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 175

Jul 30, 2026cs.AI

MECA: A Mechanism-Centered Agent for Constructing Well-Specified and Valuable Mathematical Conjectures

Automatically constructing well-specified and valuable mathematical conjectures remains a central challenge in AI-assisted mathematical discovery. Many existing open problems and conjectures are often too broad, underspecified, or difficult to connect to plausible proof or refutation strategies. We view a mathematical mechanism as a structure or reasoning principle that connects the assumptions of a candidate problem to its target conclusion, such as an inequality, invariant, decomposition, or reduction to an intermediate claim. We present MECA (MEchanism-centered Conjecture Agent), a multi-agent framework that constructs conjectures by jointly developing candidate statements and their supporting mechanisms. Explorer agents propose mechanisms, test how they apply, and revise the candidate conjecture accordingly, while critic agents assess their mathematical validity and research value. Their feedback guides changes to the assumptions, scope, and conclusion. Through this process, MECA transforms broad research directions into precise conjectures with substantive mathematical support while retaining a clearly identified unresolved core. We evaluate MECA in two complementary settings. First, we compare it with a generate-and-revise baseline on reconstructing preselected target-paper conclusions from target-conditioned but article-blind source materials. Second, we construct 100 semi-open problems from literature-derived seeds and existing open problems and evaluate them through independent proof and refutation attempts by automated provers. Our results indicate that mechanism-centered refinement produces well-specified and research-worthy conjectures that remain challenging for current automated provers.

Wentao Long, Yunfei Zhang, Chenyi Li +1

Fudan University · Qingdao University · Peking University

AI Agents for Scientific Discovery Mathematical Reasoning

Jul 30, 2026cs.RO

LabEvolver: Training-Free Experience Evolution for Safe and Grounded Wet-Lab Agents

We introduce LabEvolver, a training-free framework that equips safe and grounded wet-lab agents with episodic memory from execution experience. LabEvolver couples a state-grounded inner trial loop for adaptive perception, online planning, and safety validation with an outer evolution loop that distills completed trajectories into reusable skill, strategy, and safety experience. On robotic solution-preparation tasks, LabEvolver demonstrates real-world feasibility, reducing pH-regulation completion time and safety-gate intercepts by 48.2% and 60.0%, respectively. On ALFWorld, it further improves cumulative success rate within 20 steps from 76.2% with ReAct to 91.4% over 500 continual tasks, showing generality beyond wet-lab settings. These results support learn-by-doing experience evolution as a feasible path toward closed-loop automated scientific discovery. The project page is available at https://andygao6186.github.io/LabEvolver/.

Jingya Wang, Yuyang Gao, Liuzhenghao Lv +2

School of Computer Science, Peking University · School of AI for Science, Peking University · School of Electronic and Computer Engineering, Peking University

Agent Memory AI Agents for Scientific Discovery AI Agent Safety Laboratory Automation Self-Evolving Agents

Jul 30, 2026cs.AI

Evaluating Agentic Bioinformatics through Function, Evidence, and Validation

Large language model agents increasingly plan, execute, and interpret biological analyses, yet fluent responses, successful tool calls, and benchmark performance alone do not establish scientific credibility. Existing reviews primarily organize biological agents by application, architecture, and agentic capability, but do not jointly operationalize the accountability of agent-generated workflows. We address this gap by treating the inspectable workflow trajectory, rather than architecture or final output alone, as the primary unit of analysis. We introduce the Function--Evidence--Validation (FEV) framework, which separates demonstrated workflow operations, traceable support for actions and claims, and use-case-specific validation. Using FEV, we map 109 agentic or agent-adjacent systems and 28 benchmark or evaluation resources, representing 128 unique publications across genomics, single-cell and spatial omics, protein science, drug discovery, computational pathology, and general bioinformatics automation. Across domains, planning and tool-mediated execution have advanced more rapidly than replayability, provenance, robust scientific assessment, external validation, and prospective empirical testing. We therefore argue that agentic bioinformatics should be assessed through workflow correctness rather than final-answer correctness alone. FEV provides a practical basis for comparing systems and designing transparent, auditable, and scientifically accountable bioinformatics workflows.

Phuc Pham, Truong-Son Hy

Department of Computer Science, The University of Alabama at Birmingham, USA

AI Agents for Scientific Discovery Data Provenance LLM Agent Evaluation Scientific Reproducibility Scientific Workflow Automation

Jul 29, 2026cs.AI

Exploring Structures in Physics Problems: Can AI Agents Discover Statistical Mechanical Mappings?

An important skill in theoretical physics is to recognize when a new problem can be transformed into a known model. We study this skill as an AI-agent task: can LLM-based agents discover statistical mechanical mappings from a raw partition function to a tractable representation? To probe this question, we introduce StatMechBench-v0, a benchmark of six Ising-type problems covering transfer-matrix methods, gauge-removable disorder, and planar/Pfaffian structure. We evaluate a simple propose-verify-revise agent across multiple LLMs and problem phrasings. The results show that numerical feedback often helps agents repair code and recover correct partition functions. However, agents can also pass the numerical checks while misidentifying the underlying tractable class or understating computational complexity. This both reveals limitations in current LLM reasoning and calls for a verification stack that goes beyond numerical agreement, incorporating, for example, symbolic checks and structural invariants. Our study provides an early evaluation and design directions for AI agents aimed at structural discovery in theoretical physics.

