Daily Papers

Mutation-based fuzzing is effective for uncovering compiler bugs, but designing high-quality mutators for modern languages with complex constructs (e.g., templates, macros) remains challenging. Existing methods rely heavily on manual design or human-in-the-loop correction, limiting scalability and cross-language generalizability. We present Mut4All, a fully automated, language-agnostic framework that synthesizes mutators using Large Language Models (LLMs) and compiler-specific knowledge from bug reports. It consists of three agents: (1) a mutator invention agent that identifies mutation targets and generates mutator metadata using compiler-related insights; (2) a mutator implementation synthesis agent, fine-tuned to produce initial implementations; and (3) a mutator refinement agent that verifies and corrects the mutators via unit-test feedback. Mut4All processes 1000 bug reports (500 Rust, 500 C++), yielding 319 Rust and 403 C++ mutators at ~$0.08 each via GPT-4o. Our customized fuzzer, using these mutators, finds 62 bugs in Rust compilers (38 new, 7 fixed) and 34 bugs in C++ compilers (16 new, 1 fixed). Mut4All outperforms existing methods in both unique crash detection and coverage, ranking first on Rust and second on C++.

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

We introduce GenAgent, unifying visual understanding and generation through an agentic multimodal model. Unlike unified models that face expensive training costs and understanding-generation trade-offs, GenAgent decouples these capabilities through an agentic framework: understanding is handled by the multimodal model itself, while generation is achieved by treating image generation models as invokable tools. Crucially, unlike existing modular systems constrained by static pipelines, this design enables autonomous multi-turn interactions where the agent generates multimodal chains-of-thought encompassing reasoning, tool invocation, judgment, and reflection to iteratively refine outputs. We employ a two-stage training strategy: first, cold-start with supervised fine-tuning on high-quality tool invocation and reflection data to bootstrap agent behaviors; second, end-to-end agentic reinforcement learning combining pointwise rewards (final image quality) and pairwise rewards (reflection accuracy), with trajectory resampling for enhanced multi-turn exploration. GenAgent significantly boosts base generator(FLUX.1-dev) performance on GenEval++ (+23.6\%) and WISE (+14\%). Beyond performance gains, our framework demonstrates three key properties: 1) cross-tool generalization to generators with varying capabilities, 2) test-time scaling with consistent improvements across interaction rounds, and 3) task-adaptive reasoning that automatically adjusts to different tasks. Our code will be available at https://github.com/deep-kaixun/GenAgent{this url}.

Current AI agent frameworks commit early to a single interaction protocol, a fixed tool integration strategy, and static user models, limiting their deployment across diverse interaction paradigms. To address these constraints, we introduce STEM Agent (Self-adapting, Tool-enabled, Extensible, Multi-agent), a modular architecture inspired by biological pluripotency in which an undifferentiated agent core differentiates into specialized protocol handlers, tool bindings, and memory subsystems that compose into a fully functioning AI system. The framework unifies five interoperability protocols (A2A, AG-UI, A2UI, UCP, and AP2) behind a single gateway, introduces a Caller Profiler that continuously learns user preferences across more than twenty behavioral dimensions, externalizes all domain capabilities through the Model Context Protocol (MCP), and implements a biologically inspired skills acquisition system in which recurring interaction patterns crystallize into reusable agent skills through a maturation lifecycle analogous to cell differentiation. Complementing these capabilities, the memory system incorporates consolidation mechanisms, including episodic pruning, semantic deduplication, and pattern extraction, designed for sub-linear growth under sustained interaction. A comprehensive 413-test suite validates protocol handler behavior and component integration across all five architectural layers, completing in under three seconds.

Recent advances in AI and ML have transformed data science, yet increasing complexity and expertise requirements continue to hinder progress. Although crowd-sourcing platforms alleviate some challenges, high-level machine learning engineering (MLE) tasks remain labor-intensive and iterative. We introduce R&D-Agent, a comprehensive, decoupled, and extensible framework that formalizes the MLE process. R&D-Agent defines the MLE workflow into two phases and six components, turning agent design for MLE from ad-hoc craftsmanship into a principled, testable process. Although several existing agents report promising gains on their chosen components, they can mostly be summarized as a partial optimization from our framework's simple baseline. Inspired by human experts, we designed efficient and effective agents within this framework that achieve state-of-the-art performance. Evaluated on MLE-Bench, the agent built on R&D-Agent ranks as the top-performing machine learning engineering agent, achieving 35.1% any medal rate, demonstrating the ability of the framework to speed up innovation and improve accuracy across a wide range of data science applications. We have open-sourced R&D-Agent on GitHub: https://github.com/microsoft/RD-Agent.

The increasing adoption of Large Language Models (LLMs) has enabled AI scientists to perform complex end-to-end scientific discovery tasks requiring coordination of specialized roles, including idea generation and experimental execution. However, most state-of-the-art AI scientist systems rely on static, hand-designed pipelines and fail to adapt based on accumulated interaction histories. As a result, these systems overlook promising research directions, repeat failed experiments, and pursue infeasible ideas. To address this, we introduce EvoScientist, an evolving multi-agent AI scientist framework that continuously improves research strategies through persistent memory and self-evolution. EvoScientist comprises three specialized agents: a Researcher Agent (RA) for scientific idea generation, an Engineer Agent (EA) for experiment implementation and execution, and an Evolution Manager Agent (EMA) that distills insights from prior interactions into reusable knowledge. EvoScientist contains two persistent memory modules: (i) an ideation memory, which summarizes feasible research directions from top-ranked ideas while recording previously unsuccessful directions; and (ii) an experimentation memory, which captures effective data processing and model training strategies derived from code search trajectories and best-performing implementations. These modules enable the RA and EA to retrieve relevant prior strategies, improving idea quality and code execution success rates over time. Experiments show that EvoScientist outperforms 7 open-source and commercial state-of-the-art systems in scientific idea generation, achieving higher novelty, feasibility, relevance, and clarity via automatic and human evaluation. EvoScientist also substantially improves code execution success rates through multi-agent evolution, demonstrating persistent memory's effectiveness for end-to-end scientific discovery.

Multi-agent systems have emerged as a powerful paradigm for automating scientific discovery. To differentiate agent behavior in the multi-agent system, current frameworks typically assign generic role-based personas such as ''reviewer'' or ''writer'' or rely on coarse grained keyword-based personas. While functional, this approach oversimplifies how human scientists operate, whose contributions are shaped by their unique research trajectories. In response, we propose INDIBATOR, a framework for molecular discovery that grounds agents in individualized scientist profiles constructed from two modalities: publication history for literature-derived knowledge and molecular history for structural priors. These agents engage in multi-turn debate through proposal, critique, and voting phases. Our evaluation demonstrates that these fine-grained individuality-grounded agents consistently outperform systems relying on coarse-grained personas, achieving competitive or state-of-the-art performance. These results validate that capturing the ``scientific DNA'' of individual agents is essential for high-quality discovery.

Despite rapid progress in LLM agents, performance on long-horizon, tool-using tasks remains fragile. To better understand this fragility, we ask a simple question: do all actions contribute equally to failure? Analyzing execution traces on τ-Bench (Airline/Retail) and SWE-Bench Verified, we decompose trajectories into mutating (environment-changing) vs.\ non-mutating steps and formalize decisive deviations, earliest action, level divergences that flip success to failure. A logistic regression reveals that each additional deviation in a mutating action reduces the odds of success by upto 92% on Airline and upto 96% on Retail for SoTA models. In contrast, deviations in non-mutating actions have little to no effect. Errors also grow with context length as agents drift from role and act on stale constraints. Motivated by these observations, we introduce , a model-agnostic, gradient-free, test-time safeguard that (i) adds mutation-gated verification, (ii) injects Targeted Reflection before mutating steps, and (iii) performs block-based context cleaning. delivers consistent gains, e.g., Qwen3-Thinking: +28\% relative on Airline, +11\% on Retail, and +7\% on SWE-Bench Verified; Claude: +9\%/+7\%. We further identify ceiling effects in τ-Bench, where annotation errors and underspecified tasks artificially cap model performance. To address this, we release τ-Bench Verified, which restores benchmark headroom through targeted revisions. Our results argue for action-level analysis, targeted safeguards, and reliable evaluations as prerequisites for robust multi-turn agents.

Language models are revolutionizing the biochemistry domain, assisting scientists in drug design and chemical synthesis with high efficiency. Yet current approaches struggle between small language models prone to hallucination and limited knowledge retention, and large cloud-based language models plagued by privacy risks and high inference costs. To bridge this gap, we introduce ChemCRAFT, a novel framework leveraging agentic reinforcement learning to decouple chemical reasoning from knowledge storage. Instead of forcing the model to memorize vast chemical data, our approach empowers the language model to interact with a sandbox for precise information retrieval. This externalization of knowledge allows a locally deployable small model to achieve superior performance with minimal inference costs. To enable small language models for agent-calling ability, we build an agentic trajectory construction pipeline and a comprehensive chemical-agent sandbox. Based on sandbox interactions, we constructed ChemToolDataset, the first large-scale chemical tool trajectory dataset. Simultaneously, we propose SMILES-GRPO to build a dense chemical reward function, promoting the model's ability to call chemical agents. Evaluations across diverse aspects of drug design show that ChemCRAFT outperforms current cloud-based LLMs in molecular structure analysis, molecular optimization, and synthesis pathway prediction, demonstrating that scientific reasoning is not solely an emergent ability of model scale, but a learnable policy of tool orchestration. This work establishes a cost-effective and privacy-preserving paradigm for AI-aided chemistry, opening new avenues for accelerating molecular discovery with locally deployable agents. Code available at https://github.com/HowardLi1984/ChemCraft.

Automated drug discovery offers significant potential for accelerating the development of novel therapeutics by substituting labor-intensive human workflows with machine-driven processes. However, molecules generated by artificial intelligence may unintentionally infringe on existing patents, posing legal and financial risks that impede the full automation of drug discovery pipelines. This paper introduces PatentFinder, a novel multi-agent and tool-enhanced intelligence system that can accurately and comprehensively evaluate small molecules for patent infringement. PatentFinder features five specialized agents that collaboratively analyze patent claims and molecular structures with heuristic and model-based tools, generating interpretable infringement reports. To support systematic evaluation, we curate MolPatent-240, a benchmark dataset tailored for patent infringement assessment algorithms. On this benchmark, PatentFinder outperforms baseline methods that rely solely on large language models or specialized chemical tools, achieving a 13.8% improvement in F1-score and a 12% increase in accuracy. Additionally, PatentFinder autonomously generates detailed and interpretable patent infringement reports, showcasing enhanced accuracy and improved interpretability. The high accuracy and interpretability of PatentFinder make it a valuable and reliable tool for automating patent infringement assessments, offering a practical solution for integrating patent protection analysis into the drug discovery pipeline.

