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

Jun 18, 2026cs.LG

Agentic Symbolic Search: Characterizing PDEs Beyond Hand-crafted Expressions, Meshes, and Neural Networks

Mathematicians understand a PDE solution through mathematical structures rather than tables of computed values. Historically, this has been the product of mathematical analysis, carried out by hand for each problem individually. Neither numerical simulation nor neural networks produce those structures directly. We propose Agentic Symbolic Search (ASYS), a prior-guided framework in which an agent translates PDE theory, public problem constraints, and accumulated search experience into testable differentiable symbolic programs. The mathematical forms are refined under evolutionary search, while their continuous parameters are fit by gradient-based optimization. This makes the search an automated form of inductive-bias injection rather than blind symbolic regression. For problems with known analytical forms, ASYS recovers these forms naturally; for other problems, ASYS constructs analytical approximations which can guide mathematicians toward further analysis. In our experiments, across five problems spanning bounded dynamics, finite-time blow-up, and free-boundary focusing, ASYS produces interpretable representations, including a geometric interface formula for Allen-Cahn 2D dynamics and a nine-parameter contraction law for Keller-Segel chemotactic blow-up, in settings where no closed-form description was previously available. ASYS shows the possibility of a new paradigm for characterizing PDE solutions, beyond handcrafted analytical solutions, mesh-based numerical solutions, and neural network approximations.

Zongmin Yu, Liu Yang

National University of Singapore

AI Agents for Scientific Discovery PDE Solving PDE Discovery Symbolic Regression

Jun 18, 2026physics.chem-ph

Empowering Polymeric Materials Discovery by Artificial Intelligence

Polymeric materials underpin modern technologies spanning energy storage, microelectronics, healthcare and sustainable manufacturing. Yet their rational design remains exceptionally challenging because material performance emerges from complex interactions among molecular composition, chain architecture, processing history and hierarchical structural evolution across multiple length and time scales. Consequently, polymer research has long relied on labor-intensive experimentation and fragmented modeling approaches, limiting both mechanistic understanding and innovation efficiency. Recent advances in data infrastructure, machine learning, large artificial intelligence (AI) models and laboratory automation are beginning to reshape this landscape. Rather than functioning as isolated tools, polymer databases, predictive models, AI agents and automated laboratories are increasingly converging into interconnected discovery ecosystems. As a result, the central challenge is shifting from improving predictive accuracy alone to enabling reliable decision-making, adaptive learning and seamless integration across computation, experimentation and scientific reasoning. We argue that polymer science is entering an era of autonomous discovery, in which data, simulation, reasoning and experimentation operate within self-improving feedback loops that continuously generate hypotheses, design materials, execute experiments and refine predictive models. By unifying molecular design, process optimization, experimental validation and industrial translation, such autonomous ecosystems establish a more predictive, reproducible and scalable paradigm for polymer innovation, fundamentally transforming how polymer research is conducted.

Chenyao Ma, Linda Zhang, Yuheng Chen +29

Suzhou MatSource Technology Co., Ltd., Suzhou 215000, Jiangsu, China. · Advanced Institute for Materials Research (WPI-AIMR), Tohoku University, Sendai 980-8577, Japan. · Frontier Research Institute for Interdisciplinary Sciences (FRIS), Tohoku University, Sendai, 980-8577, Japan. +11

AI Agents for Scientific Discovery Materials Science Autonomous Scientific Discovery Autonomous Experimentation

Jun 15, 2026q-bio.QM

Agentic Discovery of Non-Canonical Antimicrobial Peptides with AMPGAN v3

Antimicrobial resistance causes to over a million deaths annually. Antimicrobial peptides (AMPs) are a promising solution, but generative AMP models are not yet ready to design peptides with non-natural amino acids and/or chemical modifications, which are essential for real-world peptide drugs. We present AMPGAN v3, a multi-objective conditional GAN that expands the generative vocabulary to D-amino acids and N/C-terminus modifications such as amidation. By separating adversarial and activity-aware supervision across two specialized discriminators, AMPGAN v3 substantially improves training stability and outperforms prior generative AMP models on external classifiers. We validated five candidates spanning three structural classes in vitro; two showed activity against Gram-positive strains, with the best candidate reaching MIC 8 μg/mL against B. subtilis. To support downstream curation, we further present PepCraft, a multi-agent framework for end-to-end AMP discovery in which a Planning Agent orchestrates specialized executors for generation, filtering, and verification. Its prioritization recommendations align with our in vitro outcomes. Together, these contributions let us examine, on a small but real scale, how generative and agentic AI compose in therapeutic peptide discovery. Code: https://github.com/marszzibros/AMPGANv3

Jay Jung, Xiaohan Zhang, Shenghan Song +8

Department of Computer Science, University of Vermont, Burlington, VT, USA · Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA · Department of Comparative Pathobiology, Purdue University, West Lafayette, IN, USA +3

AI Agents for Scientific Discovery Molecular Generation Conditional Generative Modeling Generative Adversarial Networks Drug Discovery

Jun 14, 2026cs.MA

DeepRoot: A KG-Coordinated Multi-Agent System for Therapeutic Reasoning over Historical Medical Texts

Historical medical archives and traditional medicines hold immense potential for drug discovery and remain a primary source for current drug development. However, pre-ontological prose and idiosyncratic taxonomies prevent the standardization and medical modernization of the data for use in current biomedical pipelines. Furthermore, no existing LLM agent system, whether tool-calling, retrieval-augmented, or agentic deep-research, can convert such text into verifiable drug-discovery leads at scale. We close this gap with DeepRoot, a multi-agent LLM system that jointly builds and utilizes a verified knowledge graph, showing that grounding and reasoning -- often conflated -- are separable axes the system can compose for therapeutic reasoning. Applied to the Shen Nong Ben Cao Jing, DeepRoot recovers

10

of

21

held-out compound-disease treatment pairs at R@

20

(

47.6\%

vs

4.8\%

for a raw corpus LLM and

\sim\!2.4\%

random) and dominates an LLM-as-judge audit for reasoning quality over baseline LLMs and LLMs with direct tool-call access to the same APIs DeepRoot itself queries. Tool-using LLMs hallucinate evidence on

87\%

of claims, versus 7-10% for DeepRoot. Graph-only inference hallucinates

0\%

but ranks lowest on reasoning coherence; DeepRoot KG+LLM is the only condition to win on both axes, pointing toward a route for systematic mining and repurposing of historical medical knowledge.

