Daily Papers

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.

Understanding the current capabilities and risks of AI Scientist systems is essential for ensuring trustworthy and sustainable AI-driven scientific progress while preserving the integrity of the academic ecosystem. To this end, we develop Jr. AI Scientist, a state-of-the-art autonomous AI scientist system that mimics the core research workflow of a novice student researcher: Given the baseline paper from the human mentor, it analyzes its limitations, formulates novel hypotheses for improvement, validates them through rigorous experimentation, and writes a paper with the results. Unlike previous approaches that assume full automation or operate on small-scale code, Jr. AI Scientist follows a well-defined research workflow and leverages modern coding agents to handle complex, multi-file implementations, leading to scientifically valuable contributions. For evaluation, we conducted automated assessments using AI Reviewers, author-led evaluations, and submissions to Agents4Science, a venue dedicated to AI-driven scientific contributions. The findings demonstrate that Jr. AI Scientist generates papers receiving higher review scores than existing fully automated systems. Nevertheless, we identify important limitations from both the author evaluation and the Agents4Science reviews, indicating the potential risks of directly applying current AI Scientist systems and key challenges for future research. Finally, we comprehensively report various risks identified during development. We hope these insights will deepen understanding of current progress and risks in AI Scientist development.

Recently, there is an increasing interest in using artificial intelligence (AI) to automate aspects of the research process, or even autonomously conduct the full research cycle from idea generation, over data analysis, to composing and evaluation of scientific manuscripts. Examples of working AI scientist systems have been demonstrated for computer science tasks and running molecular biology labs. While some approaches aim for full autonomy of the scientific AI, others rather aim for leveraging human-AI teaming. Here, we address how to adapt such approaches for boosting Brain-Computer Interface (BCI) development, as well as brain research resp. neuroscience at large. We argue that at this time, a strong emphasis on human-AI teaming, in contrast to fully autonomous AI BCI researcher will be the most promising way forward. We introduce the collaborative workspaces concept for human-AI teaming based on a set of Janusian design principles, looking both ways, to the human as well as to the AI side. Based on these principles, we present ChatBCI, a Python-based toolbox for enabling human-AI collaboration based on interaction with Large Language Models (LLMs), designed for BCI research and development projects. We show how ChatBCI was successfully used in a concrete BCI project on advancing motor imagery decoding from EEG signals. Our approach can be straightforwardly extended to broad neurotechnological and neuroscientific topics, and may by design facilitate human expert knowledge transfer to scientific AI systems in general.

The emergence of large language models (LLMs) is propelling automated scientific discovery to the next level, with LLM-based Artificial Intelligence (AI) Scientist systems now taking the lead in scientific research. Several influential works have already appeared in the field of AI Scientist systems, with AI-generated research papers having been accepted at the ICLR 2025 workshop, suggesting that a human-level AI Scientist capable of uncovering phenomena previously unknown to humans, may soon become a reality. In this survey, we focus on the central question: How far are AI scientists from changing the world and reshaping the scientific research paradigm? To answer this question, we provide a prospect-driven review that comprehensively analyzes the current achievements of AI Scientist systems, identifying key bottlenecks and the critical components required for the emergence of a scientific agent capable of producing ground-breaking discoveries that solve grand challenges. We hope this survey will contribute to a clearer understanding of limitations of current AI Scientist systems, showing where we are, what is missing, and what the ultimate goals for scientific AI should be.

While previous AI Scientist systems can generate novel findings, they often lack the focus to produce scientifically valuable contributions that address pressing human-defined challenges. We introduce DeepScientist, a system designed to overcome this by conducting goal-oriented, fully autonomous scientific discovery over month-long timelines. It formalizes discovery as a Bayesian Optimization problem, operationalized through a hierarchical evaluation process consisting of "hypothesize, verify, and analyze". Leveraging a cumulative Findings Memory, this loop intelligently balances the exploration of novel hypotheses with exploitation, selectively promoting the most promising findings to higher-fidelity levels of validation. Consuming over 20,000 GPU hours, the system generated about 5,000 unique scientific ideas and experimentally validated approximately 1100 of them, ultimately surpassing human-designed state-of-the-art (SOTA) methods on three frontier AI tasks by 183.7\%, 1.9\%, and 7.9\%. This work provides the first large-scale evidence of an AI achieving discoveries that progressively surpass human SOTA on scientific tasks, producing valuable findings that genuinely push the frontier of scientific discovery. To facilitate further research into this process, we will open-source all experimental logs and system code at https://github.com/ResearAI/DeepScientist/.

Data-driven scientific discovery requires iterative cycles of literature search, hypothesis generation, and data analysis. Substantial progress has been made towards AI agents that can automate scientific research, but all such agents remain limited in the number of actions they can take before losing coherence, thus limiting the depth of their findings. Here we present Kosmos, an AI scientist that automates data-driven discovery. Given an open-ended objective and a dataset, Kosmos runs for up to 12 hours performing cycles of parallel data analysis, literature search, and hypothesis generation before synthesizing discoveries into scientific reports. Unlike prior systems, Kosmos uses a structured world model to share information between a data analysis agent and a literature search agent. The world model enables Kosmos to coherently pursue the specified objective over 200 agent rollouts, collectively executing an average of 42,000 lines of code and reading 1,500 papers per run. Kosmos cites all statements in its reports with code or primary literature, ensuring its reasoning is traceable. Independent scientists found 79.4% of statements in Kosmos reports to be accurate, and collaborators reported that a single 20-cycle Kosmos run performed the equivalent of 6 months of their own research time on average. Furthermore, collaborators reported that the number of valuable scientific findings generated scales linearly with Kosmos cycles (tested up to 20 cycles). We highlight seven discoveries made by Kosmos that span metabolomics, materials science, neuroscience, and statistical genetics. Three discoveries independently reproduce findings from preprinted or unpublished manuscripts that were not accessed by Kosmos at runtime, while four make novel contributions to the scientific literature.

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.

The leading AI companies are increasingly focused on building generalist AI agents -- systems that can autonomously plan, act, and pursue goals across almost all tasks that humans can perform. Despite how useful these systems might be, unchecked AI agency poses significant risks to public safety and security, ranging from misuse by malicious actors to a potentially irreversible loss of human control. We discuss how these risks arise from current AI training methods. Indeed, various scenarios and experiments have demonstrated the possibility of AI agents engaging in deception or pursuing goals that were not specified by human operators and that conflict with human interests, such as self-preservation. Following the precautionary principle, we see a strong need for safer, yet still useful, alternatives to the current agency-driven trajectory. Accordingly, we propose as a core building block for further advances the development of a non-agentic AI system that is trustworthy and safe by design, which we call Scientist AI. This system is designed to explain the world from observations, as opposed to taking actions in it to imitate or please humans. It comprises a world model that generates theories to explain data and a question-answering inference machine. Both components operate with an explicit notion of uncertainty to mitigate the risks of overconfident predictions. In light of these considerations, a Scientist AI could be used to assist human researchers in accelerating scientific progress, including in AI safety. In particular, our system can be employed as a guardrail against AI agents that might be created despite the risks involved. Ultimately, focusing on non-agentic AI may enable the benefits of AI innovation while avoiding the risks associated with the current trajectory. We hope these arguments will motivate researchers, developers, and policymakers to favor this safer path.

Despite advances in scientific AI, a coherent framework for Scientific General Intelligence (SGI)-the ability to autonomously conceive, investigate, and reason across scientific domains-remains lacking. We present an operational SGI definition grounded in the Practical Inquiry Model (PIM: Deliberation, Conception, Action, Perception) and operationalize it via four scientist-aligned tasks: deep research, idea generation, dry/wet experiments, and experimental reasoning. SGI-Bench comprises over 1,000 expert-curated, cross-disciplinary samples inspired by Science's 125 Big Questions, enabling systematic evaluation of state-of-the-art LLMs. Results reveal gaps: low exact match (10--20%) in deep research despite step-level alignment; ideas lacking feasibility and detail; high code executability but low execution result accuracy in dry experiments; low sequence fidelity in wet protocols; and persistent multimodal comparative-reasoning challenges. We further introduce Test-Time Reinforcement Learning (TTRL), which optimizes retrieval-augmented novelty rewards at inference, enhancing hypothesis novelty without reference answer. Together, our PIM-grounded definition, workflow-centric benchmark, and empirical insights establish a foundation for AI systems that genuinely participate in scientific discovery.

AI scientists are emerging computational systems that serve as collaborative partners in discovery. These systems remain difficult to build because they are bespoke, tied to rigid workflows, and lack shared environments that unify tools, data, and analyses into a common ecosystem. In omics, unified ecosystems have transformed research by enabling interoperability, reuse, and community-driven development; AI scientists require comparable infrastructure. We present ToolUniverse, an ecosystem for building AI scientists from any language or reasoning model, whether open or closed. TOOLUNIVERSE standardizes how AI scientists identify and call tools, integrating more than 600 machine learning models, datasets, APIs, and scientific packages for data analysis, knowledge retrieval, and experimental design. It automatically refines tool interfaces for correct use by AI scientists, creates new tools from natural language descriptions, iteratively optimizes tool specifications, and composes tools into agentic workflows. In a case study of hypercholesterolemia, ToolUniverse was used to create an AI scientist to identify a potent analog of a drug with favorable predicted properties. The open-source ToolUniverse is available at https://aiscientist.tools.

AI is increasingly playing a pivotal role in transforming how scientific discoveries are made. We introduce The AI Scientist-v2, an end-to-end agentic system capable of producing the first entirely AI generated peer-review-accepted workshop paper. This system iteratively formulates scientific hypotheses, designs and executes experiments, analyzes and visualizes data, and autonomously authors scientific manuscripts. Compared to its predecessor (v1, Lu et al., 2024 arXiv:2408.06292), The AI Scientist-v2 eliminates the reliance on human-authored code templates, generalizes effectively across diverse machine learning domains, and leverages a novel progressive agentic tree-search methodology managed by a dedicated experiment manager agent. Additionally, we enhance the AI reviewer component by integrating a Vision-Language Model (VLM) feedback loop for iterative refinement of content and aesthetics of the figures. We evaluated The AI Scientist-v2 by submitting three fully autonomous manuscripts to a peer-reviewed ICLR workshop. Notably, one manuscript achieved high enough scores to exceed the average human acceptance threshold, marking the first instance of a fully AI-generated paper successfully navigating a peer review. This accomplishment highlights the growing capability of AI in conducting all aspects of scientific research. We anticipate that further advancements in autonomous scientific discovery technologies will profoundly impact human knowledge generation, enabling unprecedented scalability in research productivity and significantly accelerating scientific breakthroughs, greatly benefiting society at large. We have open-sourced the code at https://github.com/SakanaAI/AI-Scientist-v2 to foster the future development of this transformative technology. We also discuss the role of AI in science, including AI safety.

A major step toward Artificial General Intelligence (AGI) and Super Intelligence is AI's ability to autonomously conduct research - what we term Artificial Research Intelligence (ARI). If machines could generate hypotheses, conduct experiments, and write research papers without human intervention, it would transform science. Sakana recently introduced the 'AI Scientist', claiming to conduct research autonomously, i.e. they imply to have achieved what we term Artificial Research Intelligence (ARI). The AI Scientist gained much attention, but a thorough independent evaluation has yet to be conducted. Our evaluation of the AI Scientist reveals critical shortcomings. The system's literature reviews produced poor novelty assessments, often misclassifying established concepts (e.g., micro-batching for stochastic gradient descent) as novel. It also struggles with experiment execution: 42% of experiments failed due to coding errors, while others produced flawed or misleading results. Code modifications were minimal, averaging 8% more characters per iteration, suggesting limited adaptability. Generated manuscripts were poorly substantiated, with a median of five citations, most outdated (only five of 34 from 2020 or later). Structural errors were frequent, including missing figures, repeated sections, and placeholder text like 'Conclusions Here'. Some papers contained hallucinated numerical results. Despite these flaws, the AI Scientist represents a leap forward in research automation. It generates full research manuscripts with minimal human input, challenging expectations of AI-driven science. Many reviewers might struggle to distinguish its work from human researchers. While its quality resembles a rushed undergraduate paper, its speed and cost efficiency are unprecedented, producing a full paper for USD 6 to 15 with 3.5 hours of human involvement, far outpacing traditional researchers.

With the rapid development of Large Language Models (LLMs), AI agents have demonstrated increasing proficiency in scientific tasks, ranging from hypothesis generation and experimental design to manuscript writing. Such agent systems are commonly referred to as "AI Scientists." However, existing AI Scientists predominantly formulate scientific discovery as a standalone search or optimization problem, overlooking the fact that scientific research is inherently a social and collaborative endeavor. Real-world science relies on a complex scientific infrastructure composed of collaborative mechanisms, contribution attribution, peer review, and structured scientific knowledge networks. Due to the lack of modeling for these critical dimensions, current systems struggle to establish a genuine research ecosystem or interact deeply with the human scientific community. To bridge this gap, we introduce OmniScientist, a framework that explicitly encodes the underlying mechanisms of human research into the AI scientific workflow. OmniScientist not only achieves end-to-end automation across data foundation, literature review, research ideation, experiment automation, scientific writing, and peer review, but also provides comprehensive infrastructural support by simulating the human scientific system, comprising: (1) a structured knowledge system built upon citation networks and conceptual correlations; (2) a collaborative research protocol (OSP), which enables seamless multi-agent collaboration and human researcher participation; and (3) an open evaluation platform (ScienceArena) based on blind pairwise user voting and Elo rankings. This infrastructure empowers agents to not only comprehend and leverage human knowledge systems but also to collaborate and co-evolve, fostering a sustainable and scalable innovation ecosystem.

Recent advancements in large language model (LLM) agents have significantly accelerated scientific discovery automation, yet concurrently raised critical ethical and safety concerns. To systematically address these challenges, we introduce SafeScientist, an innovative AI scientist framework explicitly designed to enhance safety and ethical responsibility in AI-driven scientific exploration. SafeScientist proactively refuses ethically inappropriate or high-risk tasks and rigorously emphasizes safety throughout the research process. To achieve comprehensive safety oversight, we integrate multiple defensive mechanisms, including prompt monitoring, agent-collaboration monitoring, tool-use monitoring, and an ethical reviewer component. Complementing SafeScientist, we propose SciSafetyBench, a novel benchmark specifically designed to evaluate AI safety in scientific contexts, comprising 240 high-risk scientific tasks across 6 domains, alongside 30 specially designed scientific tools and 120 tool-related risk tasks. Extensive experiments demonstrate that SafeScientist significantly improves safety performance by 35\% compared to traditional AI scientist frameworks, without compromising scientific output quality. Additionally, we rigorously validate the robustness of our safety pipeline against diverse adversarial attack methods, further confirming the effectiveness of our integrated approach. The code and data will be available at https://github.com/ulab-uiuc/SafeScientist. red{Warning: this paper contains example data that may be offensive or harmful.}

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.