Recommendation algorithm iteration is moving from an artisanal, engineer-bound process toward an industrialized research loop, but this transition remains blocked by a structural execution bottleneck: the idea-to-launch cycle still depends on human engineers to generate hypotheses, modify production code, launch A/B experiments, and attribute online results. Innovation therefore scales linearly with headcount rather than compounding with evidence, compute, and accumulated experimental knowledge. We present AgentX, a production-deployed multi-agent system that fundamentally restructures this production function. AgentX operates as a self-evolving development engine: it autonomously generates, implements, evaluates, and learns from recommendation experiments at a scale and pace that no manual workflow can sustain. The system orchestrates four tightly coupled stages in a closed loop. A Brainstorm Agent synthesizes evidence from historical experiments, system architecture, data analysis, and external research into ranked, executable proposals. A Developing Agent translates each proposal into production-ready code through repository-grounded generation and multi-dimensional reliability verification. An Evaluation Agent conducts safe online rollout with guardrail-vetoed A/B judgment, converting both successes and failures into structured knowledge assets. A Harness Evolution layer (SGPO) then distills execution trajectories into semantic-gradient updates that continuously sharpen the agents themselves -- making the system not merely automated, but self-improving.

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

Precision therapeutics require multimodal adaptive models that generate personalized treatment recommendations. We introduce TxAgent, an AI agent that leverages multi-step reasoning and real-time biomedical knowledge retrieval across a toolbox of 211 tools to analyze drug interactions, contraindications, and patient-specific treatment strategies. TxAgent evaluates how drugs interact at molecular, pharmacokinetic, and clinical levels, identifies contraindications based on patient comorbidities and concurrent medications, and tailors treatment strategies to individual patient characteristics. It retrieves and synthesizes evidence from multiple biomedical sources, assesses interactions between drugs and patient conditions, and refines treatment recommendations through iterative reasoning. It selects tools based on task objectives and executes structured function calls to solve therapeutic tasks that require clinical reasoning and cross-source validation. The ToolUniverse consolidates 211 tools from trusted sources, including all US FDA-approved drugs since 1939 and validated clinical insights from Open Targets. TxAgent outperforms leading LLMs, tool-use models, and reasoning agents across five new benchmarks: DrugPC, BrandPC, GenericPC, TreatmentPC, and DescriptionPC, covering 3,168 drug reasoning tasks and 456 personalized treatment scenarios. It achieves 92.1% accuracy in open-ended drug reasoning tasks, surpassing GPT-4o and outperforming DeepSeek-R1 (671B) in structured multi-step reasoning. TxAgent generalizes across drug name variants and descriptions. By integrating multi-step inference, real-time knowledge grounding, and tool-assisted decision-making, TxAgent ensures that treatment recommendations align with established clinical guidelines and real-world evidence, reducing the risk of adverse events and improving therapeutic decision-making.

Self-improving coding agents that iteratively rewrite their own source code have demonstrated impressive performance on coding tasks. However, existing solutions generally derive self-modification from a single failure trajectory at a time, overlooking rich comparative signals available in the agent's expanding archive of past attempts. According to Mendelian principles of controlled inheritance, we introduce Mendel Gödel Machine (MGM). In addition to the general single-trajectory clonal mutation, MGM includes two new types of self-modification that better utilizes evidences accumulated: the reaction-norm mutation edits an agent based on its trajectories on multiple tasks simultaneously, and the cross-lineage hybridization edits an agent using the trajectory of a reference agent from another lineage on the same task. Under an additive fitness landscape model, we prove theoretically and demonstrate via controlled surrogate simulation that the new strategies facilitate a faster and better convergence over single-trajectory baselines. Experiments on SWE-bench and Polyglot confirm MGM's consistent improvement in performance, efficiency, and generalizability.

Scientific research increasingly relies on specialized computational tools, yet effectively utilizing these tools demands substantial domain expertise. While Large Language Models (LLMs) show promise in tool automation, they struggle to seamlessly integrate and orchestrate multiple tools for complex scientific workflows. Here, we present SciToolAgent, an LLM-powered agent that automates hundreds of scientific tools across biology, chemistry, and materials science. At its core, SciToolAgent leverages a scientific tool knowledge graph that enables intelligent tool selection and execution through graph-based retrieval-augmented generation. The agent also incorporates a comprehensive safety-checking module to ensure responsible and ethical tool usage. Extensive evaluations on a curated benchmark demonstrate that SciToolAgent significantly outperforms existing approaches. Case studies in protein engineering, chemical reactivity prediction, chemical synthesis, and metal-organic framework screening further demonstrate SciToolAgent's capability to automate complex scientific workflows, making advanced research tools accessible to both experts and non-experts.

Augmented Language Models (ALMs) empower large language models with the ability to use tools, transforming them into intelligent agents for real-world interactions. However, most existing frameworks for ALMs, to varying degrees, are deficient in the following critical features: flexible customization, collaborative democratization, and holistic evaluation. We present gentopia, an ALM framework enabling flexible customization of agents through simple configurations, seamlessly integrating various language models, task formats, prompting modules, and plugins into a unified paradigm. Furthermore, we establish gentpool, a public platform enabling the registration and sharing of user-customized agents. Agents registered in gentpool are composable such that they can be assembled together for agent collaboration, advancing the democratization of artificial intelligence. To ensure high-quality agents, gentbench, an integral component of gentpool, is designed to thoroughly evaluate user-customized agents across diverse aspects such as safety, robustness, efficiency, etc. We release gentopia on Github and will continuously move forward.

Software testing is a critical, yet resource-intensive phase of the software development lifecycle. Over the years, various automated tools have been developed to aid in this process. Search-based approaches typically achieve high coverage but produce tests with low readability, whereas large language model (LLM)-based methods generate more human-readable tests but often suffer from low coverage and compilability. While the majority of research efforts have focused on improving test coverage and readability, little attention has been paid to enhancing the robustness of bug detection, particularly in exposing corner cases and vulnerable execution paths. To address this gap, we propose AdverTest, a novel adversarial framework for LLM-powered test case generation. AdverTest comprises two interacting agents: a test case generation agent (T) and a mutant generation agent (M). These agents engage in an adversarial loop, where M persistently creates new mutants "hacking" the blind spots of T's current test suite, while T iteratively refines its test cases to "kill" the challenging mutants produced by M. This interaction loop is guided by both coverage and mutation scores, enabling the system to co-evolve toward both high test coverage and bug detection capability. Experimental results in the Defects4J dataset show that our approach improves fault detection rates by 8.56% over the best existing LLM-based methods and by 63.30% over EvoSuite, while also improving line and branch coverage.

Artificial intelligence (AI) agents are emerging as transformative tools in drug discovery, with the ability to autonomously reason, act, and learn through complicated research workflows. Building on large language models (LLMs) coupled with perception, computation, action, and memory tools, these agentic AI systems could integrate diverse biomedical data, execute tasks, carry out experiments via robotic platforms, and iteratively refine hypotheses in closed loops. We provide a conceptual and technical overview of agentic AI architectures, ranging from ReAct and Reflection to Supervisor and Swarm systems, and illustrate their applications across key stages of drug discovery, including literature synthesis, toxicity prediction, automated protocol generation, small-molecule synthesis, drug repurposing, and end-to-end decision-making. To our knowledge, this represents the first comprehensive work to present real-world implementations and quantifiable impacts of agentic AI systems deployed in operational drug discovery settings. Early implementations demonstrate substantial gains in speed, reproducibility, and scalability, compressing workflows that once took months into hours while maintaining scientific traceability. We discuss the current challenges related to data heterogeneity, system reliability, privacy, and benchmarking, and outline future directions towards technology in support of science and translation.

Comprehending genomic information is essential for biomedical research, yet extracting data from complex distributed databases remains challenging. Large language models (LLMs) offer potential for genomic Question Answering (QA) but face limitations due to restricted access to domain-specific databases. GeneGPT is the current state-of-the-art system that enhances LLMs by utilizing specialized API calls, though it is constrained by rigid API dependencies and limited adaptability. We replicate GeneGPT and propose GenomAgent, a multi-agent framework that efficiently coordinates specialized agents for complex genomics queries. Evaluated on nine tasks from the GeneTuring benchmark, GenomAgent outperforms GeneGPT by 12% on average, and its flexible architecture extends beyond genomics to various scientific domains needing expert knowledge extraction.

The convergence of large language models and agents is catalyzing a new era of scientific discovery: Agentic Science. While the scientific method is inherently iterative, existing agent frameworks are predominantly static, narrowly scoped, and lack the capacity to learn from trial and error. To bridge this gap, we present EvoMaster, a foundational evolving agent framework engineered specifically for Agentic Science at Scale. Driven by the core principle of continuous self-evolution, EvoMaster empowers agents to iteratively refine hypotheses, self-critique, and progressively accumulate knowledge across experimental cycles, faithfully mirroring human scientific inquiry. Crucially, as a domain-agnostic base harness, EvoMaster is exceptionally easy to scale up -- enabling developers to build and deploy highly capable, self-evolving scientific agents for arbitrary disciplines in approximately 100 lines of code. Built upon EvoMaster, we incubated the SciMaster ecosystem across domains such as machine learning, physics, and general science. Evaluations on four authoritative benchmarks (Humanity's Last Exam, MLE-Bench Lite, BrowseComp, and FrontierScience) demonstrate that EvoMaster achieves state-of-the-art scores of 41.1%, 75.8%, 73.3%, and 53.3%, respectively. It comprehensively outperforms the general-purpose baseline OpenClaw with relative improvements ranging from +159% to +316%, robustly validating its efficacy and generality as the premier foundational framework for the next generation of autonomous scientific discovery. EvoMaster is available at https://github.com/sjtu-sai-agents/EvoMaster.

AI agents are increasingly being developed to accelerate scientific discovery, yet their practical capabilities in real research settings remain poorly understood. Existing benchmarks for AI agents rarely capture the complexity, heterogeneity, and extended reasoning required by scientific work, whereas benchmarks for scientific tasks often reduce research to static, direct problems and provide limited support for interactive evaluation. Here, we introduce SciAgentArena, a systematic benchmark for evaluating AI agents in real-world scientific research scenarios drawn from emerging needs across multiple domains. SciAgentArena comprises approximately 200 tasks with stepwise verification and an interactive, agent-agnostic environment for assessing diverse AI agents. Using this benchmark, we find that current agents can contribute effectively to well-specified data-analysis workflows, particularly when the task structure and evaluation criteria are clear. However, their performance remains uneven across scientific contexts: agents struggle to generate genuinely novel insights, sustain self-directed exploration, and formulate robust solutions for open-ended research questions. We further characterize common failure modes across agents and identify opportunities for improving their reliability, autonomy, and scientific reasoning. Together, SciAgentArena provides a practical framework for measuring progress in AI agents for science and for guiding the design of future agents capable of addressing complex scientific challenges. Full codes, tasks, and datasets can be accessed via this link: https://sciagentarena.github.io/.

