Daily Papers

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

Hypothetical induction is recognized as the main reasoning type when scientists make observations about the world and try to propose hypotheses to explain those observations. Past research on hypothetical induction is under a constrained setting: (1) the observation annotations in the dataset are carefully manually handpicked sentences (resulting in a close-domain setting); and (2) the ground truth hypotheses are mostly commonsense knowledge, making the task less challenging. In this work, we tackle these problems by proposing the first dataset for social science academic hypotheses discovery, with the final goal to create systems that automatically generate valid, novel, and helpful scientific hypotheses, given only a pile of raw web corpus. Unlike previous settings, the new dataset requires (1) using open-domain data (raw web corpus) as observations; and (2) proposing hypotheses even new to humanity. A multi-module framework is developed for the task, including three different feedback mechanisms to boost performance, which exhibits superior performance in terms of both GPT-4 based and expert-based evaluation. To the best of our knowledge, this is the first work showing that LLMs are able to generate novel (''not existing in literature'') and valid (''reflecting reality'') scientific hypotheses.

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.

Literature-Based Discovery (LBD) aims to discover new scientific knowledge by mining papers and generating hypotheses. Standard LBD is limited to predicting pairwise relations between discrete concepts (e.g., drug-disease links), and ignores critical contexts like experimental settings (e.g., a specific patient population where a drug is evaluated) and background motivations (e.g., to find drugs without specific side effects). We address these limitations with a novel formulation of contextualized-LBD (C-LBD): generating scientific hypotheses in natural language, while grounding them in a context that controls the hypothesis search space. We present a modeling framework using retrieval of ``inspirations'' from past scientific papers. Our evaluations reveal that GPT-4 tends to generate ideas with overall low technical depth and novelty, while our inspiration prompting approaches partially mitigate this issue. Our work represents a first step toward building language models that generate new ideas derived from scientific literature.

Large Language Models have recently gained significant attention in scientific discovery for their extensive knowledge and advanced reasoning capabilities. However, they encounter challenges in effectively simulating observational feedback and grounding it with language to propel advancements in physical scientific discovery. Conversely, human scientists undertake scientific discovery by formulating hypotheses, conducting experiments, and revising theories through observational analysis. Inspired by this, we propose to enhance the knowledge-driven, abstract reasoning abilities of LLMs with the computational strength of simulations. We introduce Scientific Generative Agent (SGA), a bilevel optimization framework: LLMs act as knowledgeable and versatile thinkers, proposing scientific hypotheses and reason about discrete components, such as physics equations or molecule structures; meanwhile, simulations function as experimental platforms, providing observational feedback and optimizing via differentiability for continuous parts, such as physical parameters. We conduct extensive experiments to demonstrate our framework's efficacy in constitutive law discovery and molecular design, unveiling novel solutions that differ from conventional human expectations yet remain coherent upon analysis.

Autonomous systems that generate scientific hypotheses, conduct experiments, and draft manuscripts have recently emerged as a promising paradigm for accelerating discovery. However, existing AI Scientists remain largely domain-agnostic, limiting their applicability to clinical medicine, where research is required to be grounded in medical evidence with specialized data modalities. In this work, we introduce Medical AI Scientist, the first autonomous research framework tailored to clinical autonomous research. It enables clinically grounded ideation by transforming extensively surveyed literature into actionable evidence through clinician-engineer co-reasoning mechanism, which improves the traceability of generated research ideas. It further facilitates evidence-grounded manuscript drafting guided by structured medical compositional conventions and ethical policies. The framework operates under 3 research modes, namely paper-based reproduction, literature-inspired innovation, and task-driven exploration, each corresponding to a distinct level of automated scientific inquiry with progressively increasing autonomy. Comprehensive evaluations by both large language models and human experts demonstrate that the ideas generated by the Medical AI Scientist are of substantially higher quality than those produced by commercial LLMs across 171 cases, 19 clinical tasks, and 6 data modalities. Meanwhile, our system achieves strong alignment between the proposed method and its implementation, while also demonstrating significantly higher success rates in executable experiments. Double-blind evaluations by human experts and the Stanford Agentic Reviewer suggest that the generated manuscripts approach MICCAI-level quality, while consistently surpassing those from ISBI and BIBM. The proposed Medical AI Scientist highlights the potential of leveraging AI for autonomous scientific discovery in healthcare.

Generating novel and creative scientific hypotheses is a cornerstone in achieving Artificial General Intelligence. Large language and reasoning models have the potential to aid in the systematic creation, selection, and validation of scientifically informed hypotheses. However, current foundation models often struggle to produce scientific ideas that are both novel and feasible. One reason is the lack of a dedicated dataset that frames Scientific Hypothesis Generation (SHG) as a Natural Language Generation (NLG) task. In this paper, we introduce HypoGen, the first dataset of approximately 5500 structured problem-hypothesis pairs extracted from top-tier computer science conferences structured with a Bit-Flip-Spark schema, where the Bit is the conventional assumption, the Spark is the key insight or conceptual leap, and the Flip is the resulting counterproposal. HypoGen uniquely integrates an explicit Chain-of-Reasoning component that reflects the intellectual process from Bit to Flip. We demonstrate that framing hypothesis generation as conditional language modelling, with the model fine-tuned on Bit-Flip-Spark and the Chain-of-Reasoning (and where, at inference, we only provide the Bit), leads to improvements in the overall quality of the hypotheses. Our evaluation employs automated metrics and LLM judge rankings for overall quality assessment. We show that by fine-tuning on our HypoGen dataset we improve the novelty, feasibility, and overall quality of the generated hypotheses. The HypoGen dataset is publicly available at huggingface.co/datasets/UniverseTBD/hypogen-dr1.