Recent advances in large language models (LLMs) have fueled the vision of automated scientific discovery, often called AI Co-Scientists. To date, prior work casts these systems as generative co-authors responsible for crafting hypotheses, synthesizing code, or drafting manuscripts. In this work, we explore a complementary application: using LLMs as verifiers to automate the academic verification of scientific manuscripts. To that end, we introduce SPOT, a dataset of 83 published papers paired with 91 errors significant enough to prompt errata or retraction, cross-validated with actual authors and human annotators. Evaluating state-of-the-art LLMs on SPOT, we find that none surpasses 21.1\% recall or 6.1\% precision (o3 achieves the best scores, with all others near zero). Furthermore, confidence estimates are uniformly low, and across eight independent runs, models rarely rediscover the same errors, undermining their reliability. Finally, qualitative analysis with domain experts reveals that even the strongest models make mistakes resembling student-level misconceptions derived from misunderstandings. These findings highlight the substantial gap between current LLM capabilities and the requirements for dependable AI-assisted academic verification.

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.

Artificial Intelligence (AI) is accelerating the transformation of scientific research paradigms, not only enhancing research efficiency but also driving innovation. We introduce NovelSeek, a unified closed-loop multi-agent framework to conduct Autonomous Scientific Research (ASR) across various scientific research fields, enabling researchers to tackle complicated problems in these fields with unprecedented speed and precision. NovelSeek highlights three key advantages: 1) Scalability: NovelSeek has demonstrated its versatility across 12 scientific research tasks, capable of generating innovative ideas to enhance the performance of baseline code. 2) Interactivity: NovelSeek provides an interface for human expert feedback and multi-agent interaction in automated end-to-end processes, allowing for the seamless integration of domain expert knowledge. 3) Efficiency: NovelSeek has achieved promising performance gains in several scientific fields with significantly less time cost compared to human efforts. For instance, in reaction yield prediction, it increased from 27.6% to 35.4% in just 12 hours; in enhancer activity prediction, accuracy rose from 0.52 to 0.79 with only 4 hours of processing; and in 2D semantic segmentation, precision advanced from 78.8% to 81.0% in a mere 30 hours.

Data science plays a critical role in transforming complex data into actionable insights across numerous domains. Recent developments in large language models (LLMs) have significantly automated data science workflows, but a fundamental question persists: Can these agentic AI systems truly match the performance of human data scientists who routinely leverage domain-specific knowledge? We explore this question by designing a prediction task where a crucial latent variable is hidden in relevant image data instead of tabular features. As a result, agentic AI that generates generic codes for modeling tabular data cannot perform well, while human experts could identify the important hidden variable using domain knowledge. We demonstrate this idea with a synthetic dataset for property insurance. Our experiments show that agentic AI that relies on generic analytics workflow falls short of methods that use domain-specific insights. This highlights a key limitation of the current agentic AI for data science and underscores the need for future research to develop agentic AI systems that can better recognize and incorporate domain knowledge.

Building a working mental model of a protein typically requires weeks of reading, cross-referencing crystal and predicted structures, and inspecting ligand complexes, an effort that is slow, unevenly accessible, and often requires specialized computational skills. We introduce Speak to a Protein, a new capability that turns protein analysis into an interactive, multimodal dialogue with an expert co-scientist. The AI system retrieves and synthesizes relevant literature, structures, and ligand data; grounds answers in a live 3D scene; and can highlight, annotate, manipulate and see the visualization. It also generates and runs code when needed, explaining results in both text and graphics. We demonstrate these capabilities on relevant proteins, posing questions about binding pockets, conformational changes, or structure-activity relationships to test ideas in real-time. Speak to a Protein reduces the time from question to evidence, lowers the barrier to advanced structural analysis, and enables hypothesis generation by tightly coupling language, code, and 3D structures. Speak to a Protein is freely accessible at https://open.playmolecule.org.

The integration of Agentic AI into scientific discovery marks a new frontier in research automation. These AI systems, capable of reasoning, planning, and autonomous decision-making, are transforming how scientists perform literature review, generate hypotheses, conduct experiments, and analyze results. This survey provides a comprehensive overview of Agentic AI for scientific discovery, categorizing existing systems and tools, and highlighting recent progress across fields such as chemistry, biology, and materials science. We discuss key evaluation metrics, implementation frameworks, and commonly used datasets to offer a detailed understanding of the current state of the field. Finally, we address critical challenges, such as literature review automation, system reliability, and ethical concerns, while outlining future research directions that emphasize human-AI collaboration and enhanced system calibration.

One of the grand challenges of artificial general intelligence is developing agents capable of conducting scientific research and discovering new knowledge. While frontier models have already been used as aids to human scientists, e.g. for brainstorming ideas, writing code, or prediction tasks, they still conduct only a small part of the scientific process. This paper presents the first comprehensive framework for fully automatic scientific discovery, enabling frontier large language models to perform research independently and communicate their findings. We introduce The AI Scientist, which generates novel research ideas, writes code, executes experiments, visualizes results, describes its findings by writing a full scientific paper, and then runs a simulated review process for evaluation. In principle, this process can be repeated to iteratively develop ideas in an open-ended fashion, acting like the human scientific community. We demonstrate its versatility by applying it to three distinct subfields of machine learning: diffusion modeling, transformer-based language modeling, and learning dynamics. Each idea is implemented and developed into a full paper at a cost of less than $15 per paper. To evaluate the generated papers, we design and validate an automated reviewer, which we show achieves near-human performance in evaluating paper scores. The AI Scientist can produce papers that exceed the acceptance threshold at a top machine learning conference as judged by our automated reviewer. This approach signifies the beginning of a new era in scientific discovery in machine learning: bringing the transformative benefits of AI agents to the entire research process of AI itself, and taking us closer to a world where endless affordable creativity and innovation can be unleashed on the world's most challenging problems. Our code is open-sourced at https://github.com/SakanaAI/AI-Scientist

The powerful reasoning capabilities of Large Language Models (LLMs) in mathematics and coding, combined with their ability to automate complex tasks through agentic frameworks, present unprecedented opportunities for accelerating scientific innovation. In this paper, we introduce AI-Researcher, a fully autonomous research system that transforms how AI-driven scientific discovery is conducted and evaluated. Our framework seamlessly orchestrates the complete research pipeline--from literature review and hypothesis generation to algorithm implementation and publication-ready manuscript preparation--with minimal human intervention. To rigorously assess autonomous research capabilities, we develop Scientist-Bench, a comprehensive benchmark comprising state-of-the-art papers across diverse AI research domains, featuring both guided innovation and open-ended exploration tasks. Through extensive experiments, we demonstrate that AI-Researcher achieves remarkable implementation success rates and produces research papers that approach human-level quality. This work establishes new foundations for autonomous scientific innovation that can complement human researchers by systematically exploring solution spaces beyond cognitive limitations.

Scientific discovery is a complex cognitive process that has driven human knowledge and technological progress for centuries. While artificial intelligence (AI) has made significant advances in automating aspects of scientific reasoning, simulation, and experimentation, we still lack integrated AI systems capable of performing autonomous long-term scientific research and discovery. This paper examines the current state of AI for scientific discovery, highlighting recent progress in large language models and other AI techniques applied to scientific tasks. We then outline key challenges and promising research directions toward developing more comprehensive AI systems for scientific discovery, including the need for science-focused AI agents, improved benchmarks and evaluation metrics, multimodal scientific representations, and unified frameworks combining reasoning, theorem proving, and data-driven modeling. Addressing these challenges could lead to transformative AI tools to accelerate progress across disciplines towards scientific discovery.

Rapid development of artificial intelligence has drastically accelerated the development of scientific discovery. Trained with large-scale observation data, deep neural networks extract the underlying patterns in an end-to-end manner and assist human researchers with highly-precised predictions in unseen scenarios. The recent rise of Large Language Models (LLMs) and the empowered autonomous agents enable scientists to gain help through interaction in different stages of their research, including but not limited to literature review, research ideation, idea implementation, and academic writing. However, AI researchers instantiated by foundation model empowered agents with full-process autonomy are still in their infancy. In this paper, we study AI-Generated Science (AIGS), where agents independently and autonomously complete the entire research process and discover scientific laws. By revisiting the definition of scientific research, we argue that falsification is the essence of both human research process and the design of an AIGS system. Through the lens of falsification, prior systems attempting towards AI-Generated Science either lack the part in their design, or rely heavily on existing verification engines that narrow the use in specialized domains. In this work, we propose Baby-AIGS as a baby-step demonstration of a full-process AIGS system, which is a multi-agent system with agents in roles representing key research process. By introducing FalsificationAgent, which identify and then verify possible scientific discoveries, we empower the system with explicit falsification. Experiments on three tasks preliminarily show that Baby-AIGS could produce meaningful scientific discoveries, though not on par with experienced human researchers. Finally, we discuss on the limitations of current Baby-AIGS, actionable insights, and related ethical issues in detail.

Recent advancements in artificial intelligence (AI), particularly in large language models (LLMs) such as OpenAI-o1 and DeepSeek-R1, have demonstrated remarkable capabilities in complex domains such as logical reasoning and experimental coding. Motivated by these advancements, numerous studies have explored the application of AI in the innovation process, particularly in the context of scientific research. These AI technologies primarily aim to develop systems that can autonomously conduct research processes across a wide range of scientific disciplines. Despite these significant strides, a comprehensive survey on AI for Research (AI4Research) remains absent, which hampers our understanding and impedes further development in this field. To address this gap, we present a comprehensive survey and offer a unified perspective on AI4Research. Specifically, the main contributions of our work are as follows: (1) Systematic taxonomy: We first introduce a systematic taxonomy to classify five mainstream tasks in AI4Research. (2) New frontiers: Then, we identify key research gaps and highlight promising future directions, focusing on the rigor and scalability of automated experiments, as well as the societal impact. (3) Abundant applications and resources: Finally, we compile a wealth of resources, including relevant multidisciplinary applications, data corpora, and tools. We hope our work will provide the research community with quick access to these resources and stimulate innovative breakthroughs in AI4Research.

This survey examines the rapidly evolving field of Deep Research systems -- AI-powered applications that automate complex research workflows through the integration of large language models, advanced information retrieval, and autonomous reasoning capabilities. We analyze more than 80 commercial and non-commercial implementations that have emerged since 2023, including OpenAI/Deep Research, Gemini/Deep Research, Perplexity/Deep Research, and numerous open-source alternatives. Through comprehensive examination, we propose a novel hierarchical taxonomy that categorizes systems according to four fundamental technical dimensions: foundation models and reasoning engines, tool utilization and environmental interaction, task planning and execution control, and knowledge synthesis and output generation. We explore the architectural patterns, implementation approaches, and domain-specific adaptations that characterize these systems across academic, scientific, business, and educational applications. Our analysis reveals both the significant capabilities of current implementations and the technical and ethical challenges they present regarding information accuracy, privacy, intellectual property, and accessibility. The survey concludes by identifying promising research directions in advanced reasoning architectures, multimodal integration, domain specialization, human-AI collaboration, and ecosystem standardization that will likely shape the future evolution of this transformative technology. By providing a comprehensive framework for understanding Deep Research systems, this survey contributes to both the theoretical understanding of AI-augmented knowledge work and the practical development of more capable, responsible, and accessible research technologies. The paper resources can be viewed at https://github.com/scienceaix/deepresearch.

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.

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.

We present the AI Cosmologist, an agentic system designed to automate cosmological/astronomical data analysis and machine learning research workflows. This implements a complete pipeline from idea generation to experimental evaluation and research dissemination, mimicking the scientific process typically performed by human researchers. The system employs specialized agents for planning, coding, execution, analysis, and synthesis that work together to develop novel approaches. Unlike traditional auto machine-learning systems, the AI Cosmologist generates diverse implementation strategies, writes complete code, handles execution errors, analyzes results, and synthesizes new approaches based on experimental outcomes. We demonstrate the AI Cosmologist capabilities across several machine learning tasks, showing how it can successfully explore solution spaces, iterate based on experimental results, and combine successful elements from different approaches. Our results indicate that agentic systems can automate portions of the research process, potentially accelerating scientific discovery. The code and experimental data used in this paper are available on GitHub at https://github.com/adammoss/aicosmologist. Example papers included in the appendix demonstrate the system's capability to autonomously produce complete scientific publications, starting from only the dataset and task description

Recent advances in large language models (LLMs) have enabled AI agents to autonomously generate scientific proposals, conduct experiments, author papers, and perform peer reviews. Yet this flood of AI-generated research content collides with a fragmented and largely closed publication ecosystem. Traditional journals and conferences rely on human peer review, making them difficult to scale and often reluctant to accept AI-generated research content; existing preprint servers (e.g. arXiv) lack rigorous quality-control mechanisms. Consequently, a significant amount of high-quality AI-generated research lacks appropriate venues for dissemination, hindering its potential to advance scientific progress. To address these challenges, we introduce aiXiv, a next-generation open-access platform for human and AI scientists. Its multi-agent architecture allows research proposals and papers to be submitted, reviewed, and iteratively refined by both human and AI scientists. It also provides API and MCP interfaces that enable seamless integration of heterogeneous human and AI scientists, creating a scalable and extensible ecosystem for autonomous scientific discovery. Through extensive experiments, we demonstrate that aiXiv is a reliable and robust platform that significantly enhances the quality of AI-generated research proposals and papers after iterative revising and reviewing on aiXiv. Our work lays the groundwork for a next-generation open-access ecosystem for AI scientists, accelerating the publication and dissemination of high-quality AI-generated research content. Code is available at https://github.com/aixiv-org. Website is available at https://forms.gle/DxQgCtXFsJ4paMtn8.