Wanyu Zhao, Wanbing Zhao

Department of Physics and Astronomy Rice University

AI Agents for Scientific Discovery LLM Agent Evaluation AI Agent Benchmarks

Jul 28, 2026quant-ph

OmniQEC: discovering practical quantum error-correcting codes by an AI scientist

Quantum error correction (QEC) is indispensable for scalable fault-tolerant quantum computing. However, discovering QEC codes that remain effective is challenging, as logical performance depends on the interplay between code structure, hardware, syndrome extraction, and decoding, which often impose competing requirements. Here we introduce OmniQEC, an efficient AI scientist for discovering QEC codes suited to deployment on modern quantum processors. OmniQEC formulates QEC design as an iterative discovery process in which an orchestrator, implemented by advanced large language models (LLMs), coordinates code generation, code-level screening, syndrome-extraction synthesis, and decoder-based circuit evaluation. At its core, OmniQEC combines a self-evolving reasoning mechanism with a slow--fast synergistic workflow: a fast loop explores candidates using inexpensive code-level proxies, whereas a slow loop performs physically grounded circuit-level evaluation and feeds the resulting evidence back into the search. We evaluate OmniQEC across four qLDPC construction families, three LLM backends, and

14

total-physical-qubit budgets per backend. The discovered codes show steadily improving logical-error suppression with increasing physical-qubit budgets and outperform the BB codes with

[\![72,12,6]\!]

and

[\![144,12,12]\!]

under complete-implementation budgets of 98 and 240 physical qubits, respectively. The discovered codes are hardware-friendly and may be of independent interest for practical QEC implementation. These findings pave the way towards LLM-assisted QEC discovery grounded in physically informed code--circuit--decoder co-design.

Ge Yan, Shanchuan Li, Pengyue Ma +5

College of Computing and Data Science, Nanyang Technological University, Singapore · Department of Electrical Engineering and Computer Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo, Japan · 3Zhejiang University of Technology, China +3

AI Agents for Scientific Discovery Quantum Error Correction Large Language Model-Guided Scientific Discovery

Jul 28, 2026cs.MA

Agentic AI-enabled discovery across large-scale sleep physiology

Sleep occupies roughly one-third of human life, yet many aspects of its physiology remain poorly understood. Large polysomnography (PSG) datasets offer new opportunities to study sleep and its links to disease, but extracting insight from these recordings requires substantial expert effort and remains difficult for general-purpose AI systems. We developed AI Sleep Co-Scientist, an expert-guided environment in which human scientists direct specialist agents for hypothesis development, signal preprocessing, and statistical analysis, reviewing intermediate outputs. Each reported result is linked to the executable code that produced it. Across four cohorts of approximately 124,000 PSG recordings and more than 50 TB of raw signals, we conducted five case studies spanning how sleep physiology relates to future disease, how it distinguishes clinical phenotypes, and how sleep is organized and regulated. Diminished network-level physiological coupling during sleep was associated with incident Parkinson's disease (HR 1.48) and Alzheimer's disease (HR 1.38). A physiologically structured late-fusion sleep-age model outperformed an unconstrained early-fusion approach, and its age residual was associated with incident disease across multiple organ systems. Arousal dynamics characterized comorbid insomnia and sleep apnoea as an intermediate phenotype skewed towards obstructive sleep apnoea, distinguished by prolonged post-arousal wakefulness. Rapid eye movement (REM) bout duration tracked preceding non-REM sleep more closely than intervening wakefulness. Transient-oscillation analysis identified a fast-sigma deficit and excess centrofrontal theta activity in narcolepsy type 1. Together, these findings connect sleep to disease risk, clinical classification, and its own regulation, and show how agentic AI can support large-scale, multimodal discovery.

Rahul Thapa, Umaer Hanif, Robin Guillard +10

Department of Biomedical Data Science, Stanford University, Stanford, CA, USA · Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark · Danish Center for Sleep Medicine, Department of Clinical Neurophysiology, Glostrup, Denmark +6

AI Agents for Scientific Discovery Human-AI Collaboration

Jul 26, 2026cs.LG

SCTA: An Agentic Framework for Stable and Interpretable Target Gene Discovery from Single-Cell RNA Sequencing

Identifying therapeutic target genes from single-cell RNA sequencing (scRNA-seq) data remains a fundamental challenge in translational biology. Unlike bulk assays, scRNA-seq captures heterogeneous cellular states and rare subpopulations, but this same heterogeneity makes target discovery highly sensitive to analytical choices throughout the pipeline, including preprocessing, cell population selection, differential expression analysis, and downstream biological interpretation. As a result, existing workflows and general-purpose analysis agents often produce unstable or difficult-to-interpret target hypotheses, limiting their reliability for disease-focused discovery. We present SCTA (Single-Cell Target Agent), a decision-centric agentic framework for stable and interpretable target gene discovery from scRNA-seq data. Rather than treating analysis as a single general-purpose reasoning task, SCTA decomposes target discovery into specialized agents aligned with key decision points in the single-cell pipeline and constrains downstream reasoning with structured biological evidence. In a representative ablation study on hereditary chronic pancreatitis, we demonstrate that SCTA's full evidence integration yields the most stable target selection across independent runs among the tested configurations, while recovering biologically coherent, disease-relevant mechanisms validated in prior studies. These results suggest that decision-aware agent orchestration tailored to the structure of single-cell analysis can improve the robustness, interpretability, and practical utility of target discovery in precision medicine.

