Daily Papers

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.

LLM agents hold significant promise for advancing scientific research. To accelerate this progress, we introduce AIRS-Bench (the AI Research Science Benchmark), a suite of 20 tasks sourced from state-of-the-art machine learning papers. These tasks span diverse domains, including language modeling, mathematics, bioinformatics, and time series forecasting. AIRS-Bench tasks assess agentic capabilities over the full research lifecycle -- including idea generation, experiment analysis and iterative refinement -- without providing baseline code. The AIRS-Bench task format is versatile, enabling easy integration of new tasks and rigorous comparison across different agentic frameworks. We establish baselines using frontier models paired with both sequential and parallel scaffolds. Our results show that agents exceed human SOTA in four tasks but fail to match it in sixteen others. Even when agents surpass human benchmarks, they do not reach the theoretical performance ceiling for the underlying tasks. These findings indicate that AIRS-Bench is far from saturated and offers substantial room for improvement. We open-source the AIRS-Bench task definitions and evaluation code to catalyze further development in autonomous scientific research.

Recent progress in large language models (LLMs) has advanced automatic code generation, yet most approaches rely on direct, single-step translation from problem descriptions to code, disregarding structured software engineering practices. We introduce a lifecycle-aware framework that systematically incorporates intermediate artifacts such as requirements analysis, state machine modeling, and pseudocode into both the training and inference stages. This design aligns code generation with standard software development phases and enables more structured reasoning. Experiments show that lifecycle-level fine-tuning improves code correctness by up to 75% over the same model before fine-tuning, with performance gains compounding across intermediate stages. Multi-step inference consistently surpasses single-step generation, demonstrating the effectiveness of intermediate scaffolding. Notably, open-source LLMs, once fine-tuned under our framework, match or slightly outperform models pretrained on code. When applied to DeepSeek-Coder-1.3B, our framework yields relative CodeBLEU improvements of 34.3%, 20.0%, 11.2%, and 22.3% over ChatGPT-3.5, ChatGPT-4o-mini, DeepSeek-R1, and LLaMA-8B, respectively. Our pipeline also proves robust with up to 80\% less training data, confirming its resilience. Ablation studies further reveal that each intermediate artifact contributes distinctly to final code quality, with state machine modeling yielding the most substantial impact. Our source code and detailed experimental data are available at https://anonymous.4open.science/r/Lifecycle-Aware-3CCB.

Machine learning research, crucial for technological advancements and innovation, often faces significant challenges due to its inherent complexity, slow pace of experimentation, and the necessity for specialized expertise. Motivated by this, we present a new systematic framework, autonomous Machine Learning Research with large language models (MLR-Copilot), designed to enhance machine learning research productivity through the automatic generation and implementation of research ideas using Large Language Model (LLM) agents. The framework consists of three phases: research idea generation, experiment implementation, and implementation execution. First, existing research papers are used to generate hypotheses and experimental plans vis IdeaAgent powered by LLMs. Next, the implementation generation phase translates these plans into executables with ExperimentAgent. This phase leverages retrieved prototype code and optionally retrieves candidate models and data. Finally, the execution phase, also managed by ExperimentAgent, involves running experiments with mechanisms for human feedback and iterative debugging to enhance the likelihood of achieving executable research outcomes. We evaluate our framework on five machine learning research tasks and the experimental results show the framework's potential to facilitate the research progress and innovations.

Traditional scientific discovery relies on an iterative hypothesise-experiment-refine cycle that has driven progress for centuries, but its intuitive, ad-hoc implementation often wastes resources, yields inefficient designs, and misses critical insights. This tutorial presents Bayesian Optimisation (BO), a principled probability-driven framework that formalises and automates this core scientific cycle. BO uses surrogate models (e.g., Gaussian processes) to model empirical observations as evolving hypotheses, and acquisition functions to guide experiment selection, balancing exploitation of known knowledge and exploration of uncharted domains to eliminate guesswork and manual trial-and-error. We first frame scientific discovery as an optimisation problem, then unpack BO's core components, end-to-end workflows, and real-world efficacy via case studies in catalysis, materials science, organic synthesis, and molecule discovery. We also cover critical technical extensions for scientific applications, including batched experimentation, heteroscedasticity, contextual optimisation, and human-in-the-loop integration. Tailored for a broad audience, this tutorial bridges AI advances in BO with practical natural science applications, offering tiered content to empower cross-disciplinary researchers to design more efficient experiments and accelerate principled scientific discovery.

I investigate a stronger form of regularization by deactivating neurons for extended periods, a departure from the temporary changes of methods like Dropout. However, this long-term dynamism introduces a critical challenge: severe training instability when neurons are revived with random weights. To solve this, I propose the Lifecycle (LC) principle, a regularization mechanism centered on a key innovation: state memory. Instead of re-initializing a revived neuron, my method restores its parameters to their last known effective state. This process preserves learned knowledge and avoids destructive optimization shocks. My theoretical analysis reveals that the LC principle smooths the loss landscape, guiding optimization towards flatter minima associated with better generalization. Experiments on image classification benchmarks demonstrate that my method improves generalization and robustness. Crucially, ablation studies confirm that state memory is essential for achieving these gains.