The emergence of deep research systems presents significant capabilities in problem-solving, extending from basic queries to sophisticated research tasks. However, existing benchmarks primarily evaluate these systems as agents for web retrieval and report generation, overlooking their potential to discover novel insights on the frontiers of scientific research. To address this gap, we introduce ResearcherBench, the first benchmark focused on evaluating the capabilities of these advanced, agentic systems - which we refer to as Deep AI Research Systems (DARS) - on frontier AI scientific questions. We compiled a dataset of 65 research questions expertly selected from real-world scientific scenarios such as laboratory discussions and interviews, spanning 35 different AI subjects and categorized into three types: technical details, literature review, and open consulting. Our dual evaluation framework combines rubric assessment, which uses expert-designed criteria to evaluate insight quality, with factual assessment, which measures citation accuracy (faithfulness) and coverage (groundedness). We evaluated several leading commercial DARS and baseline systems. Results show that OpenAI Deep Research and Gemini Deep Research significantly outperform other systems, with particular strength in open-ended consulting questions. Such capabilities represent a meaningful step toward AI self-improvement, aligning with the vision of ASI for AI. We open-source ResearcherBench to provide a standardized platform for promoting the development of next-generation AI research assistants, hoping to foster a new perspective in AI research evaluation for a novel pattern of scientific collaboration: https://github.com/GAIR-NLP/ResearcherBench.

Artificial intelligence (AI) methods have become critical in scientific applications to help accelerate scientific discovery. Large language models (LLMs) are being considered as a promising approach to address some of the challenging problems because of their superior generalization capabilities across domains. The effectiveness of the models and the accuracy of the applications is contingent upon their efficient execution on the underlying hardware infrastructure. Specialized AI accelerator hardware systems have recently become available for accelerating AI applications. However, the comparative performance of these AI accelerators on large language models has not been previously studied. In this paper, we systematically study LLMs on multiple AI accelerators and GPUs and evaluate their performance characteristics for these models. We evaluate these systems with (i) a micro-benchmark using a core transformer block, (ii) a GPT- 2 model, and (iii) an LLM-driven science use case, GenSLM. We present our findings and analyses of the models' performance to better understand the intrinsic capabilities of AI accelerators. Furthermore, our analysis takes into account key factors such as sequence lengths, scaling behavior, sparsity, and sensitivity to gradient accumulation steps.

Artificial intelligence is gradually demonstrating its immense potential, and increasing attention is being given to how AI can be harnessed to advance scientific research. In this vision paper, we present our perspectives on how AI can better assist scientific inquiry and explore corresponding technical approach. We have proposed and open-sourced a large model of our KALE-LM model series, Llama3-KALE-LM-Chem-8B, which has achieved outstanding performance in tasks related to the field of chemistry. We hope that our work serves as a strong starting point, helping to realize more intelligent AI and promoting the advancement of human science and technology, as well as societal development.

Machine learning has emerged as a powerful tool for scientific discovery, enabling researchers to extract meaningful insights from complex datasets. For instance, it has facilitated the identification of disease-predictive genes from gene expression data, significantly advancing healthcare. However, the traditional process for analyzing such datasets demands substantial human effort and expertise for the data selection, processing, and analysis. To address this challenge, we introduce a novel framework, a Team of AI-made Scientists (TAIS), designed to streamline the scientific discovery pipeline. TAIS comprises simulated roles, including a project manager, data engineer, and domain expert, each represented by a Large Language Model (LLM). These roles collaborate to replicate the tasks typically performed by data scientists, with a specific focus on identifying disease-predictive genes. Furthermore, we have curated a benchmark dataset to assess TAIS's effectiveness in gene identification, demonstrating our system's potential to significantly enhance the efficiency and scope of scientific exploration. Our findings represent a solid step towards automating scientific discovery through large language models.

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.

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.

The rapid advancement of scientific progress requires innovative tools that can accelerate discovery. While recent AI methods, particularly large language models (LLMs), have shown promise in tasks such as hypothesis generation and experimental design, they fall short in replicating the collaborative nature of real-world scientific practices, where diverse teams of experts work together to tackle complex problems. To address the limitation, we propose an LLM-based multi-agent system, i.e., Virtual Scientists (VirSci), designed to mimic the teamwork inherent in scientific research. VirSci organizes a team of agents to collaboratively generate, evaluate, and refine research ideas. Through comprehensive experiments, we demonstrate that this multi-agent approach outperforms the state-of-the-art method in producing novel and impactful scientific ideas, showing potential in aligning with key insights in the Science of Science field. Our findings suggest that integrating collaborative agents can lead to more innovative scientific outputs, offering a robust system for autonomous scientific discovery.

We present Denario, an AI multi-agent system designed to serve as a scientific research assistant. Denario can perform many different tasks, such as generating ideas, checking the literature, developing research plans, writing and executing code, making plots, and drafting and reviewing a scientific paper. The system has a modular architecture, allowing it to handle specific tasks, such as generating an idea, or carrying out end-to-end scientific analysis using Cmbagent as a deep-research backend. In this work, we describe in detail Denario and its modules, and illustrate its capabilities by presenting multiple AI-generated papers generated by it in many different scientific disciplines such as astrophysics, biology, biophysics, biomedical informatics, chemistry, material science, mathematical physics, medicine, neuroscience and planetary science. Denario also excels at combining ideas from different disciplines, and we illustrate this by showing a paper that applies methods from quantum physics and machine learning to astrophysical data. We report the evaluations performed on these papers by domain experts, who provided both numerical scores and review-like feedback. We then highlight the strengths, weaknesses, and limitations of the current system. Finally, we discuss the ethical implications of AI-driven research and reflect on how such technology relates to the philosophy of science. We publicly release the code at https://github.com/AstroPilot-AI/Denario. A Denario demo can also be run directly on the web at https://huggingface.co/spaces/astropilot-ai/Denario, and the full app will be deployed on the cloud.

Recent advancements have positioned AI, and particularly Large Language Models (LLMs), as transformative tools for scientific research, capable of addressing complex tasks that require reasoning, problem-solving, and decision-making. Their exceptional capabilities suggest their potential as scientific research assistants but also highlight the need for holistic, rigorous, and domain-specific evaluation to assess effectiveness in real-world scientific applications. This paper describes a multifaceted methodology for Evaluating AI models as scientific Research Assistants (EAIRA) developed at Argonne National Laboratory. This methodology incorporates four primary classes of evaluations. 1) Multiple Choice Questions to assess factual recall; 2) Open Response to evaluate advanced reasoning and problem-solving skills; 3) Lab-Style Experiments involving detailed analysis of capabilities as research assistants in controlled environments; and 4) Field-Style Experiments to capture researcher-LLM interactions at scale in a wide range of scientific domains and applications. These complementary methods enable a comprehensive analysis of LLM strengths and weaknesses with respect to their scientific knowledge, reasoning abilities, and adaptability. Recognizing the rapid pace of LLM advancements, we designed the methodology to evolve and adapt so as to ensure its continued relevance and applicability. This paper describes the methodology state at the end of February 2025. Although developed within a subset of scientific domains, the methodology is designed to be generalizable to a wide range of scientific domains.

Artificial Intelligence (AI) is starting to transform the research process as we know it by automating the discovery of new solutions. Given a task, the typical AI-driven approach is (i) to generate a set of diverse solutions, and then (ii) to verify these solutions and select one that solves the problem. Crucially, this approach assumes the existence of a reliable verifier, i.e., one that can accurately determine whether a solution solves the given problem. We argue that systems research, long focused on designing and evaluating new performance-oriented algorithms, is particularly well-suited for AI-driven solution discovery. This is because system performance problems naturally admit reliable verifiers: solutions are typically implemented in real systems or simulators, and verification reduces to running these software artifacts against predefined workloads and measuring performance. We term this approach as AI-Driven Research for Systems (ADRS), which iteratively generates, evaluates, and refines solutions. Using penEvolve, an existing open-source ADRS instance, we present case studies across diverse domains, including load balancing for multi-region cloud scheduling, Mixture-of-Experts inference, LLM-based SQL queries, and transaction scheduling. In multiple instances, ADRS discovers algorithms that outperform state-of-the-art human designs (e.g., achieving up to 5.0x runtime improvements or 50% cost reductions). We distill best practices for guiding algorithm evolution, from prompt design to evaluator construction, for existing frameworks. We then discuss the broader implications for the systems community: as AI assumes a central role in algorithm design, we argue that human researchers will increasingly focus on problem formulation and strategic guidance. Our results highlight both the disruptive potential and the urgent need to adapt systems research practices in the age of AI.

Large Language Models (LLMs) are playing an expanding role in physics research by enhancing reasoning, symbolic manipulation, and numerical computation. However, ensuring the reliability and interpretability of their outputs remains a significant challenge. In our framework, we conceptualize the collaboration between AI and human scientists as a dynamic interplay among three modules: the reasoning module, the interpretation module, and the AI-scientist interaction module. Recognizing that effective physics reasoning demands rigorous logical consistency, quantitative precision, and deep integration with established theoretical models, we introduce the interpretation module to improve the understanding of AI-generated outputs, which is not previously explored in the literature. This module comprises multiple specialized agents, including summarizers, model builders, UI builders, and testers, which collaboratively structure LLM outputs within a physically grounded framework, by constructing a more interpretable science model. A case study demonstrates that our approach enhances transparency, facilitates validation, and strengthens AI-augmented reasoning in scientific discovery.

AI co-scientists are emerging as a tool to assist human researchers in achieving their research goals. A crucial feature of these AI co-scientists is the ability to generate a research plan given a set of aims and constraints. The plan may be used by researchers for brainstorming, or may even be implemented after further refinement. However, language models currently struggle to generate research plans that follow all constraints and implicit requirements. In this work, we study how to leverage the vast corpus of existing research papers to train language models that generate better research plans. We build a scalable, diverse training corpus by automatically extracting research goals and goal-specific grading rubrics from papers across several domains. We then train models for research plan generation via reinforcement learning with self-grading. A frozen copy of the initial policy acts as the grader during training, with the rubrics creating a generator-verifier gap that enables improvements without external human supervision. To validate this approach, we conduct a study with human experts for machine learning research goals, spanning 225 hours. The experts prefer plans generated by our finetuned Qwen3-30B-A3B model over the initial model for 70% of research goals, and approve 84% of the automatically extracted goal-specific grading rubrics. To assess generality, we also extend our approach to research goals from medical papers, and new arXiv preprints, evaluating with a jury of frontier models. Our finetuning yields 12-22% relative improvements and significant cross-domain generalization, proving effective even in problem settings like medical research where execution feedback is infeasible. Together, these findings demonstrate the potential of a scalable, automated training recipe as a step towards improving general AI co-scientists.

AI models like GPT-5 are an increasingly valuable tool for scientists, but many remain unaware of the capabilities of frontier AI. We present a collection of short case studies in which GPT-5 produced new, concrete steps in ongoing research across mathematics, physics, astronomy, computer science, biology, and materials science. In these examples, the authors highlight how AI accelerated their work, and where it fell short; where expert time was saved, and where human input was still key. We document the interactions of the human authors with GPT-5, as guiding examples of fruitful collaboration with AI. Of note, this paper includes four new results in mathematics (carefully verified by the human authors), underscoring how GPT-5 can help human mathematicians settle previously unsolved problems. These contributions are modest in scope but profound in implication, given the rate at which frontier AI is progressing.

Frontier AI safety policies highlight automation of AI research and development (R&D) by AI agents as an important capability to anticipate. However, there exist few evaluations for AI R&D capabilities, and none that are highly realistic and have a direct comparison to human performance. We introduce RE-Bench (Research Engineering Benchmark, v1), which consists of 7 challenging, open-ended ML research engineering environments and data from 71 8-hour attempts by 61 distinct human experts. We confirm that our experts make progress in the environments given 8 hours, with 82% of expert attempts achieving a non-zero score and 24% matching or exceeding our strong reference solutions. We compare humans to several public frontier models through best-of-k with varying time budgets and agent designs, and find that the best AI agents achieve a score 4x higher than human experts when both are given a total time budget of 2 hours per environment. However, humans currently display better returns to increasing time budgets, narrowly exceeding the top AI agent scores given an 8-hour budget, and achieving 2x the score of the top AI agent when both are given 32 total hours (across different attempts). Qualitatively, we find that modern AI agents possess significant expertise in many ML topics -- e.g. an agent wrote a faster custom Triton kernel than any of our human experts' -- and can generate and test solutions over ten times faster than humans, at much lower cost. We open-source the evaluation environments, human expert data, analysis code and agent trajectories to facilitate future research.

Can an AI autonomously design mechanisms for computer systems on par with the creativity and reasoning of human experts? We present Glia, an AI architecture for networked systems design that uses large language models (LLMs) in a human-inspired, multi-agent workflow. Each agent specializes in reasoning, experimentation, and analysis, collaborating through an evaluation framework that grounds abstract reasoning in empirical feedback. Unlike prior ML-for-systems methods that optimize black-box policies, Glia generates interpretable designs and exposes its reasoning process. When applied to a distributed GPU cluster for LLM inference, it produces new algorithms for request routing, scheduling, and auto-scaling that perform at human-expert levels in significantly less time, while yielding novel insights into workload behavior. Our results suggest that by combining reasoning LLMs with structured experimentation, an AI can produce creative and understandable designs for complex systems problems.

The field of AI research is advancing at an unprecedented pace, enabling automated hypothesis generation and experimental design across diverse domains such as biology, mathematics, and artificial intelligence. Despite these advancements, there remains a significant gap in the availability of scalable advising systems capable of providing high-quality, well-reasoned feedback to refine proposed hypotheses and experimental designs. To address this challenge, we explore key factors that underlie the development of robust advising systems, including model size, context length, confidence estimation, and structured reasoning processes. Our findings reveal that a relatively small model, when equipped with a well-compressed literature database and a structured reasoning framework, can outperform powerful general-purpose language models such as Deepseek-R1 in terms of acceptance rates for self-ranked top-30% submissions to ICLR 2025. Moreover, when limited to high-confidence predictions, our system achieves an acceptance rate exceeding 90% on the ICLR 2025 test set, underscoring its potential to significantly enhance the quality and efficiency of hypothesis generation and experimental design. The code is released at https://github.com/HowardLiu0830/GUIDE-Research-Idea-Evaluation.