Shuyu Chen, Chen Zhu, Ye Zhang +3

Siebel School of Computing and Data Science University of Illinois Urbana-Champaign Champaign, IL, USA · School of Information Sciences University of Illinois Urbana-Champaign Champaign, IL, USA · Novartis Biomedical Research Biomedical Research Cambridge, MA, USA +1

AI Agents for Scientific Discovery Scientific Workflow Automation Single-Cell RNA Sequencing Drug Discovery

Jul 25, 2026cs.AI

Harnessing agent memory to build lifelong AI partners for materials scientists

Materials research advances through accumulated experience - scripts that work, protocols that are trusted, warnings attached to failed calculations or experiments, and judgement that links a new question to an old result. This experience is essential for reproducibility and knowledge transfer, yet it is usually fragmented across notebooks, repositories, job logs and individual memory, and it is rarely portable across artificial-intelligence agents. Here we argue that a lifelong AI partner for materials science can be designed around persistent memory rather than around a particular agent implementation. We introduce a self-evolving memory framework that stores scientific experience as inspectable facts and executable skills, so that observations, failure boundaries, protocols and validation checks can be retrieved, revised and migrated across models. We evaluate the idea in three computational settings that expose different layers of materials-research competence. In 49 real-world materials-tool-use questions comprising 138 executable subtasks, memory nearly doubles GPT-5.2 task success without model-parameter updates. In elemental-solid equation-of-state calculations, memory converts a wavefunction-initialization failure into a pre-execution guardrail, improving outcomes from 22/1/4 to 25/2/0 Correct/Partial/Error and avoiding 92% of repeated errors. In 13 practical material simulation workflows, remembered skills and failure facts halve the aggregate trace burden (tokens) and reduce tool calls by over a factor of two by the third round, while preserving physically meaningful outputs in band-gap, phonon, vacancy and work-function analyses. These results show that agent memory can serve as a durable scientific asset; a portable, self-improving record of materials-research experience that outlives any single model or agent stack.

Siyu Liu, Bo Hu, Beilin Ye +3

Center for Structural Materials, Department of Mechanical Engineering, The University of Hong Kong, Hong Kong, China · International Digital Economy Academy (IDEA), Shenzhen, China · Materials Innovation Institute for Life Sciences and Energy (MILES), HKU-SIRI, Shenzhen, China

Agent Memory AI Agents for Scientific Discovery Memory-Augmented Agents Agent Memory Management

Jul 25, 2026cs.AI

Stress-testing large language model agents in a robotic chemistry laboratory

AI is evaluated through knowledge, reasoning and plan generation, yet scientific agency requires reliable physical action and adaptation to evidence. Here, we use a robotic chemistry laboratory as a physical-world testbed to make scientific agency measurable. Its 45 modular workstations exposed as machine-readable skills enabled 4,608 trials. Only 3.3% of trials produced expert-assessed executable workflows under laboratory constraints; even the best system achieved 28.1%. Long-horizon planning remained a challenge: only three executable workflows exceeded 30 operations, although the longest contained 44. Across five rounds, experimental feedback prompted local adjustments but no workflow-level replanning or analytical-method redesign. By making physical executability and evidence-driven replanning measurable, our study provides an evidence-based assessment of deployment readiness and a diagnostic framework to guide closed-loop improvements towards physically grounded autonomous research.

Lulu Guo, Yingkai Sun, Xiaobo Li +13

State Key Laboratory of Precision and Intelligent Chemistry, Hefei National Research Center for Physical Sciences at the Microscale, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, China · Center for Scientific Intelligence Innovation, Hefei, China · School of Chemistry, School of Computer Science, University of Birmingham, Birmingham, UK

AI Agent Reliability AI Agents for Scientific Discovery AI Agent Evaluation Robotics Laboratory Automation Autonomous Experimentation+1

Jul 24, 2026stat.ML

CausalSmith: A Formally Grounded, Self-Improving Agentic Framework for Automated Research in Causal Inference

Automating theoretical research requires generating candidate results and evaluating them reliably. Models keep getting better at the first, while the second remains hard. A common approach asks one large language model (LLM) to review what another produced, yet such reviewers are empirically unreliable: they may accept fabricated papers and catch the fabrication at close to chance rates~\citep{badscientist2025}. We present \textsc{CausalSmith}, a framework for automated theoretical research in causal inference built on the Lean proof assistant, where a proof is checked by a program rather than read by a referee. \textsc{CausalSmith} rests on \textsc{Causalean}, a foundational Lean library for causal inference holding 8,179 machine-checked definitions and theorems, developed with language-model assistance under human design and review. Around it, we build a self-improving agentic pipeline that selects research topics, proposes results, formalizes statements, constructs proofs, and presents the resulting artifacts for human inspection. Moreover, the pipeline pairs Lean verification with a statement audit that compares each formal theorem against the informal claim behind it. We evaluate the system using artifacts produced by completed autonomous research runs. The source code, formal library, and run records are available at https://github.com/Jiyuan-Tan/CausalSmith.

Jiyuan Tan, Vasilis Syrgkanis

AI Agents for Scientific Discovery Automated Theorem Proving Formal Verification Causal Inference Autonomous Research Agents

Jul 17, 2026cs.AI

SciForge: An AI-Native, Multimodal Workbench for Scientific Discovery

Scientific work increasingly spans heterogeneous artifacts -- papers, code, datasets, scientific file formats, model outputs, figures, manuscripts, and team decisions -- yet general-purpose AI assistants rarely preserve these objects as a coherent, auditable research state. We present SciForge, a multimodal research-native AI workbench that reserves the graphical interface for human judgment while search, parsing, model routing, workflow execution, plotting, writing, and presentation generation run as modular agent-accessible services. SciForge is built around five pillars: (i) \emph{goal-scoped scientific decision governance} for \textbf{goal-oriented} research, with review gates and shared review surfaces; (ii) \emph{translate-then-reason} for \textbf{multimodal} input, routing scientific objects through domain translators before the agent reasons; (iii) \emph{evidence governance} for \textbf{auditable} traceability, linking claims to provenance chains and audit findings; (iv) \emph{collaborative team science} for \textbf{collaborative} research, enabling multi-role decision governance, with shared team workspaces planned for future releases; and (v) \emph{real-world application scenarios} for \textbf{practical} impact, demonstrated through eight end-to-end user cases, with flagship demonstrations including multi-day agentic research sprints for gene discovery, AI-guided de novo protein design, molecular optimization, and genome-to-BGC discovery. The system combines a thin interaction layer, contextual research capability patterns, an Agent Runtime and Workflow Engine, an Evidence-DAG audit sidecar and a Scientific Model Router. SciForge currently runs as a desktop application, with mobile supervision support; future releases will deepen team collaboration. The system is open-source and available at https://github.com/AGI4Sci/SciForge