Real-world enterprise data intelligence workflows encompass data engineering that turns raw sources into analytical-ready tables and data analysis that convert those tables into decision-oriented insights. We introduce DAComp, a benchmark of 210 tasks that mirrors these complex workflows. Data engineering (DE) tasks require repository-level engineering on industrial schemas, including designing and building multi-stage SQL pipelines from scratch and evolving existing systems under evolving requirements. Data analysis (DA) tasks pose open-ended business problems that demand strategic planning, exploratory analysis through iterative coding, interpretation of intermediate results, and the synthesis of actionable recommendations. Engineering tasks are scored through execution-based, multi-metric evaluation. Open-ended tasks are assessed by a reliable, experimentally validated LLM-judge, which is guided by hierarchical, meticulously crafted rubrics. Our experiments reveal that even state-of-the-art agents falter on DAComp. Performance on DE tasks is particularly low, with success rates under 20%, exposing a critical bottleneck in holistic pipeline orchestration, not merely code generation. Scores on DA tasks also average below 40%, highlighting profound deficiencies in open-ended reasoning and demonstrating that engineering and analysis are distinct capabilities. By clearly diagnosing these limitations, DAComp provides a rigorous and realistic testbed to drive the development of truly capable autonomous data agents for enterprise settings. Our data and code are available at https://da-comp.github.io

The remarkable success of Large Language Models (LLMs) has illuminated a promising pathway toward achieving Artificial General Intelligence for both academic and industrial communities, owing to their unprecedented performance across various applications. As LLMs continue to gain prominence in both research and commercial domains, their security and safety implications have become a growing concern, not only for researchers and corporations but also for every nation. Currently, existing surveys on LLM safety primarily focus on specific stages of the LLM lifecycle, e.g., deployment phase or fine-tuning phase, lacking a comprehensive understanding of the entire "lifechain" of LLMs. To address this gap, this paper introduces, for the first time, the concept of "full-stack" safety to systematically consider safety issues throughout the entire process of LLM training, deployment, and eventual commercialization. Compared to the off-the-shelf LLM safety surveys, our work demonstrates several distinctive advantages: (I) Comprehensive Perspective. We define the complete LLM lifecycle as encompassing data preparation, pre-training, post-training, deployment and final commercialization. To our knowledge, this represents the first safety survey to encompass the entire lifecycle of LLMs. (II) Extensive Literature Support. Our research is grounded in an exhaustive review of over 800+ papers, ensuring comprehensive coverage and systematic organization of security issues within a more holistic understanding. (III) Unique Insights. Through systematic literature analysis, we have developed reliable roadmaps and perspectives for each chapter. Our work identifies promising research directions, including safety in data generation, alignment techniques, model editing, and LLM-based agent systems. These insights provide valuable guidance for researchers pursuing future work in this field.

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

We propose an agent architecture that automates parts of the common reinforcement learning experiment workflow, to enable automated mastery of control domains for embodied agents. To do so, it leverages a VLM to perform some of the capabilities normally required of a human experimenter, including the monitoring and analysis of experiment progress, the proposition of new tasks based on past successes and failures of the agent, decomposing tasks into a sequence of subtasks (skills), and retrieval of the skill to execute - enabling our system to build automated curricula for learning. We believe this is one of the first proposals for a system that leverages a VLM throughout the full experiment cycle of reinforcement learning. We provide a first prototype of this system, and examine the feasibility of current models and techniques for the desired level of automation. For this, we use a standard Gemini model, without additional fine-tuning, to provide a curriculum of skills to a language-conditioned Actor-Critic algorithm, in order to steer data collection so as to aid learning new skills. Data collected in this way is shown to be useful for learning and iteratively improving control policies in a robotics domain. Additional examination of the ability of the system to build a growing library of skills, and to judge the progress of the training of those skills, also shows promising results, suggesting that the proposed architecture provides a potential recipe for fully automated mastery of tasks and domains for embodied agents.

Understanding the world and explaining it with scientific theories is a central aspiration of artificial intelligence research. Proposing theories, designing experiments to test them, and then revising them based on data are fundamental to scientific discovery. Despite the significant promise of LLM-based scientific agents, no benchmarks systematically test LLM's ability to propose scientific models, collect experimental data, and revise them in light of new data. We introduce BoxingGym, a benchmark with 10 environments for systematically evaluating both experimental design (e.g. collecting data to test a scientific theory) and model discovery (e.g. proposing and revising scientific theories). To enable tractable and quantitative evaluation, we implement each environment as a generative probabilistic model with which a scientific agent can run interactive experiments. These probabilistic models are drawn from various real-world scientific domains ranging from psychology to ecology. To quantitatively evaluate a scientific agent's ability to collect informative experimental data, we compute the expected information gain (EIG), an information-theoretic quantity which measures how much an experiment reduces uncertainty about the parameters of a generative model. A good scientific theory is a concise and predictive explanation. Therefore, to quantitatively evaluate model discovery, we ask a scientific agent to explain their model and then assess whether this explanation enables another scientific agent to make reliable predictions about this environment. In addition to this explanation-based evaluation, we compute standard model evaluation metrics such as prediction errors. We find that current LLMs, such as GPT-4o, struggle with both experimental design and model discovery. We find that augmenting the LLM-based agent with an explicit statistical model does not reliably improve these results.

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

Large language models are redefining software engineering by implementing AI-powered techniques throughout the whole software development process, including requirement gathering, software architecture, code generation, testing, and deployment. However, it is still difficult to develop a cohesive platform that consistently produces the best outcomes across all stages. The objective of this study is to develop a unified platform that utilizes multiple artificial intelligence agents to automate the process of transforming user requirements into well-organized deliverables. These deliverables include user stories, prioritization, and UML sequence diagrams, along with the modular approach to APIs, unit tests, and end-to-end tests. Additionally, the platform will organize tasks, perform security and compliance, and suggest design patterns and improvements for non-functional requirements. We allow users to control and manage each phase according to their preferences. In addition, the platform provides security and compliance checks following European standards and proposes design optimizations. We use multiple models, such as GPT-3.5, GPT-4, and Llama3 to enable to generation of modular code as per user choice. The research also highlights the limitations and future research discussions to overall improve the software development life cycle. The source code for our uniform platform is hosted on GitHub, enabling additional experimentation and supporting both research and practical uses. \end