Reducing hallucination of Large Language Models (LLMs) is imperative for use in the sciences where reproducibility is crucial. However, LLMs inherently lack long-term memory, making it a nontrivial, ad hoc, and inevitably biased task to fine-tune them on domain-specific literature and data. Here we introduce LLaMP, a multimodal retrieval-augmented generation (RAG) framework of multiple data-aware reasoning-and-acting (ReAct) agents that dynamically interact with computational and experimental data on Materials Project (MP). Without fine-tuning, LLaMP demonstrates an ability to comprehend and integrate various modalities of materials science concepts, fetch relevant data stores on the fly, process higher-order data (such as crystal structures and elastic tensors), and summarize multi-step procedures for solid-state synthesis. We show that LLaMP effectively corrects errors in GPT-3.5's intrinsic knowledge, reducing a 5.21% MAPE on frequently-documented bandgaps and a significant 1103.54% MAPE on formation energies -- errors that GPT-3.5 seems to derive from mixed data sources. Additionally, LLaMP substantially reduces the hallucinated volumetric strain in a diamond cubic silicon structure from 66.3% to 0. The proposed framework offers an intuitive and nearly hallucination-free approach to exploring materials informatics and establishes a pathway for knowledge distillation and fine-tuning other language models. We envision the framework as a valuable component for scientific hypotheses and a foundation for future autonomous laboratories where multiple LLM agents communicate and cooperate with robotics to drive material synthesis and chemical reactions without hard-coded human logic and intervention.

Large language models (LLMs) have demonstrated potential in assisting scientific research, yet their ability to discover high-quality research hypotheses remains unexamined due to the lack of a dedicated benchmark. To address this gap, we introduce the first large-scale benchmark for evaluating LLMs with a near-sufficient set of sub-tasks of scientific discovery: inspiration retrieval, hypothesis composition, and hypothesis ranking. We develop an automated framework that extracts critical components - research questions, background surveys, inspirations, and hypotheses - from scientific papers across 12 disciplines, with expert validation confirming its accuracy. To prevent data contamination, we focus exclusively on papers published in 2024, ensuring minimal overlap with LLM pretraining data. Our evaluation reveals that LLMs perform well in retrieving inspirations, an out-of-distribution task, suggesting their ability to surface novel knowledge associations. This positions LLMs as "research hypothesis mines", capable of facilitating automated scientific discovery by generating innovative hypotheses at scale with minimal human intervention.

Large language models hold promise as scientific assistants, yet existing agents either rely solely on algorithm evolution or on deep research in isolation, both of which face critical limitations. Pure algorithm evolution, as in AlphaEvolve, depends only on the internal knowledge of LLMs and quickly plateaus in complex domains, while pure deep research proposes ideas without validation, resulting in unrealistic or unimplementable solutions. We present DeepEvolve, an agent that integrates deep research with algorithm evolution, uniting external knowledge retrieval, cross-file code editing, and systematic debugging under a feedback-driven iterative loop. Each iteration not only proposes new hypotheses but also refines, implements, and tests them, avoiding both shallow improvements and unproductive over-refinements. Across nine benchmarks in chemistry, mathematics, biology, materials, and patents, DeepEvolve consistently improves the initial algorithm, producing executable new algorithms with sustained gains. By bridging the gap between unguided evolution and research without grounding, DeepEvolve provides a reliable framework for advancing scientific algorithm discovery. Our code is available at https://github.com/liugangcode/deepevolve.

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.

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

Large Language Model (LLM)-based multi-agent systems (MAS) demonstrate remarkable potential for scientific discovery. Existing approaches, however, often automate scientific discovery using predefined workflows that lack rationality constraints. This often leads to aimless hypothesizing and a failure to consistently link hypotheses with evidence, thereby hindering systematic uncertainty reduction. Overcoming these limitations fundamentally requires systematic uncertainty reduction. We introduce PiFlow, an information-theoretical framework, treating automated scientific discovery as a structured uncertainty reduction problem guided by principles (e.g., scientific laws). In evaluations across three distinct scientific domains -- discovering nanomaterial structures, bio-molecules, and superconductor candidates with targeted properties -- our method significantly improves discovery efficiency, reflected by a 73.55\% increase in the Area Under the Curve (AUC) of property values versus exploration steps, and enhances solution quality by 94.06\% compared to a vanilla agent system. Overall, PiFlow serves as a Plug-and-Play method, establishing a novel paradigm shift in highly efficient automated scientific discovery, paving the way for more robust and accelerated AI-driven research. Code is publicly available at our https://github.com/amair-lab/PiFlow{GitHub}.

Scientific idea generation lies at the heart of scientific discovery and has driven human progress-whether by solving unsolved problems or proposing novel hypotheses to explain unknown phenomena. Unlike standard scientific reasoning or general creative generation, idea generation in science is a multi-objective and open-ended task, where the novelty of a contribution is as essential as its empirical soundness. Large language models (LLMs) have recently emerged as promising generators of scientific ideas, capable of producing coherent and factual outputs with surprising intuition and acceptable reasoning, yet their creative capacity remains inconsistent and poorly understood. This survey provides a structured synthesis of methods for LLM-driven scientific ideation, examining how different approaches balance creativity with scientific soundness. We categorize existing methods into five complementary families: External knowledge augmentation, Prompt-based distributional steering, Inference-time scaling, Multi-agent collaboration, and Parameter-level adaptation. To interpret their contributions, we employ two complementary frameworks: Boden's taxonomy of Combinatorial, Exploratory and Transformational creativity to characterize the level of ideas each family expected to generate, and Rhodes' 4Ps framework-Person, Process, Press, and Product-to locate the aspect or source of creativity that each method emphasizes. By aligning methodological advances with creativity frameworks, this survey clarifies the state of the field and outlines key directions toward reliable, systematic, and transformative applications of LLMs in scientific discovery.

