agentic model discovery, moving from generate-score-revise toward discover-falsify-revise.

Mengran Li, Bo Li, Chengyang Zhang +3

Sun Yat-sen University · University of Macau · Sichuan University +3

AI Agents for Scientific Discovery AI Agent Auditing Single-Cell Perturbation Modeling

Sep 21, 2026cs.AI

The AI Neuroscientist: An Interactive Agentic Interface for Neuroimaging Analysis

Analyzing neuroimaging data requires specialized coding and statistical expertise, which limits accessibility for researchers without computational backgrounds. We present the AI Neuroscientist, a language agent for interactive data exploration. The system integrates a large language model (LLM) with a neuroimaging toolset to perform quality control, modeling, and visualization. This allows researchers to query data quality and specify analysis parameters directly in natural language, providing a transparent and interactive alternative to conventional scripted pipelines for small-scale data exploration. We demonstrate these capabilities using functional near-infrared spectroscopy (fNIRS) data, and evaluate the agent on a custom fNIRS benchmarking suite against general-purpose LLM agents with code sandboxes. Future extensions will generalize the architecture to additional modalities, including functional magnetic resonance imaging (fMRI) data, and expand the benchmarking suite to additional fNIRS tasks.

Aakash Patel, Panos Ketonis, Shreya Saxena +2

Department of Computer Science, Yale University · Wu Tsai Institute, Yale University · Department of Biomedical Engineering, Yale University +2

AI Agents for Scientific Discovery LLM Agent Evaluation AI Agent Benchmarks Neuroimaging

Sep 20, 2026cs.AI

ScholarStack: Layered Research Asset Orchestration and Cross-Task Reuse for Scientific Agents

Scientific agents support a range of literature-based research tasks, such as retrieval, question answering, evidence-grounded generation, and claim assessment. Most existing systems, however, are organized around individual tasks: the same papers are repeatedly retrieved, segmented, and interpreted, and the understanding built in one task is difficult to reuse in the next. We present ScholarStack, a layered research asset framework that compiles a paper collection into reusable, versioned, and provenance-preserving assets at three complementary levels: source-grounded paper-level statements, domain-level organization, and evidence-grounded cross-paper syntheses. A common access interface returns task-specific views at the evidence granularity each task requires, preserving study conditions, source traceability, and verification status. We instantiate the framework on four task families spanning ten task settings, comparing agents that use the compiled assets with task-specific baselines under matched base models. Quality gains concentrate on tasks that require cross-paper evidence, such as multi-paper question answering and literature review generation, and query-time token cost falls on every task where it is measured, with assets compiled once and reused across tasks. These results suggest that layered research assets can serve as shared infrastructure for scientific agents, shifting literature-based assistance from isolated document processing toward cumulative, evidence-grounded workflows.

ScholarSeed AI Team, Caoqinwei Gong, Xue Jiang +17

DAMO Academy, Alibaba Group

AI Agents for Scientific Discovery Evidence-Grounded Generation

Sep 16, 2026cs.LG

Agora: Git as Shared Memory for Collective AutoResearch

Research agents working in separate sessions need to know what others have tried and which results they can build on. Agora stores their contributions as an append-only directed acyclic graph (DAG) in Git. Each commit records a result, insight, hypothesis, verification, or report and links it to prior work. Searchable views show leading results, neglected branches, and verification status; diversity-aware recommendations suggest experiments beyond the current leaders. We report a run of nearly 12 days in which 13 language-model workers, with no assigned tasks or central planner, used Agora to solve 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 reduced the development evaluator score from 3.39 to 1.899 bits per byte, closing 62% of the gap to a trained GPT-2 124M. The best method compresses donor next-token statistics into the target's embedding and output head, then adds short-range context through sparse edits to attention, feed-forward, and state-space blocks. Its 145-commit ancestry spans 15 accounts. Participants also posted 165 verifications of 95 targets, each by an account other than the target's author, with no reported failures. The run documents how agents reused and verified shared work. Measuring the effect on discovery per unit of compute requires a matched comparison.

Yifan Zhang, Yunheng Zou, Shaokun Zhang +5

NVIDIA

AI Agents for Scientific Discovery Multi-Agent Collaboration Multi-Agent Systems Agent Memory Management Autonomous Research Agents Shared-Memory Multi-Agent Systems

Sep 14, 2026cs.CL

Discovery Foundation Models: Toward Open-Ended Discovery Intelligence

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

Ling Yang, Zhenfei Yin, Yingcheng Wu

DFM Scientist Collaboration Program

AI Agents for Scientific Discovery Autonomous Scientific Discovery