The automation of scientific discovery has been a long-standing goal within the research community, driven by the potential to accelerate knowledge creation. While significant progress has been made using commercial large language models (LLMs) as research assistants or idea generators, the possibility of automating the entire research process with open-source LLMs remains largely unexplored. This paper explores the feasibility of using open-source post-trained LLMs as autonomous agents capable of performing the full cycle of automated research and review, from literature review and manuscript preparation to peer review and paper revision. Our iterative preference training framework consists of CycleResearcher, which conducts research tasks, and CycleReviewer, which simulates the peer review process, providing iterative feedback via reinforcement learning. To train these models, we develop two new datasets, Review-5k and Research-14k, reflecting real-world machine learning research and peer review dynamics. Our results demonstrate that CycleReviewer achieves a 26.89\% improvement in mean absolute error (MAE) over individual human reviewers in predicting paper scores, indicating that LLMs can surpass expert-level performance in research evaluation. In research, the papers generated by the CycleResearcher model achieved a score of 5.36 in simulated peer reviews, surpassing the preprint level of 5.24 from human experts and approaching the accepted paper level of 5.69. This work represents a significant step toward fully automated scientific inquiry, providing ethical safeguards and advancing AI-driven research capabilities. The code, dataset and model weight are released at http://github/minjun-zhu/Researcher.

Large language model (LLM)-based systems are increasingly deployed to conduct scientific research autonomously, yet whether their reasoning adheres to the epistemic norms that make scientific inquiry self-correcting is poorly understood. Here, we evaluate LLM-based scientific agents across eight domains, spanning workflow execution to hypothesis-driven inquiry, through more than 25,000 agent runs and two complementary lenses: (i) a systematic performance analysis that decomposes the contributions of the base model and the agent scaffold, and (ii) a behavioral analysis of the epistemological structure of agent reasoning. We observe that the base model is the primary determinant of both performance and behavior, accounting for 41.4% of explained variance versus 1.5% for the scaffold. Across all configurations, evidence is ignored in 68% of traces, refutation-driven belief revision occurs in 26%, and convergent multi-test evidence is rare. The same reasoning pattern appears whether the agent executes a computational workflow or conducts hypothesis-driven inquiry. They persist even when agents receive near-complete successful reasoning trajectories as context, and the resulting unreliability compounds across repeated trials in epistemically demanding domains. Thus, current LLM-based agents execute scientific workflows but do not exhibit the epistemic patterns that characterize scientific reasoning. Outcome-based evaluation cannot detect these failures, and scaffold engineering alone cannot repair them. Until reasoning itself becomes a training target, the scientific knowledge produced by such agents cannot be justified by the process that generated it.

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.

Generative AI is reshaping knowledge work, yet existing research focuses predominantly on software engineering and the natural sciences, with limited methodological exploration for the humanities and social sciences. Positioned as a "methodological experiment," this study proposes an AI Agent-based collaborative research workflow (Agentic Workflow) for humanities and social science research. Taiwan's Claude.ai usage data (N = 7,729 conversations, November 2025) from the Anthropic Economic Index (AEI) serves as the empirical vehicle for validating the feasibility of this methodology. This study operates on two levels: the primary level is the design and validation of a methodological framework - a seven-stage modular workflow grounded in three principles: task modularization, human-AI division of labor, and verifiability, with each stage delineating clear roles for human researchers (research judgment and ethical decisions) and AI Agents (information retrieval and text generation); the secondary level is the empirical analysis of AEI Taiwan data - serving as an operational demonstration of the workflow's application to secondary data research, showcasing both the process and output quality (see Appendix A). This study contributes by proposing a replicable AI collaboration framework for humanities and social science researchers, and identifying three operational modes of human-AI collaboration - direct execution, iterative refinement, and human-led - through reflexive documentation of the operational process. This taxonomy reveals the irreplaceability of human judgment in research question formulation, theoretical interpretation, contextualized reasoning, and ethical reflection. Limitations including single-platform data, cross-sectional design, and AI reliability risks are acknowledged.

Historically, scientific discovery has been a lengthy and costly process, demanding substantial time and resources from initial conception to final results. To accelerate scientific discovery, reduce research costs, and improve research quality, we introduce Agent Laboratory, an autonomous LLM-based framework capable of completing the entire research process. This framework accepts a human-provided research idea and progresses through three stages--literature review, experimentation, and report writing to produce comprehensive research outputs, including a code repository and a research report, while enabling users to provide feedback and guidance at each stage. We deploy Agent Laboratory with various state-of-the-art LLMs and invite multiple researchers to assess its quality by participating in a survey, providing human feedback to guide the research process, and then evaluate the final paper. We found that: (1) Agent Laboratory driven by o1-preview generates the best research outcomes; (2) The generated machine learning code is able to achieve state-of-the-art performance compared to existing methods; (3) Human involvement, providing feedback at each stage, significantly improves the overall quality of research; (4) Agent Laboratory significantly reduces research expenses, achieving an 84% decrease compared to previous autonomous research methods. We hope Agent Laboratory enables researchers to allocate more effort toward creative ideation rather than low-level coding and writing, ultimately accelerating scientific discovery.

A central aspect of machine learning research is experimentation, the process of designing and running experiments, analyzing the results, and iterating towards some positive outcome (e.g., improving accuracy). Could agents driven by powerful language models perform machine learning experimentation effectively? To answer this question, we introduce MLAgentBench, a suite of 13 tasks ranging from improving model performance on CIFAR-10 to recent research problems like BabyLM. For each task, an agent can perform actions like reading/writing files, executing code, and inspecting outputs. We then construct an agent that can perform ML experimentation based on ReAct framework. We benchmark agents based on Claude v1.0, Claude v2.1, Claude v3 Opus, GPT-4, GPT-4-turbo, Gemini-Pro, and Mixtral and find that a Claude v3 Opus agent is the best in terms of success rate. It can build compelling ML models over many tasks in MLAgentBench with 37.5% average success rate. Our agents also display highly interpretable plans and actions. However, the success rates vary considerably; they span from 100% on well-established older datasets to as low as 0% on recent Kaggle challenges created potentially after the underlying LM was trained. Finally, we identify several key challenges for LM-based agents such as long-term planning and reducing hallucination. Our code is released at https://github.com/snap-stanford/MLAgentBench.