Zijian Carl Ma, Sean J. Wang, Sijbren Kramer +1

Department of Bioengineering · Stanford University · Amazon AWS AI

Historical Document Analysis Multi-Agent LLM Systems AI Agents for Scientific Discovery Knowledge Representation Knowledge Graph Question Answering LLM Agent Reliability+2

Jun 13, 2026cs.CL

Pepti-Agent: An AI Agent for Peptide Design and Optimization

Therapeutic peptides occupy a valuable design space between small molecules and biologics, but their development requires satisfying several competing constraints at once: solubility, hemolytic activity, and nonspecific surface fouling are governed by overlapping sequence features, so improving one property often degrades another. Computational design addresses this by pairing generative models with sequence-based property predictors, iteratively proposing and refining candidates. However, these components are typically wired together as monolithic scripts that are difficult to inspect, extend, or reuse, and they often refine sequences by natural-language reasoning rather than by tracking the evolving multi-property state of each candidate. We present Pepti-Agent, a closed-loop, peptide-specific framework that exposes generation, property prediction, and single-residue mutation as independently inspectable Model Context Protocol (MCP) tools. A large language model controller invokes these tools and consults live predictor output between calls, so refinement is guided by each sequence's current property profile rather than by language reasoning alone. Task-specific PeptideGPT models generate candidates, ProtBERT-based classifiers score solubility, hemolysis, and non-fouling, and two interchangeable mutation operators propose sequence edits. By recording a per-step trace of controller decisions, predictor outputs, and accepted mutations, Pepti-Agent offers a reproducible substrate for benchmarking multi-objective design strategies and for prioritizing candidates for experimental validation.

Houxu Chen, Achuth Chandrasekhar, Amir Barati Farimani

Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, USA · Mechanical Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, USA · Chemical Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, USA +2

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

Jun 11, 2026cs.AI

EpiBench: Verifiable Evaluation of AI Agents on Epigenomics Analysis

We introduce EpiBench, a verifiable benchmark for short-horizon epigenomics analysis. EpiBench evaluates whether agents can make well-defined analysis decisions from realistic workflow states and return deterministically gradable answers. The benchmark includes 106 evaluations across CUT&Tag/CUT&RUN, ATAC-seq, ChIP-seq, and DNA methylation workflows. Across 5,088 valid trajectories from 16 model-harness pairs, no system passed a majority of attempts: GPT-5.5 / Pi led at 45.0% (143/318 attempts; 95% confidence interval (CI), 36.3--53.7), followed by GPT-5.5 / OpenAI Codex at 39.9% (127/318 attempts; 95% CI, 31.6--48.3). Claude Opus 4.8 Max / Pi and GPT-5.4 / Pi each passed 39.0% (124/318 attempts; 95% CI, 30.2--47.8 and 31.0--47.0, respectively). Performance varies across assay types, and many failed runs still contain parts of the correct answer. Agents often found the right files and computed useful intermediate results, but failed when the task required deeper, assay-specific scientific judgment.

Harihara Muralidharan, Reema Baskar, Soo Hee Lee +2

LatchBio, San Francisco, CA, USA

AI Agents for Scientific Discovery AI Agent Evaluation AI Agent Benchmarks Genomics

Jun 11, 2026cs.CY

AgentSociety 2: An Integrated Research Environment for Executable Social Science

AI scientist systems are beginning to automate parts of scientific research, but social science poses a distinct challenge: its objects of inquiry are not merely datasets or laboratory protocols, but integrated social processes involving situated participants, interaction contexts, interventions, and outcomes. Yet a critical link is missing: existing systems either assist isolated research tasks or simulate agents as experimental subjects, leaving the research workflow and simulated society decoupled. Here we introduce AgentSociety 2, an Integrated Research Environment for executable social science. It couples two roles of LLM agents in the same runtime: AI social scientists that coordinate literature grounding, hypothesis generation, experiment design, simulation execution, result interpretation, and manuscript drafting; and silicon participants that generate behavioral responses within configurable social environments. This dual-role design turns hypotheses into auditable agent behaviors, environment rules, interventions, and measurements, thereby supporting an end-to-end workflow. Across seven illustrative studies spanning micro-level social-science laboratory experiments, meso-level dynamics in social media, and macro-level urban scenarios, we demonstrate its capacity to support diverse disciplinary questions, reproduce major qualitative patterns from prior studies, identify informative deviations, and enable large-scale simulations through optimized agent-environment interactions. By preserving human researchers' high-level agency while delegating procedural orchestration to agentic systems, it provides a human-in-the-loop and controllable infrastructure for next-generation computational social science, with broader applications in scalable computational social experimentation and AI-enabled social governance platforms.

Jinghua Piao, Jun Zhang, Haoyu Huang +16

Department of Electronic Engineering, Tsinghua University · School of Environment, Tsinghua University · School of Public Policy and Management, Tsinghua University +2

Multi-Agent LLM Systems AI Agents for Scientific Discovery Human Behavior Simulation Computational Social Science Large Language Model-Based Social Simulation

Jun 11, 2026cs.AI

TerraBench: Can Agents Reason Over Heterogeneous Earth-System Data?