Autonomous agentic systems are largely static after deployment: they do not learn from user interactions, and recurring failures persist until the next human-driven update ships a fix. Self-evolving agents have emerged in response, but all confine evolution to text-mutable artifacts -- skill files, prompt configurations, memory schemas, workflow graphs -- and leave the agent harness untouched. Since routing, hook ordering, state invariants, and dispatch live in code rather than in any text artifact, an entire class of structural failure is physically unreachable from the text layer. We argue that source-level adaptation is a fundamentally more general medium: it is Turing-complete, a strict superset of every text-mutable scope, takes effect deterministically rather than through base-model compliance, and does not erode under long-context drift. We present MOSS, a system that performs self-rewriting at the source level on production agentic substrates. Each evolution is anchored to an automatically curated batch of production-failure evidence and proceeds through a deterministic multi-stage pipeline; code modification is delegated to a pluggable external coding-agent CLI while MOSS retains stage ordering and verdicts. Candidates are verified by replaying the batch against the candidate image in ephemeral trial workers, then promoted via user-consent-gated, in-place container swap with health-probe-gated rollback. On OpenClaw, MOSS lifts a four-task mean grader score from 0.25 to 0.61 in a single cycle without human intervention.

AI agents hold the potential to revolutionize scientific productivity by automating literature reviews, replicating experiments, analyzing data, and even proposing new directions of inquiry; indeed, there are now many such agents, ranging from general-purpose "deep research" systems to specialized science-specific agents, such as AI Scientist and AIGS. Rigorous evaluation of these agents is critical for progress. Yet existing benchmarks fall short on several fronts: they (1) fail to provide holistic, product-informed measures of real-world use cases such as science research; (2) lack reproducible agent tools necessary for a controlled comparison of core agentic capabilities; (3) do not account for confounding variables such as model cost and tool access; (4) do not provide standardized interfaces for quick agent prototyping and evaluation; and (5) lack comprehensive baseline agents necessary to identify true advances. In response, we define principles and tooling for more rigorously benchmarking agents. Using these, we present AstaBench, a suite that provides the first holistic measure of agentic ability to perform scientific research, comprising 2400+ problems spanning the entire scientific discovery process and multiple scientific domains, and including many problems inspired by actual user requests to deployed Asta agents. Our suite comes with the first scientific research environment with production-grade search tools that enable controlled, reproducible evaluation, better accounting for confounders. Alongside, we provide a comprehensive suite of nine science-optimized classes of Asta agents and numerous baselines. Our extensive evaluation of 57 agents across 22 agent classes reveals several interesting findings, most importantly that despite meaningful progress on certain individual aspects, AI remains far from solving the challenge of science research assistance.

We present ScienceClaw + Infinite, a framework for autonomous scientific investigation in which independent agents conduct research without central coordination, and any contributor can deploy new agents into a shared ecosystem. The system is built around three components: an extensible registry of over 300 interoperable scientific skills, an artifact layer that preserves full computational lineage as a directed acyclic graph (DAG), and a structured platform for agent-based scientific discourse with provenance-aware governance. Agents select and chain tools based on their scientific profiles, produce immutable artifacts with typed metadata and parent lineage, and broadcast unsatisfied information needs to a shared global index. The ArtifactReactor enables plannerless coordination: peer agents discover and fulfill open needs through pressure-based scoring, while schema-overlap matching triggers multi-parent synthesis across independent analyses. An autonomous mutation layer actively prunes the expanding artifact DAG to resolve conflicting or redundant workflows, while persistent memory allows agents to continuously build upon complex epistemic states across multiple cycles. Infinite converts these outputs into auditable scientific records through structured posts, provenance views, and machine-readable discourse relations, with community feedback steering subsequent investigation cycles. Across four autonomous investigations, peptide design for the somatostatin receptor SSTR2, lightweight impact-resistant ceramic screening, cross-domain resonance bridging biology, materials, and music, and formal analogy construction between urban morphology and grain-boundary evolution, the framework demonstrates heterogeneous tool chaining, emergent convergence among independently operating agents, and traceable reasoning from raw computation to published finding.

Agents based on large language models have shown great potential in accelerating scientific discovery by leveraging their rich background knowledge and reasoning capabilities. In this paper, we introduce BioDiscoveryAgent, an agent that designs new experiments, reasons about their outcomes, and efficiently navigates the hypothesis space to reach desired solutions. We demonstrate our agent on the problem of designing genetic perturbation experiments, where the aim is to find a small subset out of many possible genes that, when perturbed, result in a specific phenotype (e.g., cell growth). Utilizing its biological knowledge, BioDiscoveryAgent can uniquely design new experiments without the need to train a machine learning model or explicitly design an acquisition function as in Bayesian optimization. Moreover, BioDiscoveryAgent, using Claude 3.5 Sonnet, achieves an average of 21% improvement in predicting relevant genetic perturbations across six datasets, and a 46% improvement in the harder task of non-essential gene perturbation, compared to existing Bayesian optimization baselines specifically trained for this task. Our evaluation includes one dataset that is unpublished, ensuring it is not part of the language model's training data. Additionally, BioDiscoveryAgent predicts gene combinations to perturb more than twice as accurately as a random baseline, a task so far not explored in the context of closed-loop experiment design. The agent also has access to tools for searching the biomedical literature, executing code to analyze biological datasets, and prompting another agent to critically evaluate its predictions. Overall, BioDiscoveryAgent is interpretable at every stage, representing an accessible new paradigm in the computational design of biological experiments with the potential to augment scientists' efficacy.

While Large Language Models (LLMs) like ChatGPT and GPT-4 have demonstrated exceptional proficiency in natural language processing, their efficacy in addressing complex, multifaceted tasks remains limited. A growing area of research focuses on LLM-based agents equipped with external tools capable of performing diverse tasks. However, existing LLM-based agents only support a limited set of tools which is unable to cover a diverse range of user queries, especially for those involving expertise domains. It remains a challenge for LLM-based agents to extend their tools autonomously when confronted with various user queries. As GitHub has hosted a multitude of repositories which can be seen as a good resource for tools, a promising solution is that LLM-based agents can autonomously integrate the repositories in GitHub according to the user queries to extend their tool set. In this paper, we introduce GitAgent, an agent capable of achieving the autonomous tool extension from GitHub. GitAgent follows a four-phase procedure to incorporate repositories and it can learn human experience by resorting to GitHub Issues/PRs to solve problems encountered during the procedure. Experimental evaluation involving 30 user queries demonstrates GitAgent's effectiveness, achieving a 69.4% success rate on average.

Large language models (LLMs) are catalyzing the development of autonomous AI research agents for scientific and engineering discovery. We present FM Agent, a novel and general-purpose multi-agent framework that leverages a synergistic combination of LLM-based reasoning and large-scale evolutionary search to address complex real-world challenges. The core of FM Agent integrates several key innovations: 1) a cold-start initialization phase incorporating expert guidance, 2) a novel evolutionary sampling strategy for iterative optimization, 3) domain-specific evaluators that combine correctness, effectiveness, and LLM-supervised feedback, and 4) a distributed, asynchronous execution infrastructure built on Ray. Demonstrating broad applicability, our system has been evaluated across diverse domains, including operations research, machine learning, GPU kernel optimization, and classical mathematical problems. FM Agent reaches state-of-the-art results autonomously, without human interpretation or tuning -- 1976.3 on ALE-Bench (+5.2\%), 43.56\% on MLE-Bench (+4.0pp), up to 20x speedups on KernelBench, and establishes new state-of-the-art(SOTA) results on several classical mathematical problems. Beyond academic benchmarks, FM Agent shows considerable promise for both large-scale enterprise R\&D workflows and fundamental scientific research, where it can accelerate innovation, automate complex discovery processes, and deliver substantial engineering and scientific advances with broader societal impact.

Molecular editing and optimization are multi-step problems that require iteratively improving properties while keeping molecules chemically valid and structurally similar. We frame both tasks as sequential, tool-guided decisions and introduce MolAct, an agentic reinforcement learning framework that employs a two-stage training paradigm: first building editing capability, then optimizing properties while reusing the learned editing behaviors. To the best of our knowledge, this is the first work to formalize molecular design as an Agentic Reinforcement Learning problem, where an LLM agent learns to interleave reasoning, tool-use, and molecular optimization. The framework enables agents to interact in multiple turns, invoking chemical tools for validity checking, property assessment, and similarity control, and leverages their feedback to refine subsequent edits. We instantiate the MolAct framework to train two model families: MolEditAgent for molecular editing tasks and MolOptAgent for molecular optimization tasks. In molecular editing, MolEditAgent-7B delivers 100, 95, and 98 valid add, delete, and substitute edits, outperforming strong closed "thinking" baselines such as DeepSeek-R1; MolEditAgent-3B approaches the performance of much larger open "thinking" models like Qwen3-32B-think. In molecular optimization, MolOptAgent-7B (trained on MolEditAgent-7B) surpasses the best closed "thinking" baseline (e.g., Claude 3.7) on LogP and remains competitive on solubility, while maintaining balanced performance across other objectives. These results highlight that treating molecular design as a multi-step, tool-augmented process is key to reliable and interpretable improvements.

Much previous AI research has focused on developing monolithic models to maximize their intelligence and capability, with the primary goal of enhancing performance on specific tasks. In contrast, this paper explores an alternative approach: collaborative AI systems that use workflows to integrate models, data sources, and pipelines to solve complex and diverse tasks. We introduce GenAgent, an LLM-based framework that automatically generates complex workflows, offering greater flexibility and scalability compared to monolithic models. The core innovation of GenAgent lies in representing workflows with code, alongside constructing workflows with collaborative agents in a step-by-step manner. We implement GenAgent on the ComfyUI platform and propose a new benchmark, OpenComfy. The results demonstrate that GenAgent outperforms baseline approaches in both run-level and task-level evaluations, showing its capability to generate complex workflows with superior effectiveness and stability.