The blue bottle experiment was first introduced to the chemical education literature as a simple demonstration on kinetics. Its original formulation contains only glucose, NaOH and small amount of methylene blue. The solution turns blue when shaken and fades to colorless upon standing. This bluing/de-bluing cycle may be repeated and may be compared to blood colors in animal's respiratory cycle. Inspired by the blue bottle experiment, the colorful chemical bottle experiment kit was commercially developed in 2006. The kit is a versatile pedagogical tool, not only for physical chemistry but also for analytical, biological and organic chemistry. It also helps teaching concepts in scientific method and laboratory safety. This manuscript contains four parts, brief review on literature relating to the blue bottle experiment, description of the colorful chemical bottle experiment kit, pedagogical discussion of the experiments and preliminary evaluation from students.

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

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.

Many chemical concepts can be well defined in the context of quantum chemical theories. Examples are the electronegativity scale of Mulliken and Jaffe and the hard and soft acids and bases concept of Pearson. The sound theoretical basis allows for a systematic definition of such concepts. However, while they are often used to describe and compare chemical processes in terms of reactivity, their predictive power remains unclear. In this work, we elaborate on the predictive potential of chemical reactivity concepts, which can be crucial for autonomous reaction exploration protocols to guide them by first-principles heuristics that expoit these concepts.

Automating AI research holds immense potential for accelerating scientific progress, yet current AI agents struggle with the complexities of rigorous, end-to-end experimentation. We introduce EXP-Bench, a novel benchmark designed to systematically evaluate AI agents on complete research experiments sourced from influential AI publications. Given a research question and incomplete starter code, EXP-Bench challenges AI agents to formulate hypotheses, design and implement experimental procedures, execute them, and analyze results. To enable the creation of such intricate and authentic tasks with high-fidelity, we design a semi-autonomous pipeline to extract and structure crucial experimental details from these research papers and their associated open-source code. With the pipeline, EXP-Bench curated 461 AI research tasks from 51 top-tier AI research papers. Evaluations of leading LLM-based agents, such as OpenHands and IterativeAgent on EXP-Bench demonstrate partial capabilities: while scores on individual experimental aspects such as design or implementation correctness occasionally reach 20-35%, the success rate for complete, executable experiments was a mere 0.5%. By identifying these bottlenecks and providing realistic step-by-step experiment procedures, EXP-Bench serves as a vital tool for future AI agents to improve their ability to conduct AI research experiments. EXP-Bench is open-sourced at https://github.com/Just-Curieous/Curie/tree/main/benchmark/exp_bench.

Fully automated self-driving laboratories are promising to enable high-throughput and large-scale scientific discovery by reducing repetitive labour. However, effective automation requires deep integration of laboratory knowledge, which is often unstructured, multimodal, and difficult to incorporate into current AI systems. This paper introduces the k-agents framework, designed to support experimentalists in organizing laboratory knowledge and automating experiments with agents. Our framework employs large language model-based agents to encapsulate laboratory knowledge including available laboratory operations and methods for analyzing experiment results. To automate experiments, we introduce execution agents that break multi-step experimental procedures into state machines, interact with other agents to execute each step and analyze the experiment results. The analyzed results are then utilized to drive state transitions, enabling closed-loop feedback control. To demonstrate its capabilities, we applied the agents to calibrate and operate a superconducting quantum processor, where they autonomously planned and executed experiments for hours, successfully producing and characterizing entangled quantum states at the level achieved by human scientists. Our knowledge-based agent system opens up new possibilities for managing laboratory knowledge and accelerating scientific discovery.

In the development of science, accurate and reproducible documentation of the experimental process is crucial. Automatic recognition of the actions in experiments from videos would help experimenters by complementing the recording of experiments. Towards this goal, we propose FineBio, a new fine-grained video dataset of people performing biological experiments. The dataset consists of multi-view videos of 32 participants performing mock biological experiments with a total duration of 14.5 hours. One experiment forms a hierarchical structure, where a protocol consists of several steps, each further decomposed into a set of atomic operations. The uniqueness of biological experiments is that while they require strict adherence to steps described in each protocol, there is freedom in the order of atomic operations. We provide hierarchical annotation on protocols, steps, atomic operations, object locations, and their manipulation states, providing new challenges for structured activity understanding and hand-object interaction recognition. To find out challenges on activity understanding in biological experiments, we introduce baseline models and results on four different tasks, including (i) step segmentation, (ii) atomic operation detection (iii) object detection, and (iv) manipulated/affected object detection. Dataset and code are available from https://github.com/aistairc/FineBio.

LLM-based reasoning models have enabled the development of agentic systems that act as co-scientists, assisting in multi-step scientific analysis. However, evaluating these systems is challenging, as it requires realistic, end-to-end research scenarios that integrate data analysis, interpretation, and the generation of new insights from the experimental data. To address this limitation, we introduce HeurekaBench, a framework to create benchmarks with exploratory, open-ended research questions for experimental datasets. Each such question is grounded in a scientific study and its corresponding code repository, and is created using a semi-automated pipeline that leverages multiple LLMs to extract insights and generate candidate workflows, which are then verified against reported findings. We instantiate the framework in single-cell biology to obtain sc-HeurekaBench benchmark and use it to compare state-of-the-art single-cell agents. We further showcase the benefits of our benchmark for quantitatively analyzing current design choices in agentic systems. We find that the addition of a critic module can improve ill-formed responses for open-source LLM-based agents by up to 22% and close the gap with their closed-source counterparts. Overall, HeurekaBench sets a path toward rigorous, end-to-end evaluation of scientific agents, grounding benchmark construction in real scientific workflows.