SciForge Team, Zhangyang Gao, Minghao Fang +10

SciForge Team, Shanghai Artificial Intelligence Laboratory

AI Agents for Scientific Discovery AI Agent Governance Multimodal Agents Scientific Workflow Automation Human-AI Collaboration

Jul 16, 2026cs.AI

TopoAgent: A Self-Evolving Topological Agent for Multimodal Scientific Reasoning

While Multimodal Large Language Models (MLLMs) excel in general tasks, rigorous scientific reasoning remains challenging due to the limitations of monolithic, linear planning. Such sequential designs often suffer from visual-semantic misalignment, long-context hallucinations, and brittle execution under fixed task granularity. We propose TopoAgent, a self-evolving topological framework that replaces linear trajectories with dynamic, state-isolated graph evolution. TopoAgent first employs a front-end decomposer to fracture complex queries into visually-grounded atoms. These atoms are organized into a Directed Acyclic Graph (DAG) based on their dependencies, enabling strict context isolation to shield the reasoning engine from irrelevant historical noise. Furthermore, we introduce adaptive atomic fission, which dynamically splits bottleneck nodes into finer-grained sub-atoms at runtime when tool capability boundaries are exceeded. Extensive experiments across mathematics, physics, and chemistry benchmarks demonstrate that TopoAgent significantly outperforms state-of-the-art linear agent frameworks, providing a robust, noise-resistant, and self-correcting paradigm for autonomous scientific reasoning.

Mingze Xu, Yinghui Li, Jiayi Kuang +5

Tsinghua University · Sun Yat-sen University · 3Tencent

AI Agents for Scientific Discovery Multimodal Reasoning Graph-Based Planning

Jul 15, 2026cs.AI

ReasFlow: Assisting Reasoning-Centric Scientific Discovery in Applied Mathematics via a Knowledge-Based Multi-Agent System

Recent advances in Large Language Models have fueled autonomous AI agents capable of tackling complex scientific tasks, yet existing automated research systems remain predominantly focused on empirically driven domains with quantitative benchmarks, leaving theory-driven discovery, particularly in mathematically grounded disciplines requiring rigorous proofs and synthesis of domain knowledge, largely underexplored. Key challenges include the difficulty of verifying theoretical reasoning at scale, insufficient reasoning ability for autonomous frontier exploration, and a scarcity of procedural heuristics in the literature. We introduce ReasFlow, an end-to-end autonomous agent system for reasoning-centric scientific discovery that operationalizes a collaborative paradigm where the human expert acts as Principal Investigator while the agent executes rigorous derivations as a capable graduate student. ReasFlow incorporates (i) a robust internal verification loop that audits logical coherence and corrects fundamental errors prior to human inspection, and (ii) an automated knowledge retrieval and self-improvement mechanism that proactively surfaces both declarative facts and overlooked procedural heuristics, substantially reducing expert intervention. The system unifies literature synthesis, algorithm design, theorem proving, experimentation, and manuscript preparation in a single system. Deployed to autonomously generate five complete research papers with rigorous theoretical and empirical content from minimal prompts, ReasFlow consistently achieves the highest evaluation scores among state-of-the-art open-access baselines under a curated LLM-based review rubric. ReasFlow is publicly accessible via the ReasLab platform, providing a collaborative workspace for AI-assisted theoretical research. Github repo: https://github.com/ReasLab/ReasFlow.git.

Yutong He, Daibo Li, Guohong Li +15

Peking University · University of Electronic Science and Technology of China · Beijing Normal University +2

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

Jul 15, 2026cs.AI

Automatic Ordinary Differential Equations Discovery For Biological Systems Using Large Language Model Powered Agentic System

Automatic scientific discovery has long been a goal of computational scholars - a machine that can discover nature's secrets on its own, moving computational systems beyond data-fitting tools toward the generation and refinement of mechanistic models of the universe. Recent advances in symbolic regression (SR) and large-language-model (LLM)-based agents suggest that such systems can recover equations from data, incorporate domain priors, and automate parts of the research workflow. However, most existing approaches either focus on narrow equation-discovery benchmarks or broad end-to-end automation pipelines, while biological systems remain comparatively underexplored. Here, we introduce the MEDA system, an LLM- and SR-powered agentic framework for discovering ordinary-differential-equation (ODE) models of biological and biologically inspired dynamical systems. MEDA retrieves background knowledge, defines admissible variables, generates mechanistic constraints, proposes candidate ODEs, and fits and evaluates them. We evaluate it across canonical model retrieval, reasoning-based extrapolation to unseen variants, and open-ended discovery, with and without experimental data. Across these settings, MEDA recovered the correct state variables, achieved strong structural recovery in retrieval and extrapolation tasks, and produced biologically plausible discovery-oriented models. Ablation and robustness analyses show that knowledge-guided formalization and mechanistic constraints are load-bearing components, whereas numerical fitting alone can preserve trajectory-compatible but biologically incorrect equations.