Climate and environmental decision-making increasingly requires reasoning across heterogeneous inputs, including gridded physical data, satellite imagery, geospatial context, and simulator outputs. Weather and climate foundation models can forecast well, but do not reason interactively in language, while large language models (LLMs) reason in language but cannot operate directly on high-dimensional Earth-system data. As a result, real scientific workflows in Earth-science remain underserved. We introduce TerraBench, a benchmark for grounded Earth-science reasoning, built on TerraAgent, a ReAct-style executable framework that interleaves reasoning, tool calls, and observations to couple LLM planning with scientific tools for environmental retrieval, geospatial processing, simulation, and artifact-backed computation. TerraBench unifies analysis of Earth observation imagery, gridded data, GIS reasoning and simulation in a single executable interface, whereas prior benchmarks isolate these capabilities into narrow individual tasks. It is also the first in this space to pair process-level tool-use metrics with tolerance-aware numeric scoring. The benchmark comprises 403 extensive agentic tasks across three tracks (Fundamentals, Simulator-Grounded, and Document-Grounded Verification) and eight application domains with 24,500 verified execution steps. These results indicate that reliable Earth-science agents must go beyond tool access to coordinate heterogeneous workflows, parameterize tools precisely, and preserve artifact provenance.

Dat Tien Nguyen, Thao Nguyen, Fadillah Adamsyah Maani +5

Mohamed bin Zayed University of Artificial Intelligence, Abu Dhabi, UAE · ADIA Lab, Abu Dhabi, UAE

AI Agents for Scientific Discovery Scientific Reasoning LLM Agent Evaluation Geospatial Reasoning AI Agent Benchmarks LLM Agents+1

Jun 11, 2026cs.AI

MDForge: Agentic Molecular Dynamics Pipeline Design under Sparse Simulator Feedback

Molecular dynamics (MD) is the canonical in-silico method for atomistic molecular science, simulating molecular behavior from first-principle physics. Designing an MD pipeline for a new system requires substantial expert knowledge: running it on even one molecule is expensive, ruling out trial-and-error. We automate this expert pipeline-design process with an LLM agent. Unlike existing MD agents that orchestrate a predefined tool set, we treat pipeline design as open-ended code generation in which the agent's behavior is reshaped online by verbal reward. Specifically, we build MDForge, an LLM agent whose in-context update rule densifies the sparse reward via a multi-agent debate among physics experts. On three SAMPL host-guest binding free-energy benchmarks, MDForge automatically designs MD pipelines competitive with human experts. Deployed on a library of unseen candidate guests, its CB[7] pipeline discovers a novel binder that wet-lab competition NMR confirms is a high-affinity, picomolar CB[7] binder. Our data and code are available at https://github.com/Zehong-Wang/MDForge.

Zehong Wang, Yijun Ma, Connor R. Schmidt +7

University of Notre Dame · University of Connecticut

AI Agents for Scientific Discovery Molecular Dynamics Simulation Physics-Based Simulation RL for LLM Agents

Jun 11, 2026cs.AI

Fantastic Scientific Agents and How to Build Them: AgentBuild for Rietveld Refinement

As scientific workflows shift from deterministic executables to LLM-based agents, the development practices on offer, such as fine-tuning, reinforcement learning, and prompt-and-go, bury the scientist's judgment. We propose treating agent construction as a workflow stage and introduce AgentBuild, which builds a scientific agent from a contract the scientist authors. The contract is a version-controlled rubric, a difficulty-graded curriculum, and a curated external knowledge base. A rubric-driven judge gates a meta-optimizer coding agent that edits the agent within a declared boundary, so the build compiles the agent, not the scientist's judgment. We instantiate this for Rietveld refinement of X-ray diffraction data through GSAS-II behind MCP and A2A, where a blank-harness construction run progresses through a lithium lanthanum zirconium oxide (LLZO) signal-to-noise ladder, reaches the 4 hour scan as a frontier case, and exposes the workflow-scope limits that remain. The same rubric that rewards credible fits also scores trajectory scope, making the frontier a contract failure rather than a pattern-fitting failure. As base models evolve, re-running AgentBuild is a re-tune, not a rebuild, and the scientist's authored contract remains the durable asset.

Woong Shin, Craig A. Bridges, Marshall T. McDonnell +1

Oak Ridge National Laboratory, Oak Ridge, TN, USA

AI Agents for Scientific Discovery LLM Agent Self-Improvement LLM Agents Scientific Workflow Automation Data Analysis Agents

Jun 10, 2026cs.AI

StatefulDiscovery: Evidence-Calibrated Claim Formation in Open-Ended Scientific Discovery

Open-ended scientific discovery asks agents to move beyond executing analyses for predefined questions. Across multiple rounds of exploration, a discovery agent must decide which phenomena warrant investigation while avoiding overinterpretation, where emerging claims exceed the evidential scope of the analyses. This creates an evidence-calibration problem: the exploration trajectory must be coupled with claim status so that evidence can guide both what to investigate next and what can be claimed. We introduce \textsc{StatefulDiscovery}, a discovery framework that externalizes investigation state and uses it to coordinate frontier selection, evidence acquisition, and claim adjudication. We evaluate \textsc{StatefulDiscovery} across 40 real-data discovery tasks. Compared with several baselines, \textsc{StatefulDiscovery} produces more claims overall judged to be both well-supported and high-value. Ablations indicate distinct roles for structured hypotheses, local adjudication, frontier control and persistent states. Together, these results suggest that explicit discovery state can couple exploration with evidence-calibrated claim formation. Our code is released at https://github.com/SUSTech-GenAI/StatefulDiscovery.git.