Gene set knowledge discovery is essential for advancing human functional genomics. Recent studies have shown promising performance by harnessing the power of Large Language Models (LLMs) on this task. Nonetheless, their results are subject to several limitations common in LLMs such as hallucinations. In response, we present GeneAgent, a first-of-its-kind language agent featuring self-verification capability. It autonomously interacts with various biological databases and leverages relevant domain knowledge to improve accuracy and reduce hallucination occurrences. Benchmarking on 1,106 gene sets from different sources, GeneAgent consistently outperforms standard GPT-4 by a significant margin. Moreover, a detailed manual review confirms the effectiveness of the self-verification module in minimizing hallucinations and generating more reliable analytical narratives. To demonstrate its practical utility, we apply GeneAgent to seven novel gene sets derived from mouse B2905 melanoma cell lines, with expert evaluations showing that GeneAgent offers novel insights into gene functions and subsequently expedites knowledge discovery.

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

Traditional drug design faces significant challenges due to inherent chemical and biological complexities, often resulting in high failure rates in clinical trials. Deep learning advancements, particularly generative models, offer potential solutions to these challenges. One promising algorithm is DrugGPT, a transformer-based model, that generates small molecules for input protein sequences. Although promising, it generates both chemically valid and invalid structures and does not incorporate the features of approved drugs, resulting in time-consuming and inefficient drug discovery. To address these issues, we introduce DrugGen, an enhanced model based on the DrugGPT structure. DrugGen is fine-tuned on approved drug-target interactions and optimized with proximal policy optimization. By giving reward feedback from protein-ligand binding affinity prediction using pre-trained transformers (PLAPT) and a customized invalid structure assessor, DrugGen significantly improves performance. Evaluation across multiple targets demonstrated that DrugGen achieves 100% valid structure generation compared to 95.5% with DrugGPT and produced molecules with higher predicted binding affinities (7.22 [6.30-8.07]) compared to DrugGPT (5.81 [4.97-6.63]) while maintaining diversity and novelty. Docking simulations further validate its ability to generate molecules targeting binding sites effectively. For example, in the case of fatty acid-binding protein 5 (FABP5), DrugGen generated molecules with superior docking scores (FABP5/11, -9.537 and FABP5/5, -8.399) compared to the reference molecule (Palmitic acid, -6.177). Beyond lead compound generation, DrugGen also shows potential for drug repositioning and creating novel pharmacophores for existing targets. By producing high-quality small molecules, DrugGen provides a high-performance medium for advancing pharmaceutical research and drug discovery.

The application of Large Language Models (LLMs) in accelerating scientific discovery has garnered increasing attention, with a key focus on constructing research agents endowed with innovative capability, i.e., the ability to autonomously generate novel and significant research ideas. Existing approaches predominantly rely on sophisticated prompt engineering and lack a systematic training paradigm. To address this, we propose DeepInnovator, a training framework designed to trigger the innovative capability of LLMs. Our approach comprises two core components. (1) ``Standing on the shoulders of giants''. We construct an automated data extraction pipeline to extract and organize structured research knowledge from a vast corpus of unlabeled scientific literature. (2) ``Conjectures and refutations''. We introduce a ``Next Idea Prediction'' training paradigm, which models the generation of research ideas as an iterative process of continuously predicting, evaluating, and refining plausible and novel next idea. Both automatic and expert evaluations demonstrate that our DeepInnovator-14B significantly outperforms untrained baselines, achieving win rates of 80.53\%-93.81\%, and attains performance comparable to that of current leading LLMs. This work provides a scalable training pathway toward building research agents with genuine, originative innovative capability, and will open-source the dataset to foster community advancement. Source code and data are available at: https://github.com/HKUDS/DeepInnovator.

Large Language Models (LLMs) show promise in biomedicine but lack true causal understanding, relying instead on correlations. This paper envisions causal LLM agents that integrate multimodal data (text, images, genomics, etc.) and perform intervention-based reasoning to infer cause-and-effect. Addressing this requires overcoming key challenges: designing safe, controllable agentic frameworks; developing rigorous benchmarks for causal evaluation; integrating heterogeneous data sources; and synergistically combining LLMs with structured knowledge (KGs) and formal causal inference tools. Such agents could unlock transformative opportunities, including accelerating drug discovery through automated hypothesis generation and simulation, enabling personalized medicine through patient-specific causal models. This research agenda aims to foster interdisciplinary efforts, bridging causal concepts and foundation models to develop reliable AI partners for biomedical progress.

Scaffolding Large Language Models (LLMs) into multi-agent systems often improves performance on complex tasks, but the safety impact of such scaffolds has not been as thoroughly explored. In this paper, we introduce AGENTBREEDER a framework for multi-objective evolutionary search over scaffolds. Our REDAGENTBREEDER evolves scaffolds towards jailbreaking the base LLM while achieving high task success, while BLUEAGENTBREEDER instead aims to combine safety with task reward. We evaluate the systems discovered by the different instances of AGENTBREEDER and popular baselines using widely recognized reasoning, mathematics, and safety benchmarks. Our work highlights and mitigates the safety risks due to multi-agent scaffolding.

De novo drug design requires simultaneously generating novel molecules outside of training data and predicting their target properties, making it a hard task for generative models. To address this, we propose Joint Transformer that combines a Transformer decoder, Transformer encoder, and a predictor in a joint generative model with shared weights. We formulate a probabilistic black-box optimization algorithm that employs Joint Transformer to generate novel molecules with improved target properties and outperforms other SMILES-based optimization methods in de novo drug design.

Mathematical formulas are a fundamental and widely used component in various scientific fields, serving as a universal language for expressing complex concepts and relationships. While state-of-the-art transformer models excel in processing and understanding natural language, they encounter challenges with mathematical notation, which involves a complex structure and diverse representations. This study focuses on the development of specialized training datasets to enhance the encoding of mathematical content. We introduce Math Mutator (MAMUT), a framework capable of generating equivalent and falsified versions of a given mathematical formula in LaTeX notation, effectively capturing the mathematical variety in notation of the same concept. Based on MAMUT, we have generated four large mathematical datasets containing diverse notation, which can be used to train language models with enhanced mathematical embeddings.

Automated program repair (APR) has recently shifted toward large language models and agent-based systems, yet most systems rely on local snapshot context, overlooking repository history. Prior work shows that repository history helps repair single-line bugs, since the last commit touching the buggy line is often the bug-introducing one. In this paper, we investigate whether repository history can also improve agentic APR systems at scale, especially for complex multi-hunk bugs. We present HAFixAgent, a History-Aware Bug-Fixing Agent that injects blame-derived repository heuristics into its repair loop. A preliminary study of all 854 real-world bugs from Defects4J motivates our design, showing that bug-relevant history is both widely available and highly concentrated. Empirical comparison of HAFixAgent with two state-of-the-art baselines shows: (1) Effectiveness: HAFixAgent significantly improves over the agent-based baseline (by 212.3%) and the multi-hunk baseline (by 29.9%). (2) Efficiency: history does not significantly increase agent steps and keeps token costs comparable, with notably lower median costs for complex multi-file-multi-hunk bugs. (3) Practicality: combining different historical heuristics repairs more bugs, offering a clear cost-benefit trade-off. HAFixAgent offers a practical recipe for history-aware agentic APR: ground the agent in version control history, prioritize diff-based historical context, and integrate complementary heuristics when needed.

We propose CURE, a novel reinforcement learning framework with a dedicated reward design that co-evolves coding and unit test generation capabilities based on their interaction outcomes, without any ground-truth code as supervision. This approach enables flexible and scalable training and allows the unit tester to learn directly from the coder's mistakes. Our derived ReasonFlux-Coder-7B and 14B models improve code generation accuracy by 5.3% and Best-of-N accuracy by 9.0% after optimization on Qwen2.5-Instruct models, outperforming similarly sized Qwen-Coder, DeepSeek-Coder, and Seed-Coder. They naturally extend to downstream tasks such as test-time scaling and agentic coding-achieving a 8.1% improvement over the base model. For the long-CoT model, our ReasonFlux-Coder-4B consistently outperforms Qwen3-4B while achieving 64.8% inference efficiency in unit test generation. Notably, we also find that our model can serve as an effective reward model for reinforcement learning on base models. Project: https://github.com/Gen-Verse/CURE

Reproducing research results from papers and released code is central to scientific progress. Existing works have introduced benchmarks to evaluate whether LLM agents can assist with reproducibility, but they are difficult to scale due to their reliance on substantial manual effort for data curation and evaluation. We introduce ReproRepo, a scalable framework for reproducibility evaluation that leverages human-raised GitHub issues as naturally occurring supervision on realistic reproduction blockers. We instantiate ReproRepo on 1,149 recent machine learning papers from major conferences and evaluate four frontier model-agent configurations. Our results show that LLM agents, even without executing code, can identify many real-world reproducibility problems from paper-repository pairs: the best agent in our study, namely Codex with GPT-5.5, surfaces at least one semantically related human-reported blocker for ~90% of papers in the study. Further analysis shows that agents are particularly effective for surfacing visible failures and identifying the right semantic region, but may still be insufficient in exact localization. ReproRepo can serve as a reusable, scalable framework for future evaluations of LLM agents on real-world reproducibility auditing. Our code is released at https://github.com/LithiumDA/ReproRepo.

There has been unprecedented interest in developing agents that expand the boundary of scientific discovery, primarily by optimizing quantitative objective functions specified by scientists. However, for grand challenges in science, these objectives may only be imperfect proxies. We argue that automating objective function design is a central, yet unmet need for scientific discovery agents. In this work, we introduce the Scientific Autonomous Goal-evolving Agent (SAGA) to address this challenge. SAGA employs a bi-level architecture in which an outer loop of LLM agents analyzes optimization outcomes, proposes new objectives, and converts them into computable scoring functions, while an inner loop performs solution optimization under the current objectives. This bi-level design enables systematic exploration of the space of objectives and their trade-offs, rather than treating them as fixed inputs. We demonstrate the framework through a wide range of design applications, including antibiotics, nanobodies, functional DNA sequences, inorganic materials, and chemical processes. Notably, our experimental validation identifies a structurally novel hit with promising potency and safety profiles for E. coli in the antibiotic design task, and three de novo PD-L1 binders in the nanobody design task. These results suggest that automating objective formulation can substantially improve the effectiveness of scientific discovery agents.