Language models are increasingly used in scientific discovery to generate hypotheses, propose candidate solutions, implement systems, and iteratively refine them. At the core of these trial-and-error loops lies evaluation: the process of obtaining feedback on candidate solutions via verifiers, simulators, or task-specific scoring functions. While prior work has highlighted the importance of evaluation, it has not explicitly formulated the problem of how evaluation-driven discovery loops can be scaled up in a principled and effective manner to push the boundaries of scientific discovery, a problem this paper seeks to address. We introduce Simple Test-time Evaluation-driven Scaling (SimpleTES), a general framework that strategically combines parallel exploration, feedback-driven refinement, and local selection, revealing substantial gains unlocked by scaling evaluation-driven discovery loops along the right dimensions. Across 21 scientific problems spanning six domains, SimpleTES discovers state-of-the-art solutions using gpt-oss models, consistently outperforming both frontier-model baselines and sophisticated optimization pipelines. Particularly, we sped up the widely used LASSO algorithm by over 2x, designed quantum circuit routing policies that reduce gate overhead by 24.5%, and discovered new Erdos minimum overlap constructions that surpass the best-known results. Beyond novel discoveries, SimpleTES produces trajectory-level histories that naturally supervise feedback-driven learning. When post-trained on successful trajectories, models not only improve efficiency on seen problems but also generalize to unseen problems, discovering solutions that base models fail to uncover. Together, our results establish effective evaluation-driven loop scaling as a central axis for advancing LLM-driven scientific discovery, and provide a simple yet practical framework for realizing these gains.

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

Large language models (LLMs) have shown promise in automating scientific hypothesis generation, yet existing approaches primarily yield coarse-grained hypotheses lacking critical methodological and experimental details. We introduce and formally define the novel task of fine-grained scientific hypothesis discovery, which entails generating detailed, experimentally actionable hypotheses from coarse initial research directions. We frame this as a combinatorial optimization problem and investigate the upper limits of LLMs' capacity to solve it when maximally leveraged. Specifically, we explore four foundational questions: (1) how to best harness an LLM's internal heuristics to formulate the fine-grained hypothesis it itself would judge as the most promising among all the possible hypotheses it might generate, based on its own internal scoring-thus defining a latent reward landscape over the hypothesis space; (2) whether such LLM-judged better hypotheses exhibit stronger alignment with ground-truth hypotheses; (3) whether shaping the reward landscape using an ensemble of diverse LLMs of similar capacity yields better outcomes than defining it with repeated instances of the strongest LLM among them; and (4) whether an ensemble of identical LLMs provides a more reliable reward landscape than a single LLM. To address these questions, we propose a hierarchical search method that incrementally proposes and integrates details into the hypothesis, progressing from general concepts to specific experimental configurations. We show that this hierarchical process smooths the reward landscape and enables more effective optimization. Empirical evaluations on a new benchmark of expert-annotated fine-grained hypotheses from recent chemistry literature show that our method consistently outperforms strong baselines.

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/.

The rapid growth of biomedical literature and curated databases has made it increasingly difficult for researchers to systematically connect biomarker mechanisms to actionable drug combination hypotheses. We present AI Co-Scientist (CoDHy), an interactive, human-in-the-loop system for biomarker-guided drug combination hypothesis generation in cancer research. CoDHy integrates structured biomedical databases and unstructured literature evidence into a task-specific knowledge graph, which serves as the basis for graph-based reasoning and hypothesis construction. The system combines knowledge graph embeddings with agent-based reasoning to generate, validate, and rank candidate drug combinations, while explicitly grounding each hypothesis in retrievable evidence. Through a web-based interface, users can configure the scientific context, inspect intermediate results, and iteratively refine hypotheses, enabling transparent and researcher-steerable exploration rather than automated decision-making. We demonstrate CoDHy as a system for exploratory hypothesis generation and decision support in translational oncology, highlighting its design, interaction workflow, and practical use cases.

Scientific inquiry requires systems-level reasoning that integrates heterogeneous experimental data, cross-domain knowledge, and mechanistic evidence into coherent explanations. While Large Language Models (LLMs) offer inferential capabilities, they often depend on retrieval-augmented contexts that lack structural depth. Traditional Knowledge Graphs (KGs) attempt to bridge this gap, yet their pairwise constraints fail to capture the irreducible higher-order interactions that govern emergent physical behavior. To address this, we introduce a methodology for constructing hypergraph-based knowledge representations that faithfully encode multi-entity relationships. Applied to a corpus of ~1,100 manuscripts on biocomposite scaffolds, our framework constructs a global hypergraph of 161,172 nodes and 320,201 hyperedges, revealing a scale-free topology (power law exponent ~1.23) organized around highly connected conceptual hubs. This representation prevents the combinatorial explosion typical of pairwise expansions and explicitly preserves the co-occurrence context of scientific formulations. We further demonstrate that equipping agentic systems with hypergraph traversal tools, specifically using node-intersection constraints, enables them to bridge semantically distant concepts. By exploiting these higher-order pathways, the system successfully generates grounded mechanistic hypotheses for novel composite materials, such as linking cerium oxide to PCL scaffolds via chitosan intermediates. This work establishes a "teacherless" agentic reasoning system where hypergraph topology acts as a verifiable guardrail, accelerating scientific discovery by uncovering relationships obscured by traditional graph methods.

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.

Introduction: The scientific publishing landscape is expanding rapidly, creating challenges for researchers to stay up-to-date with the evolution of the literature. Natural Language Processing (NLP) has emerged as a potent approach to automating knowledge extraction from this vast amount of publications and preprints. Tasks such as Named-Entity Recognition (NER) and Named-Entity Linking (NEL), in conjunction with context-dependent semantic interpretation, offer promising and complementary approaches to extracting structured information and revealing key concepts. Results: We present the SourceData-NLP dataset produced through the routine curation of papers during the publication process. A unique feature of this dataset is its emphasis on the annotation of bioentities in figure legends. We annotate eight classes of biomedical entities (small molecules, gene products, subcellular components, cell lines, cell types, tissues, organisms, and diseases), their role in the experimental design, and the nature of the experimental method as an additional class. SourceData-NLP contains more than 620,000 annotated biomedical entities, curated from 18,689 figures in 3,223 papers in molecular and cell biology. We illustrate the dataset's usefulness by assessing BioLinkBERT and PubmedBERT, two transformers-based models, fine-tuned on the SourceData-NLP dataset for NER. We also introduce a novel context-dependent semantic task that infers whether an entity is the target of a controlled intervention or the object of measurement. Conclusions: SourceData-NLP's scale highlights the value of integrating curation into publishing. Models trained with SourceData-NLP will furthermore enable the development of tools able to extract causal hypotheses from the literature and assemble them into knowledge graphs.