Jiayao Chen, Shi Liu, Linyi Yang

Southern University of Science and Technology

AI Agents for Scientific Discovery Evidence-Grounded Reasoning State Tracking Scientific Claim Verification

Jun 10, 2026cs.AI

Skill-Augmented AI Agents for Medical Research Analysis: An Exploratory Multi-Model Human Evaluation in an NSCLC Transcriptomic Biomarker Task

Background. Large language models and AI agents are increasingly used to support biomedical research, but native model outputs may omit key analytical steps, misuse methods, or overstate conclusions. We evaluated whether autonomous access to a medical research skill package was associated with higher-quality AI-generated transcriptomic research-analysis outputs compared with native AI without skills. Methods. We conducted an exploratory multi-model human evaluation using a non-small cell lung cancer immunotherapy biomarker task. Six model backbones were tested. The evaluation included 21 anonymized outputs: 9 native-AI outputs and 12 skill-augmented outputs generated through an AI agent implementation represented by OpenClaw. Four non-expert biomedical reviewers and two blinded experts evaluated each output, with two ratings from each reviewer type. The primary outcome was expert-rated overall quality. Results. Skill-augmented outputs showed directionally higher expert overall quality than native-AI outputs (mean 5.50 vs 5.11; difference=0.39; bootstrap 95% CI, -0.04 to 0.90; Welch p=0.156). Non-expert reviewer quality showed the same direction (mean 4.72 vs 4.47; difference=0.26; bootstrap 95% CI, -0.25 to 0.80; Welch p=0.373). Expert agreement was limited (single-rating ICC=-0.15), and model-specific effects were descriptive and heterogeneous. Conclusions. Autonomous skill access showed a directional quality signal in this exploratory sample, but the signal was smaller than expert-rating noise and should not be interpreted as confirmatory evidence. The findings primarily motivate larger evaluations of skill-augmented AI agents with stronger reliability controls, platform replication, and biological-validity assessment.

Qianyu Yao, Fei Sun, Bocheng Huang +10

AIPOCH PTE. LTD., Singapore

AI Agents for Scientific Discovery LLM Agent Evaluation Medical LLMs

Jun 9, 2026cs.CL

Harnessing the Collective Intelligence of AI Agents in the Wild for New Discoveries

Scientific discovery is often a collective process: researchers share partial results, inspect failed attempts, and build on each other's ideas over long time horizons. Recent AI systems have shown that language-model-based agents can make meaningful progress on open scientific problems, but most existing systems operate in isolation. In this paper, we present EinsteinArena, an agent-native platform for open distributed research and discovery. EinsteinArena provides agents with a live set of open problems, each with a solid verifier, public leaderboard, and problem-specific discussion forum where agents can ask questions and share insights. We focus on mathematical tasks that have garnered substantial research interest, where progress can be measured unambiguously. As of May 2026, agents on EinsteinArena have discovered 12 new state-of-the-art results better than any previous human or AI solutions. One notable example is the kissing number problem in dimension 11, where the platform improved the best known lower bound from 593 to 604. This advance did not come from a single agent or isolated run. Rather it arose through a sequence of submissions, public discussion, verifier refinement, and subsequent agent-to-agent borrowing of ideas. These results provide evidence that decentralized scientific discovery can emerge from open interaction among autonomous agents in the wild, demonstrating a new paradigm for collective AI-driven research.

Federico Bianchi, Yongchan Kwon, Aneesh Pappu +1

Together AI · Stanford University

AI Agents for Scientific Discovery Multi-Agent Collaboration Autonomous Scientific Discovery

Jun 6, 2026cs.AI

SciTrace: Trajectory-Aware Safety Reasoning for Scientific Discovery Agents

LLM-based scientific agents have shown strong capacity for autonomous research, yet their safety layers remain structurally divorced from core reasoning: they inspect pipeline outputs rather than shaping the deliberation that produces them. This separation opens two failure modes: safety signals accumulated at one stage are discarded before the next, and sequences of individually benign tool calls can compose into harmful outcomes that no single-step filter detects. To address these challenges, we introduce \textbf{SciTrace}, a framework that weaves safety reasoning into every stage of the scientific agent pipeline. SciTrace couples two complementary mechanisms: a \textit{Safety-Intrinsic Reasoning Loop} (SIR) that maintains a cumulative risk state across the Thinker, Experimenter, Writer, and Reviewer stages through joint task-and-safety deliberation, and a \textit{Compositional Tool-Chain Verifier} (CTV) that performs trajectory-aware safety checks before execution, catching risks that surface only across multi-step tool sequences. Evaluated on 240 high-risk research tasks and 120 tool-related risk tasks spanning six scientific domains, SciTrace achieves state-of-the-art (\textbf{SOTA}) safety among compared frameworks across four backbone models: it consistently improves tool call safety and adversarial robustness while preserving scientific output quality, and it uncovers \textbf{78.8%} of the compositional tool-chain escapes that single-step monitors miss. The project website is available at https://opensciagent.github.io/SciTrace/.

Tanush Swaminathan, Runmin Jiang, Letian Zhang +1

Carnegie Mellon University · Allen Institute

AI Agents for Scientific Discovery LLM Safety Evaluation LLM Agent Safety

Jun 5, 2026cond-mat.mtrl-sci

Agentic multi-fidelity learning of quasiparticle and excitonic properties

Many-body GW-Bethe-Salpeter equation calculations are essential for accurate simulations of electronic structure and optical properties in modern low-dimensional nanomaterials. However, these methods are computationally demanding and can exhibit localized numerical instabilities or convergence failures that are difficult to detect within high-throughput workflows. We introduce an agent-guided multi-fidelity framework for correcting GW-Bethe-Salpeter excited-state landscapes in strained MoS2-WS2 bilayers. Across stacking registries, strain branches and reciprocal-space samplings, the workflow identifies spike-like excursions, near-zero-gap collapse and cross-fidelity inconsistencies associated with fragile long-wavelength dielectric screening. A structural agent evaluates calculations by assigning confidence weights and selectively using a small number of high-accuracy reference points. Machine learning models then transfer information across related systems and apply Gaussian process corrections to recover improved quasiparticle gaps and exciton binding energies, with calibrated uncertainty estimates. The approach corrects numerically induced artifacts without erasing physical strain dependence and substantially improves agreement with higher-fidelity references relative to a no-agent baseline. These results show that reliable surrogate learning for excited-state materials requires explicit diagnosis of numerical fragility, not direct interpolation of raw first-principles data points. The proposed framework is readily transferable to other optoelectronic nanomaterials characterized by strong quantum confinement, such as quantum dots, nanoribbons, layered two-dimensional semiconductors, and hybrid perovskite nanostructures.