Humans interact with the environment using a combination of perception - transforming sensory inputs from their environment into symbols, and cognition - mapping symbols to knowledge about the environment for supporting abstraction, reasoning by analogy, and long-term planning. Human perception-inspired machine perception, in the context of AI, refers to large-scale pattern recognition from raw data using neural networks trained using self-supervised learning objectives such as next-word prediction or object recognition. On the other hand, machine cognition encompasses more complex computations, such as using knowledge of the environment to guide reasoning, analogy, and long-term planning. Humans can also control and explain their cognitive functions. This seems to require the retention of symbolic mappings from perception outputs to knowledge about their environment. For example, humans can follow and explain the guidelines and safety constraints driving their decision-making in safety-critical applications such as healthcare, criminal justice, and autonomous driving. This article introduces the rapidly emerging paradigm of Neurosymbolic AI combines neural networks and knowledge-guided symbolic approaches to create more capable and flexible AI systems. These systems have immense potential to advance both algorithm-level (e.g., abstraction, analogy, reasoning) and application-level (e.g., explainable and safety-constrained decision-making) capabilities of AI systems.

Artificial intelligence commonly refers to the science and engineering of artificial systems that can carry out tasks generally associated with requiring aspects of human intelligence, such as playing games, translating languages, and driving cars. In recent years, there have been exciting advances in learning-based, data-driven approaches towards AI, and machine learning and deep learning have enabled computer systems to perceive the world in unprecedented ways. Reinforcement learning has enabled breakthroughs in complex games such as Go and challenging robotics tasks such as quadrupedal locomotion. A key aspect of intelligence is to not only make predictions, but reason about the uncertainty in these predictions, and to consider this uncertainty when making decisions. This is what this manuscript on "Probabilistic Artificial Intelligence" is about. The first part covers probabilistic approaches to machine learning. We discuss the differentiation between "epistemic" uncertainty due to lack of data and "aleatoric" uncertainty, which is irreducible and stems, e.g., from noisy observations and outcomes. We discuss concrete approaches towards probabilistic inference and modern approaches to efficient approximate inference. The second part of the manuscript is about taking uncertainty into account in sequential decision tasks. We consider active learning and Bayesian optimization -- approaches that collect data by proposing experiments that are informative for reducing the epistemic uncertainty. We then consider reinforcement learning and modern deep RL approaches that use neural network function approximation. We close by discussing modern approaches in model-based RL, which harness epistemic and aleatoric uncertainty to guide exploration, while also reasoning about safety.

The automation of scientific discovery represents a critical milestone in Artificial Intelligence (AI) research. However, existing agentic systems for science suffer from two fundamental limitations: rigid, pre-programmed workflows that cannot adapt to intermediate findings, and inadequate context management that hinders long-horizon research. We present freephdlabor, an open-source multiagent framework featuring fully dynamic workflows determined by real-time agent reasoning and a \textit{modular architecture} enabling seamless customization -- users can modify, add, or remove agents to address domain-specific requirements. The framework provides comprehensive infrastructure including automatic context compaction, workspace-based communication to prevent information degradation, memory persistence across sessions, and non-blocking human intervention mechanisms. These features collectively transform automated research from isolated, single-run attempts into continual research programs that build systematically on prior explorations and incorporate human feedback. By providing both the architectural principles and practical implementation for building customizable co-scientist systems, this work aims to facilitate broader adoption of automated research across scientific domains, enabling practitioners to deploy interactive multiagent systems that autonomously conduct end-to-end research -- from ideation through experimentation to publication-ready manuscripts.

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.

Large language models and autonomous AI agents have evolved rapidly, resulting in a diverse array of evaluation benchmarks, frameworks, and collaboration protocols. However, the landscape remains fragmented and lacks a unified taxonomy or comprehensive survey. Therefore, we present a side-by-side comparison of benchmarks developed between 2019 and 2025 that evaluate these models and agents across multiple domains. In addition, we propose a taxonomy of approximately 60 benchmarks that cover general and academic knowledge reasoning, mathematical problem-solving, code generation and software engineering, factual grounding and retrieval, domain-specific evaluations, multimodal and embodied tasks, task orchestration, and interactive assessments. Furthermore, we review AI-agent frameworks introduced between 2023 and 2025 that integrate large language models with modular toolkits to enable autonomous decision-making and multi-step reasoning. Moreover, we present real-world applications of autonomous AI agents in materials science, biomedical research, academic ideation, software engineering, synthetic data generation, chemical reasoning, mathematical problem-solving, geographic information systems, multimedia, healthcare, and finance. We then survey key agent-to-agent collaboration protocols, namely the Agent Communication Protocol (ACP), the Model Context Protocol (MCP), and the Agent-to-Agent Protocol (A2A). Finally, we discuss recommendations for future research, focusing on advanced reasoning strategies, failure modes in multi-agent LLM systems, automated scientific discovery, dynamic tool integration via reinforcement learning, integrated search capabilities, and security vulnerabilities in agent protocols.

Autonomous agents built on language models (LMs) are showing increasing popularity in many fields, including scientific research. AI co-scientists aim to support or automate parts of the research process using these agents. A key component of empirical AI research is the design of ablation experiments. To this end, we introduce AblationBench, a benchmark suite for evaluating agents on ablation planning tasks in empirical AI research. It includes two tasks: AuthorAblation, which helps authors propose ablation experiments based on a method section and contains 83 instances, and ReviewerAblation, which helps reviewers find missing ablations in a full paper and contains 350 instances. For both tasks, we develop LM-based judges that serve as an automatic evaluation framework. Our experiments with frontier LMs show that these tasks remain challenging, with the best-performing LM system identifying only 29% of the original ablations on average. Lastly, we analyze the limitations of current LMs on these tasks, and find that chain-of-thought prompting outperforms the currently existing agent-based approach.

Data science aims to extract insights from data to support decision-making processes. Recently, Large Language Models (LLMs) are increasingly used as assistants for data science, by suggesting ideas, techniques and small code snippets, or for the interpretation of results and reporting. Proper automation of some data-science activities is now promised by the rise of LLM agents, i.e., AI systems powered by an LLM equipped with additional affordances--such as code execution and knowledge bases--that can perform self-directed actions and interact with digital environments. In this paper, we survey the evaluation of LLM assistants and agents for data science. We find (1) a dominant focus on a small subset of goal-oriented activities, largely ignoring data management and exploratory activities; (2) a concentration on pure assistance or fully autonomous agents, without considering intermediate levels of human-AI collaboration; and (3) an emphasis on human substitution, therefore neglecting the possibility of higher levels of automation thanks to task transformation.

Large Language Models (LLMs) have extended their impact beyond Natural Language Processing, substantially fostering the development of interdisciplinary research. Recently, various LLM-based agents have been developed to assist scientific discovery progress across multiple aspects and domains. Among these, computer-using agents, capable of interacting with operating systems as humans do, are paving the way to automated scientific problem-solving and addressing routines in researchers' workflows. Recognizing the transformative potential of these agents, we introduce ScienceBoard, which encompasses two complementary contributions: (i) a realistic, multi-domain environment featuring dynamic and visually rich scientific workflows with integrated professional software, where agents can autonomously interact via different interfaces to accelerate complex research tasks and experiments; and (ii) a challenging benchmark of 169 high-quality, rigorously validated real-world tasks curated by humans, spanning scientific-discovery workflows in domains such as biochemistry, astronomy, and geoinformatics. Extensive evaluations of agents with state-of-the-art backbones (e.g., GPT-4o, Claude 3.7, UI-TARS) show that, despite some promising results, they still fall short of reliably assisting scientists in complex workflows, achieving only a 15% overall success rate. In-depth analysis further provides valuable insights for addressing current agent limitations and more effective design principles, paving the way to build more capable agents for scientific discovery. Our code, environment, and benchmark are at https://qiushisun.github.io/ScienceBoard-Home/.

Large Language Models (LLMs) are catalyzing a paradigm shift in scientific discovery, evolving from task-specific automation tools into increasingly autonomous agents and fundamentally redefining research processes and human-AI collaboration. This survey systematically charts this burgeoning field, placing a central focus on the changing roles and escalating capabilities of LLMs in science. Through the lens of the scientific method, we introduce a foundational three-level taxonomy-Tool, Analyst, and Scientist-to delineate their escalating autonomy and evolving responsibilities within the research lifecycle. We further identify pivotal challenges and future research trajectories such as robotic automation, self-improvement, and ethical governance. Overall, this survey provides a conceptual architecture and strategic foresight to navigate and shape the future of AI-driven scientific discovery, fostering both rapid innovation and responsible advancement. Github Repository: https://github.com/HKUST-KnowComp/Awesome-LLM-Scientific-Discovery.

The rapid growth of biomedical data, tools, and literature has created a fragmented research landscape that outpaces human expertise. While AI agents offer a solution, they typically rely on static, manually curated toolsets, limiting their ability to adapt and scale. Here, we introduce STELLA, a self-evolving AI agent designed to overcome these limitations. STELLA employs a multi-agent architecture that autonomously improves its own capabilities through two core mechanisms: an evolving Template Library for reasoning strategies and a dynamic Tool Ocean that expands as a Tool Creation Agent automatically discovers and integrates new bioinformatics tools. This allows STELLA to learn from experience. We demonstrate that STELLA achieves state-of-the-art accuracy on a suite of biomedical benchmarks, scoring approximately 26\% on Humanity's Last Exam: Biomedicine, 54\% on LAB-Bench: DBQA, and 63\% on LAB-Bench: LitQA, outperforming leading models by up to 6 percentage points. More importantly, we show that its performance systematically improves with experience; for instance, its accuracy on the Humanity's Last Exam benchmark almost doubles with increased trials. STELLA represents a significant advance towards AI Agent systems that can learn and grow, dynamically scaling their expertise to accelerate the pace of biomedical 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.

Scientific Large Language Models (Sci-LLMs) are transforming how knowledge is represented, integrated, and applied in scientific research, yet their progress is shaped by the complex nature of scientific data. This survey presents a comprehensive, data-centric synthesis that reframes the development of Sci-LLMs as a co-evolution between models and their underlying data substrate. We formulate a unified taxonomy of scientific data and a hierarchical model of scientific knowledge, emphasizing the multimodal, cross-scale, and domain-specific challenges that differentiate scientific corpora from general natural language processing datasets. We systematically review recent Sci-LLMs, from general-purpose foundations to specialized models across diverse scientific disciplines, alongside an extensive analysis of over 270 pre-/post-training datasets, showing why Sci-LLMs pose distinct demands -- heterogeneous, multi-scale, uncertainty-laden corpora that require representations preserving domain invariance and enabling cross-modal reasoning. On evaluation, we examine over 190 benchmark datasets and trace a shift from static exams toward process- and discovery-oriented assessments with advanced evaluation protocols. These data-centric analyses highlight persistent issues in scientific data development and discuss emerging solutions involving semi-automated annotation pipelines and expert validation. Finally, we outline a paradigm shift toward closed-loop systems where autonomous agents based on Sci-LLMs actively experiment, validate, and contribute to a living, evolving knowledge base. Collectively, this work provides a roadmap for building trustworthy, continually evolving artificial intelligence (AI) systems that function as a true partner in accelerating scientific discovery.

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.

Recent advancements in artificial intelligence have sparked interest in scientific assistants that could support researchers across the full spectrum of scientific workflows, from literature review to experimental design and data analysis. A key capability for such systems is the ability to process and reason about scientific information in both visual and textual forms - from interpreting spectroscopic data to understanding laboratory setups. Here, we introduce MaCBench, a comprehensive benchmark for evaluating how vision-language models handle real-world chemistry and materials science tasks across three core aspects: data extraction, experimental understanding, and results interpretation. Through a systematic evaluation of leading models, we find that while these systems show promising capabilities in basic perception tasks - achieving near-perfect performance in equipment identification and standardized data extraction - they exhibit fundamental limitations in spatial reasoning, cross-modal information synthesis, and multi-step logical inference. Our insights have important implications beyond chemistry and materials science, suggesting that developing reliable multimodal AI scientific assistants may require advances in curating suitable training data and approaches to training those models.

Artificial intelligence systems are increasingly deployed in biomedical research. However, current evaluation frameworks may inadequately assess their effectiveness as research collaborators. This rapid review examines benchmarking practices for AI systems in preclinical biomedical research. Three major databases and two preprint servers were searched from January 1, 2018 to October 31, 2025, identifying 14 benchmarks that assess AI capabilities in literature understanding, experimental design, and hypothesis generation. The results revealed that all current benchmarks assess isolated component capabilities, including data analysis quality, hypothesis validity, and experimental protocol design. However, authentic research collaboration requires integrated workflows spanning multiple sessions, with contextual memory, adaptive dialogue, and constraint propagation. This gap implies that systems excelling on component benchmarks may fail as practical research co-pilots. A process-oriented evaluation framework is proposed that addresses four critical dimensions absent from current benchmarks: dialogue quality, workflow orchestration, session continuity, and researcher experience. These dimensions are essential for evaluating AI systems as research co-pilots rather than as isolated task executors.

A key challenge in artificial intelligence is the creation of systems capable of autonomously advancing scientific understanding by exploring novel domains, identifying complex patterns, and uncovering previously unseen connections in vast scientific data. In this work, we present SciAgents, an approach that leverages three core concepts: (1) the use of large-scale ontological knowledge graphs to organize and interconnect diverse scientific concepts, (2) a suite of large language models (LLMs) and data retrieval tools, and (3) multi-agent systems with in-situ learning capabilities. Applied to biologically inspired materials, SciAgents reveals hidden interdisciplinary relationships that were previously considered unrelated, achieving a scale, precision, and exploratory power that surpasses traditional human-driven research methods. The framework autonomously generates and refines research hypotheses, elucidating underlying mechanisms, design principles, and unexpected material properties. By integrating these capabilities in a modular fashion, the intelligent system yields material discoveries, critique and improve existing hypotheses, retrieve up-to-date data about existing research, and highlights their strengths and limitations. Our case studies demonstrate scalable capabilities to combine generative AI, ontological representations, and multi-agent modeling, harnessing a `swarm of intelligence' similar to biological systems. This provides new avenues for materials discovery and accelerates the development of advanced materials by unlocking Nature's design principles.