With the growing availability of data within various scientific domains, generative models hold enormous potential to accelerate scientific discovery. They harness powerful representations learned from datasets to speed up the formulation of novel hypotheses with the potential to impact material discovery broadly. We present the Generative Toolkit for Scientific Discovery (GT4SD). This extensible open-source library enables scientists, developers, and researchers to train and use state-of-the-art generative models to accelerate scientific discovery focused on material design.

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

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

Large Language Models (LLMs) are accelerating scientific idea generation, but rigorously evaluating these numerous, often superficial, AI-generated propositions for novelty and factual accuracy is a critical bottleneck; manual verification is too slow. Existing validation methods are inadequate: LLMs as standalone verifiers may hallucinate and lack domain knowledge (our findings show 60% unawareness of relevant papers in specific domains), while traditional citation networks lack explicit causality and narrative surveys are unstructured. This underscores a core challenge: the absence of structured, verifiable, and causally-linked historical data of scientific evolution.To address this,we introduce THE-Tree (Technology History Evolution Tree), a computational framework that constructs such domain-specific evolution trees from scientific literature. THE-Tree employs a search algorithm to explore evolutionary paths. During its node expansion, it utilizes a novel "Think-Verbalize-Cite-Verify" process: an LLM proposes potential advancements and cites supporting literature. Critically, each proposed evolutionary link is then validated for logical coherence and evidential support by a recovered natural language inference mechanism that interrogates the cited literature, ensuring that each step is grounded. We construct and validate 88 THE-Trees across diverse domains and release a benchmark dataset including up to 71k fact verifications covering 27k papers to foster further research. Experiments demonstrate that i) in graph completion, our THE-Tree improves hit@1 by 8% to 14% across multiple models compared to traditional citation networks; ii) for predicting future scientific developments, it improves hit@1 metric by nearly 10%; and iii) when combined with other methods, it boosts the performance of evaluating important scientific papers by almost 100%.

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

Verifying scientific claims presents a significantly greater challenge than verifying political or news-related claims. Unlike the relatively broad audience for political claims, the users of scientific claim verification systems can vary widely, ranging from researchers testing specific hypotheses to everyday users seeking information on a medication. Additionally, the evidence for scientific claims is often highly complex, involving technical terminology and intricate domain-specific concepts that require specialized models for accurate verification. Despite considerable interest from the research community, there is a noticeable lack of large-scale scientific claim verification datasets to benchmark and train effective models. To bridge this gap, we introduce two large-scale datasets, SciClaimHunt and SciClaimHunt_Num, derived from scientific research papers. We propose several baseline models tailored for scientific claim verification to assess the effectiveness of these datasets. Additionally, we evaluate models trained on SciClaimHunt and SciClaimHunt_Num against existing scientific claim verification datasets to gauge their quality and reliability. Furthermore, we conduct human evaluations of the claims in proposed datasets and perform error analysis to assess the effectiveness of the proposed baseline models. Our findings indicate that SciClaimHunt and SciClaimHunt_Num serve as highly reliable resources for training models in scientific claim verification.

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 Machine Learning (SciML) integrates data-driven inference with physical modeling to solve complex problems in science and engineering. However, the design of SciML architectures, loss formulations, and training strategies remains an expert-driven research process, requiring extensive experimentation and problem-specific insights. Here we introduce AgenticSciML, a collaborative multi-agent system in which over 10 specialized AI agents collaborate to propose, critique, and refine SciML solutions through structured reasoning and iterative evolution. The framework integrates structured debate, retrieval-augmented method memory, and ensemble-guided evolutionary search, enabling the agents to generate and assess new hypotheses about architectures and optimization procedures. Across physics-informed learning and operator learning tasks, the framework discovers solution methods that outperform single-agent and human-designed baselines by up to four orders of magnitude in error reduction. The agents produce novel strategies -- including adaptive mixture-of-expert architectures, decomposition-based PINNs, and physics-informed operator learning models -- that do not appear explicitly in the curated knowledge base. These results show that collaborative reasoning among AI agents can yield emergent methodological innovation, suggesting a path toward scalable, transparent, and autonomous discovery in scientific computing.

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.

Traditionally, theory and practice of Cognitive Control are linked via literature reviews by human domain experts. This approach, however, is inadequate to track the ever-growing literature. It may also be biased, and yield redundancies and confusion. Here we present an alternative approach. We performed automated text analyses on a large body of scientific texts to create a joint representation of tasks and constructs. More specifically, 385,705 scientific abstracts were first mapped into an embedding space using a transformers-based language model. Document embeddings were then used to identify a task-construct graph embedding that grounds constructs on tasks and supports nuanced meaning of the constructs by taking advantage of constrained random walks in the graph. This joint task-construct graph embedding, can be queried to generate task batteries targeting specific constructs, may reveal knowledge gaps in the literature, and inspire new tasks and novel hypotheses.

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.

There is growing excitement about the potential of Language Models (LMs) to accelerate scientific discovery. Falsifying hypotheses is key to scientific progress, as it allows claims to be iteratively refined over time. This process requires significant researcher effort, reasoning, and ingenuity. Yet current benchmarks for LMs predominantly assess their ability to generate solutions rather than challenge them. We advocate for developing benchmarks that evaluate this inverse capability - creating counterexamples for subtly incorrect solutions. To demonstrate this approach, we start with the domain of algorithmic problem solving, where counterexamples can be evaluated automatically using code execution. Specifically, we introduce REFUTE, a dynamically updating benchmark that includes recent problems and incorrect submissions from programming competitions, where human experts successfully identified counterexamples. Our analysis finds that the best reasoning agents, even OpenAI o3-mini (high) with code execution feedback, can create counterexamples for only <9% of incorrect solutions in REFUTE, even though ratings indicate its ability to solve up to 48% of these problems from scratch. We hope our work spurs progress in evaluating and enhancing LMs' ability to falsify incorrect solutions - a capability that is crucial for both accelerating research and making models self-improve through reliable reflective reasoning.