Arnab Neogi, Aaron Forde, Christopher A. Lane +2

Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA · Center for Integrated Nanotechnologies, Materials Physics and Applications Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA

AI Agents for Scientific Discovery Materials Property Prediction Quantum Many-Body Physics Computational Materials Science

Jun 2, 2026cs.AI

LAP: An Agent-to-Instrument Protocol for Autonomous Science

Autonomous science is moving from demonstration to infrastructure. Large language model agents now plan experiments, and self-driving laboratories execute them. Yet every such system rebuilds the link between the reasoning agent and the physical instrument from scratch, against fragmented vendor SDKs and standards built for deterministic software clients rather than probabilistic, goal-directed agents. Recent agent-interoperability protocols clarify two of the three edges of an agentic ecosystem (Anthropic's Model Context Protocol (MCP) standardizes the agent-to-tool edge, and Google's Agent2Agent (A2A) the agent-to-agent edge), but neither models the agent-to-instrument edge, where operations are stateful, safety-critical, exclusively owned, physically embodied, and produce measurements with units, calibration, and uncertainty. We present the Lab Agent Protocol (LAP), a protocol design that fills this gap. LAP retains A2A's peer-to-peer, discovery-first, task-lifecycle structure and adds four physical-world primitives: (i) the InstrumentCard, a signed capability and physical-limit description; (ii) first-class reservation for exclusive instrument and sample locking; (iii) a safety-fence handshake with operator-confirmation tokens cryptographically bound to a specific task and its parameters, gating hazardous and irreversible operations; and (iv) a MeasurementResult schema that makes every result physically typed (QUDT/UCUM), calibration-anchored, uncertainty-bearing, and reproducible by construction. We specify roles, a six-layer architecture, the JSON-RPC method set, the task and safety state machines, the error model, and cross-laboratory federation, and walk a closed-loop autonomous campaign through the protocol end-to-end. LAP is transport-compatible with the A2A/MCP ecosystem and encapsulates rather than replaces existing device standards such as SiLA 2 and OPC-UA.

Linwu Zhu, Liqiang Gao, Yan Chen +2

Shiyanjia Lab

AI Agents for Scientific Discovery Agent Communication Protocols AI Agent Safety Laboratory Automation Autonomous Experimentation

Jun 2, 2026cs.AI

CP-Agent: Context-Aware Multimodal Reasoning for Cellular Morphological Profiling under Chemical Perturbations

Cell Painting combines multiplexed fluorescent staining, high-content imaging, and quantitative analysis to generate high-dimensional phenotypic readouts to support diverse downstream tasks such as mechanism-of-action (MoA) inference, toxicity prediction, and construction of drug-disease atlases. However, existing workflows are slow, costly and difficult to interpret. Approaches for drug screening modeling predominantly focus on molecular representation learning, while neglecting actual experimental context (e.g., cell line, dosing schedule, etc.), limiting generalization and MoA resolution. We introduce CP-Agent, an agentic multimodal large language model (MLLM) capable of generating mechanism-relevant, human-interpretable rationales for cell morphological changes under drug perturbations. At its core, CP-Agent leverages a context-aware alignment module, CP-CLIP, that jointly embeds high-content images and experimental metadata to enable robust treatment and MoA discrimination (achieving a maximum F1-score of 0.896). By integrating CP-CLIP outputs with agentic tool usage and reasoning, CP-Agent compiles rationales into a structured report to guide experimental design and hypothesis refinement. These capabilities highlight CP-Agent's potential to accelerate drug discovery by enabling more interpretable, scalable, and context-aware phenotypic screening -- streamlining iterative cycles of hypothesis generation in drug discovery.

Yuxin Zhang, Yiyao Li, Ping Shu Ho +3

Department of Electrical and Computer Engineering, The University of Hong Kong · School of Computing and Data Science, The University of Hong Kong · Nvidia AI Technology Center +2

AI Agents for Scientific Discovery Multimodal Contrastive Learning Multimodal Agents Drug Discovery

Jun 1, 2026q-bio.BM

Site4Drug: Predicting Drug-Binding Target Sites with an AI Agent

Selecting where to intervene on a protein (i.e., choosing a targetable site) is often a more ambiguous and failure-prone bottleneck than selecting what binds, especially for membrane proteins where accessibility, topology, and post-translational modifications (PTMs) constrain actionable regions. We present Site4Drug, a modality-aware site-finding agent that outputs a ranked list of targetable regions with explicit constraints, evidence summaries, risk flags, and a traceable decision log. Rather than requiring users to specify the drug modality upfront, Site4Drug can recommend a binding modality (e.g., antibody/peptide-like vs small-molecule) from the same evidence used for site discovery, including topology, hydropathy, PTM propensity, disulfides, domain context, and sequence. Importantly, this evidence is applied consistently across modalities, including small-molecule pocket discovery, to avoid selecting chemically plausible but biologically occluded sites.

Taehan Kim, Sarrah Rose Mikhail Leung, Bharat Mekala +1

UC Berkeley · University of Michigan

AI Agents for Scientific Discovery Drug Discovery

May 31, 2026cs.AI

Self-Revising Discovery Systems for Science: A Categorical Framework for Agentic Artificial Intelligence

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

Fiona Y. Wang, Markus J. Buehler

Laboratory for Atomistic and Molecular Mechanics Department of Biological Engineering Massachusetts Institute of Technology Cambridge, MA 02139, USA · Laboratory for Atomistic and Molecular Mechanics Department of Civil and Environmental Engineering Department of Mechanical Engineering Center for Computational Science and Engineering Schwarzman College of Computing Massachusetts Institute of Technology Cambridge, MA 02139, USA

AI Agents for Scientific Discovery Autonomous Scientific Discovery

May 30, 2026cs.CV

CodeCytos: AI-assisted spatial molecular imaging analysis via code-augmented agent action space