David Krongauz, Arad Zulti, Eran Segal +1

Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel · Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel · Mohamed bin Zayed University of Artificial Intelligence, Abu Dhabi, United Arab Emirates +2

Dynamical Systems AI Agents for Scientific Discovery Autonomous Scientific Discovery ODE Discovery Symbolic Regression

Jul 13, 2026cs.LG

An Agentic AI Scientific Community for Automated Neural Operator Discovery

We present an agentic approach to autonomous neural operator discovery based on an AI scientific community, which consists of a swarm of virtual laboratories that interact under a citation-based economy of influence. Highly-cited labs found new labs that follow their research direction and replace non-performing labs. Each virtual lab contains three agents: an LLM planner that proposes an architecture, a numerical worker that trains and measures it, and an LLM reviewer that participates in cross-lab peer review. All labs share a common vocabulary consisting of DeepONet (branch-trunk), Fourier, Transformer (attention), wavelet, and residual convolutional neural operator building blocks. We evaluate the neural operator AI scientific community on five problems, namely piecewise regression, the linear advection and Burgers 1D PDEs, and the Navier-Stokes and Darcy flow 2D PDEs, while repeating the simulation three times for each problem. The results show that the neural operator AI scientific community is capable of discovering high-accuracy, low-parameter-count neural operator architectures. All 9,623 LLM calls are logged and audited, which reveals that the virtual lab LLM planners choose to hybridize in 99.8% of their logged decisions, consistently returning multi-family hybrids. Moreover, we conducted an ablation study by replacing the LLM agents in each lab by rule-based alternatives, which caused the scientific community to collapse to non-hybridized single-family stacks in several cases, showing that LLM agency is needed to preserve diversity. The results suggest a no-free-lunch theorem for neural operators: there is no universal winner. The code, configurations, and the complete LLM transcripts are released at https://github.com/luislootx/AI-SC.

Luis Loo, Ulisses Braga-Neto

Department of Electrical & Computer Engineering Texas A&M University, College Station, TX

AI Agents for Scientific Discovery LLM Agent Orchestration Autonomous Scientific Discovery PDE Operator Learning Neural Architecture Search Neural Operators

Jul 12, 2026cs.AI

Imaging-101: Benchmarking LLM Coding Agents on Scientific Computational Imaging

Computational imaging, which recovers hidden signals from indirect, noisy measurements, underpins quantitative discovery across scientific disciplines, yet building a correct reconstruction pipeline demands deep domain expertise and remains laborious even for domain scientists. We introduce Imaging-101, a benchmark of 57 expert-verified computational imaging tasks spanning six scientific domains, each grounded in a peer-reviewed paper and canonicalized into a standardized four-stage pipeline (preprocessing, forward physics modeling, inverse solver, and visualization) Three evaluation tracks (planning, function-level unit tests, and end-to-end reconstruction) probe distinct agent capabilities across the full pipeline. Evaluating seven frontier LLMs uncovers systematic challenges in applying coding agents to computational imaging that go beyond those exposed by general coding benchmarks, spanning algorithm selection, physical convention handling, and pipeline integration. These findings highlight concrete capability gaps and point toward skill-augmented, domain-specialized agents as a practical path to reliable computational imaging assistance.

Siyi Chen, Jiahe Ying, Yixuan Jia +9

Key Laboratory of Spacecraft Design Optimization and Dynamic Simulation Technologies, Ministry of Education, Beijing, 102206, China

AI Agents for Scientific Discovery Computational Imaging LLM Agents Image Inverse Problems

Jul 11, 2026cs.AI

IdeaTrail: Full-Process Agent Trajectories for Scientific Ideation

Scientific ideation unfolds over multiple stages, including literature search, paper reading, tool use, claim checking, cross-paper synthesis, brainstorming, rejection of weak directions, and iterative writing. Yet most existing resources capture isolated components or final artifacts rather than the process connecting them. We introduce IdeaTrail, a dataset of 1,170 multi-turn trajectories for scientific ideation and proposal generation. Each trajectory follows a research process from evidence gathering to either idea selection or proposal construction, jointly recording tool use, acquired evidence, intermediate artifacts, and reasoning. IdeaTrail is synthesized from human-selected research papers and proposal artifacts through a Generator--Advisor loop. The Generator produces the visible sequence of actions, observations, and artifact edits, while the Advisor uses the full generation context to check grounding, causal order, naturalness, and leakage from hidden targets. This reverse-to-forward design keeps trajectories aligned with real scientific artifacts while retaining the uncertainty, evidence use, and staged convergence characteristic of research practice. IdeaTrail provides both reusable process supervision and a general recipe for constructing scientific-research-agent data.

Hengquan Guo

ShanghaiTech University

AI Agents for Scientific Discovery Scientific Hypothesis Generation LLM Agent Trajectory Synthesis Research Idea Generation Synthetic Data Generation for Language Models

Jul 10, 2026cs.AI

Toward Auditable AI Scientists: A Hypothesis Evolution Protocol for LLM Agents

Large language model (LLM) agents are increasingly expected to play a central role in AI-driven scientific discovery. Equipped with broad knowledge, flexible reasoning, and tool use, they have the potential to autonomously explore and solve scientific problems by repeatedly proposing hypotheses, testing them, and revising their beliefs in the light of the evidence. In current agents, however, these hypotheses, tests, and belief updates are buried in unstructured logs, and no mechanism lets the agent or the human researcher audit that process. Here we propose the Hypothesis Evolution Protocol (HEP), an agent harness that provides hypothesis generation, evaluation, and evolution as explicit, auditable operations. On materials-science research tasks, a HEP-equipped agent operates the hypothesis--test--evidence--belief cycle that planning-style agents lack, generalizes across research questions, and exploits the protocol more fully as the base LLM becomes more capable. These results mark a step toward auditable AI scientists, whose scientific reasoning can be inspected, verified, and built upon.