Large language models (LLMs) have shown significant potential in scientific disciplines such as biomedicine, particularly in hypothesis generation, where they can analyze vast literature, identify patterns, and suggest research directions. However, a key challenge lies in evaluating the truthfulness of generated hypotheses, as verifying their accuracy often requires substantial time and resources. Additionally, the hallucination problem in LLMs can lead to the generation of hypotheses that appear plausible but are ultimately incorrect, undermining their reliability. To facilitate the systematic study of these challenges, we introduce TruthHypo, a benchmark for assessing the capabilities of LLMs in generating truthful biomedical hypotheses, and KnowHD, a knowledge-based hallucination detector to evaluate how well hypotheses are grounded in existing knowledge. Our results show that LLMs struggle to generate truthful hypotheses. By analyzing hallucinations in reasoning steps, we demonstrate that the groundedness scores provided by KnowHD serve as an effective metric for filtering truthful hypotheses from the diverse outputs of LLMs. Human evaluations further validate the utility of KnowHD in identifying truthful hypotheses and accelerating scientific discovery. Our data and source code are available at https://github.com/Teddy-XiongGZ/TruthHypo.

Large language models (LLMs) have demonstrated significant potential to accelerate scientific discovery as valuable tools for analyzing data, generating hypotheses, and supporting innovative approaches in various scientific fields. In this work, we investigate how LLMs can handle the transition from conceptual research ideas to well-structured research plans. Effective research planning not only supports scientists in advancing their research but also represents a crucial capability for the development of autonomous research agents. Despite its importance, the field lacks a systematic understanding of LLMs' research planning capability. To rigorously measure this capability, we introduce the Idea2Plan task and Idea2Plan Bench, a benchmark built from 200 ICML 2025 Spotlight and Oral papers released after major LLM training cutoffs. Each benchmark instance includes a research idea and a grading rubric capturing the key components of valid plans. We further propose Idea2Plan JudgeEval, a complementary benchmark to assess the reliability of LLM-based judges against expert annotations. Experimental results show that GPT-5 and GPT-5-mini achieve the strongest performance on the benchmark, though substantial headroom remains for future improvement. Our study provides new insights into LLMs' capability for research planning and lay the groundwork for future progress.

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.

Large Language Models (LLMs) are transforming scientific hypothesis generation and validation by enabling information synthesis, latent relationship discovery, and reasoning augmentation. This survey provides a structured overview of LLM-driven approaches, including symbolic frameworks, generative models, hybrid systems, and multi-agent architectures. We examine techniques such as retrieval-augmented generation, knowledge-graph completion, simulation, causal inference, and tool-assisted reasoning, highlighting trade-offs in interpretability, novelty, and domain alignment. We contrast early symbolic discovery systems (e.g., BACON, KEKADA) with modern LLM pipelines that leverage in-context learning and domain adaptation via fine-tuning, retrieval, and symbolic grounding. For validation, we review simulation, human-AI collaboration, causal modeling, and uncertainty quantification, emphasizing iterative assessment in open-world contexts. The survey maps datasets across biomedicine, materials science, environmental science, and social science, introducing new resources like AHTech and CSKG-600. Finally, we outline a roadmap emphasizing novelty-aware generation, multimodal-symbolic integration, human-in-the-loop systems, and ethical safeguards, positioning LLMs as agents for principled, scalable scientific discovery.

A hallmark of human innovation is the process of recombination -- creating original ideas by integrating elements of existing mechanisms and concepts. In this work, we automatically mine the scientific literature and build CHIMERA: a large-scale knowledge base (KB) of recombination examples. CHIMERA can be used to empirically explore at scale how scientists recombine concepts and take inspiration from different areas, or to train supervised machine learning models that learn to predict new creative cross-domain directions. To build this KB, we present a novel information extraction task of extracting recombination from scientific paper abstracts, collect a high-quality corpus of hundreds of manually annotated abstracts, and use it to train an LLM-based extraction model. The model is applied to a large corpus of papers in the AI domain, yielding a KB of over 28K recombination examples. We analyze CHIMERA to explore the properties of recombination in different subareas of AI. Finally, we train a scientific hypothesis generation model using the KB, which predicts new recombination directions that real-world researchers find inspiring. Our data and code are available at https://github.cs.huji.ac.il/tomhope-lab/CHIMERA

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

AI holds promise for transforming scientific processes, including hypothesis generation. Prior work on hypothesis generation can be broadly categorized into theory-driven and data-driven approaches. While both have proven effective in generating novel and plausible hypotheses, it remains an open question whether they can complement each other. To address this, we develop the first method that combines literature-based insights with data to perform LLM-powered hypothesis generation. We apply our method on five different datasets and demonstrate that integrating literature and data outperforms other baselines (8.97\% over few-shot, 15.75\% over literature-based alone, and 3.37\% over data-driven alone). Additionally, we conduct the first human evaluation to assess the utility of LLM-generated hypotheses in assisting human decision-making on two challenging tasks: deception detection and AI generated content detection. Our results show that human accuracy improves significantly by 7.44\% and 14.19\% on these tasks, respectively. These findings suggest that integrating literature-based and data-driven approaches provides a comprehensive and nuanced framework for hypothesis generation and could open new avenues for scientific inquiry.

In science and medicine, model interpretations may be reported as discoveries of natural phenomena or used to guide patient treatments. In such high-stakes tasks, false discoveries may lead investigators astray. These applications would therefore benefit from control over the finite-sample error rate of interpretations. We reframe black box model interpretability as a multiple hypothesis testing problem. The task is to discover "important" features by testing whether the model prediction is significantly different from what would be expected if the features were replaced with uninformative counterfactuals. We propose two testing methods: one that provably controls the false discovery rate but which is not yet feasible for large-scale applications, and an approximate testing method which can be applied to real-world data sets. In simulation, both tests have high power relative to existing interpretability methods. When applied to state-of-the-art vision and language models, the framework selects features that intuitively explain model predictions. The resulting explanations have the additional advantage that they are themselves easy to interpret.