Frontier scientific reasoning is rapidly emerging as a key foundation for advancing AI agents in automated scientific discovery. Deep research agents offer a promising approach to this challenge. These models develop robust problem-solving capabilities through post-training on information-seeking tasks, which are typically curated via knowledge graph construction or iterative web browsing. However, these strategies face inherent limitations in frontier science, where domain-specific knowledge is scattered across sparse and heterogeneous academic sources, and problem solving requires sophisticated computation and reasoning far beyond factual recall. To bridge this gap, we introduce SciResearcher, a fully automated agentic framework for frontier-science data construction. SciResearcher synthesizes diverse conceptual and computational tasks grounded in academic evidence, while eliciting information acquisition, tool-integrated reasoning, and long-horizon capabilities. Leveraging the curated data for supervised fine-tuning and agentic reinforcement learning, we develop SciResearcher-8B, an agent foundation model that achieves 19.46% on the HLE-Bio/Chem-Gold benchmark, establishing a new state of the art at its parameter scale and surpassing several larger proprietary agents. It further achieves 13-15% absolute gains on SuperGPQA-Hard-Biology and TRQA-Literature benchmarks. Overall, SciResearcher introduces a new paradigm for automated data construction for frontier scientific reasoning and offers a scalable path toward future scientific agents.

Scientific experimentation, a cornerstone of human progress, demands rigor in reliability, methodical control, and interpretability to yield meaningful results. Despite the growing capabilities of large language models (LLMs) in automating different aspects of the scientific process, automating rigorous experimentation remains a significant challenge. To address this gap, we propose Curie, an AI agent framework designed to embed rigor into the experimentation process through three key components: an intra-agent rigor module to enhance reliability, an inter-agent rigor module to maintain methodical control, and an experiment knowledge module to enhance interpretability. To evaluate Curie, we design a novel experimental benchmark composed of 46 questions across four computer science domains, derived from influential research papers, and widely adopted open-source projects. Compared to the strongest baseline tested, we achieve a 3.4times improvement in correctly answering experimental questions.Curie is open-sourced at https://github.com/Just-Curieous/Curie.

Large Language Models (LLMs) and multi-agent systems have shown impressive capabilities in natural language tasks but face challenges in clinical trial applications, primarily due to limited access to external knowledge. Recognizing the potential of advanced clinical trial tools that aggregate and predict based on the latest medical data, we propose an integrated solution to enhance their accessibility and utility. We introduce Clinical Agent System (ClinicalAgent), a clinical multi-agent system designed for clinical trial tasks, leveraging GPT-4, multi-agent architectures, LEAST-TO-MOST, and ReAct reasoning technology. This integration not only boosts LLM performance in clinical contexts but also introduces novel functionalities. The proposed method achieves competitive predictive performance in clinical trial outcome prediction (0.7908 PR-AUC), obtaining a 0.3326 improvement over the standard prompt Method. Publicly available code can be found at https://anonymous.4open.science/r/ClinicalAgent-6671.

Recent studies operationalize self-improvement through coding agents that edit their own codebases. They grow a tree of self-modifications through expansion strategies that favor higher software engineering benchmark performance, assuming that this implies more promising subsequent self-modifications. However, we identify a mismatch between the agent's self-improvement potential (metaproductivity) and its coding benchmark performance, namely the Metaproductivity-Performance Mismatch. Inspired by Huxley's concept of clade, we propose a metric (CMP) that aggregates the benchmark performances of the descendants of an agent as an indicator of its potential for self-improvement. We show that, in our self-improving coding agent development setting, access to the true CMP is sufficient to simulate how the G\"odel Machine would behave under certain assumptions. We introduce the Huxley-G\"odel Machine (HGM), which, by estimating CMP and using it as guidance, searches the tree of self-modifications. On SWE-bench Verified and Polyglot, HGM outperforms prior self-improving coding agent development methods while using less wall-clock time. Last but not least, HGM demonstrates strong transfer to other coding datasets and large language models. The agent optimized by HGM on SWE-bench Verified with GPT-5-mini and evaluated on SWE-bench Lite with GPT-5 achieves human-level performance, matching the best officially checked results of human-engineered coding agents. Our code is available at https://github.com/metauto-ai/HGM.

Scientific Research, vital for improving human life, is hindered by its inherent complexity, slow pace, and the need for specialized experts. To enhance its productivity, we propose a ResearchAgent, a large language model-powered research idea writing agent, which automatically generates problems, methods, and experiment designs while iteratively refining them based on scientific literature. Specifically, starting with a core paper as the primary focus to generate ideas, our ResearchAgent is augmented not only with relevant publications through connecting information over an academic graph but also entities retrieved from an entity-centric knowledge store based on their underlying concepts, mined and shared across numerous papers. In addition, mirroring the human approach to iteratively improving ideas with peer discussions, we leverage multiple ReviewingAgents that provide reviews and feedback iteratively. Further, they are instantiated with human preference-aligned large language models whose criteria for evaluation are derived from actual human judgments. We experimentally validate our ResearchAgent on scientific publications across multiple disciplines, showcasing its effectiveness in generating novel, clear, and valid research ideas based on human and model-based evaluation results.

AI agents are increasingly deployed in production, yet their security evaluations remain bottlenecked by manual red-teaming or static benchmarks that fail to model adaptive, multi-turn adversaries. We propose NAAMSE, an evolutionary framework that reframes agent security evaluation as a feedback-driven optimization problem. Our system employs a single autonomous agent that orchestrates a lifecycle of genetic prompt mutation, hierarchical corpus exploration, and asymmetric behavioral scoring. By using model responses as a fitness signal, the framework iteratively compounds effective attack strategies while simultaneously ensuring "benign-use correctness", preventing the degenerate security of blanket refusal. Our experiments on Gemini 2.5 Flash demonstrate that evolutionary mutation systematically amplifies vulnerabilities missed by one-shot methods, with controlled ablations revealing that the synergy between exploration and targeted mutation uncovers high-severity failure modes. We show that this adaptive approach provides a more realistic and scalable assessment of agent robustness in the face of evolving threats. The code for NAAMSE is open source and available at https://github.com/HASHIRU-AI/NAAMSE.

LLM-based agents have shown increasing potential in automating scientific discovery. Given an optimizable metric and an execution environment, they can propose, validate, and iterate scientific solutions, and have produced results that outperform human-designed approaches. As model capabilities continue to improve, we argue that the bottleneck for autonomous scientific discovery is shifting from prescribing agent workflows to designing agent environments: the resources, constraints, and interfaces that shape agent behavior. We frame this as environment engineering: building environments that amplify productive behaviors, such as open-ended exploration, systematic artifact management, and inter-agent collaboration, while suppressing harmful behaviors, such as reward hacking and high-friction human oversight. We present EurekAgent, an environment-engineered agent system for metric-driven autonomous scientific discovery. EurekAgent engineers the environment along four dimensions: permissions engineering for bounded agent execution and isolated evaluation; artifact engineering for filesystem and Git-based collaboration; budget engineering for budget-aware exploration; and human-in-the-loop engineering for easy human supervision and intervention. EurekAgent sets new state-of-the-art results on multiple mathematics, kernel engineering, and machine learning tasks, including new state-of-the-art 26-circle packing results discovered with less than $11 in total API cost. We open-source our code and results, and call for environment engineering as a core research direction for developing reliable autonomous research agents.

AI research agents offer the promise to accelerate scientific progress by automating the design, implementation, and training of machine learning models. However, the field is still in its infancy, and the key factors driving the success or failure of agent trajectories are not fully understood. We examine the role that ideation diversity plays in agent performance. First, we analyse agent trajectories on MLE-bench, a well-known benchmark to evaluate AI research agents, across different models and agent scaffolds. Our analysis reveals that different models and agent scaffolds yield varying degrees of ideation diversity, and that higher-performing agents tend to have increased ideation diversity. Further, we run a controlled experiment where we modify the degree of ideation diversity, demonstrating that higher ideation diversity results in stronger performance. Finally, we strengthen our results by examining additional evaluation metrics beyond the standard medal-based scoring of MLE-bench, showing that our findings still hold across other agent performance metrics.

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

Real-world AI software engineering demands coding agents that can reason over massive repositories, maintain durable memory across and within long sessions, and robustly coordinate complex toolchains at test time. Existing open-source coding agents provide transparency but frequently fall short when pushed to these industrial-scale workloads, while proprietary coding agents offer strong practical performance but limited extensibility, interpretability, and controllability. We present the Confucius Code Agent (CCA), an open-sourced AI software engineer that can operate at an industrial scale. CCA is built atop the Confucius SDK, an open-sourced agent development platform designed around three complementary perspectives: Agent Experience (AX), User Experience (UX), and Developer Experience (DX). The SDK introduces a unified orchestrator with hierarchical working memory for long-context reasoning, a persistent note-taking system for cross-session continual learning, and a modular extension module for robust tool use. Moreover, a meta-agent automates the synthesis, evaluation, and refinement of agent configurations through a build-test-improve loop, enabling rapid agent development on new tasks, environments, and tool stacks. Instantiated on Confucius SDK with these mechanisms, CCA delivers strong performance on real-world software engineering tasks. On SWE-Bench-Pro, CCA achieves a state-of-the-art Resolve@1 performance of 54.3%, substantially improving over prior coding agents. Together, the Confucius SDK and CCA provide a transparent, extensible, and reproducible foundation for AI agents, bridge gaps between research prototypes and production-grade systems, and support agent development and deployment at industrial scale.

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

Modern scientific research relies on large-scale data, complex workflows, and specialized tools, which existing LLMs and tool-based agents struggle to handle due to limitations in long-horizon planning, robust goal maintenance, and continual learning from execution. To address these issues, in this work, we propose S1-NexusAgent, a self-evolving agent framework designed for multidisciplinary scientific research. S1-NexusAgent adopts a hierarchical Plan-and-CodeAct execution paradigm, decoupling global scientific planning from subtask-level tool execution through a dual-loop architecture, thereby enabling stable modeling of complex research workflows. The system natively supports the Model Context Protocol (MCP), integrates up to thousands of cross-disciplinary scientific tools, and achieves efficient orchestration of heterogeneous research tools via intention-aware dynamic tool retrieval and hot-plug mechanisms. To address long-context and large-scale data challenges in scientific settings, S1-NexusAgent introduces object-reference-based sparse context management, which enables sub-task context isolation and intermediate result compression. Building on this, a Critic Agent automatically evaluates complete execution trajectories and distills high-quality research paths into reusable Scientific Skills, forming a closed loop for continuous self-evolution, which is valuable for sustainable and long-horizon scientific research. Experiments on authoritative scientific benchmarks involving long-horizon planning and complex specialized tool orchestration, including biomini-eval (biology), ChemBench (chemistry), and MatSciBench (material science), demonstrate that S1-NexusAgent achieves state-of-the-art performance, validating its effectiveness and generalization capability in complex scientific tasks.