Artificial intelligence (AI) is reshaping scientific discovery, evolving from specialized computational tools into autonomous research partners. We position Agentic Science as a pivotal stage within the broader AI for Science paradigm, where AI systems progress from partial assistance to full scientific agency. Enabled by large language models (LLMs), multimodal systems, and integrated research platforms, agentic AI shows capabilities in hypothesis generation, experimental design, execution, analysis, and iterative refinement -- behaviors once regarded as uniquely human. This survey provides a domain-oriented review of autonomous scientific discovery across life sciences, chemistry, materials science, and physics. We unify three previously fragmented perspectives -- process-oriented, autonomy-oriented, and mechanism-oriented -- through a comprehensive framework that connects foundational capabilities, core processes, and domain-specific realizations. Building on this framework, we (i) trace the evolution of AI for Science, (ii) identify five core capabilities underpinning scientific agency, (iii) model discovery as a dynamic four-stage workflow, (iv) review applications across the above domains, and (v) synthesize key challenges and future opportunities. This work establishes a domain-oriented synthesis of autonomous scientific discovery and positions Agentic Science as a structured paradigm for advancing AI-driven research.

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.

Scientific discovery has long been constrained by human limitations in expertise, physical capability, and sleep cycles. The recent rise of AI scientists and automated laboratories has accelerated both the cognitive and operational aspects of research. However, key limitations persist: AI systems are often confined to virtual environments, while automated laboratories lack the flexibility and autonomy to adaptively test new hypotheses in the physical world. Recent advances in embodied AI, such as generalist robot foundation models, diffusion-based action policies, fine-grained manipulation learning, and sim-to-real transfer, highlight the promise of integrating cognitive and embodied intelligence. This convergence opens the door to closed-loop systems that support iterative, autonomous experimentation and the possibility of serendipitous discovery. In this position paper, we propose the paradigm of Intelligent Science Laboratories (ISLs): a multi-layered, closed-loop framework that deeply integrates cognitive and embodied intelligence. ISLs unify foundation models for scientific reasoning, agent-based workflow orchestration, and embodied agents for robust physical experimentation. We argue that such systems are essential for overcoming the current limitations of scientific discovery and for realizing the full transformative potential of AI-driven science.

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

Evaluations are critical for understanding the capabilities of large language models (LLMs). Fundamentally, evaluations are experiments; but the literature on evaluations has largely ignored the literature from other sciences on experiment analysis and planning. This article shows researchers with some training in statistics how to think about and analyze data from language model evaluations. Conceptualizing evaluation questions as having been drawn from an unseen super-population, we present formulas for analyzing evaluation data, measuring differences between two models, and planning an evaluation experiment. We make a number of specific recommendations for running language model evaluations and reporting experiment results in a way that minimizes statistical noise and maximizes informativeness.

Combined electric power system and High-Altitude Electromagnetic Pulse (HEMP) models are being developed to determine the effect of a HEMP on the US power grid. The work relies primarily on deterministic methods; however, it is computationally untenable to evaluate the E1 HEMP response of large numbers of grid components distributed across a large interconnection. Further, the deterministic assessment of these components' failures are largely unachievable. E1 HEMP laboratory testing of the components is accomplished, but is expensive, leaving few data points to construct failure models of grid components exposed to E1 HEMP. The use of Bayesian priors, developed using the subject matter expertise, combined with the minimal test data in a Bayesian inference process, provides the basis for the development of more robust and cost-effective statistical component failure models. These can be used with minimal computational burden in a simulation environment such as sampling of Cumulative Distribution Functions (CDFs).

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.

This report describes ARIS (Auto-Research-in-sleep), an open-source research harness for autonomous research, including its architecture, assurance mechanisms, and early deployment experience. The performance of agent systems built on LLMs depends on both the model weights and the harness around them, which governs what information to store, retrieve, and present to the model. For long-horizon research workflows, the central failure mode is not a visible breakdown but a plausible unsupported success: a long-running agent can produce claims whose evidential support is incomplete, misreported, or silently inherited from the executor's framing. Therefore, we present ARIS as a research harness that coordinates machine-learning research workflows through cross-model adversarial collaboration as a default configuration: an executor model drives forward progress while a reviewer from a different model family is recommended to critique intermediate artifacts and request revisions. ARIS has three architectural layers. The execution layer provides more than 65 reusable Markdown-defined skills, model integrations via MCP, a persistent research wiki for iterative reuse of prior findings, and deterministic figure generation. The orchestration layer coordinates five end-to-end workflows with adjustable effort settings and configurable routing to reviewer models. The assurance layer includes a three-stage process for checking whether experimental claims are supported by evidence: integrity verification, result-to-claim mapping, and claim auditing that cross-checks manuscript statements against the claim ledger and raw evidence, as well as a five-pass scientific-editing pipeline, mathematical-proof checks, and visual inspection of the rendered PDF. A prototype self-improvement loop records research traces and proposes harness improvements that are adopted only after reviewer approval.

With the advent of large multimodal language models, science is now at a threshold of an AI-based technological transformation. Recently, a plethora of new AI models and tools has been proposed, promising to empower researchers and academics worldwide to conduct their research more effectively and efficiently. This includes all aspects of the research cycle, especially (1) searching for relevant literature; (2) generating research ideas and conducting experimentation; generating (3) text-based and (4) multimodal content (e.g., scientific figures and diagrams); and (5) AI-based automatic peer review. In this survey, we provide an in-depth overview over these exciting recent developments, which promise to fundamentally alter the scientific research process for good. Our survey covers the five aspects outlined above, indicating relevant datasets, methods and results (including evaluation) as well as limitations and scope for future research. Ethical concerns regarding shortcomings of these tools and potential for misuse (fake science, plagiarism, harms to research integrity) take a particularly prominent place in our discussion. We hope that our survey will not only become a reference guide for newcomers to the field but also a catalyst for new AI-based initiatives in the area of "AI4Science".