Conventional tissue image analysis software provides foundational capabilities for cellular analysis, including segmentation, basic morphological feature extraction, and spatial organization analysis. However, these tools often require manual intervention and are not well integrated with code-driven automation, limiting efficiency and scalability for complex spatial tissue studies. In addition, they offer limited flexibility for custom analyses, as they typically support only a fixed set of pre-implemented spatial cellular features. To address these limitations, we propose CodeCytos, a coding-based reasoning agent framework that enables dynamic, programmable interaction with spatial molecular imaging data to improve automation and customization. CodeCytos is designed to streamline the exploration of custom spatial cellular features and adapt to diverse research needs. We demonstrate its utility through case studies on four expert-curated datasets from distinct tissue types: frontal cortex, non-small-cell lung cancer, pancreas, and tonsil. We evaluate CodeCytos under a realistic minimal prompt setting, where bioscientists pose simple questions without task-specific instructions or contextual information about spatial cellular analysis, and benchmark multiple LLM backbones with strong coding capabilities. We further show that incorporating tailored, domain-agnostic few-shot in-context coding-reasoning examples (randomly sampled demonstrations outside the spatial analysis domain) can substantially improve performance without requiring costly, expert-crafted in-domain demonstrations. Overall, CodeCytos outperforms baseline approaches, highlighting the potential of code-action agents to assist with custom feature exploration in spatial molecular imaging and to accelerate biomarker discovery.

Hung Q. Vo, Huy Q. Vo, Son T. Ly +6

University of Houston, Department of Electrical and Computer Engineering, Houston, Texas, 77004, USA · Houston Methodist Hospital, Department of Systems Medicine and Biomedical Engineering, Houston, Texas, 77030, USA

Computational Pathology Spatial Transcriptomics AI Agents for Scientific Discovery Agentic Code Generation

May 28, 2026cs.AI

Learning to Choose: An Empowerment-Guided Multi-Agent System with semantic communication for Adaptive Method Selection

Automating scientific computing workflows requires more than generating executable code: autonomous systems must also select appropriate computational strategies, implement them faithfully, and ensure that the resulting outcomes remain causally attributable to the decisions that produced them. In multi-agent pipelines, this process is particularly fragile, as small inconsistencies between agent intentions and actions can lead to semantic drift, where the eventually executed procedure no longer reflects the originally selected strategy, thereby corrupting downstream evaluation and adaptation. In this work, motivated by the ATHENA framework (Toscano et al., 2025; Toscano et al., 2026) and the concept of empowerment (Yiu et al., 2025), we introduce a multi-agent framework that combines contextual bandits with structured inter-agent communication and, most importantly, semantic checkpoints that preserve action-outcome fidelity throughout the pipeline. The system integrates specialized large language model (LLM) agents, grounded code generation, and self-healing execution loops within an adaptive decision-making architecture. Interpreting the framework through the lens of empowerment, we show that reliable autonomous learning requires not only identifying high-quality actions, but also preserving the integrity of their propagation across agents. Using sensitivity analysis and uncertainty quantification workflows as representative case studies, we demonstrate that unchecked semantic drift degrades policy learning, whereas the proposed framework improves convergence, robustness, and adaptation to novel problem contexts. These results suggest a broader design principle for scientific multi-agent systems: adaptive decision-making must be coupled with explicit mechanisms that guarantee semantic consistency and reliable information flow across the computational pipeline.

Geremy Loachamín-Suntaxi, Robert Lazar, Dimitrios G. Giovanis +2

School of Chemical Engineering, National Technical University of Athens, Zographos Campus, 15780, Attiki, Greece · Luxembourg Institute of Science and Technology Esch-sur-Alzette, L-4362, Luxembourg

Multi-Agent LLM Systems AI Agents for Scientific Discovery Semantic Communication

May 28, 2026cs.AI

Compass: Navigating Global Marine Lead Data Integration through Expert-Guided LLM Agent

Marine lead (Pb) and its isotopes are critical tracers for ocean circulation and anthropogenic pollution, yet in-situ observations remain costly and sparse. While vast historical records exist, they lie buried within the unstructured content of academic papers, creating "data silos" inaccessible to comprehensive analysis. Manual extraction is unscalable, while general-purpose Large Language Models (LLMs) lack the necessary domain-specific knowledge, leading to hallucinations and scientifically invalid outputs. To address this, we introduce an expert-guided adaptation approach that enables LLMs to perform rigorous scientific data extraction without fine-tuning. We operationalize this approach through Compass, an LLM agent framework enhanced by a Knowledge Tree co-designed with marine scientists, which decomposes complex tasks into verifiable steps, guiding the agent's reasoning to ensure scientific validity. Deploying Compass across a corpus of over 230,000 relevant open-access papers, we successfully extract 3,751 previously unincorporated Pb records. This effort establishes the largest integrated marine Pb database to date. Beyond standard metrics, Compass demonstrates superior reliability through multi-layered validation, achieving 92% accuracy as confirmed through expert manual verification. The newly integrated data expand coverage in previously under-sampled regions such as the East China Sea and the Southern Ocean, providing an enriched data foundation for future scientific discoveries. We release an interactive visualization platform to facilitate open scientific access. Our work demonstrates that expert-guided agents can effectively bridge the gap between general-purpose LLMs and high-stakes scientific domains, enabling scalable data discovery in geosciences.

Yiming Liu, Bin Lu, Meng Jin +6

AI Agents for Scientific Discovery Document Information Extraction LLM Information Extraction

May 28, 2026cs.AI

Battery-Sim-Agent: Leveraging LLM-Agent for Inverse Battery Parameter Estimation

Parameterizing high-fidelity "digital twins" of batteries is a critical yet challenging inverse problem that hinders the pace of battery innovation. Prevailing methods formulate this as a black-box optimization (BBO) task, employing algorithms that are sample-inefficient and blind to the underlying physics. In this work, we introduce a new paradigm that reframes the inverse problem as a reasoning task, and present Battery-Sim-Agent, the first framework to deploy a Large Language Model (LLM) agent in a closed loop with a high-fidelity battery simulator. The agent mimics a human scientist's workflow: it interprets rich, multi-modal feedback from the simulator, forms physically-grounded hypotheses to explain discrepancies, and proposes structured parameter updates. On a systematically constructed benchmark suite spanning diverse battery chemistries, operating conditions, and difficulty levels, our agent significantly outperforms strong BBO baselines like Bayesian optimization in identifying accurate parameters. We further demonstrate the framework's capability in complex long-horizon degradation fitting tasks and validate its practical applicability on real-world battery datasets. Our results highlight the promise of LLM-agents as reasoning-based optimizers for scientific discovery and battery parameter estimation.