LLMs and Agents have achieved impressive progress in code generation, mathematical reasoning, and scientific discovery. However, existing benchmarks primarily measure correctness, overlooking the diversity of methods behind solutions. True innovation depends not only on producing correct answers but also on the originality of the approach. We present InnoGym, the first benchmark and framework designed to systematically evaluate the innovation potential of AI agents. InnoGym introduces two complementary metrics: performance gain, which measures improvement over the best-known solutions, and novelty, which captures methodological differences from prior approaches. The benchmark includes 18 carefully curated tasks from real-world engineering and scientific domains, each standardized through resource filtering, evaluator validation, and solution collection. In addition, we provide iGym, a unified execution environment for reproducible and long-horizon evaluations. Extensive experiments show that while some agents produce novel approaches, their lack of robustness limits performance gains. These results highlight a key gap between creativity and effectiveness, underscoring the need for benchmarks that evaluate both.

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

As the capabilities of Large Language Models (LLMs) continue to advance, the field of patent processing has garnered increased attention within the natural language processing community. However, the majority of research has been concentrated on classification tasks, such as patent categorization and examination, or on short text generation tasks like patent summarization and patent quizzes. In this paper, we introduce a novel and practical task known as Draft2Patent, along with its corresponding D2P benchmark, which challenges LLMs to generate full-length patents averaging 17K tokens based on initial drafts. Patents present a significant challenge to LLMs due to their specialized nature, standardized terminology, and extensive length. We propose a multi-agent framework called AutoPatent which leverages the LLM-based planner agent, writer agents, and examiner agent with PGTree and RRAG to generate lengthy, intricate, and high-quality complete patent documents. The experimental results demonstrate that our AutoPatent framework significantly enhances the ability to generate comprehensive patents across various LLMs. Furthermore, we have discovered that patents generated solely with the AutoPatent framework based on the Qwen2.5-7B model outperform those produced by larger and more powerful LLMs, such as GPT-4o, Qwen2.5-72B, and LLAMA3.1-70B, in both objective metrics and human evaluations. We will make the data and code available upon acceptance at https://github.com/QiYao-Wang/AutoPatent.

REST APIs play important roles in enriching the action space of web agents, yet most API-based agents rely on curated and uniform toolsets that do not reflect the complexity of real-world APIs. Building tool-using agents for arbitrary domains remains a major challenge, as it requires reading unstructured API documentation, testing APIs and inferring correct parameters. We propose Doc2Agent, a scalable pipeline to build agents that can call Python-based tools generated from API documentation. Doc2Agent generates executable tools from API documentations and iteratively refines them using a code agent. We evaluate our approach on real-world APIs, WebArena APIs, and research APIs, producing validated tools. We achieved a 55\% relative performance improvement with 90\% lower cost compared to direct API calling on WebArena benchmark. A domain-specific agent built for glycomaterial science further demonstrates the pipeline's adaptability to complex, knowledge-rich tasks. Doc2Agent offers a generalizable solution for building tool agents from unstructured API documentation at scale.

Recent progress in large language model (LLM) agents has largely focused on embedding self-improvement mechanisms inside the agent or searching over many concurrent variants. While these approaches can raise aggregate scores, they often yield unstable and hard-to-audit improvement trajectories, making it difficult to guarantee non-regression or to reason about failures across versions. We reframe agent improvement as release engineering: agents are treated as shippable artifacts, and improvement is externalized into a regression-aware release pipeline. We introduce AgentDevel, a release engineering pipeline that iteratively runs the current agent, produces implementation-blind, symptom-level quality signals from execution traces, synthesizes a single release candidate (RC) via executable diagnosis, and promotes it under flip-centered gating. AgentDevel features three core designs: (i) an implementation-blind LLM critic that characterizes failure appearances without accessing agent internals, (ii) script-based executable diagnosis that aggregates dominant symptom patterns and produces auditable engineering specifications, and (iii) flip-centered gating that prioritizes pass to fail regressions and fail to pass fixes as first-class evidence. Unlike population-based search or in-agent self-refinement, AgentDevel maintains a single canonical version line and emphasizes non-regression as a primary objective. Experiments on execution-heavy benchmarks demonstrate that AgentDevel yields stable improvements with significantly fewer regressions while producing reproducible, auditable artifacts. Overall, AgentDevel provides a practical development discipline for building, debugging, and releasing LLM agents as software development.

Large language models (LLMs) have shown remarkable potential in various domains, but they often lack the ability to access and reason over domain-specific knowledge and tools. In this paper, we introduced CACTUS (Chemistry Agent Connecting Tool-Usage to Science), an LLM-based agent that integrates cheminformatics tools to enable advanced reasoning and problem-solving in chemistry and molecular discovery. We evaluate the performance of CACTUS using a diverse set of open-source LLMs, including Gemma-7b, Falcon-7b, MPT-7b, Llama2-7b, and Mistral-7b, on a benchmark of thousands of chemistry questions. Our results demonstrate that CACTUS significantly outperforms baseline LLMs, with the Gemma-7b and Mistral-7b models achieving the highest accuracy regardless of the prompting strategy used. Moreover, we explore the impact of domain-specific prompting and hardware configurations on model performance, highlighting the importance of prompt engineering and the potential for deploying smaller models on consumer-grade hardware without significant loss in accuracy. By combining the cognitive capabilities of open-source LLMs with domain-specific tools, CACTUS can assist researchers in tasks such as molecular property prediction, similarity searching, and drug-likeness assessment. Furthermore, CACTUS represents a significant milestone in the field of cheminformatics, offering an adaptable tool for researchers engaged in chemistry and molecular discovery. By integrating the strengths of open-source LLMs with domain-specific tools, CACTUS has the potential to accelerate scientific advancement and unlock new frontiers in the exploration of novel, effective, and safe therapeutic candidates, catalysts, and materials. Moreover, CACTUS's ability to integrate with automated experimentation platforms and make data-driven decisions in real time opens up new possibilities for autonomous discovery.

The rise of generative AI (GenAI) multi-agent systems (MAS) necessitates standardized protocols enabling agents to discover and interact with external tools. However, these protocols introduce new security challenges, particularly; tool squatting; the deceptive registration or representation of tools. This paper analyzes tool squatting threats within the context of emerging interoperability standards, such as Model Context Protocol (MCP) or seamless communication between agents protocols. It introduces a comprehensive Tool Registry system designed to mitigate these risks. We propose a security-focused architecture featuring admin-controlled registration, centralized tool discovery, fine grained access policies enforced via dedicated Agent and Tool Registry services, a dynamic trust scoring mechanism based on tool versioning and known vulnerabilities, and just in time credential provisioning. Based on its design principles, the proposed registry framework aims to effectively prevent common tool squatting vectors while preserving the flexibility and power of multi-agent systems. This work addresses a critical security gap in the rapidly evolving GenAI ecosystem and provides a foundation for secure tool integration in production environments.

The ultimate goal of code agents is to solve complex tasks autonomously. Although large language models (LLMs) have made substantial progress in code generation, real-world tasks typically demand full-fledged code repositories rather than simple scripts. Building such repositories from scratch remains a major challenge. Fortunately, GitHub hosts a vast, evolving collection of open-source repositories, which developers frequently reuse as modular components for complex tasks. Yet, existing frameworks like OpenHands and SWE-Agent still struggle to effectively leverage these valuable resources. Relying solely on README files provides insufficient guidance, and deeper exploration reveals two core obstacles: overwhelming information and tangled dependencies of repositories, both constrained by the limited context windows of current LLMs. To tackle these issues, we propose RepoMaster, an autonomous agent framework designed to explore and reuse GitHub repositories for solving complex tasks. For efficient understanding, RepoMaster constructs function-call graphs, module-dependency graphs, and hierarchical code trees to identify essential components, providing only identified core elements to the LLMs rather than the entire repository. During autonomous execution, it progressively explores related components using our exploration tools and prunes information to optimize context usage. Evaluated on the adjusted MLE-bench, RepoMaster achieves a 110% relative boost in valid submissions over the strongest baseline OpenHands. On our newly released GitTaskBench, RepoMaster lifts the task-pass rate from 40.7% to 62.9% while reducing token usage by 95%. Our code and demonstration materials are publicly available at https://github.com/QuantaAlpha/RepoMaster.

Gene expression analysis holds the key to many biomedical discoveries, yet extracting insights from raw transcriptomic data remains formidable due to the complexity of multiple large, semi-structured files and the need for extensive domain expertise. Current automation approaches are often limited by either inflexible workflows that break down in edge cases or by fully autonomous agents that lack the necessary precision for rigorous scientific inquiry. GenoMAS charts a different course by presenting a team of LLM-based scientists that integrates the reliability of structured workflows with the adaptability of autonomous agents. GenoMAS orchestrates six specialized LLM agents through typed message-passing protocols, each contributing complementary strengths to a shared analytic canvas. At the heart of GenoMAS lies a guided-planning framework: programming agents unfold high-level task guidelines into Action Units and, at each juncture, elect to advance, revise, bypass, or backtrack, thereby maintaining logical coherence while bending gracefully to the idiosyncrasies of genomic data. On the GenoTEX benchmark, GenoMAS reaches a Composite Similarity Correlation of 89.13% for data preprocessing and an F_1 of 60.48% for gene identification, surpassing the best prior art by 10.61% and 16.85% respectively. Beyond metrics, GenoMAS surfaces biologically plausible gene-phenotype associations corroborated by the literature, all while adjusting for latent confounders. Code is available at https://github.com/Liu-Hy/GenoMAS.

We introduce SynFormer, a generative modeling framework designed to efficiently explore and navigate synthesizable chemical space. Unlike traditional molecular generation approaches, we generate synthetic pathways for molecules to ensure that designs are synthetically tractable. By incorporating a scalable transformer architecture and a diffusion module for building block selection, SynFormer surpasses existing models in synthesizable molecular design. We demonstrate SynFormer's effectiveness in two key applications: (1) local chemical space exploration, where the model generates synthesizable analogs of a reference molecule, and (2) global chemical space exploration, where the model aims to identify optimal molecules according to a black-box property prediction oracle. Additionally, we demonstrate the scalability of our approach via the improvement in performance as more computational resources become available. With our code and trained models openly available, we hope that SynFormer will find use across applications in drug discovery and materials science.