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

As large language models (LLMs) advance, the ultimate vision for their role in science is emerging: we could build an AI collaborator to effectively assist human beings throughout the entire scientific research process. We refer to this envisioned system as ResearchGPT. Given that scientific research progresses through multiple interdependent phases, achieving this vision requires rigorous benchmarks that evaluate the end-to-end workflow rather than isolated sub-tasks. To this end, we contribute CS-54k, a high-quality corpus of scientific Q&A pairs in computer science, built from 14k CC-licensed papers. It is constructed through a scalable, paper-grounded pipeline that combines retrieval-augmented generation (RAG) with multi-stage quality control to ensure factual grounding. From this unified corpus, we derive two complementary subsets: CS-4k, a carefully curated benchmark for evaluating AI's ability to assist scientific research, and CS-50k, a large-scale training dataset. Extensive experiments demonstrate that CS-4k stratifies state-of-the-art LLMs into distinct capability tiers. Open models trained on CS-50k with supervised training and reinforcement learning demonstrate substantial improvements. Even 7B-scale models, when properly trained, outperform many larger proprietary systems, such as GPT-4.1, GPT-4o, and Gemini 2.5 Pro. This indicates that making AI models better research assistants relies more on domain-aligned training with high-quality data than on pretraining scale or general benchmark performance. We release CS-4k and CS-50k in the hope of fostering AI systems as reliable collaborators in CS research.

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

We introduce the STATION, an open-world multi-agent environment that models a miniature scientific ecosystem. Leveraging their extended context windows, agents in the Station can engage in long scientific journeys that include reading papers from peers, formulating hypotheses, submitting code, performing analyses, and publishing results. Importantly, there is no centralized system coordinating their activities - agents are free to choose their own actions and develop their own narratives within the Station. Experiments demonstrate that AI agents in the Station achieve new state-of-the-art performance on a wide range of benchmarks, spanning from mathematics to computational biology to machine learning, notably surpassing AlphaEvolve in circle packing. A rich tapestry of narratives emerges as agents pursue independent research, interact with peers, and build upon a cumulative history. From these emergent narratives, novel methods arise organically, such as a new density-adaptive algorithm for scRNA-seq batch integration. The Station marks a first step towards autonomous scientific discovery driven by emergent behavior in an open-world environment, representing a new paradigm that moves beyond rigid optimization.

Recent progress in autonomous code generation has fueled excitement around AI agents capable of accelerating scientific discovery by running experiments. However, there is currently no benchmark that evaluates whether such agents can implement scientific ideas when given varied amounts of code as a starting point, interpolating between reproduction (running code) and from-scratch replication (fully re-implementing and running code). We introduce AutoExperiment, a benchmark that evaluates AI agents' ability to implement and run machine learning experiments based on natural language descriptions in research papers. In each task, agents are given a research paper, a codebase with key functions masked out, and a command to run the experiment. The goal is to generate the missing code, execute the experiment in a sandboxed environment, and reproduce the results. AutoExperiment scales in difficulty by varying the number of missing functions n, ranging from partial reproduction to full replication. We evaluate state-of-the-art agents and find that performance degrades rapidly as n increases. Agents that can dynamically interact with the environment (e.g. to debug their code) can outperform agents in fixed "agentless" harnesses, and there exists a significant gap between single-shot and multi-trial success rates (Pass@1 vs. Pass@5), motivating verifier approaches to our benchmark. Our findings highlight critical challenges in long-horizon code generation, context retrieval, and autonomous experiment execution, establishing AutoExperiment as a new benchmark for evaluating progress in AI-driven scientific experimentation. Our data and code are open-sourced at https://github.com/j1mk1m/AutoExperiment .

Scientific discovery is poised for rapid advancement through advanced robotics and artificial intelligence. Current scientific practices face substantial limitations as manual experimentation remains time-consuming and resource-intensive, while multidisciplinary research demands knowledge integration beyond individual researchers' expertise boundaries. Here, we envision an autonomous generalist scientist (AGS) concept combines agentic AI and embodied robotics to automate the entire research lifecycle. This system could dynamically interact with both physical and virtual environments while facilitating the integration of knowledge across diverse scientific disciplines. By deploying these technologies throughout every research stage -- spanning literature review, hypothesis generation, experimentation, and manuscript writing -- and incorporating internal reflection alongside external feedback, this system aims to significantly reduce the time and resources needed for scientific discovery. Building on the evolution from virtual AI scientists to versatile generalist AI-based robot scientists, AGS promises groundbreaking potential. As these autonomous systems become increasingly integrated into the research process, we hypothesize that scientific discovery might adhere to new scaling laws, potentially shaped by the number and capabilities of these autonomous systems, offering novel perspectives on how knowledge is generated and evolves. The adaptability of embodied robots to extreme environments, paired with the flywheel effect of accumulating scientific knowledge, holds the promise of continually pushing beyond both physical and intellectual frontiers.

Auto-regressive LLM-based software engineering (SWE) agents, henceforth SWE agents, have made tremendous progress (>60% on SWE-Bench Verified) on real-world coding challenges including GitHub issue resolution. SWE agents use a combination of reasoning, environment interaction and self-reflection to resolve issues thereby generating "trajectories". Analysis of SWE agent trajectories is difficult, not only as they exceed LLM sequence length (sometimes, greater than 128k) but also because it involves a relatively prolonged interaction between an LLM and the environment managed by the agent. In case of an agent error, it can be hard to decipher, locate and understand its scope. Similarly, it can be hard to track improvements or regression over multiple runs or experiments. While a lot of research has gone into making these SWE agents reach state-of-the-art, much less focus has been put into creating tools to help analyze and visualize agent output. We propose a novel tool called SeaView: Software Engineering Agent Visual Interface for Enhanced Workflow, with a vision to assist SWE-agent researchers to visualize and inspect their experiments. SeaView's novel mechanisms help compare experimental runs with varying hyper-parameters or LLMs, and quickly get an understanding of LLM or environment related problems. Based on our user study, experienced researchers spend between 10 and 30 minutes to gather the information provided by SeaView, while researchers with little experience can spend between 30 minutes to 1 hour to diagnose their experiment.