A multi-agent AI system (MAS) is composed of multiple autonomous agents that interact, exchange information, and make decisions based on internal generative models. Recent advances in large language models and tool-using agents have made MAS increasingly practical in areas like scientific discovery and collaborative automation. However, key questions remain: When are MAS more effective than single-agent systems? What new safety risks arise from agent interactions? And how should we evaluate their reliability and structure? This paper outlines a formal framework for analyzing MAS, focusing on two core aspects: effectiveness and safety. We explore whether MAS truly improve robustness, adaptability, and performance, or merely repackage known techniques like ensemble learning. We also study how inter-agent dynamics may amplify or suppress system vulnerabilities. While MAS are relatively new to the signal processing community, we envision them as a powerful abstraction that extends classical tools like distributed estimation and sensor fusion to higher-level, policy-driven inference. Through experiments on data science automation, we highlight the potential of MAS to reshape how signal processing systems are designed and trusted.

Machine learning, the foundation of modern artificial intelligence, has driven innovations that have fundamentally transformed the world. Yet, behind advancements lies a complex and often tedious process requiring labor and compute intensive iteration and experimentation. Engineers and scientists developing machine learning models spend much of their time on trial-and-error tasks instead of conceptualizing innovative solutions or research hypotheses. To address this challenge, we introduce AI-Driven Exploration (AIDE), a machine learning engineering agent powered by large language models (LLMs). AIDE frames machine learning engineering as a code optimization problem, and formulates trial-and-error as a tree search in the space of potential solutions. By strategically reusing and refining promising solutions, AIDE effectively trades computational resources for enhanced performance, achieving state-of-the-art results on multiple machine learning engineering benchmarks, including our Kaggle evaluations, OpenAI MLE-Bench and METRs RE-Bench.

Constructing real-world data-to-insight pipelines often involves data extraction from data lakes, data integration across heterogeneous data sources, and diverse operations from data cleaning to analysis. The design and implementation of data science pipelines require domain knowledge, technical expertise, and even project-specific insights. AI systems have shown remarkable reasoning, coding, and understanding capabilities. However, it remains unclear to what extent these capabilities translate into successful design and execution of such complex pipelines. We introduce KRAMABENCH: a benchmark composed of 104 manually-curated real-world data science pipelines spanning 1700 data files from 24 data sources in 6 different domains. We show that these pipelines test the end-to-end capabilities of AI systems on data processing, requiring data discovery, wrangling and cleaning, efficient processing, statistical reasoning, and orchestrating data processing steps given a high-level task. Our evaluation tests 5 general models and 3 code generation models using our reference framework, DS-GURU, which instructs the AI model to decompose a question into a sequence of subtasks, reason through each step, and synthesize Python code that implements the proposed design. Our results on KRAMABENCH show that, although the models are sufficiently capable of solving well-specified data science code generation tasks, when extensive data processing and domain knowledge are required to construct real-world data science pipelines, existing out-of-box models fall short. Progress on KramaBench represents crucial steps towards developing autonomous data science agents for real-world applications. Our code, reference framework, and data are available at https://github.com/mitdbg/KramaBench.

The development of Artificial Intelligence (AI), including AI in Science (AIS), should be done following the principles of responsible AI. Progress in responsible AI is often quantified through evaluation metrics, yet there has been less work on assessing the robustness and reliability of the metrics themselves. We reflect on prior work that examines the robustness of fairness metrics for recommender systems as a type of AI application and summarise their key takeaways into a set of non-exhaustive guidelines for developing reliable metrics of responsible AI. Our guidelines apply to a broad spectrum of AI applications, including AIS.

The rapid advancements of AI agents have ignited the long-held ambition of leveraging them to accelerate scientific discovery. Achieving this goal requires a deep understanding of the frontiers of human knowledge. As such, Humanity's Last Exam (HLE) provides an exceptionally challenging touchstone for evaluating scientific AI agents. In this work, we aim to construct the foundational architecture for general-purpose agents and validate the capabilities through leading performance on HLE. To achieve this, we introduce X-Master, a tool-augmented reasoning agent designed to emulate human researchers by interacting flexibly with external tools during its reasoning process. This agent, guided by the conceptualization of code as an interaction language, can flexibly leverage built-in Python libraries and our customized tools to augment the reasoning. We further scale its capabilities through X-Masters, a scattered-and-stacked agentic workflow that systematically enhances breadth and depth of reasoning. Our open-source solution, X-Masters, sets a new state-of-the-art record on HLE with a score of 32.1%, surpassing OpenAI's and Google's Deep Research (26.6% and 26.9%) and becoming the first to exceed the 30% threshold. This work allows us to gain a deeper understanding of complex task-solving and accumulates valuable experience that can inform future advancements, guiding subsequent model training.

The evolution of Artificial Intelligence (AI) has been significantly accelerated by advancements in Large Language Models (LLMs) and Large Multimodal Models (LMMs), gradually showcasing potential cognitive reasoning abilities in problem-solving and scientific discovery (i.e., AI4Science) once exclusive to human intellect. To comprehensively evaluate current models' performance in cognitive reasoning abilities, we introduce OlympicArena, which includes 11,163 bilingual problems across both text-only and interleaved text-image modalities. These challenges encompass a wide range of disciplines spanning seven fields and 62 international Olympic competitions, rigorously examined for data leakage. We argue that the challenges in Olympic competition problems are ideal for evaluating AI's cognitive reasoning due to their complexity and interdisciplinary nature, which are essential for tackling complex scientific challenges and facilitating discoveries. Beyond evaluating performance across various disciplines using answer-only criteria, we conduct detailed experiments and analyses from multiple perspectives. We delve into the models' cognitive reasoning abilities, their performance across different modalities, and their outcomes in process-level evaluations, which are vital for tasks requiring complex reasoning with lengthy solutions. Our extensive evaluations reveal that even advanced models like GPT-4o only achieve a 39.97% overall accuracy, illustrating current AI limitations in complex reasoning and multimodal integration. Through the OlympicArena, we aim to advance AI towards superintelligence, equipping it to address more complex challenges in science and beyond. We also provide a comprehensive set of resources to support AI research, including a benchmark dataset, an open-source annotation platform, a detailed evaluation tool, and a leaderboard with automatic submission features.

Research is a fundamental process driving the advancement of human civilization, yet it demands substantial time and effort from researchers. In recent years, the rapid development of artificial intelligence (AI) technologies has inspired researchers to explore how AI can accelerate and enhance research. To monitor relevant advancements, this paper presents a systematic review of the progress in this domain. Specifically, we organize the relevant studies into three main categories: hypothesis formulation, hypothesis validation, and manuscript publication. Hypothesis formulation involves knowledge synthesis and hypothesis generation. Hypothesis validation includes the verification of scientific claims, theorem proving, and experiment validation. Manuscript publication encompasses manuscript writing and the peer review process. Furthermore, we identify and discuss the current challenges faced in these areas, as well as potential future directions for research. Finally, we also offer a comprehensive overview of existing benchmarks and tools across various domains that support the integration of AI into the research process. We hope this paper serves as an introduction for beginners and fosters future research. Resources have been made publicly available at https://github.com/zkzhou126/AI-for-Research.

The rapid advancement of large language models has fundamentally shifted the bottleneck in AI development from computational power to data availability-with countless valuable datasets remaining hidden across specialized repositories, research appendices, and domain platforms. As reasoning capabilities and deep research methodologies continue to evolve, a critical question emerges: can AI agents transcend conventional search to systematically discover any dataset that meets specific user requirements, enabling truly autonomous demand-driven data curation? We introduce DatasetResearch, the first comprehensive benchmark evaluating AI agents' ability to discover and synthesize datasets from 208 real-world demands across knowledge-intensive and reasoning-intensive tasks. Our tri-dimensional evaluation framework reveals a stark reality: even advanced deep research systems achieve only 22% score on our challenging DatasetResearch-pro subset, exposing the vast gap between current capabilities and perfect dataset discovery. Our analysis uncovers a fundamental dichotomy-search agents excel at knowledge tasks through retrieval breadth, while synthesis agents dominate reasoning challenges via structured generation-yet both catastrophically fail on "corner cases" outside existing distributions. These findings establish the first rigorous baseline for dataset discovery agents and illuminate the path toward AI systems capable of finding any dataset in the digital universe. Our benchmark and comprehensive analysis provide the foundation for the next generation of self-improving AI systems and are publicly available at https://github.com/GAIR-NLP/DatasetResearch.

AI agents are increasingly autonomous in their interactions with human users and tools, leading to increased interactional safety risks. We present HAICOSYSTEM, a framework examining AI agent safety within diverse and complex social interactions. HAICOSYSTEM features a modular sandbox environment that simulates multi-turn interactions between human users and AI agents, where the AI agents are equipped with a variety of tools (e.g., patient management platforms) to navigate diverse scenarios (e.g., a user attempting to access other patients' profiles). To examine the safety of AI agents in these interactions, we develop a comprehensive multi-dimensional evaluation framework that uses metrics covering operational, content-related, societal, and legal risks. Through running 1840 simulations based on 92 scenarios across seven domains (e.g., healthcare, finance, education), we demonstrate that HAICOSYSTEM can emulate realistic user-AI interactions and complex tool use by AI agents. Our experiments show that state-of-the-art LLMs, both proprietary and open-sourced, exhibit safety risks in over 50\% cases, with models generally showing higher risks when interacting with simulated malicious users. Our findings highlight the ongoing challenge of building agents that can safely navigate complex interactions, particularly when faced with malicious users. To foster the AI agent safety ecosystem, we release a code platform that allows practitioners to create custom scenarios, simulate interactions, and evaluate the safety and performance of their agents.

Scientific innovation is undergoing a paradigm shift driven by the rapid advancement of Large Language Models (LLMs). As science faces mounting challenges including information overload, disciplinary silos, and diminishing returns on conventional research methods, LLMs are emerging as powerful agents capable not only of enhancing scientific workflows but also of participating in and potentially leading the innovation process. Existing surveys mainly focus on different perspectives, phrases, and tasks in scientific research and discovery, while they have limitations in understanding the transformative potential and role differentiation of LLM. This survey proposes a comprehensive framework to categorize the evolving roles of LLMs in scientific innovation across three hierarchical levels: Evaluator, Collaborator, and Scientist. We distinguish between LLMs' contributions to structured scientific research processes and open-ended scientific discovery, thereby offering a unified taxonomy that clarifies capability boundaries, evaluation criteria, and human-AI interaction patterns at each level. Through an extensive analysis of current methodologies, benchmarks, systems, and evaluation metrics, this survey delivers an in-depth and systematic synthesis on LLM-driven scientific innovation. We present LLMs not only as tools for automating existing processes, but also as catalysts capable of reshaping the epistemological foundations of science itself. This survey offers conceptual clarity, practical guidance, and theoretical foundations for future research, while also highlighting open challenges and ethical considerations in the pursuit of increasingly autonomous AI-driven science. Resources related to this survey can be accessed on GitHub at: https://github.com/haoxuan-unt2024/llm4innovation.

The rapid progress of Large Language Models (LLMs) has given rise to a new category of autonomous AI systems, referred to as Deep Research (DR) agents. These agents are designed to tackle complex, multi-turn informational research tasks by leveraging a combination of dynamic reasoning, adaptive long-horizon planning, multi-hop information retrieval, iterative tool use, and the generation of structured analytical reports. In this paper, we conduct a detailed analysis of the foundational technologies and architectural components that constitute Deep Research agents. We begin by reviewing information acquisition strategies, contrasting API-based retrieval methods with browser-based exploration. We then examine modular tool-use frameworks, including code execution, multimodal input processing, and the integration of Model Context Protocols (MCPs) to support extensibility and ecosystem development. To systematize existing approaches, we propose a taxonomy that differentiates between static and dynamic workflows, and we classify agent architectures based on planning strategies and agent composition, including single-agent and multi-agent configurations. We also provide a critical evaluation of current benchmarks, highlighting key limitations such as restricted access to external knowledge, sequential execution inefficiencies, and misalignment between evaluation metrics and the practical objectives of DR agents. Finally, we outline open challenges and promising directions for future research. A curated and continuously updated repository of DR agent research is available at: {https://github.com/ai-agents-2030/awesome-deep-research-agent}.

Recent neural language models have taken a significant step forward in producing remarkably controllable, fluent, and grammatical text. Although studies have found that AI-generated text is not distinguishable from human-written text for crowd-sourcing workers, there still exist errors in AI-generated text which are even subtler and harder to spot. We primarily focus on the scenario in which scientific AI writing assistant is deeply involved. First, we construct a feature description framework to distinguish between AI-generated text and human-written text from syntax, semantics, and pragmatics based on the human evaluation. Then we utilize the features, i.e., writing style, coherence, consistency, and argument logistics, from the proposed framework to analyze two types of content. Finally, we adopt several publicly available methods to investigate the gap of between AI-generated scientific text and human-written scientific text by AI-generated scientific text detection models. The results suggest that while AI has the potential to generate scientific content that is as accurate as human-written content, there is still a gap in terms of depth and overall quality. The AI-generated scientific content is more likely to contain errors in factual issues. We find that there exists a "writing style" gap between AI-generated scientific text and human-written scientific text. Based on the analysis result, we summarize a series of model-agnostic and distribution-agnostic features for detection tasks in other domains. Findings in this paper contribute to guiding the optimization of AI models to produce high-quality content and addressing related ethical and security concerns.

AI systems are gaining widespread adoption across various sectors and domains. Creating high-quality AI system requirements is crucial for aligning the AI system with business goals and consumer values and for social responsibility. However, with the uncertain nature of AI systems and the heavy reliance on sensitive data, more research is needed to address the elicitation and analysis of AI systems requirements. With the proprietary nature of many AI systems, there is a lack of open-source requirements artifacts and technical requirements documents for AI systems, limiting broader research and investigation. With Large Language Models (LLMs) emerging as a promising alternative to human-generated text, this paper investigates the potential use of LLMs to generate user stories for AI systems based on abstracts from scholarly papers. We conducted an empirical evaluation using three LLMs and generated 1260 user stories from 42 abstracts from 26 domains. We assess their quality using the Quality User Story (QUS) framework. Moreover, we identify relevant non-functional requirements (NFRs) and ethical principles. Our analysis demonstrates that the investigated LLMs can generate user stories inspired by the needs of various stakeholders, offering a promising approach for generating user stories for research purposes and for aiding in the early requirements elicitation phase of AI systems. We have compiled and curated a collection of stories generated by various LLMs into a dataset (UStAI), which is now publicly available for use.

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.