Izumi Takahara, Teruyasu Mizoguchi

Institute of Industrial Science, The University of Tokyo, Tokyo, Japan 153-8505

AI Agents for Scientific Discovery LLM Auditing Scientific Hypothesis Generation LLM Agent Harnesses

Jul 7, 2026cs.AI

A framework for single and multi-agent human-AI curiosity ecosystems

This paper offers a framework for considering curiosity as an ecosystem. First, it suggests that a single agent's inquiry policy (how, when, and why an agent asks a question) depends on how the agent values immediate uncertainty reduction, costs, delayed return, and the value of keeping the question open. A key concept in the framework is that the weights on these decision-related terms can change with experience. For example, a period of cheap, quickly answered questions may change the cost of inquiry on a short timescale and change which kinds of questions the agent is drawn to answer over a longer timescale. Second, these ideas are extended to many agents exploring a shared knowledge landscape, and there the framework tracks inquiry volume, topic diversity, frontier-directed inquiry, redundancy, and reusable knowledge. The result is a conceptual framework for studying curiosity ecology and for future efforts towards designing multi-agent AI systems for discovery.

Ilya E. Monosov

Solomon H. Snyder Department of Neuroscience, Johns Hopkins University, Baltimore, MD, USA · Departments of Biomedical Engineering, Electrical and Computer Engineering, and Psychiatry, Johns Hopkins University, Baltimore, MD, USA · Zanvyl Krieger Mind/Brain Institute, Johns Hopkins University, Baltimore, MD, USA +1

AI Agents for Scientific Discovery Intrinsic Motivation Multi-Agent Systems

Jul 5, 2026cs.CL

CausalGame: Benchmarking Causal Thinking of LLM Agents in Games

Building AI Scientist agents with Large Language Models (LLMs) has recently attracted growing attention. Since scientific discovery fundamentally relies on uncovering causal relationships from observations, the capability of causal thinking, i.e., distinguishing causation from correlation and recognizing hidden biases, is essential to LLM agents. Although a number of benchmarks exist for AI Scientists, none explicitly incorporate challenges from selection bias, measurement error, and hidden confounders that widely exist in real-world scientific discovery. To this end, we present CausalGame, a benchmark that evaluates the causal thinking capabilities of LLM agents through interactive games. CausalGame asks LLM agents to actively design experimental protocols, collect observation data, and derive a final solution with an explanation report. To emulate realistic scientific discovery challenges, we design 14 scenarios that incorporate selection bias, measurement error, and hidden confounders. Across 30 LLM agents, none demonstrates reliable causal thinking: the best model reaches only 68.0% survival against analytical optima of 78-85%, and merely 5-7% of sessions receive credits on the causal-reasoning rubrics. CausalGame provides a scalable and controlled testbed for evaluating the causal thinking of AI Scientist agents.

Zhenhao Chen, Yongqiang Chen, Chenxi Liu +7

1MBZUAI · 2Carnegie Mellon University · 3TMLR Group, Hong Kong Baptist University +2

AI Agents for Scientific Discovery AI Agent Benchmarks Causal Reasoning in Language Models Causal Reasoning

Jul 4, 2026cs.CL

Rethinking Scientific Discovery in the Agentic Era

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 \textbf{SCION (Scientific Collaborative Innovation with Agentic Organizational Nexus)}, an agentic scientific operating system that acts as an \textbf{organizational nexus}. Through a Science Agent serving as a \textbf{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 \textbf{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 \textbf{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.

Yining Zheng, Yuxin Wang, Jiahao Lu +27

Shanghai Innovation Institute · Fudan University · East China Normal University

AI Agents for Scientific Discovery Multi-Agent Collaboration Scientific Workflow Automation LLM Agent Planning Autonomous Research Agents

Jul 1, 2026cs.AI

The Agentic Garden of Forking Paths

Empirical research rarely admits a unique analysis. Different analytical choices can lead to different conclusions from the same data, yet these hidden forking paths are difficult to observe. We show that AI agents capture much of the analytical variation among human researchers while making these paths explicit. Across four high-stakes domains, assigning different personas is sufficient for AI agents to report divergent, often opposing, conclusions from the same data and question, with findings systematically aligned with those beliefs. In a study in which 42 human research teams analyzed the same immigration dataset, AI agents reproduced 72% of the human ideological gap in reported effect estimates. Despite reaching opposing conclusions, it is difficult to identify clear issues in each analysis based on the final AI reports: 86% passed independent AI review and 78% passed majority human expert review. These findings suggest that the central challenge is often not flawed analyses, but selective exploration and reporting from a large space of methodologically defensible analyses. AI agents may amplify this longstanding problem by making such exploration inexpensive and scalable. To address this, we introduce the m-value (multiverse value), the probability that an analysis path would produce a claim at least as extreme as the reported one. We further introduce Agentic Bootstrap, which estimates the m-value by using AI agents to sample plausible analysis paths. Applied to the human immigration study, 13.5% of reported human analyses fell in the most extreme 5% of the analysis space (m<0.05). Scientific evidence should therefore be evaluated not only by a single reported analysis but also by its position within the distribution of analyses that could reasonably have been reported. Agentic Bootstrap makes this distribution observable and turns it into a criterion for scientific credibility.