We describe HypotheSAEs, a general method to hypothesize interpretable relationships between text data (e.g., headlines) and a target variable (e.g., clicks). HypotheSAEs has three steps: (1) train a sparse autoencoder on text embeddings to produce interpretable features describing the data distribution, (2) select features that predict the target variable, and (3) generate a natural language interpretation of each feature (e.g., "mentions being surprised or shocked") using an LLM. Each interpretation serves as a hypothesis about what predicts the target variable. Compared to baselines, our method better identifies reference hypotheses on synthetic datasets (at least +0.06 in F1) and produces more predictive hypotheses on real datasets (~twice as many significant findings), despite requiring 1-2 orders of magnitude less compute than recent LLM-based methods. HypotheSAEs also produces novel discoveries on two well-studied tasks: explaining partisan differences in Congressional speeches and identifying drivers of engagement with online headlines.

In recent years, the rapid advancement of Large Language Models (LLMs) has transformed the landscape of scientific research, offering unprecedented support across various stages of the research cycle. This paper presents the first systematic survey dedicated to exploring how LLMs are revolutionizing the scientific research process. We analyze the unique roles LLMs play across four critical stages of research: hypothesis discovery, experiment planning and implementation, scientific writing, and peer reviewing. Our review comprehensively showcases the task-specific methodologies and evaluation benchmarks. By identifying current challenges and proposing future research directions, this survey not only highlights the transformative potential of LLMs, but also aims to inspire and guide researchers and practitioners in leveraging LLMs to advance scientific inquiry. Resources are available at the following repository: https://github.com/du-nlp-lab/LLM4SR

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 equation discovery is a fundamental task in the history of scientific progress, enabling the derivation of laws governing natural phenomena. Recently, Large Language Models (LLMs) have gained interest for this task due to their potential to leverage embedded scientific knowledge for hypothesis generation. However, evaluating the true discovery capabilities of these methods remains challenging, as existing benchmarks often rely on common equations that are susceptible to memorization by LLMs, leading to inflated performance metrics that do not reflect discovery. In this paper, we introduce LLM-SRBench, a comprehensive benchmark with 239 challenging problems across four scientific domains specifically designed to evaluate LLM-based scientific equation discovery methods while preventing trivial memorization. Our benchmark comprises two main categories: LSR-Transform, which transforms common physical models into less common mathematical representations to test reasoning beyond memorized forms, and LSR-Synth, which introduces synthetic, discovery-driven problems requiring data-driven reasoning. Through extensive evaluation of several state-of-the-art methods, using both open and closed LLMs, we find that the best-performing system so far achieves only 31.5% symbolic accuracy. These findings highlight the challenges of scientific equation discovery, positioning LLM-SRBench as a valuable resource for future research.

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.

Hypothesis generation is a fundamental step in scientific discovery, yet it is increasingly challenged by information overload and disciplinary fragmentation. Recent advances in Large Language Models (LLMs) have sparked growing interest in their potential to enhance and automate this process. This paper presents a comprehensive survey of hypothesis generation with LLMs by (i) reviewing existing methods, from simple prompting techniques to more complex frameworks, and proposing a taxonomy that categorizes these approaches; (ii) analyzing techniques for improving hypothesis quality, such as novelty boosting and structured reasoning; (iii) providing an overview of evaluation strategies; and (iv) discussing key challenges and future directions, including multimodal integration and human-AI collaboration. Our survey aims to serve as a reference for researchers exploring LLMs for hypothesis generation.

We introduce scientific claim verification, a new task to select abstracts from the research literature containing evidence that SUPPORTS or REFUTES a given scientific claim, and to identify rationales justifying each decision. To study this task, we construct SciFact, a dataset of 1.4K expert-written scientific claims paired with evidence-containing abstracts annotated with labels and rationales. We develop baseline models for SciFact, and demonstrate that simple domain adaptation techniques substantially improve performance compared to models trained on Wikipedia or political news. We show that our system is able to verify claims related to COVID-19 by identifying evidence from the CORD-19 corpus. Our experiments indicate that SciFact will provide a challenging testbed for the development of new systems designed to retrieve and reason over corpora containing specialized domain knowledge. Data and code for this new task are publicly available at https://github.com/allenai/scifact. A leaderboard and COVID-19 fact-checking demo are available at https://scifact.apps.allenai.org.

There is growing interest in hypothesis generation with large language models (LLMs). However, fundamental questions remain: what makes a good hypothesis, and how can we systematically evaluate methods for hypothesis generation? To address this, we introduce HypoBench, a novel benchmark designed to evaluate LLMs and hypothesis generation methods across multiple aspects, including practical utility, generalizability, and hypothesis discovery rate. HypoBench includes 7 real-world tasks and 5 synthetic tasks with 194 distinct datasets. We evaluate four state-of-the-art LLMs combined with six existing hypothesis-generation methods. Overall, our results suggest that existing methods are capable of discovering valid and novel patterns in the data. However, the results from synthetic datasets indicate that there is still significant room for improvement, as current hypothesis generation methods do not fully uncover all relevant or meaningful patterns. Specifically, in synthetic settings, as task difficulty increases, performance significantly drops, with best models and methods only recovering 38.8% of the ground-truth hypotheses. These findings highlight challenges in hypothesis generation and demonstrate that HypoBench serves as a valuable resource for improving AI systems designed to assist scientific discovery.

We consider the problem of performing Bayesian inference in probabilistic models where observations are accompanied by uncertainty, referred to as "uncertain evidence." We explore how to interpret uncertain evidence, and by extension the importance of proper interpretation as it pertains to inference about latent variables. We consider a recently-proposed method "distributional evidence" as well as revisit two older methods: Jeffrey's rule and virtual evidence. We devise guidelines on how to account for uncertain evidence and we provide new insights, particularly regarding consistency. To showcase the impact of different interpretations of the same uncertain evidence, we carry out experiments in which one interpretation is defined as "correct." We then compare inference results from each different interpretation illustrating the importance of careful consideration of uncertain evidence.

We examine how well the state-of-the-art (SOTA) models used in legal reasoning support abductive reasoning tasks. Abductive reasoning is a form of logical inference in which a hypothesis is formulated from a set of observations, and that hypothesis is used to explain the observations. The ability to formulate such hypotheses is important for lawyers and legal scholars as it helps them articulate logical arguments, interpret laws, and develop legal theories. Our motivation is to consider the belief that deep learning models, especially large language models (LLMs), will soon replace lawyers because they perform well on tasks related to legal text processing. But to do so, we believe, requires some form of abductive hypothesis formation. In other words, while LLMs become more popular and powerful, we want to investigate their capacity for abductive reasoning. To pursue this goal, we start by building a logic-augmented dataset for abductive reasoning with 498,697 samples and then use it to evaluate the performance of a SOTA model in the legal field. Our experimental results show that although these models can perform well on tasks related to some aspects of legal text processing, they still fall short in supporting abductive reasoning tasks.