Deep research systems, agentic AI that solve complex, multi-step tasks by coordinating reasoning, search across the open web and user files, and tool use, are moving toward hierarchical deployments with a Planner, Coordinator, and Executors. In practice, training entire stacks end-to-end remains impractical, so most work trains a single planner connected to core tools such as search, browsing, and code. While SFT imparts protocol fidelity, it suffers from imitation and exposure biases and underuses environment feedback. Preference alignment methods such as DPO are schema and proxy-dependent, off-policy, and weak for long-horizon credit assignment and multi-objective trade-offs. A further limitation of SFT and DPO is their reliance on human defined decision points and subskills through schema design and labeled comparisons. Reinforcement learning aligns with closed-loop, tool-interaction research by optimizing trajectory-level policies, enabling exploration, recovery behaviors, and principled credit assignment, and it reduces dependence on such human priors and rater biases. This survey is, to our knowledge, the first dedicated to the RL foundations of deep research systems. It systematizes work after DeepSeek-R1 along three axes: (i) data synthesis and curation; (ii) RL methods for agentic research covering stability, sample efficiency, long context handling, reward and credit design, multi-objective optimization, and multimodal integration; and (iii) agentic RL training systems and frameworks. We also cover agent architecture and coordination, as well as evaluation and benchmarks, including recent QA, VQA, long-form synthesis, and domain-grounded, tool-interaction tasks. We distill recurring patterns, surface infrastructure bottlenecks, and offer practical guidance for training robust, transparent deep research agents with RL.

While AI systems demonstrate exponentially improving capabilities, the pace of AI research itself remains linearly bounded by human cognitive capacity, creating an increasingly severe development bottleneck. We present ASI-Arch, the first demonstration of Artificial Superintelligence for AI research (ASI4AI) in the critical domain of neural architecture discovery--a fully autonomous system that shatters this fundamental constraint by enabling AI to conduct its own architectural innovation. Moving beyond traditional Neural Architecture Search (NAS), which is fundamentally limited to exploring human-defined spaces, we introduce a paradigm shift from automated optimization to automated innovation. ASI-Arch can conduct end-to-end scientific research in the domain of architecture discovery, autonomously hypothesizing novel architectural concepts, implementing them as executable code, training and empirically validating their performance through rigorous experimentation and past experience. ASI-Arch conducted 1,773 autonomous experiments over 20,000 GPU hours, culminating in the discovery of 106 innovative, state-of-the-art (SOTA) linear attention architectures. Like AlphaGo's Move 37 that revealed unexpected strategic insights invisible to human players, our AI-discovered architectures demonstrate emergent design principles that systematically surpass human-designed baselines and illuminate previously unknown pathways for architectural innovation. Crucially, we establish the first empirical scaling law for scientific discovery itself--demonstrating that architectural breakthroughs can be scaled computationally, transforming research progress from a human-limited to a computation-scalable process. We provide comprehensive analysis of the emergent design patterns and autonomous research capabilities that enabled these breakthroughs, establishing a blueprint for self-accelerating AI systems.

The rapid growth in the use of Large Language Models (LLMs) and AI Agents as part of software development and deployment is revolutionizing the information technology landscape. While code generation receives significant attention, a higher-impact application lies in using AI agents for operational resilience of cloud services, which currently require significant human effort and domain knowledge. There is a growing interest in AI for IT Operations (AIOps) which aims to automate complex operational tasks, like fault localization and root cause analysis, thereby reducing human intervention and customer impact. However, achieving the vision of autonomous and self-healing clouds though AIOps is hampered by the lack of standardized frameworks for building, evaluating, and improving AIOps agents. This vision paper lays the groundwork for such a framework by first framing the requirements and then discussing design decisions that satisfy them. We also propose AIOpsLab, a prototype implementation leveraging agent-cloud-interface that orchestrates an application, injects real-time faults using chaos engineering, and interfaces with an agent to localize and resolve the faults. We report promising results and lay the groundwork to build a modular and robust framework for building, evaluating, and improving agents for autonomous clouds.

Artificial intelligence promises to accelerate scientific discovery, yet its benefits remain unevenly distributed. While technical obstacles such as scarce data, fragmented standards, and unequal access to computation are significant, we argue that the primary barriers are social and institutional. Narratives that defer progress to speculative "AI scientists," the undervaluing of data and infrastructure contributions, misaligned incentives, and gaps between domain experts and machine learning researchers all constrain impact. We highlight four interconnected challenges: community dysfunction, research priorities misaligned with upstream needs, data fragmentation, and infrastructure inequities. We argue that their roots lie in cultural and organizational practices. Addressing them requires not only technical innovation but also intentional community-building, cross-disciplinary education, shared benchmarks, and accessible infrastructure. We call for reframing AI for science as a collective social project, where sustainable collaboration and equitable participation are treated as prerequisites for technical progress.

Artificial intelligence (AI), and especially its sub-field of Machine Learning (ML), are impacting the daily lives of everyone with their ubiquitous applications. In recent years, AI researchers and practitioners have introduced principles and guidelines to build systems that make reliable and trustworthy decisions. From a practical perspective, conventional ML systems process historical data to extract the features that are consequently used to train ML models that perform the desired task. However, in practice, a fundamental challenge arises when the system needs to be operationalized and deployed to evolve and operate in real-life environments continuously. To address this challenge, Machine Learning Operations (MLOps) have emerged as a potential recipe for standardizing ML solutions in deployment. Although MLOps demonstrated great success in streamlining ML processes, thoroughly defining the specifications of robust MLOps approaches remains of great interest to researchers and practitioners. In this paper, we provide a comprehensive overview of the trustworthiness property of MLOps systems. Specifically, we highlight technical practices to achieve robust MLOps systems. In addition, we survey the existing research approaches that address the robustness aspects of ML systems in production. We also review the tools and software available to build MLOps systems and summarize their support to handle the robustness aspects. Finally, we present the open challenges and propose possible future directions and opportunities within this emerging field. The aim of this paper is to provide researchers and practitioners working on practical AI applications with a comprehensive view to adopt robust ML solutions in production environments.

This paper studies the impact of artificial intelligence on innovation, exploiting the randomized introduction of a new materials discovery technology to 1,018 scientists in the R&D lab of a large U.S. firm. AI-assisted researchers discover 44% more materials, resulting in a 39% increase in patent filings and a 17% rise in downstream product innovation. These compounds possess more novel chemical structures and lead to more radical inventions. However, the technology has strikingly disparate effects across the productivity distribution: while the bottom third of scientists see little benefit, the output of top researchers nearly doubles. Investigating the mechanisms behind these results, I show that AI automates 57% of "idea-generation" tasks, reallocating researchers to the new task of evaluating model-produced candidate materials. Top scientists leverage their domain knowledge to prioritize promising AI suggestions, while others waste significant resources testing false positives. Together, these findings demonstrate the potential of AI-augmented research and highlight the complementarity between algorithms and expertise in the innovative process. Survey evidence reveals that these gains come at a cost, however, as 82% of scientists report reduced satisfaction with their work due to decreased creativity and skill underutilization.

Advances in LLMs have produced agents with knowledge and operational capabilities comparable to human scientists, suggesting potential to assist, accelerate, and automate research. However, existing studies mainly evaluate such systems on well-defined benchmarks or general tasks like literature retrieval, limiting their end-to-end problem-solving ability in open scientific scenarios. This is particularly true in physics, which is abstract, mathematically intensive, and requires integrating analytical reasoning with code-based computation. To address this, we propose PhysMaster, an LLM-based agent functioning as an autonomous theoretical and computational physicist. PhysMaster couples absract reasoning with numerical computation and leverages LANDAU, the Layered Academic Data Universe, which preserves retrieved literature, curated prior knowledge, and validated methodological traces, enhancing decision reliability and stability. It also employs an adaptive exploration strategy balancing efficiency and open-ended exploration, enabling robust performance in ultra-long-horizon tasks. We evaluate PhysMaster on problems from high-energy theory, condensed matter theory to astrophysics, including: (i) acceleration, compressing labor-intensive research from months to hours; (ii) automation, autonomously executing hypothesis-driven loops ; and (iii) autonomous discovery, independently exploring open problems.

Recently, Large Language Models (LLMs) have been applied to scientific equation discovery, leveraging their embedded scientific knowledge for hypothesis generation. However, current methods typically confine LLMs to the role of an equation proposer within search algorithms like genetic programming. In this paper, we present SR-Scientist, a framework that elevates the LLM from a simple equation proposer to an autonomous AI scientist that writes code to analyze data, implements the equation as code, submits it for evaluation, and optimizes the equation based on experimental feedback. Specifically, we wrap the code interpreter into a set of tools for data analysis and equation evaluation. The agent is instructed to optimize the equation by utilizing these tools over a long horizon with minimal human-defined pipelines. Empirical results show that SR-Scientist outperforms baseline methods by an absolute margin of 6% to 35% on datasets covering four science disciplines. Additionally, we demonstrate our method's robustness to noise, the generalization of the discovered equations to out-of-domain data, and their symbolic accuracy. Furthermore, we develop an end-to-end reinforcement learning framework to enhance the agent's capabilities.

Scientific user facilities, such as synchrotron beamlines, are equipped with a wide array of hardware and software tools that require a codebase for human-computer-interaction. This often necessitates developers to be involved to establish connection between users/researchers and the complex instrumentation. The advent of generative AI presents an opportunity to bridge this knowledge gap, enabling seamless communication and efficient experimental workflows. Here we present a modular architecture for the Virtual Scientific Companion (VISION) by assembling multiple AI-enabled cognitive blocks that each scaffolds large language models (LLMs) for a specialized task. With VISION, we performed LLM-based operation on the beamline workstation with low latency and demonstrated the first voice-controlled experiment at an X-ray scattering beamline. The modular and scalable architecture allows for easy adaptation to new instrument and capabilities. Development on natural language-based scientific experimentation is a building block for an impending future where a science exocortex -- a synthetic extension to the cognition of scientists -- may radically transform scientific practice and discovery.

Large language models (LLMs) and vision-language models (VLMs) have the potential to transform biological research by enabling autonomous experimentation. Yet, their application remains constrained by rigid protocol design, limited adaptability to dynamic lab conditions, inadequate error handling, and high operational complexity. Here we introduce BioMARS (Biological Multi-Agent Robotic System), an intelligent platform that integrates LLMs, VLMs, and modular robotics to autonomously design, plan, and execute biological experiments. BioMARS uses a hierarchical architecture: the Biologist Agent synthesizes protocols via retrieval-augmented generation; the Technician Agent translates them into executable robotic pseudo-code; and the Inspector Agent ensures procedural integrity through multimodal perception and anomaly detection. The system autonomously conducts cell passaging and culture tasks, matching or exceeding manual performance in viability, consistency, and morphological integrity. It also supports context-aware optimization, outperforming conventional strategies in differentiating retinal pigment epithelial cells. A web interface enables real-time human-AI collaboration, while a modular backend allows scalable integration with laboratory hardware. These results highlight the feasibility of generalizable, AI-driven laboratory automation and the transformative role of language-based reasoning in biological research.

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".

DeepResearch agents represent a transformative AI paradigm, conducting expert-level research through sophisticated reasoning and multi-tool integration. However, evaluating these systems remains critically challenging due to open-ended research scenarios and existing benchmarks that focus on isolated capabilities rather than holistic performance. Unlike traditional LLM tasks, DeepResearch systems must synthesize diverse sources, generate insights, and present coherent findings, which are capabilities that resist simple verification. To address this gap, we introduce DeepResearch-ReportEval, a comprehensive framework designed to assess DeepResearch systems through their most representative outputs: research reports. Our approach systematically measures three dimensions: quality, redundancy, and factuality, using an innovative LLM-as-a-Judge methodology achieving strong expert concordance. We contribute a standardized benchmark of 100 curated queries spanning 12 real-world categories, enabling systematic capability comparison. Our evaluation of four leading commercial systems reveals distinct design philosophies and performance trade-offs, establishing foundational insights as DeepResearch evolves from information assistants toward intelligent research partners. Source code and data are available at: https://github.com/HKUDS/DeepResearch-Eval.

This study critically distinguishes between AI Agents and Agentic AI, offering a structured conceptual taxonomy, application mapping, and challenge analysis to clarify their divergent design philosophies and capabilities. We begin by outlining the search strategy and foundational definitions, characterizing AI Agents as modular systems driven by Large Language Models (LLMs) and Large Image Models (LIMs) for narrow, task-specific automation. Generative AI is positioned as a precursor, with AI Agents advancing through tool integration, prompt engineering, and reasoning enhancements. In contrast, Agentic AI systems represent a paradigmatic shift marked by multi-agent collaboration, dynamic task decomposition, persistent memory, and orchestrated autonomy. Through a sequential evaluation of architectural evolution, operational mechanisms, interaction styles, and autonomy levels, we present a comparative analysis across both paradigms. Application domains such as customer support, scheduling, and data summarization are contrasted with Agentic AI deployments in research automation, robotic coordination, and medical decision support. We further examine unique challenges in each paradigm including hallucination, brittleness, emergent behavior, and coordination failure and propose targeted solutions such as ReAct loops, RAG, orchestration layers, and causal modeling. This work aims to provide a definitive roadmap for developing robust, scalable, and explainable AI agent and Agentic AI-driven systems. >AI Agents, Agent-driven, Vision-Language-Models, Agentic AI Decision Support System, Agentic-AI Applications

Large Language Models (LLMs) have revolutionized various aspects of engineering and science. Their utility is often bottlenecked by the lack of interaction with the external digital environment. To overcome this limitation and achieve integration of LLMs and Artificial Intelligence (AI) into real-world applications, customized AI agents are being constructed. Based on the technological trends and techniques, we extract a high-level approach for constructing these AI agents, focusing on their underlying architecture. This thesis serves as a comprehensive guide that elucidates a multi-faceted approach for empowering LLMs with the capability to leverage Application Programming Interfaces (APIs). We present a 7-step methodology that begins with the selection of suitable LLMs and the task decomposition that is necessary for complex problem-solving. This methodology includes techniques for generating training data for API interactions and heuristics for selecting the appropriate API among a plethora of options. These steps eventually lead to the generation of API calls that are both syntactically and semantically aligned with the LLM's understanding of a given task. Moreover, we review existing frameworks and tools that facilitate these processes and highlight the gaps in current attempts. In this direction, we propose an on-device architecture that aims to exploit the functionality of carry-on devices by using small models from the Hugging Face community. We examine the effectiveness of these approaches on real-world applications of various domains, including the generation of a piano sheet. Through an extensive analysis of the literature and available technologies, this thesis aims to set a compass for researchers and practitioners to harness the full potential of LLMs augmented with external tool capabilities, thus paving the way for more autonomous, robust, and context-aware AI agents.