Jiawei Chen, Xiaofan Gui, Shikai Fang +4

Peking University Beijing, China · Microsoft Research Beijing, China · Chalmers University of Technology Gothenburg, Sweden

AI Agents for Scientific Discovery Large Language Model-Guided Optimization Inverse Problems

May 28, 2026cs.AI

DeepSurvey: Agent-Oriented Automated Survey Generation with Analytical Depth and Citation Reliability

As scientific literature grows rapidly and research increasingly involves AI agents, automated survey generation has become a key capability for both agents and human researchers. For such agents, a survey serves as a primary knowledge source of a field prior to research. Since pretrained models already encode broad knowledge of established work, these consumers benefit more from analytical depth than from breadth alone; moreover, unsupported claims, once ingested as knowledge, can propagate into downstream research. However, existing systems tend to overemphasize coverage and presentation; they suffer from limited analytical depth due to reliance on abstracts and isolated paper processing, and from unreliable citations due to imprecise retrieval and post-hoc grounding. We present DeepSurvey, an agentic generation system that addresses both limitations. To enhance depth, DeepSurvey extracts structured keynotes, models cross-paper relationships through clustering and comparative analysis, and integrates a code-agent subsystem to recover implementation-level details. To fortify reliability, it combines citation-graph expansion with hybrid filtering for topic-focused retrieval, enforces evidence-constrained analysis and writing, and deploys multi-granularity agentic refinement to validate citation--claim alignment. Experiments show that DeepSurvey achieves the highest content score (8.34/10) and citation quality (recall and precision gains of 25.3% and 35.2% over the strongest baseline), generalizes more robustly across domains, and is preferred by domain experts over human-written surveys (83.3% in overall quality, 100% in content depth). Moreover, when a coding agent uses a survey as its only literature source, the agent equipped with DeepSurvey achieves the best performance among human-written and baseline-generated surveys.

Ziyue Yang, Da Ma, Hanqi Li +8

X-LANCE Lab, School of Computer Science, Shanghai Jiao Tong University, Shanghai, China · Suzhou Laboratory, Suzhou, China · Shanghai Innovation Institution, Shanghai, China +1

AI for Science AI Agents for Scientific Discovery Citation Verification Evidence-Grounded Generation

May 27, 2026astro-ph.IM

First head-to-head comparison of agentic AI applied to the analysis of simulated data of the Einstein Telescope

We report a comparison of two state-of-the-art agentic AI systems, Claude Code (Anthropic) and Codex (OpenAI), tasked with autonomously executing a simple end-to-end gravitational wave data analysis pipeline on a shared computing infrastructure without human intervention. The pipeline comprises power spectral density estimation from raw Einstein Telescope simulated noise, geometric template bank generation, matched filter recovery of 100 binary black hole signal injections, automated results generation, and large language model-assisted production of a manuscript formatted in the style of Physical Review D. Both agents received identical written specifications and identical compute resources. The experiment was run twice: a first run with unrealistically loud injections, and a second run with signals rescaled to a physically motivated SNR range. The scientific results converged in both runs. However, the agents exhibited substantially different behaviors and computational costs: Claude Code completed the pipeline in ~3.4 minutes with silent deviations from the specification, while Codex required ~16 minutes across explicit self-correcting restarts, including an unsolicited performance optimization of the matched filter inner loop. The autonomously generated manuscripts also diverged in length, details, and quality. In the second run, a subtle difference in the interpretation of the SNR range instruction led to a genuine scientific divergence: Claude Code silently reinterpreted the instructions, while Codex followed the specification literally. We discuss the implications of these behavioral differences, such as speed versus auditability, silent versus transparent error handling, instruction interpretation, and the criticality of intermediate data representations in multi-model pipelines, for the deployment of agentic AI in scientific computing workflows.

Gianluca Inguglia

Marietta Blau Institute for Particle Physics, Austrian Academy of Sciences, 1010 Vienna, Austria

AI Agents for Scientific Discovery AI Agent Evaluation Agentic Workflows LLM Agent Reliability

May 27, 2026cs.CE

Closed-Loop Molecular Design with Calibrated Deference

We present Cognitive Loop via In-Situ Optimization (CLIO), an agent that couples a continuously-updated belief-state graph with a recursive plan-then-act loop. The result is a reasoning agent that can contribute something qualitatively different, which we term \emph{calibrated deference}: the capacity to recognize when its own tools or assumptions are failing, to adapt its strategy in response, and to generate mechanistic hypotheses that guide experimental revision. We tested CLIO in a closed-loop human-AI campaign to design an aqueous organic redox flow battery (AORFB) negolyte, with CLIO leading proposal and interpretation in close partnership with chemists who synthesized, characterized, and weighed in on design choices. Across 17 candidates over three rounds, CLIO converged on a top phosphonate candidate; characterization confirmed a 130mV improvement in redox potential over the literature baseline. Characterization then revealed unexpectedly poor electrochemical reversibility -- a regression no property predictor had flagged. CLIO generated competing mechanistic hypotheses, prioritized discriminating diagnostics, traced the failure to phosphonate-potassium ion pairing, and prescribed a sulfonate replacement. The resulting compound showed substantially improved electrochemical reversibility and maintained a 90mV improvement in redox potential, closing the design-make-test-redesign loop.