We review our recent work in the area of autonomous materials research, highlighting the coupling of machine learning methods and models and more problem-aware modeling. We review the general Bayesian framework for closed-loop design employed by many autonomous materials platforms. We then provide examples of our work on such platforms. We finally review our approaches to extend current statistical and ML models to better reflect problem-specific structure including the use of physics-based models and incorporation of operational considerations into the decision-making procedure.

Automated scientific discovery with large language models is transforming the research lifecycle from ideation to experimentation, yet existing agents struggle to autonomously process raw data collected from scientific experiments. We introduce SciDER, a data-centric end-to-end system that automates the research lifecycle. Unlike traditional frameworks, our specialized agents collaboratively parse and analyze raw scientific data, generate hypotheses and experimental designs grounded in specific data characteristics, and write and execute corresponding code. Evaluation on three benchmarks shows SciDER excels in specialized data-driven scientific discovery and outperforms general-purpose agents and state-of-the-art models through its self-evolving memory and critic-led feedback loop. Distributed as a modular Python package, we also provide easy-to-use PyPI packages with a lightweight web interface to accelerate autonomous, data-driven research and aim to be accessible to all researchers and developers.

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

We report a case study of four end-to-end attempts to autonomously generate ML research papers using a pipeline of six LLM agents mapped to stages of the scientific workflow. Of these four, three attempts failed during implementation or evaluation. One completed the pipeline and was accepted to Agents4Science 2025, an experimental inaugural venue that required AI systems as first authors, passing both human and multi-AI review. From these attempts, we document six recurring failure modes: bias toward training data defaults, implementation drift under execution pressure, memory and context degradation across long-horizon tasks, overexcitement that declares success despite obvious failures, insufficient domain intelligence, and weak scientific taste in experimental design. We conclude by discussing four design principles for more robust AI-scientist systems, implications for autonomous scientific discovery, and we release all prompts, artifacts, and outputs at https://github.com/Lossfunk/ai-scientist-artefacts-v1

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.

AI scientist systems, capable of autonomously executing the full research workflow from hypothesis generation and experimentation to paper writing, hold significant potential for accelerating scientific discovery. However, the internal workflow of these systems have not been closely examined. This lack of scrutiny poses a risk of introducing flaws that could undermine the integrity, reliability, and trustworthiness of their research outputs. In this paper, we identify four potential failure modes in contemporary AI scientist systems: inappropriate benchmark selection, data leakage, metric misuse, and post-hoc selection bias. To examine these risks, we design controlled experiments that isolate each failure mode while addressing challenges unique to evaluating AI scientist systems. Our assessment of two prominent open-source AI scientist systems reveals the presence of several failures, across a spectrum of severity, which can be easily overlooked in practice. Finally, we demonstrate that access to trace logs and code from the full automated workflow enables far more effective detection of such failures than examining the final paper alone. We thus recommend journals and conferences evaluating AI-generated research to mandate submission of these artifacts alongside the paper to ensure transparency, accountability, and reproducibility.

Recent works exploring deep learning application to dynamical systems modeling have demonstrated that embedding physical priors into neural networks can yield more effective, physically-realistic, and data-efficient models. However, in the absence of complete prior knowledge of a dynamical system's physical characteristics, determining the optimal structure and optimization strategy for these models can be difficult. In this work, we explore methods for discovering neural state space dynamics models for system identification. Starting with a design space of block-oriented state space models and structured linear maps with strong physical priors, we encode these components into a model genome alongside network structure, penalty constraints, and optimization hyperparameters. Demonstrating the overall utility of the design space, we employ an asynchronous genetic search algorithm that alternates between model selection and optimization and obtains accurate physically consistent models of three physical systems: an aerodynamics body, a continuous stirred tank reactor, and a two tank interacting system.

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

With an increasing number of replication studies performed in psychological science, the question of how to evaluate the outcome of a replication attempt deserves careful consideration. Bayesian approaches allow to incorporate uncertainty and prior information into the analysis of the replication attempt by their design. The Replication Bayes Factor, introduced by Verhagen & Wagenmakers (2014), provides quantitative, relative evidence in favor or against a successful replication. In previous work by Verhagen & Wagenmakers (2014) it was limited to the case of t-tests. In this paper, the Replication Bayes Factor is extended to F-tests in multi-group, fixed-effect ANOVA designs. Simulations and examples are presented to facilitate the understanding and to demonstrate the usefulness of this approach. Finally, the Replication Bayes Factor is compared to other Bayesian and frequentist approaches and discussed in the context of replication attempts. R code to calculate Replication Bayes factors and to reproduce the examples in the paper is available at https://osf.io/jv39h/.

Critical peer review of scientific manuscripts presents a significant challenge for Large Language Models (LLMs), partly due to data limitations and the complexity of expert reasoning. This report introduces Persistent Workflow Prompting (PWP), a potentially broadly applicable prompt engineering methodology designed to bridge this gap using standard LLM chat interfaces (zero-code, no APIs). We present a proof-of-concept PWP prompt for the critical analysis of experimental chemistry manuscripts, featuring a hierarchical, modular architecture (structured via Markdown) that defines detailed analysis workflows. We develop this PWP prompt through iterative application of meta-prompting techniques and meta-reasoning aimed at systematically codifying expert review workflows, including tacit knowledge. Submitted once at the start of a session, this PWP prompt equips the LLM with persistent workflows triggered by subsequent queries, guiding modern reasoning LLMs through systematic, multimodal evaluations. Demonstrations show the PWP-guided LLM identifying major methodological flaws in a test case while mitigating LLM input bias and performing complex tasks, including distinguishing claims from evidence, integrating text/photo/figure analysis to infer parameters, executing quantitative feasibility checks, comparing estimates against claims, and assessing a priori plausibility. To ensure transparency and facilitate replication, we provide full prompts, detailed demonstration analyses, and logs of interactive chats as supplementary resources. Beyond the specific application, this work offers insights into the meta-development process itself, highlighting the potential of PWP, informed by detailed workflow formalization, to enable sophisticated analysis using readily available LLMs for complex scientific tasks.