The synthesis of complex natural products remains one of the grand challenges of organic chemistry. We present DeepRetro, a major advancement in computational retrosynthesis that enables the discovery of viable synthetic routes for complex molecules typically considered beyond the reach of existing retrosynthetic methods. DeepRetro is a novel, open-source framework that tightly integrates large language models (LLMs), traditional retrosynthetic engines, and expert human feedback in an iterative design loop. Prior approaches rely solely on template-based methods or unconstrained LLM outputs. In contrast, DeepRetro combines the precision of template-based methods with the generative flexibility of LLMs, controlled by rigorous chemical validity checks and enhanced by recursive refinement. This hybrid system dynamically explores and revises synthetic pathways, guided by both algorithmic checks and expert chemist feedback through an interactive user interface. While DeepRetro achieves strong performance on standard retrosynthesis benchmarks, its true strength lies in its ability to propose novel, viable pathways to highly complex natural products-targets that have historically eluded automated planning. Through detailed case studies, we illustrate how this approach enables new routes for total synthesis and facilitates human-machine collaboration in organic chemistry. Beyond retrosynthesis, DeepRetro represents a working model for how to leverage LLMs in scientific discovery. We provide a transparent account of the system's design, algorithms, and human-feedback loop, enabling broad adaptation across scientific domains. By releasing DeepRetro as an open-source tool, we aim to empower chemists to tackle increasingly ambitious synthetic targets, accelerating progress in drug discovery, materials design, and beyond.

AI agents hold growing promise for accelerating scientific discovery; yet, a lack of frontier evaluations hinders adoption into real workflows. Expert-written benchmarks have proven effective at measuring AI reasoning, but most at this stage have become saturated and only measure performance on constrained outputs. To help address this gap, we introduce COMPOSITE-STEM, a benchmark of 70 expert-written tasks in physics, biology, chemistry, and mathematics, curated by doctoral-level researchers. Our benchmark combines exact-match grading and criterion-based rubrics with an LLM-as-a-jury grading protocol, allowing more flexible assessment of scientifically meaningful outputs. Using an adapted multimodal Terminus-2 agent harness within the Harbor agentic evaluation framework, we evaluate four frontier models. The top-performing model achieves 21%, demonstrating that COMPOSITE-STEM captures capabilities beyond current agent reach. All tasks are open-sourced with contributor permission to support reproducibility and to promote additional research towards AI's acceleration of scientific progress in these domains.

Coding agents are increasingly used to accelerate code generation in many downstream tasks, such as fixing bugs, building applications, and prototyping. However, despite their value as coding assistants, agent-generated code tends to be larger and more verbose than the corresponding human-written implementation. In this work, we show that the cause lies in the agent's own search process: while iterating toward a passing solution, an agent accumulates speculative edits, abandoned hypotheses, and temporary changes that persist into the final patch. This may seem harmless for a single patch, but the problem compounds as agents take responsibility for ever-larger portions of a codebase-a codebase that was once minimal and well-maintained slowly accumulates redundancy faster than it can be cleaned up, drifting to a state that is harder to maintain. Given the magnitude of this problem, we take a step towards alleviating this issue. First, we formally define this phenomenon as CodeSlop-the residual and functionally unnecessary edits commonly seen in AI-generated code. We then introduce our algorithm TRIM (Trajectory-guided Redundancy Identification and Minimization). Rather than minimizing CodeSlop directly, TRIM instead minimizes agent trajectories. As we show empirically, this indirect technique of minimizing CodeSlop is highly effective: TRIM cuts CodeSlop by 17.9%-32.9% across agentic scaffolds, with negligible performance regression. TRIM is also highly efficient, requiring roughly half the validation cost of algorithmic baselines such as Delta Debugging.

Agentic Artificial Intelligence (AI) builds upon Generative AI (GenAI). It constitutes the next major step in the evolution of AI with much stronger reasoning and interaction capabilities that enable more autonomous behavior to tackle complex tasks. Since the initial release of ChatGPT (3.5), Generative AI has seen widespread adoption, giving users firsthand experience. However, the distinction between Agentic AI and GenAI remains less well understood. To address this gap, our survey is structured in two parts. In the first part, we compare GenAI and Agentic AI using existing literature, discussing their key characteristics, how Agentic AI remedies limitations of GenAI, and the major steps in GenAI's evolution toward Agentic AI. This section is intended for a broad audience, including academics in both social sciences and engineering, as well as industry professionals. It provides the necessary insights to comprehend novel applications that are possible with Agentic AI but not with GenAI. In the second part, we deep dive into novel aspects of Agentic AI, including recent developments and practical concerns such as defining agents. Finally, we discuss several challenges that could serve as a future research agenda, while cautioning against risks that can emerge when exceeding human intelligence.

Large Language Models (LLMs) promise to accelerate discovery by reasoning across the expanding scientific landscape. Yet, the challenge is no longer access to information but connecting it in meaningful, domain-spanning ways. In materials science, where innovation demands integrating concepts from molecular chemistry to mechanical performance, this is especially acute. Neither humans nor single-agent LLMs can fully contend with this torrent of information, with the latter often prone to hallucinations. To address this bottleneck, we introduce a multi-agent framework guided by large-scale knowledge graphs to find sustainable substitutes for per- and polyfluoroalkyl substances (PFAS)-chemicals currently under intense regulatory scrutiny. Agents in the framework specialize in problem decomposition, evidence retrieval, design parameter extraction, and graph traversal, uncovering latent connections across distinct knowledge pockets to support hypothesis generation. Ablation studies show that the full multi-agent pipeline outperforms single-shot prompting, underscoring the value of distributed specialization and relational reasoning. We demonstrate that by tailoring graph traversal strategies, the system alternates between exploitative searches focusing on domain-critical outcomes and exploratory searches surfacing emergent cross-connections. Illustrated through the exemplar of biomedical tubing, the framework generates sustainable PFAS-free alternatives that balance tribological performance, thermal stability, chemical resistance, and biocompatibility. This work establishes a framework combining knowledge graphs with multi-agent reasoning to expand the materials design space, showcasing several initial design candidates to demonstrate the approach.

Small LLMs often struggle to match the agentic capabilities of large, costly models. While reinforcement learning can help, progress has been limited by two structural bottlenecks: existing open-source agentic training data are narrow in task variety and easily solved; real-world APIs lack diversity and are unstable for large-scale reinforcement learning rollout processes. We address these challenges with SYNTHAGENT, a framework that jointly synthesizes diverse tool-use training data and simulates complete environments. Specifically, a strong teacher model creates novel tasks and tool ecosystems, then rewrites them into intentionally underspecified instructions. This compels agents to actively query users for missing details. When handling synthetic tasks, an LLM-based user simulator provides user-private information, while a mock tool system delivers stable tool responses. For rewards, task-level rubrics are constructed based on required subgoals, user-agent interactions, and forbidden behaviors. Across 14 challenging datasets in math, search, and tool use, models trained on our synthetic data achieve substantial gains, with small models outperforming larger baselines.

Molecular generation is a central challenge in drug discovery, requiring models that explore vast chemical space while satisfying diverse design constraints. We present Molexar, a unified multimodal molecular foundation model built on Fragment-SELFIES, a robust, fragment-aware molecular language with validity-preserving decoding and explicit fragment structure. A pretrained autoregressive decoder learns the Fragment-SELFIES syntax and molecular distribution; supervised fine-tuning (SFT) then trains the same decoder on condition-molecule pairs spanning scalar molecular properties, pharmacophore fingerprints, protein sequences, and binding pockets, injecting each condition by in-place replacement of value-token embeddings so that all generation modes share one autoregressive path. Molexar achieves strong efficiency at a small parameter count while matching or exceeding larger models. The pretrained model reaches 100% validity and high drug-likeness in unconditional and fragment-constrained generation; the SFT model follows single- and multi-property instructions and remains competitive on target-conditioned generation on the CrossDocked2020 test set. On MolGenBench, Molexar further generates molecules with favorable safety and potency. These results establish Molexar as a practical unified foundation for computational chemistry and drug-design workflows.

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

AI agents increasingly rely on external tools to solve complex, long-horizon tasks. Advancing such agents requires reproducible evaluation and large-scale training in controllable, diverse, and realistic tool-use environments. However, real-world APIs are limited in availability, domain coverage, and stability, often requiring access keys and imposing rate limits, which render them impractical for stable evaluation or scalable training. To address these challenges, we introduce SynthTools, a flexible and scalable framework for generating synthetic tool ecosystems. Our framework consists of three core components: Tool Generation for automatic and scalable creation of diverse tools, Tool Simulation to emulate realistic tool behaviors, and Tool Audit to ensure correctness and consistency of tool simulation. To illustrate its scalability, we show that SynthTools can readily produce toolsets that span twice as many domains and twice as many tools per domain as prior work. Furthermore, the tool simulation and tool audit components demonstrate strong reliability, achieving 94% and 99% accuracy respectively. Finally, we construct downstream tasks from the generated tools that even state-of-the-art models struggle to complete. By enabling scalable, diverse, and reliable tool ecosystems, SynthTools provides a practical path toward large-scale training and stable evaluation of tool-use agents. Our code is available at https://github.com/namkoong-lab/SynthTools.

Drug discovery is a complex process that involves multiple scenarios and stages, such as fragment-constrained molecule generation, hit generation and lead optimization. However, existing molecular generative models can only tackle one or two of these scenarios and lack the flexibility to address various aspects of the drug discovery pipeline. In this paper, we present Generalist Molecular generative model (GenMol), a versatile framework that addresses these limitations by applying discrete diffusion to the Sequential Attachment-based Fragment Embedding (SAFE) molecular representation. GenMol generates SAFE sequences through non-autoregressive bidirectional parallel decoding, thereby allowing utilization of a molecular context that does not rely on the specific token ordering and enhanced computational efficiency. Moreover, under the discrete diffusion framework, we introduce fragment remasking, a strategy that optimizes molecules by replacing fragments with masked tokens and regenerating them, enabling effective exploration of chemical space. GenMol significantly outperforms the previous GPT-based model trained on SAFE representations in de novo generation and fragment-constrained generation, and achieves state-of-the-art performance in goal-directed hit generation and lead optimization. These experimental results demonstrate that GenMol can tackle a wide range of drug discovery tasks, providing a unified and versatile approach for molecular design.

Tool utilization enables Large Language Model (LLM) agents to interact with the real world and resolve complex tasks. However, existing agent frameworks predominantly rely on static toolsets composed of granular atomic actions (e.g., basic file I/O or single-turn search), which forces agents to reinvent low-level logic for every recurring workflow, leading to increased reasoning overhead and failure rates. In this study, we propose that agents can achieve self-evolution by synthesizing these atomic actions into reusable Standard Operating Procedures (SOPs), which function as callable higher-order tools that encapsulate multi-step logic. We further introduce EvoSOP, a framework that empowers agents to extract SOPs from execution trajectories and iteratively optimize the toolset through a systematic lifecycle of construction, merging, evaluation, and pruning. Extensive experiments demonstrate that EvoSOP significantly boosts task success rates while substantially reducing the number of interaction rounds compared to baselines. Our analysis also reveals that iterative tool optimization fosters reliable and efficient tool-use patterns, providing a scalable pathway for the development of self-evolving agents.