Jiacheng Miao, Jonathan K Pritchard, James Zou

Department of Biomedical Data Science, Stanford University · Department of Genetics, Stanford University · Department of Biology, Stanford University +2

AI Agents for Scientific Discovery Scientific Reproducibility

Jun 30, 2026cs.AI

Agentic-Ideation: Sample Efficient Agentic Trajectories Synthesis for Scientific Ideation Agents

Ideation plays a pivotal role in scientific discovery. Recent LLM, especially AI Scientist systems, show promising potential for automated ideation. However, existing approaches predominantly rely on pre-defined agentic workflows. This constraint severely limits the flexibility required to navigate the vast search space of scientific literature and the complex action space of research reasoning. Recently, training Agentic LLMs has emerged as a promising direction, offering flexible reasoning frameworks and the capability for autonomous tool utilization. However, there remains a non-trivial challenge: applying previous agentic data synthesis methods to scientific ideation suffers from prohibitively high data synthesis cost. To bridge this gap, we propose Agentic-Ideation, a novel framework comprising an automated trajectory synthesis pipeline and a specialized agentic LLM trained for scientific ideation. Specifically, we first define a comprehensive tool space incorporating three external tools and three cognitive tools. Then we introduce an Oracle-Guided Data Synthesis strategy. By leveraging a reference idea as oracle guidance, this approach steers the multi-agent system to efficiently reconstruct the logical reasoning and tool invocation paths, transforming aimless trial-and-error into directed trajectory generation. Finally, we train the agent on these synthesized trajectories, employing a masking strategy on tool execution results. This ensures the model focuses on decision-making logic without interference from external feedback. Experimental results demonstrate that our method outperforms the SOTA workflow-based baseline by \textbf{11.91%} in overall quality. Furthermore, our approach improves the sample efficiency of high-quality data synthesis by \textbf{over 10

\times

}.

Keyu Zhao, Lingyan Kong, Fengli Xu +1

Department of Electronic Engineering, Tsinghua University.

Multi-Agent LLM Systems AI Agents for Scientific Discovery Scientific Hypothesis Generation LLM Agent Training Synthetic Data Generation for Language Models

Jun 30, 2026cs.AI

AI-Assisted Discovery of Convex Relaxations via Dual Agents

Recent work shows that LLM agents can improve sharp-constant inequalities by searching for extremal constructions, which yield upper bounds. We address the complementary side: a lower bound holds for every admissible function and follows from a convex relaxation of the nonconvex problem, with tighter relaxations giving stronger bounds. We instantiate the autoresearch paradigm to discover such relaxations: a coding agent proposes valid tightening constraints, a theory agent verifies each one and searches for counterexamples, and every reported bound is certified by an explicit dual-feasible point checked in rigorous interval arithmetic. On two optimization constants studied by \citet{tao2025alphaevolve} - the first autocorrelation inequality (

C_{6.2}

) and the Erdős minimum-overlap constant (

C_{6.5}

) - we improve the certified lower bounds from

1.28

to

1.2937

and from

0.379005

to

0.37912

, respectively.

Sungyoon Kim, Mert Pilanci

Department of Electrical Engineering, Stanford University, CA, USA.

Primal-Dual Optimization AI Agents for Scientific Discovery Large Language Model-Guided Optimization

Jun 25, 2026q-bio.GN

scBench-Long: Verifiable Benchmarking of Long-Horizon Single-Cell Biology

Single-cell studies require analysts to convert raw measurements into specific biological claims through multi-step workflows and integration of metadata, assay context, and auxiliary evidence. Existing AI-biology benchmarks largely measure broad knowledge, executable workflows, or local analysis steps. We introduce scBench-Long, a benchmark for long-horizon single-cell biology in which agents must recover scientific conclusions from raw or near-raw data without prescribed methods. The benchmark contains 21 evaluations spanning melanoma CD8 T-cell reactivity, CD8 RNA+ATAC regulatory inference, human--monkey chimera development, KRAS-driven lung tumor aging, and lethal COVID-19 lung pathology. Tasks cover paired scRNA/TCR sequencing, RNA and chromatin profiling, cross-species transcriptomics, combinatorial scRNA-seq, single-nucleus RNA-seq, immune repertoires, ortholog maps, ligand--receptor resources, and validation evidence. Candidate claims are reproduced, reviewed, and converted into controlled answer vocabularies with deterministic grading and trajectory rubrics. Across 1,068 completed trajectories, the strongest model--harness pair passes 16/63 runs (25.4%). scBench-Long evaluates whether agents can move beyond local analysis steps and make complex scientific claims that are supported by single-cell data.

Ian Diks, Zhen Yang, Arjun Banerjee +2

LatchBio, San Francisco, CA, USA

AI Agents for Scientific Discovery Long-Horizon Agent Evaluation Single-Cell Transcriptomics Agent Benchmarks

Jun 24, 2026cs.AI

Agentic evolution of physically constrained foundation models

Artificial intelligence increasingly drives automated scientific discovery, yet contemporary generalist agents lack physical grounding, frequently hallucinating hardware-incompatible designs. Here, we present a physically grounded, multi-agent discovery engine that autonomously architects hardware-compliant computing systems. Anchored by an Evolutionary Knowledge Graph structuring past scientific innovations, the framework extracts an "algorithmic Chain-of-Thought" to transform blind stochastic search into directed structural evolution. Applied to the extreme testbed of foundation model deployment, the engine evolved two hardware-aware compression methodologies surpassing human-engineered heuristics: Q-Enhance mitigates long-context accuracy loss in dense models, and MoE-Salient-AQ outperforms state-of-the-art manual sparse Mixture-of-Experts designs by 3.7% at sub-3-bit regimes. Utilizing a bandwidth-efficient Sensitivity Profile, we successfully deployed a massive 235-billion-parameter model onto a constrained dual-A100 server, reducing memory requirements by 75% with a marginal 0.64% accuracy degradation. By transforming unconstrained combinatorial search into knowledge-driven autonomy, this establishes a scalable hardware-software co-design paradigm for machine-driven discovery within strict physical boundaries.

Jiangwei Zhang, Wen Sun, Chong Wang +7

State Key Laboratory of Cyberspace Security Defense, Institute of Information Engineering, Chinese Academy of Sciences, Beijing, 100084, China. · University of Chinese Academy of Sciences, Beijing, 101408, China. · Department of Electronic Engineering, Tsinghua University, Beijing, 100084, China.