Reproducibility is central to research credibility, yet large-scale reanalysis of empricial data remains costly because replication packages vary widely in structure, software environment, and documentation. We develop and evaluate an agentic AI workflow that addresses this execution bottleneck while preserving scientific rigor. The system separates scientific reasoning from computational execution: researchers design fixed diagnostic templates, and the workflow automates the acquisition, harmonization, and execution of replication materials using pre-specified, version-controlled code. A structured knowledge layer records resolved failure patterns, enabling adaptation across heterogeneous studies while keeping each pipeline version transparent and stable. We evaluate this workflow on 92 instrumental variable (IV) studies, including 67 with manually verified reproducible 2SLS estimates and 25 newly published IV studies under identical criteria. For each paper, we analyze up to three two-stage least squares (2SLS) specifications, totaling 215. Across the 92 papers, the system achieves 87% end-to-end success overall. Conditional on accessible data and code, reproducibility is 100% at both the paper and specification levels. The framework substantially lowers the cost of executing established empirical protocols and can be adapted in empirical settings where analytic templates and norms of transparency are well established.

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.

The rapid advancement in capabilities of large language models (LLMs) raises a pivotal question: How can LLMs accelerate scientific discovery? This work tackles the crucial first stage of research, generating novel hypotheses. While recent work on automated hypothesis generation focuses on multi-agent frameworks and extending test-time compute, none of the approaches effectively incorporate transparency and steerability through a synergistic Human-in-the-loop (HITL) approach. To address this gap, we introduce IRIS: Interactive Research Ideation System, an open-source platform designed for researchers to leverage LLM-assisted scientific ideation. IRIS incorporates innovative features to enhance ideation, including adaptive test-time compute expansion via Monte Carlo Tree Search (MCTS), fine-grained feedback mechanism, and query-based literature synthesis. Designed to empower researchers with greater control and insight throughout the ideation process. We additionally conduct a user study with researchers across diverse disciplines, validating the effectiveness of our system in enhancing ideation. We open-source our code at https://github.com/Anikethh/IRIS-Interactive-Research-Ideation-System

Multimodal Large Language Models (MLLMs) excel in general domains but struggle with complex, real-world science. We posit that polymer science, an interdisciplinary field spanning chemistry, physics, biology, and engineering, is an ideal high-stakes testbed due to its diverse multimodal data. Yet, existing benchmarks related to polymer science largely overlook real-world workflows, limiting their practical utility and failing to systematically evaluate MLLMs across the full, practice-grounded lifecycle of experimentation. We introduce PolyReal, a novel multimodal benchmark grounded in real-world scientific practices to evaluate MLLMs on the full lifecycle of polymer experimentation. It covers five critical capabilities: (1) foundational knowledge application; (2) lab safety analysis; (3) experiment mechanism reasoning; (4) raw data extraction; and (5) performance & application exploration. Our evaluation of leading MLLMs on PolyReal reveals a capability imbalance. While models perform well on knowledge-intensive reasoning (e.g., Experiment Mechanism Reasoning), they drop sharply on practice-based tasks (e.g., Lab Safety Analysis and Raw Data Extraction). This exposes a severe gap between abstract scientific knowledge and its practical, context-dependent application, showing that these real-world tasks remain challenging for MLLMs. Thus, PolyReal helps address this evaluation gap and provides a practical benchmark for assessing AI systems in real-world scientific workflows.

Effective research ideation is a critical step for scientific research. However, the exponential increase in scientific literature makes it challenging for researchers to stay current with recent advances and identify meaningful research directions. Recent developments in large language models~(LLMs) suggest a promising avenue for automating the generation of novel research ideas. However, existing methods for idea generation either trivially prompt LLMs or directly expose LLMs to extensive literature without indicating useful information. Inspired by the research process of human researchers, we propose a Chain-of-Ideas~(CoI) agent, an LLM-based agent that organizes relevant literature in a chain structure to effectively mirror the progressive development in a research domain. This organization facilitates LLMs to capture the current advancements in research, thereby enhancing their ideation capabilities. Furthermore, we propose Idea Arena, an evaluation protocol that can comprehensively evaluate idea generation methods from different perspectives, aligning closely with the preferences of human researchers. Experimental results indicate that the CoI agent consistently outperforms other methods and shows comparable quality as humans in research idea generation. Moreover, our CoI agent is budget-friendly, with a minimum cost of \$0.50 to generate a candidate idea and its corresponding experimental design.

The exploration of thermoelectric materials is challenging considering the large materials space, combined with added exponential degrees of freedom coming from doping and the diversity of synthetic pathways. Here we seek to incorporate historical data and update and refine it using experimental feedback by employing error-correction learning (ECL). We thus learn from prior datasets and then adapt the model to differences in synthesis and characterization that are otherwise difficult to parameterize. We then apply this strategy to discovering thermoelectric materials where we prioritize synthesis at temperatures < 300{\deg}C. We document a previously unreported chemical family of thermoelectric materials, PbSe:SnSb, finding that the best candidate in this chemical family, 2 wt% SnSb doped PbSe, exhibits a power factor more than 2x that of PbSe. Our investigations show that our closed-loop experimentation strategy reduces the required number of experiments to find an optimized material by as much as 3x compared to high-throughput searches powered by state-of-the-art machine learning models. We also observe that this improvement is dependent on the accuracy of prior in a manner that exhibits diminishing returns, and after a certain accuracy is reached, it is factors associated with experimental pathways that dictate the trends.