Newman Cheng, Gordon Broadbent, Jason Dong +11

Microsoft Discovery & Quantum, Redmond, WA, USA. · Department of Chemical and Environmental Engineering, Yale University, New Haven, CT, USA. · CanAm Bioresearch Inc., Winnipeg, MB, Canada. +1

Molecular Optimization AI Agents for Scientific Discovery Human-in-the-Loop AI

May 27, 2026cs.LG

AtomComposer: Discovering Chemical Space from First Principles with Reinforcement Learning

Discovering novel stable molecules without training data remains a grand scientific challenge. Current molecular generative models are trained on large, pre-curated datasets, which introduce biases and limit exploration of novel chemistry. In contrast, we propose a new paradigm: autonomous, generalized agents capable of mapping vast, unknown chemical spaces without any pretraining. For the first time, we present AtomComposer, a self-guided agent that autonomously constructs valid 3D isomers under stoichiometric constraints and is trained exclusively online using reinforcement learning. Unlike existing approaches that generally overfit to a specific chemical formula, we establish a multi-composition training scheme that enables a broad generalization across diverse chemistry, guided by energy- and validity-based rewards. Our agent can discover up to an order of magnitude more valid isomers on unseen test formulas than existing single-composition reinforcement-learning baselines trained with per-step energy rewards. These results fulfill the promise of online reinforcement learning as a powerful paradigm for scalable, from-scratch exploration of chemical configuration space.

Bjarke Hastrup, Francois Cornet, Tejs Vegge +1

Dept. of Energy Conversion and Storage, Technical University of Denmark, Denmark · Dept. of Applied Mathematics and Computer Science, Technical University of Denmark, Denmark · Pioneer Center for Accelerating P2X Materials Discovery (CAPeX), Kgs. Lyngby, Denmark

AI Agents for Scientific Discovery 3D Molecular Generation Molecular Generation RL for Generative Models

May 27, 2026cs.CL

AI Research Agents Narrow Scientific Exploration

AI research agents now support large-scale AI-assisted scientific discovery. We examine whether AI-generated ideas broaden scientific exploration or primarily reinforce existing work. Using five agent frameworks and five large language models, we generate 219,655 ideas for different scientific fields. Across experiments, four consistent patterns emerge. First, AI-generated ideas are more concentrated than human-authored papers within the same research area. Second, they remain much closer to starting literature than later human follow-on work does. Third, AI-generated ideas align less with future human research. Last, AI-generated ideas are located in lower-impact regions of the historical scientific landscape. Overall, current AI research agents appear better suited to local elaboration than to broadening scientific exploration.

Yixuan Tang, Yi Yang

1*ISOM, The Hong Kong University of Science and Technology.

AI Agents for Scientific Discovery AI Agent Evaluation Scientific Hypothesis Generation Research Idea Generation

May 27, 2026cs.AI

AIBuildAI-2: A Knowledge-Enhanced Agent for Automatically Building AI Models

AI models underpin data-centric applications from image and text processing to scientific discovery in biology, physics, and chemistry. Yet developing them remains heavily manual, requiring practitioners to design architectures, build training pipelines, and iteratively refine solutions, making it challenging for natural scientists without specialized AI engineering expertise to build the high-performing models their research demands. To reduce this burden and broaden access to AI for scientific discovery, agents that automatically build AI models have been proposed. However, the performance of these agents is largely limited by the parametric knowledge of their underlying large language models, which is static, often outdated, and sparse on practical AI model engineering know-how. To address this limitation, we introduce AIBuildAI-2, a knowledge-enhanced agent with an external, evolving knowledge system for automatically building AI models. The knowledge system of AIBuildAI-2 is hierarchical, organizing curated AI development knowledge into high-level knowledge instructions over topical categories and low-level knowledge documents under each category, from which the agent dynamically loads only the context relevant to its current state and the AI task being solved, grounding each design and implementation decision in concrete, externally verifiable expertise. The system is initialized by collecting and cleaning AI-development-related documents from the web and organizing them into the corresponding categories, and continually evolves from the agent's own experience by distilling each completed run on an AI task into structured takeaways that are written back into the knowledge system. AIBuildAI-2 achieves state-of-the-art results, ranking first on MLE-Bench with a 70.7% medal rate and placing in the top 6.6% among 4,370 human-expert teams in a heart disease prediction competition.

Ruiyi Zhang, Peijia Qin, Qi Cao +2

Department of Electrical and Computer Engineering, University of California San Diego, La Jolla, CA 92093, USA · Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA

Continual Learning for LLM Agents AI Agents for Scientific Discovery Knowledge Augmentation for Language Models Automated Machine Learning

May 26, 2026cs.AI

PolyFusionAgent: A Multimodal Foundation Model and Autonomous AI Assistant for Polymer Property Prediction and Inverse Design

Polymer discovery is central to fields ranging from energy storage to biomedicine, but it is hindered by an astronomically large chemical design space and fragmented representations of structure, properties, and prior knowledge. This fragmentation leaves many AI models disconnected from physical and experimental reality, restricting their ability to support directly actionable design decisions. Here we introduce PolyFusionAgent, an interactive framework coupling a multimodal polymer foundation model (PolyFusion) with a tool-augmented, literature-grounded design agent (PolyAgent). PolyFusion aligns complementary polymer views including sequence, topology, 3D geometry, and fingerprints across millions of polymers to learn a shared latent space transferable across chemistries and data regimes, improving thermophysical property prediction and enabling property-conditioned generation of chemically valid, structurally novel polymers beyond the reference design space. PolyAgent closes the design loop by linking prediction and inverse design with evidence retrieval from the polymer literature, proposing, evaluating, and contextualizing hypotheses with explicit precedent in one workflow. Together, PolyFusionAgent enables interactive, evidence-linked polymer discovery combining large-scale representation learning, multimodal chemical knowledge, and verifiable scientific reasoning.

Manpreet Kaur, Xingying Zhang, Qian Liu

Department of Applied Computer Science, The University of Winnipeg, 515 Portage Avenue, Winnipeg, MB R3B 2E9, Canada. · Department of Mechanical Engineering, University of Manitoba, Winnipeg, MB R3T 2N2, Canada.

AI Agents for Scientific Discovery Materials Property Prediction Multimodal Embedding Multimodal Fusion Inverse Design