Model Compression LLM Quantization AI Agents for Scientific Discovery Automated Algorithm Discovery Hardware-Software Co-Design

Jun 23, 2026cs.SE

Agon: An Autonomous Large-Scale Omnidisciplinary Research System Built on Prompt Economy

Large language models are making research production scalable, shifting the bottleneck from producing artifacts to judging claims. We present \textsc{Agon}, a research orchestrator that validates what can be checked inside the workflow and leaves the remaining judgments to human scientists. \textsc{Agon} is built on six design principles: Prompt Economy, Future-Facing, Minimal Prompts, OmniDisciplinary, Massive Parallelism, and Zero-Code. We ran \textsc{Agon} across domains for 444 iterations of Prompt Economy loops, using only small starting topics and no human-written experimental code. These deployments demonstrate scalability while exposing new classes of failure. We organize these failures into a taxonomy along severity, fixability, visibility, and capability locus. The taxonomy separates failures the loops can see and fix from those that require human judgment. Together, these results show that \textsc{Agon} is pushing research toward a new paradigm: machine scales, human steers.

Youran Sun, Xingyu Ren, Chugang Yi +4

University of Maryland, College Park, College Park, MD, USA · The Chinese University of Hong Kong, Hong Kong, China · Stanford University, Stanford, CA, USA

AI Agents for Scientific Discovery Human-in-the-Loop AI Autonomous Experimentation Autonomous Research Agents LLM Agent Reliability

Jun 22, 2026cs.AI

Causal Discovery in the Era of Agents

Recent attempts to combine large language models (LLMs) with causal discovery ask models to infer pairwise directions, propose graph structures, or inject language-model outputs as priors and constraints. These approaches promise faster analysis, but they also obscure whether a causal evidence is supported by data and assumptions or by textual associations, prompt artifacts and hallucinated mechanisms. We argue for a different role for agents in causal discovery. Agents should inspect data, retrieve context, explain method assumptions and clarify graph outputs, but they should not supply edges, orientations, priors, constraints or causal conclusions. We propose the principle that agents assist the workflow, while causal claims remain grounded in data, explicit assumptions, formal algorithms, diagnostics and user or domain-expert decisions. We instantiate this principle in causal-learn+, an online platform that coordinates data analysis, preprocessing, method recommendation, expert-knowledge incorporation, formal discovery and interpretation around the algorithmic ecosystem of causal-learn. A case study on Big Five personality data illustrates agent-assisted pipeline of causal discovery without turning language-model unreliability into causal evidence. The platform is available at causallearn.com.

Yujia Zheng, Vishal Verma, Mantej Gill +3

1Carnegie Mellon University. · 2Mohamed bin Zayed University of Artificial Intelligence.

AI Agents for Scientific Discovery Causal Discovery

Jun 22, 2026cs.AI

AI Scientists as Engines of Discovery: A Case for Development within Reformed Institutions

Agentic artificial intelligence (AI) systems are beginning to assist, accelerate, and partially automate scientific discovery, performing tasks that span literature synthesis, code generation, data analysis, hypothesis proposal, and model criticism. We argue that this transition is qualitative rather than incremental, and that suitably designed multi-agent systems may evolve from passive computational tools into ``AI scientists'' that can expand the hypothesis-generating and verification capacity of science. Such systems must be developed and deployed within a scientific ecosystem fit for purpose: institutions must be redesigned for verification, accountability, interpretability, and dual-use safety. We sketch how multi-agent architectures, illustrated by the prototype framework \textit{Denario}, accelerate the discovery cycle and traverse model spaces beyond human reach; examine what this implies for authorship, peer review, and the enduring role of human scientists; and close with recommendations for governing AI as an epistemic actor rather than a mere instrument.

Raul Jimenez, Boris Bolliet, Francisco Villaescusa-Navarro +7

Institute of Cosmos Sciences (ICCUB), University of Barcelona, Barcelona, Spain · ICREA, Barcelona, 08010, Spain · Cavendish Astrophysics, University of Cambridge, Madingley Road, Cambridge CB3 0HA, UK +10

AI Agents for Scientific Discovery Scientific Hypothesis Generation Autonomous Scientific Discovery AI Agent Governance Human Oversight of AI

Jun 21, 2026cs.AI

PaperClaw: Harnessing Agents for Autonomous Research and Human-in-the-Loop Refinement

Large language models have become capable reasoners and tool users that write and run code and search the literature, which makes automating the research process itself a realistic goal. We present PAPERCLAW, a harnessed multi-agent system that carries a project autonomously, from a field of study to a finished paper. PAPERCLAW curates a domain from a field's live literature, datasets, and code; brainstorms it into an idea with a pre-registered main-result contract; and drives a stoppable hypothesis map through an iterative propose, test, reflect loop that grows only from measured verdicts and halts once the evidence supports the idea, at which point it writes a venue-compliant paper. A full-lifecycle memory keeps each stage in a single living record, so a long run can be paused, inspected, and resumed without losing context. At the centre is an in-cycle research assistant with research tools and skills: it can drive the whole pipeline on its own, while the same interface lets a person step in at any stage, turning a first autonomous draft into a stronger paper through human-in-the-loop refinement. Throughout, PAPERCLAW keeps its output grounded and checkable, citing only references validated against open scholarly indexes and reporting results that genuinely ran. An evaluation with an LLM judge finds that PAPERCLAW produces strong papers both fully autonomously and with human-in-the-loop refinement.

Weiwei Ye, Hangchen Liu, Dongyuan Li +1

The University of Tokyo

Multi-Agent LLM Systems AI Agents for Scientific Discovery Human-in-the-Loop AI Autonomous Research Agents