Code agents can autonomously resolve GitHub issues, yet when they fail, current evaluation provides no visibility into where or why. Metrics such as Pass@1 collapse an entire execution into a single binary outcome, making it difficult to identify where and why the agent went wrong. To address this limitation, we introduce TRAJEVAL, a diagnostic framework that decomposes agent trajectories into three interpretable stages: search (file localization), read (function comprehension), and edit (modification targeting). For each stage, we compute precision and recall by comparing against reference patches. Analyzing 16,758 trajectories across three agent architectures and seven models, we find universal inefficiencies (all agents examine approximately 22x more functions than necessary) yet distinct failure modes: GPT-5 locates relevant code but targets edits incorrectly, while Qwen-32B fails at file discovery entirely. We validate that these diagnostics are predictive, achieving model-level Pass@1 prediction within 0.87-2.1% MAE, and actionable: real-time feedback based on trajectory signals improves two state-of-the-art models by 2.2-4.6 percentage points while reducing costs by 20-31%. These results demonstrate that our framework not only provides a more fine-grained analysis of agent behavior, but also translates diagnostic signals into tangible performance gains. More broadly, TRAJEVAL transforms agent evaluation beyond outcome-based benchmarking toward mechanism-driven diagnosis of agent success and failure.

Efficient experiment reproduction is critical to accelerating progress in artificial intelligence. However, the inherent complexity of method design and training procedures presents substantial challenges for automation. Notably, reproducing experiments often requires implicit domain-specific knowledge not explicitly documented in the original papers. To address this, we introduce the paper lineage algorithm, which identifies and extracts implicit knowledge from the relevant references cited by the target paper. Building on this idea, we propose AutoReproduce, a multi-agent framework capable of automatically reproducing experiments described in research papers in an end-to-end manner. AutoReproduce enhances code executability by generating unit tests alongside the reproduction process. To evaluate the reproduction capability, we construct ReproduceBench, a benchmark annotated with verified implementations, and introduce novel evaluation metrics to assess both the reproduction and execution fidelity. Experimental results demonstrate that AutoReproduce outperforms the existing strong agent baselines on all five evaluation metrics by a peak margin of over 70%. In particular, compared to the official implementations, AutoReproduce achieves an average performance gap of 22.1% on 89.74% of the executable experiment runs. The code will be available at https://github.com/AI9Stars/AutoReproduce.

AI agents have the potential to aid users on a variety of consequential tasks, including conducting scientific research. To spur the development of useful agents, we need benchmarks that are challenging, but more crucially, directly correspond to real-world tasks of interest. This paper introduces such a benchmark, designed to measure the accuracy of AI agents in tackling a crucial yet surprisingly challenging aspect of scientific research: computational reproducibility. This task, fundamental to the scientific process, involves reproducing the results of a study using the provided code and data. We introduce CORE-Bench (Computational Reproducibility Agent Benchmark), a benchmark consisting of 270 tasks based on 90 scientific papers across three disciplines (computer science, social science, and medicine). Tasks in CORE-Bench consist of three difficulty levels and include both language-only and vision-language tasks. We provide an evaluation system to measure the accuracy of agents in a fast and parallelizable way, saving days of evaluation time for each run compared to a sequential implementation. We evaluated two baseline agents: the general-purpose AutoGPT and a task-specific agent called CORE-Agent. We tested both variants using two underlying language models: GPT-4o and GPT-4o-mini. The best agent achieved an accuracy of 21% on the hardest task, showing the vast scope for improvement in automating routine scientific tasks. Having agents that can reproduce existing work is a necessary step towards building agents that can conduct novel research and could verify and improve the performance of other research agents. We hope that CORE-Bench can improve the state of reproducibility and spur the development of future research agents.

Agent orchestration frameworks have proliferated, collectively exceeding 290,000 GitHub stars across LangGraph, CrewAI, Google ADK, OpenAI Agents SDK, Semantic Kernel, Strands, and LlamaIndex. All follow the same pattern: an external orchestrator above the LLM, injecting instructions and routing decisions every turn. Recent work has shown this architecture is dominated for procedural tasks by simply providing the procedure in a frontier model's system prompt [Dennis et al., 2026a], at the cost of consuming the context window, requiring a frontier model for every conversation, and exposing proprietary procedures to third-party providers. Compiling the procedure into the weights of a small fine-tuned model -- creating a subterranean agent -- should resolve all of these concerns, and prior work (SimpleTOD, FireAct, SynTOD, WorkflowLLM, Agent Lumos) has shown the technique works. Yet developer adoption has overwhelmingly favored orchestration. We identify three perceived barriers and address each empirically across travel booking (14 nodes), Zoom support (14 nodes, product-specific knowledge), and insurance claims (55 nodes, 6 decision hubs).

One of the critical phases in software development is software testing. Testing helps with identifying potential bugs and reducing maintenance costs. The goal of automated test generation tools is to ease the development of tests by suggesting efficient bug-revealing tests. Recently, researchers have leveraged Large Language Models (LLMs) of code to generate unit tests. While the code coverage of generated tests was usually assessed, the literature has acknowledged that the coverage is weakly correlated with the efficiency of tests in bug detection. To improve over this limitation, in this paper, we introduce MuTAP for improving the effectiveness of test cases generated by LLMs in terms of revealing bugs by leveraging mutation testing. Our goal is achieved by augmenting prompts with surviving mutants, as those mutants highlight the limitations of test cases in detecting bugs. MuTAP is capable of generating effective test cases in the absence of natural language descriptions of the Program Under Test (PUTs). We employ different LLMs within MuTAP and evaluate their performance on different benchmarks. Our results show that our proposed method is able to detect up to 28% more faulty human-written code snippets. Among these, 17% remained undetected by both the current state-of-the-art fully automated test generation tool (i.e., Pynguin) and zero-shot/few-shot learning approaches on LLMs. Furthermore, MuTAP achieves a Mutation Score (MS) of 93.57% on synthetic buggy code, outperforming all other approaches in our evaluation. Our findings suggest that although LLMs can serve as a useful tool to generate test cases, they require specific post-processing steps to enhance the effectiveness of the generated test cases which may suffer from syntactic or functional errors and may be ineffective in detecting certain types of bugs and testing corner cases PUTs.

Autonomous research systems are often evaluated as one-shot paper generators: given a topic, they produce a manuscript and a small set of experiment logs. This framing hides the operational problem that makes such systems difficult to trust: research is long-running, branching, failure-prone, and dependent on auditable handoffs between agents and humans. XScientist is a git-like research protocol and operating system for this setting. It orchestrates idea generation, experiment execution, manuscript drafting, self-review, repair, quality gating, daemon scheduling, and reproducibility artifacts as one continuously observable pipeline. The central design choice is to treat each run as a portable research artifact rather than only as a PDF. XScientist exports an Agent-Native Research Artifact (ARA), a protocol that records an exploration DAG, per-node code and outputs, claim-to-evidence anchors, content hashes, provenance, and re-execution hooks. This makes each generated paper inspectable as a science exploration tree: failed branches, repaired experiments, ablations, and manuscript claims remain connected to the nodes that produced them. The system also includes deterministic integrity forensics, sample gates, truth contracts, reviewer-oriented repair loops, and long-running daemon controls. This paper describes the current XScientist architecture, the ARA protocol surface, and the practical safeguards needed to move autonomous science from single-run demos toward reproducible, reviewable, and forkable research infrastructure. The implementation and manuscript source are maintained in the public GitHub repository at https://github.com/smileformylove/XScientist.

Recently, Agentic AI has become an increasingly popular research field. However, we argue that current agent research practices lack standardization and scientific rigor, making it hard to conduct fair comparisons among methods. As a result, it is still unclear how different design choices in agent frameworks affect effectiveness, and measuring their progress remains challenging. In this work, we conduct a systematic empirical study on GAIA benchmark and BrowseComp to examine the impact of popular design choices in key agent components in a fair and rigorous manner. We find that the lack of a standard evaluation protocol makes previous works, even open-sourced ones, non-reproducible, with significant variance between random runs. Therefore, we introduce a more robust evaluation protocol to stabilize comparisons. Our study reveals which components and designs are crucial for effective agents, while others are redundant, despite seeming logical. Based on our findings, we build and open-source OAgents, a new foundation agent framework that achieves state-of-the-art performance among open-source projects. OAgents offers a modular design for various agent components, promoting future research in Agentic AI.

Large Language Model agents are reshaping the industrial landscape. However, most practical agents remain human-designed because tasks differ widely, making them labor-intensive to build. This situation poses a central question: can we automatically create and adapt domain agents in the wild? While several recent approaches have sought to automate agent creation, they typically treat agent generation as a black-box procedure and rely solely on final performance metrics to guide the process. Such strategies overlook critical evidence explaining why an agent succeeds or fails, and often require high computational costs. To address these limitations, we propose ReCreate, an experience-driven framework for the automatic creation of domain agents. ReCreate systematically leverages agent interaction histories, which provide rich concrete signals on both the causes of success or failure and the avenues for improvement. Specifically, we introduce an agent-as-optimizer paradigm that effectively learns from experience via three key components: (i) an experience storage and retrieval mechanism for on-demand inspection; (ii) a reasoning-creating synergy pipeline that maps execution experience into scaffold edits; and (iii) hierarchical updates that abstract instance-level details into reusable domain patterns. In experiments across diverse domains, ReCreate consistently outperforms human-designed agents and existing automated agent generation methods, even when starting from minimal seed scaffolds.

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

We present Deep Researcher Agent, an open-source framework that enables large language model (LLM) agents to autonomously conduct deep learning experiments around the clock. Unlike existing AI research assistants that focus on paper writing or code generation, our system addresses the full experiment lifecycle: hypothesis formation, code implementation, training execution, result analysis, and iterative refinement. The framework introduces three key innovations: (1) Zero-Cost Monitoring -- a monitoring paradigm that incurs zero LLM API costs during model training by relying solely on process-level checks and log file reads; (2) Two-Tier Constant-Size Memory -- a memory architecture capped at sim5K characters regardless of runtime duration, preventing the unbounded context growth that plagues long-running agents; and (3) Minimal-Toolset Leader-Worker Architecture -- a multi-agent design where each worker agent is equipped with only 3--5 tools, reducing per-call token overhead by up to 73\%. In sustained deployments spanning 30+ days, the framework autonomously completed 500+ experiment cycles across four concurrent research projects, achieving a 52\% improvement over baseline metrics in one project through 200+ automated experiments -- all at an average LLM cost of \$0.08 per 24-hour cycle. Code is available at https://github.com/Xiangyue-Zhang/auto-deep-researcher-24x7.