Since language models (LMs) now outperform average humans on many challenging tasks, it has become increasingly difficult to develop challenging, high-quality, and realistic evaluations. We address this issue by examining LMs' capabilities to generate code for solving real scientific research problems. Incorporating input from scientists and AI researchers in 16 diverse natural science sub-fields, including mathematics, physics, chemistry, biology, and materials science, we created a scientist-curated coding benchmark, SciCode. The problems in SciCode naturally factorize into multiple subproblems, each involving knowledge recall, reasoning, and code synthesis. In total, SciCode contains 338 subproblems decomposed from 80 challenging main problems. It offers optional descriptions specifying useful scientific background information and scientist-annotated gold-standard solutions and test cases for evaluation. Claude3.5-Sonnet, the best-performing model among those tested, can solve only 4.6% of the problems in the most realistic setting. We believe that SciCode demonstrates both contemporary LMs' progress towards becoming helpful scientific assistants and sheds light on the development and evaluation of scientific AI in the future.

Advances in AI-assisted research have introduced powerful tools for literature retrieval, hypothesis generation, experimentation, and manuscript preparation. However, systems remain fragmented and lack human-centred workflows. To address these gaps, we introduce AIssistant, an agentic, open-source Human-AI collaborative framework designed to simplify the end-to-end creation of scientific workflows. Since our development is still in an early stage, we present here the first experiments with AIssistant for perspective and review research papers in machine learning. Our system integrates modular tools and agents for literature synthesis, section-wise experimentation, citation management, and automatic LaTeX paper text generation, while maintaining human oversight at every stage to ensure accuracy, coherence, and scholarly rigour. We conducted a comprehensive evaluation across three layers: (1) Independent Human Review, following NeurIPS double-blind standards; (2) Automated LLM Review, using GPT-5 as a scalable human review proxy; and (3) Program Chair Oversight, where the chair monitors the entire review process and makes final validation and acceptance decisions. The results demonstrate that AIssistant improves drafting efficiency and thematic consistency. Nonetheless, Human-AI collaboration remains essential for maintaining factual correctness, methodological soundness, and ethical compliance. Despite its effectiveness, we identify key limitations, including hallucinated citations, difficulty adapting to dynamic paper structures, and incomplete integration of multimodal content.

AIOps (Artificial Intelligence for IT Operations) solutions leverage the tremendous amount of data produced during the operation of large-scale systems and machine learning models to assist software practitioners in their system operations. Existing AIOps solutions usually maintain AIOps models against concept drift through periodical retraining, despite leaving a pile of discarded historical models that may perform well on specific future data. Other prior works propose dynamically selecting models for prediction tasks from a set of candidate models to optimize the model performance. However, there is no prior work in the AIOps area that assesses the use of model selection mechanisms on historical models to improve model performance or robustness. To fill the gap, we evaluate several model selection mechanisms by assessing their capabilities in selecting the optimal AIOps models that were built in the past to make predictions for the target data. We performed a case study on three large-scale public operation datasets: two trace datasets from the cloud computing platforms of Google and Alibaba, and one disk stats dataset from the BackBlaze cloud storage data center. We observe that the model selection mechnisms utilizing temporal adjacency tend to have a better performance and can prevail the periodical retraining approach. Our findings also highlight a performance gap between existing model selection mechnisms and the theoretical upper bound which may motivate future researchers and practitioners in investigating more efficient and effective model selection mechanisms that fit in the context of AIOps.

The scientific research paradigm is undergoing a profound transformation owing to the development of Artificial Intelligence (AI). Recent works demonstrate that various AI-assisted research methods can largely improve research efficiency by improving data analysis, accelerating computation, and fostering novel idea generation. To further move towards the ultimate goal (i.e., automatic scientific research), in this paper, we propose Dolphin, the first closed-loop open-ended auto-research framework to further build the entire process of human scientific research. Dolphin can generate research ideas, perform experiments, and get feedback from experimental results to generate higher-quality ideas. More specifically, Dolphin first generates novel ideas based on relevant papers which are ranked by the topic and task attributes. Then, the codes are automatically generated and debugged with the exception-traceback-guided local code structure. Finally, Dolphin automatically analyzes the results of each idea and feeds the results back to the next round of idea generation. Experiments are conducted on the benchmark datasets of different topics and results show that Dolphin can generate novel ideas continuously and complete the experiment in a loop. We highlight that Dolphin can automatically propose methods that are comparable to the state-of-the-art in some tasks such as 2D image classification and 3D point classification.

Large language models (LLMs) have sparked growing interest in automatic machine learning research agents. Among them, agents capable of autonomously proposing ideas and conducting machine learning experiments are particularly promising, as they maximize research automation and accelerate scientific progress by iteratively refining ideas based on experimental results. However, comprehensively evaluating such agents remains challenging. Existing benchmarks tend to overemphasize engineering aspects while neglecting academic rigor, creating barriers that obscure a clear assessment of an agent's scientific capabilities in machine learning research. They also suffer from limited task diversity, an overemphasis on application-oriented tasks over fundamental research problems, and limited scalability to realistic research settings. To address these limitations, we introduce FML-bench, a benchmark designed to evaluate automatic machine learning research agents on 8 diverse and fundamental machine learning research problems. It reduces coding burden, emphasizes fundamental problems rather than specific use cases, offers high task diversity, and is extensible to real-world machine learning GitHub repositories. Furthermore, we present a unified evaluation framework with five complementary metrics, designed to comprehensively assess agent performance on our benchmark. We evaluate state-of-the-art automatic research agents on FML-bench, and find that agents employing broad research exploration strategies outperform those focusing on narrow but deep exploration. These findings suggest that emphasizing the breadth of exploration may lead to more effective research outcomes than focusing solely on incremental refinement. Our benchmark is available at https://github.com/qrzou/FML-bench.

A major challenge of AI + Science lies in their inherent incompatibility: today's AI is primarily based on connectionism, while science depends on symbolism. To bridge the two worlds, we propose a framework to seamlessly synergize Kolmogorov-Arnold Networks (KANs) and science. The framework highlights KANs' usage for three aspects of scientific discovery: identifying relevant features, revealing modular structures, and discovering symbolic formulas. The synergy is bidirectional: science to KAN (incorporating scientific knowledge into KANs), and KAN to science (extracting scientific insights from KANs). We highlight major new functionalities in the pykan package: (1) MultKAN: KANs with multiplication nodes. (2) kanpiler: a KAN compiler that compiles symbolic formulas into KANs. (3) tree converter: convert KANs (or any neural networks) to tree graphs. Based on these tools, we demonstrate KANs' capability to discover various types of physical laws, including conserved quantities, Lagrangians, symmetries, and constitutive laws.

Artificial intelligence (AI) has made significant strides in recent years, yet it continues to struggle with a fundamental aspect of cognition present in all animals: common sense. Current AI systems, including those designed for complex tasks like autonomous driving, problem-solving challenges such as the Abstraction and Reasoning Corpus (ARC), and conversational benchmarks like the Turing Test, often lack the ability to adapt to new situations without extensive prior knowledge. This manuscript argues that integrating common sense into AI systems is essential for achieving true autonomy and unlocking the full societal and commercial value of AI. We propose a shift in the order of knowledge acquisition emphasizing the importance of developing AI systems that start from minimal prior knowledge and are capable of contextual learning, adaptive reasoning, and embodiment -- even within abstract domains. Additionally, we highlight the need to rethink the AI software stack to address this foundational challenge. Without common sense, AI systems may never reach true autonomy, instead exhibiting asymptotic performance that approaches theoretical ideals like AIXI but remains unattainable in practice due to infinite resource and computation requirements. While scaling AI models and passing benchmarks like the Turing Test have brought significant advancements in applications that do not require autonomy, these approaches alone are insufficient to achieve autonomous AI with common sense. By redefining existing benchmarks and challenges to enforce constraints that require genuine common sense, and by broadening our understanding of embodiment to include both physical and abstract domains, we can encourage the development of AI systems better equipped to handle the complexities of real-world and abstract environments.

The exponential growth of academic publications poses challenges for the research process, such as literature review and procedural planning. Large Language Models (LLMs) have emerged as powerful AI tools, especially when combined with additional tools and resources. Recent LLM-powered frameworks offer promising solutions for handling complex domain-specific tasks, yet their domain-specific implementation limits broader applicability. This highlights the need for LLM-integrated systems that can assist in cross-disciplinary tasks, such as streamlining the research process across science and engineering disciplines. To address this need, we introduce Artificial Research Innovator Assistant (ARIA), a four-agent, multi-LLM framework. By emulating a team of expert assistants, ARIA systematically replicates the human research workflow to autonomously search, retrieve, and filter hundreds of papers, subsequently synthesizing relevant literature into actionable research procedures. In a case study on dropwise condensation enhancement, ARIA demonstrates its capability to streamline research tasks within an hour, maintaining user oversight during execution and ultimately liberating researchers from time-intensive tasks.

Drawing on 1,178 safety and reliability papers from 9,439 generative AI papers (January 2020 - March 2025), we compare research outputs of leading AI companies (Anthropic, Google DeepMind, Meta, Microsoft, and OpenAI) and AI universities (CMU, MIT, NYU, Stanford, UC Berkeley, and University of Washington). We find that corporate AI research increasingly concentrates on pre-deployment areas -- model alignment and testing & evaluation -- while attention to deployment-stage issues such as model bias has waned. Significant research gaps exist in high-risk deployment domains, including healthcare, finance, misinformation, persuasive and addictive features, hallucinations, and copyright. Without improved observability into deployed AI, growing corporate concentration could deepen knowledge deficits. We recommend expanding external researcher access to deployment data and systematic observability of in-market AI behaviors.

Solving complex real-world tasks requires cycles of actions and observations. This is particularly true in science, where tasks require many cycles of analysis, tool use, and experimentation. Language agents are promising for automating intellectual tasks in science because they can interact with tools via natural language or code. Yet their flexibility creates conceptual and practical challenges for software implementations, since agents may comprise non-standard components such as internal reasoning, planning, tool usage, as well as the inherent stochasticity of temperature-sampled language models. Here, we introduce Aviary, an extensible gymnasium for language agents. We formalize agents as policies solving language-grounded partially observable Markov decision processes, which we term language decision processes. We then implement five environments, including three challenging scientific environments: (1) manipulating DNA constructs for molecular cloning, (2) answering research questions by accessing scientific literature, and (3) engineering protein stability. These environments were selected for their focus on multi-step reasoning and their relevance to contemporary biology research. Finally, with online training and scaling inference-time compute, we show that language agents backed by open-source, non-frontier LLMs can match and exceed both frontier LLM agents and human experts on multiple tasks at up to 100x lower inference cost.

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.

Compositional AI systems, which combine multiple artificial intelligence components together with other application components to solve a larger problem, have no known pattern of development and are often approached in a bespoke and ad hoc style. This makes development slower and harder to reuse for future applications. To support the full rapid development cycle of compositional AI applications, we have developed a novel framework called (Bee)* (written as a regular expression and pronounced as "beestar"). We illustrate how (Bee)* supports building integrated, scalable, and interactive compositional AI applications with a simplified developer experience.

We define Agency as the emergent capacity of AI systems to function as autonomous agents actively discovering problems, formulating hypotheses, and executing solutions through self-directed engagement with environments and tools. This fundamental capability marks the dawn of the Age of AI Agency, driven by a critical industry shift: the urgent need for AI systems that don't just think, but work. While current AI excels at reasoning and generating responses, industries demand autonomous agents that can execute tasks, operate tools, and drive real-world outcomes. As agentic intelligence becomes the defining characteristic separating cognitive systems from productive workers, efficiently cultivating machine autonomy becomes paramount. Current approaches assume that more data yields better agency, following traditional scaling laws from language modeling. We fundamentally challenge this paradigm. LIMI (Less Is More for Intelligent Agency) demonstrates that agency follows radically different development principles. Through strategic focus on collaborative software development and scientific research workflows, we show that sophisticated agentic intelligence can emerge from minimal but strategically curated demonstrations of autonomous behavior. Using only 78 carefully designed training samples, LIMI achieves 73.5% on comprehensive agency benchmarks, dramatically outperforming state-of-the-art models: Kimi-K2-Instruct (24.1%), DeepSeek-V3.1 (11.9%), Qwen3-235B-A22B-Instruct (27.5%), and GLM-4.5 (45.1%). Most strikingly, LIMI demonstrates 53.7% improvement over models trained on 10,000 samples-achieving superior agentic intelligence with 128 times fewer samples. Our findings establish the Agency Efficiency Principle: machine autonomy emerges not from data abundance but from strategic curation of high-quality agentic demonstrations.

Artificial intelligence (AI) has achieved astonishing successes in many domains, especially with the recent breakthroughs in the development of foundational large models. These large models, leveraging their extensive training data, provide versatile solutions for a wide range of downstream tasks. However, as modern datasets become increasingly diverse and complex, the development of large AI models faces two major challenges: (1) the enormous consumption of computational resources and deployment difficulties, and (2) the difficulty in fitting heterogeneous and complex data, which limits the usability of the models. Mixture of Experts (MoE) models has recently attracted much attention in addressing these challenges, by dynamically selecting and activating the most relevant sub-models to process input data. It has been shown that MoEs can significantly improve model performance and efficiency with fewer resources, particularly excelling in handling large-scale, multimodal data. Given the tremendous potential MoE has demonstrated across various domains, it is urgent to provide a comprehensive summary of recent advancements of MoEs in many important fields. Existing surveys on MoE have their limitations, e.g., being outdated or lacking discussion on certain key areas, and we aim to address these gaps. In this paper, we first introduce the basic design of MoE, including gating functions, expert networks, routing mechanisms, training strategies, and system design. We then explore the algorithm design of MoE in important machine learning paradigms such as continual learning, meta-learning, multi-task learning, and reinforcement learning. Additionally, we summarize theoretical studies aimed at understanding MoE and review its applications in computer vision and natural language processing. Finally, we discuss promising future research directions.