Large Language Models (LLMs) have transformed how people interact with artificial intelligence (AI) systems, achieving state-of-the-art results in various tasks, including scientific discovery and hypothesis generation. However, the lack of a comprehensive and systematic evaluation framework for generating research ideas using LLMs poses a significant obstacle to understanding and assessing their generative capabilities in scientific discovery. To address this gap, we propose IdeaBench, a benchmark system that includes a comprehensive dataset and an evaluation framework for standardizing the assessment of research idea generation using LLMs. Our dataset comprises titles and abstracts from a diverse range of influential papers, along with their referenced works. To emulate the human process of generating research ideas, we profile LLMs as domain-specific researchers and ground them in the same context considered by human researchers. This maximizes the utilization of the LLMs' parametric knowledge to dynamically generate new research ideas. We also introduce an evaluation framework for assessing the quality of generated research ideas. Our evaluation framework is a two-stage process: first, using GPT-4o to rank ideas based on user-specified quality indicators such as novelty and feasibility, enabling scalable personalization; and second, calculating relative ranking based "Insight Score" to quantify the chosen quality indicator. The proposed benchmark system will be a valuable asset for the community to measure and compare different LLMs, ultimately advancing the automation of the scientific discovery process.

Misinformation about climate change is a complex societal issue requiring holistic, interdisciplinary solutions at the intersection between technology and psychology. One proposed solution is a "technocognitive" approach, involving the synthesis of psychological and computer science research. Psychological research has identified that interventions in response to misinformation require both fact-based (e.g., factual explanations) and technique-based (e.g., explanations of misleading techniques) content. However, little progress has been made on documenting and detecting fallacies in climate misinformation. In this study, we apply a previously developed critical thinking methodology for deconstructing climate misinformation, in order to develop a dataset mapping different types of climate misinformation to reasoning fallacies. This dataset is used to train a model to detect fallacies in climate misinformation. Our study shows F1 scores that are 2.5 to 3.5 better than previous works. The fallacies that are easiest to detect include fake experts and anecdotal arguments, while fallacies that require background knowledge, such as oversimplification, misrepresentation, and slothful induction, are relatively more difficult to detect. This research lays the groundwork for development of solutions where automatically detected climate misinformation can be countered with generative technique-based corrections.

A great deal of effort has been devoted to reducing the risk of spurious scientific discoveries, from the use of sophisticated validation techniques, to deep statistical methods for controlling the false discovery rate in multiple hypothesis testing. However, there is a fundamental disconnect between the theoretical results and the practice of data analysis: the theory of statistical inference assumes a fixed collection of hypotheses to be tested, or learning algorithms to be applied, selected non-adaptively before the data are gathered, whereas in practice data is shared and reused with hypotheses and new analyses being generated on the basis of data exploration and the outcomes of previous analyses. In this work we initiate a principled study of how to guarantee the validity of statistical inference in adaptive data analysis. As an instance of this problem, we propose and investigate the question of estimating the expectations of m adaptively chosen functions on an unknown distribution given n random samples. We show that, surprisingly, there is a way to estimate an exponential in n number of expectations accurately even if the functions are chosen adaptively. This gives an exponential improvement over standard empirical estimators that are limited to a linear number of estimates. Our result follows from a general technique that counter-intuitively involves actively perturbing and coordinating the estimates, using techniques developed for privacy preservation. We give additional applications of this technique to our question.

With the exponential growth of research facilitated by modern technology and improved accessibility, scientific discoveries have become increasingly fragmented within and across fields. This makes it challenging to assess the significance, novelty, incremental findings, and equivalent ideas between related works, particularly those from different research communities. Large language models (LLMs) have recently demonstrated strong quantitative and qualitative reasoning abilities, and multi-agent LLM debates have shown promise in handling complex reasoning tasks by exploring diverse perspectives and reasoning paths. Inspired by this, we introduce Tree-of-Debate (ToD), a framework which converts scientific papers into LLM personas that debate their respective novelties. To emphasize structured, critical reasoning rather than focusing solely on outcomes, ToD dynamically constructs a debate tree, enabling fine-grained analysis of independent novelty arguments within scholarly articles. Through experiments on scientific literature across various domains, evaluated by expert researchers, we demonstrate that ToD generates informative arguments, effectively contrasts papers, and supports researchers in their literature review.

The rapid growth of biomedical knowledge has outpaced our ability to efficiently extract insights and generate novel hypotheses. Large language models (LLMs) have emerged as a promising tool to revolutionize knowledge interaction and potentially accelerate biomedical discovery. In this paper, we present a comprehensive evaluation of LLMs as biomedical hypothesis generators. We construct a dataset of background-hypothesis pairs from biomedical literature, carefully partitioned into training, seen, and unseen test sets based on publication date to mitigate data contamination. Using this dataset, we assess the hypothesis generation capabilities of top-tier instructed models in zero-shot, few-shot, and fine-tuning settings. To enhance the exploration of uncertainty, a crucial aspect of scientific discovery, we incorporate tool use and multi-agent interactions in our evaluation framework. Furthermore, we propose four novel metrics grounded in extensive literature review to evaluate the quality of generated hypotheses, considering both LLM-based and human assessments. Our experiments yield two key findings: 1) LLMs can generate novel and validated hypotheses, even when tested on literature unseen during training, and 2) Increasing uncertainty through multi-agent interactions and tool use can facilitate diverse candidate generation and improve zero-shot hypothesis generation performance. However, we also observe that the integration of additional knowledge through few-shot learning and tool use may not always lead to performance gains, highlighting the need for careful consideration of the type and scope of external knowledge incorporated. These findings underscore the potential of LLMs as powerful aids in biomedical hypothesis generation and provide valuable insights to guide further research in this area.