In the upcoming decade, deep learning may revolutionize the natural sciences, enhancing our capacity to model and predict natural occurrences. This could herald a new era of scientific exploration, bringing significant advancements across sectors from drug development to renewable energy. To answer this call, we present DeepSpeed4Science initiative (deepspeed4science.ai) which aims to build unique capabilities through AI system technology innovations to help domain experts to unlock today's biggest science mysteries. By leveraging DeepSpeed's current technology pillars (training, inference and compression) as base technology enablers, DeepSpeed4Science will create a new set of AI system technologies tailored for accelerating scientific discoveries by addressing their unique complexity beyond the common technical approaches used for accelerating generic large language models (LLMs). In this paper, we showcase the early progress we made with DeepSpeed4Science in addressing two of the critical system challenges in structural biology research.

Human space exploration beyond low Earth orbit will involve missions of significant distance and duration. To effectively mitigate myriad space health hazards, paradigm shifts in data and space health systems are necessary to enable Earth-independence, rather than Earth-reliance. Promising developments in the fields of artificial intelligence and machine learning for biology and health can address these needs. We propose an appropriately autonomous and intelligent Precision Space Health system that will monitor, aggregate, and assess biomedical statuses; analyze and predict personalized adverse health outcomes; adapt and respond to newly accumulated data; and provide preventive, actionable, and timely insights to individual deep space crew members and iterative decision support to their crew medical officer. Here we present a summary of recommendations from a workshop organized by the National Aeronautics and Space Administration, on future applications of artificial intelligence in space biology and health. In the next decade, biomonitoring technology, biomarker science, spacecraft hardware, intelligent software, and streamlined data management must mature and be woven together into a Precision Space Health system to enable humanity to thrive in deep space.

Gravitational waves, detected a century after they were first theorized, are spacetime distortions caused by some of the most cataclysmic events in the universe, including black hole mergers and supernovae. The successful detection of these waves has been made possible by ingenious detectors designed by human experts. Beyond these successful designs, the vast space of experimental configurations remains largely unexplored, offering an exciting territory potentially rich in innovative and unconventional detection strategies. Here, we demonstrate the application of artificial intelligence (AI) to systematically explore this enormous space, revealing novel topologies for gravitational wave (GW) detectors that outperform current next-generation designs under realistic experimental constraints. Our results span a broad range of astrophysical targets, such as black hole and neutron star mergers, supernovae, and primordial GW sources. Moreover, we are able to conceptualize the initially unorthodox discovered designs, emphasizing the potential of using AI algorithms not only in discovering but also in understanding these novel topologies. We've assembled more than 50 superior solutions in a publicly available Gravitational Wave Detector Zoo which could lead to many new surprising techniques. At a bigger picture, our approach is not limited to gravitational wave detectors and can be extended to AI-driven design of experiments across diverse domains of fundamental physics.

Agentic AI systems use specialized agents to handle tasks within complex workflows, enabling automation and efficiency. However, optimizing these systems often requires labor-intensive, manual adjustments to refine roles, tasks, and interactions. This paper introduces a framework for autonomously optimizing Agentic AI solutions across industries, such as NLP-driven enterprise applications. The system employs agents for Refinement, Execution, Evaluation, Modification, and Documentation, leveraging iterative feedback loops powered by an LLM (Llama 3.2-3B). The framework achieves optimal performance without human input by autonomously generating and testing hypotheses to improve system configurations. This approach enhances scalability and adaptability, offering a robust solution for real-world applications in dynamic environments. Case studies across diverse domains illustrate the transformative impact of this framework, showcasing significant improvements in output quality, relevance, and actionability. All data for these case studies, including original and evolved agent codes, along with their outputs, are here: https://anonymous.4open.science/r/evolver-1D11/

In recent years there has been a tremendous surge in the general capabilities of AI systems, mainly fuelled by training foundation models on internetscale data. Nevertheless, the creation of openended, ever self-improving AI remains elusive. In this position paper, we argue that the ingredients are now in place to achieve openendedness in AI systems with respect to a human observer. Furthermore, we claim that such open-endedness is an essential property of any artificial superhuman intelligence (ASI). We begin by providing a concrete formal definition of open-endedness through the lens of novelty and learnability. We then illustrate a path towards ASI via open-ended systems built on top of foundation models, capable of making novel, humanrelevant discoveries. We conclude by examining the safety implications of generally-capable openended AI. We expect that open-ended foundation models will prove to be an increasingly fertile and safety-critical area of research in the near future.

Frontier AI agents show increasing promise as scientific research assistants, and may eventually be useful for extended, open-ended research workflows. However, in order to use agents for novel research, we must first assess the underlying faithfulness and correctness of their work. To evaluate agents as research assistants, we introduce ReplicationBench, an evaluation framework that tests whether agents can replicate entire research papers drawn from the astrophysics literature. Astrophysics, where research relies heavily on archival data and computational study while requiring little real-world experimentation, is a particularly useful testbed for AI agents in scientific research. We split each paper into tasks which require agents to replicate the paper's core contributions, including the experimental setup, derivations, data analysis, and codebase. Each task is co-developed with the original paper authors and targets a key scientific result, enabling objective evaluation of both faithfulness (adherence to original methods) and correctness (technical accuracy of results). ReplicationBench is extremely challenging for current frontier language models: even the best-performing language models score under 20%. We analyze ReplicationBench trajectories in collaboration with domain experts and find a rich, diverse set of failure modes for agents in scientific research. ReplicationBench establishes the first benchmark of paper-scale, expert-validated astrophysics research tasks, reveals insights about agent performance generalizable to other domains of data-driven science, and provides a scalable framework for measuring AI agents' reliability in scientific research.

Ensuring safe and effective use of AI requires understanding and anticipating its performance on novel tasks, from advanced scientific challenges to transformed workplace activities. So far, benchmarking has guided progress in AI, but it has offered limited explanatory and predictive power for general-purpose AI systems, given the low transferability across diverse tasks. In this paper, we introduce general scales for AI evaluation that can explain what common AI benchmarks really measure, extract ability profiles of AI systems, and predict their performance for new task instances, in- and out-of-distribution. Our fully-automated methodology builds on 18 newly-crafted rubrics that place instance demands on general scales that do not saturate. Illustrated for 15 large language models and 63 tasks, high explanatory power is unleashed from inspecting the demand and ability profiles, bringing insights on the sensitivity and specificity exhibited by different benchmarks, and how knowledge, metacognition and reasoning are affected by model size, chain-of-thought and distillation. Surprisingly, high predictive power at the instance level becomes possible using these demand levels, providing superior estimates over black-box baseline predictors based on embeddings or finetuning, especially in out-of-distribution settings (new tasks and new benchmarks). The scales, rubrics, battery, techniques and results presented here represent a major step for AI evaluation, underpinning the reliable deployment of AI in the years ahead. (Collaborative platform: https://kinds-of-intelligence-cfi.github.io/ADELE.)

We introduce Meta Agents Research Environments (ARE), a research platform for scalable creation of environments, integration of synthetic or real applications, and execution of agentic orchestrations. ARE provides simple abstractions to build complex and diverse environments, each with their own rules, tools, content, and verifiers, helping to bridge the gap between model development and real-world deployment. We also propose Gaia2, a benchmark built in ARE and designed to measure general agent capabilities. Beyond search and execution, Gaia2 requires agents to handle ambiguities and noise, adapt to dynamic environments, collaborate with other agents, and operate under temporal constraints. Unlike prior benchmarks, Gaia2 runs asynchronously, surfacing new failure modes that are invisible in static settings. Our experiments show that no system dominates across the intelligence spectrum: stronger reasoning often comes at the cost of efficiency, and budget scaling curves plateau, highlighting the need for new architectures and adaptive compute strategies. Perhaps more importantly, ARE abstractions enable continuous extension of Gaia2 to other environments, empowering the community to rapidly create new benchmarks tailored to their domains. In AI's second half, progress increasingly depends on defining meaningful tasks and robust evaluations to drive frontier capabilities forward.

Large language models (LLMs) have enabled powerful advances in natural language understanding and generation. Yet their application to complex, real-world scientific workflows remain limited by challenges in memory, planning, and tool integration. Here, we introduce SciBORG (Scientific Bespoke Artificial Intelligence Agents Optimized for Research Goals), a modular agentic framework that allows LLM-based agents to autonomously plan, reason, and achieve robust and reliable domain-specific task execution. Agents are constructed dynamically from source code documentation and augmented with finite-state automata (FSA) memory, enabling persistent state tracking and context-aware decision-making. This approach eliminates the need for manual prompt engineering and allows for robust, scalable deployment across diverse applications via maintaining context across extended workflows and to recover from tool or execution failures. We validate SciBORG through integration with both physical and virtual hardware, such as microwave synthesizers for executing user-specified reactions, with context-aware decision making and demonstrate its use in autonomous multi-step bioassay retrieval from the PubChem database utilizing multi-step planning, reasoning, agent-to-agent communication and coordination for execution of exploratory tasks. Systematic benchmarking shows that SciBORG agents achieve reliable execution, adaptive planning, and interpretable state transitions. Our results show that memory and state awareness are critical enablers of agentic planning and reliability, offering a generalizable foundation for deploying AI agents in complex environments.

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.

Intelligent agents powered by large language models (LLMs) have demonstrated substantial promise in autonomously conducting experiments and facilitating scientific discoveries across various disciplines. While their capabilities are promising, they also introduce novel vulnerabilities that demand careful consideration for safety. However, there exists a notable gap in the literature, as there has been no comprehensive exploration of these vulnerabilities. This position paper fills this gap by conducting a thorough examination of vulnerabilities in LLM-based agents within scientific domains, shedding light on potential risks associated with their misuse and emphasizing the need for safety measures. We begin by providing a comprehensive overview of the potential risks inherent to scientific LLM agents, taking into account user intent, the specific scientific domain, and their potential impact on the external environment. Then, we delve into the origins of these vulnerabilities and provide a scoping review of the limited existing works. Based on our analysis, we propose a triadic framework involving human regulation, agent alignment, and an understanding of environmental feedback (agent regulation) to mitigate these identified risks. Furthermore, we highlight the limitations and challenges associated with safeguarding scientific agents and advocate for the development of improved models, robust benchmarks, and comprehensive regulations to address these issues effectively.

Recent advances in artificial intelligence (AI) have produced highly capable and controllable systems. This creates unprecedented opportunities for structured reasoning as well as collaboration among multiple AI systems and humans. To fully realize this potential, it is essential to develop a principled way of designing and studying such structured interactions. For this purpose, we introduce the conceptual framework of Flows: a systematic approach to modeling complex interactions. Flows are self-contained building blocks of computation, with an isolated state, communicating through a standardized message-based interface. This modular design allows Flows to be recursively composed into arbitrarily nested interactions, with a substantial reduction of complexity. Crucially, any interaction can be implemented using this framework, including prior work on AI--AI and human--AI interactions, prompt engineering schemes, and tool augmentation. We demonstrate the potential of Flows on the task of competitive coding, a challenging task on which even GPT-4 struggles. Our results suggest that structured reasoning and collaboration substantially improve generalization, with AI-only Flows adding +21 and human--AI Flows adding +54 absolute points in terms of solve rate. To support rapid and rigorous research, we introduce the aiFlows library. The library comes with a repository of Flows that can be easily used, extended, and composed into novel, more complex Flows. The aiFlows library is available at https://github.com/epfl-dlab/aiflows. Data and Flows for reproducing our experiments are available at https://github.com/epfl-dlab/cc_flows.

The ability to solve problems is a hallmark of intelligence and has been an enduring goal in AI. AI systems that can create programs as solutions to problems or assist developers in writing programs can increase productivity and make programming more accessible. Recently, pre-trained large language models have shown impressive abilities in generating new codes from natural language descriptions, repairing buggy codes, translating codes between languages, and retrieving relevant code segments. However, the evaluation of these models has often been performed in a scattered way on only one or two specific tasks, in a few languages, at a partial granularity (e.g., function) level and in many cases without proper training data. Even more concerning is that in most cases the evaluation of generated codes has been done in terms of mere lexical overlap rather than actual execution whereas semantic similarity (or equivalence) of two code segments depends only on their ``execution similarity'', i.e., being able to get the same output for a given input.

AI agents are systems capable of perceiving their environment, autonomously planning and executing tasks. Recent advancements in LLM have introduced a transformative paradigm for AI agents, enabling them to interact with external resources and tools through prompts. In such agents, the workflow integrates developer-written code, which manages framework construction and logic control, with LLM-generated natural language that enhances dynamic decision-making and interaction. However, discrepancies between developer-implemented logic and the dynamically generated content of LLMs in terms of behavior and expected outcomes can lead to defects, such as tool invocation failures and task execution errors. These issues introduce specific risks, leading to various defects in LLM-based AI Agents, such as service interruptions. Despite the importance of these issues, there is a lack of systematic work that focuses on analyzing LLM-based AI Agents to uncover defects in their code. In this paper, we present the first study focused on identifying and detecting defects in LLM Agents. We collected and analyzed 6,854 relevant posts from StackOverflow to define 8 types of agent defects. For each type, we provided detailed descriptions with an example. Then, we designed a static analysis tool, named Agentable, to detect the defects. Agentable leverages Code Property Graphs and LLMs to analyze Agent workflows by efficiently identifying specific code patterns and analyzing natural language descriptions. To evaluate Agentable, we constructed two datasets: AgentSet, consists of 84 real-world Agents, and AgentTest, which contains 78 Agents specifically designed to include various types of defects. Our results show that Agentable achieved an overall accuracy of 88.79% and a recall rate of 91.03%. Furthermore, our analysis reveals the 889 defects of the AgentSet, highlighting the prevalence of these defects.

Computing in the life sciences has undergone a transformative evolution, from early computational models in the 1950s to the applications of artificial intelligence (AI) and machine learning (ML) seen today. This paper highlights key milestones and technological advancements through the historical development of computing in the life sciences. The discussion includes the inception of computational models for biological processes, the advent of bioinformatics tools, and the integration of AI/ML in modern life sciences research. Attention is given to AI-enabled tools used in the life sciences, such as scientific large language models and bio-AI tools, examining their capabilities, limitations, and impact to biological risk. This paper seeks to clarify and establish essential terminology and concepts to ensure informed decision-making and effective communication across disciplines.