Early warning signals have been proposed to forecast the possibility of a critical transition, such as the eutrophication of a lake, the collapse of a coral reef, or the end of a glacial period. Because such transitions often unfold on temporal and spatial scales that can be difficult to approach by experimental manipulation, research has often relied on historical observations as a source of natural experiments. Here we examine a critical difference between selecting systems for study based on the fact that we have observed a critical transition and those systems for which we wish to forecast the approach of a transition. This difference arises by conditionally selecting systems known to experience a transition of some sort and failing to account for the bias this introduces -- a statistical error often known as the Prosecutor's Fallacy. By analysing simulated systems that have experienced transitions purely by chance, we reveal an elevated rate of false positives in common warning signal statistics. We further demonstrate a model-based approach that is less subject to this bias than these more commonly used summary statistics. We note that experimental studies with replicates avoid this pitfall entirely.

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

Artificial intelligence has made great strides in the last decade but still falls short of the human brain, the best-known example of intelligence. Not much is known of the neural processes that allow the brain to make the leap to achieve so much from so little beyond its ability to create knowledge structures that can be flexibly and dynamically combined, recombined, and applied in new and novel ways. This paper proposes a mathematical approach using graph theory and spectral graph theory, to hypothesize how to constrain these neural clusters of information based on eigen-relationships. This same hypothesis is hierarchically applied to scale up from the smallest to the largest clusters of knowledge that eventually lead to model building and reasoning.

Building upon our previous investigations of O1 replication (Part 1: Journey Learning [Qin et al., 2024] and Part 2: Distillation [Huang et al., 2024]), this work explores the potential of inference-time scaling in large language models (LLMs) for medical reasoning tasks, ranging from diagnostic decision-making to treatment planning. Through extensive experiments on medical benchmarks of varying complexity (MedQA, Medbullets, and JAMA Clinical Challenges), our investigation reveals several key insights: (1) Increasing inference time does lead to improved performance. With a modest training set of 500 samples, our model yields substantial performance improvements of 6%-11%. (2) Task complexity directly correlates with the required length of reasoning chains, confirming the necessity of extended thought processes for challenging problems. (3) The differential diagnoses generated by our model adhere to the principles of the hypothetico-deductive method, producing a list of potential conditions that may explain a patient's symptoms and systematically narrowing these possibilities by evaluating the evidence. These findings demonstrate the promising synergy between inference-time scaling and journey learning in advancing LLMs' real-world clinical reasoning capabilities.

Probabilistic text generators have been used to produce fake scientific papers for more than a decade. Such nonsensical papers are easily detected by both human and machine. Now more complex AI-powered generation techniques produce texts indistinguishable from that of humans and the generation of scientific texts from a few keywords has been documented. Our study introduces the concept of tortured phrases: unexpected weird phrases in lieu of established ones, such as 'counterfeit consciousness' instead of 'artificial intelligence.' We combed the literature for tortured phrases and study one reputable journal where these concentrated en masse. Hypothesising the use of advanced language models we ran a detector on the abstracts of recent articles of this journal and on several control sets. The pairwise comparisons reveal a concentration of abstracts flagged as 'synthetic' in the journal. We also highlight irregularities in its operation, such as abrupt changes in editorial timelines. We substantiate our call for investigation by analysing several individual dubious articles, stressing questionable features: tortured writing style, citation of non-existent literature, and unacknowledged image reuse. Surprisingly, some websites offer to rewrite texts for free, generating gobbledegook full of tortured phrases. We believe some authors used rewritten texts to pad their manuscripts. We wish to raise the awareness on publications containing such questionable AI-generated or rewritten texts that passed (poor) peer review. Deception with synthetic texts threatens the integrity of the scientific literature.

Scientific discovery is a cumulative process and requires new ideas to be situated within an ever-expanding landscape of existing knowledge. An emerging and critical challenge is how to identify conceptually relevant prior work from rapidly growing literature, and assess how a new idea differentiates from existing research. Current embedding approaches typically conflate distinct conceptual aspects into single representations and cannot support fine-grained literature retrieval; meanwhile, LLM-based evaluators are subject to sycophancy biases, failing to provide discriminative novelty assessment. To tackle these challenges, we introduce the Ideation Space, a structured representation that decomposes scientific knowledge into three distinct dimensions, i.e., research problem, methodology, and core findings, each learned through contrastive training. This framework enables principled measurement of conceptual distance between ideas, and modeling of ideation transitions that capture the logical connections within a proposed idea. Building upon this representation, we propose a Hierarchical Sub-Space Retrieval framework for efficient, targeted literature retrieval, and a Decomposed Novelty Assessment algorithm that identifies which aspects of an idea are novel. Extensive experiments demonstrate substantial improvements, where our approach achieves Recall@30 of 0.329 (16.7% over baselines), our ideation transition retrieval reaches Hit Rate@30 of 0.643, and novelty assessment attains 0.37 correlation with expert judgments. In summary, our work provides a promising paradigm for future research on accelerating and evaluating scientific discovery.

This paper introduces a novel approach to data analysis designed for the needs of specialists in psychology of religion. We detect developmental and cross-cultural patterns in children's drawings of God(s) and other supernatural agents. We develop methods to objectively evaluate our empirical observations of the drawings with respect to: (1) the gravity center, (2) the average intensities of the colors green and yellow, (3) the use of different colors (palette) and (4) the visual complexity of the drawings. We find statistically significant differences across ages and countries in the gravity centers and in the average intensities of colors. These findings support the hypotheses of the experts and raise new questions for further investigation.

Large language models (LLMs) are increasingly being used for complex research tasks such as literature review, idea generation, and scientific paper analysis, yet their ability to truly understand and process the intricate relationships within complex research papers, such as the logical links between claims and supporting evidence remains largely unexplored. In this study, we present CLAIM-BENCH, a comprehensive benchmark for evaluating LLMs' capabilities in scientific claim-evidence extraction and validation, a task that reflects deeper comprehension of scientific argumentation. We systematically compare three approaches which are inspired by divide and conquer approaches, across six diverse LLMs, highlighting model-specific strengths and weaknesses in scientific comprehension. Through evaluation involving over 300 claim-evidence pairs across multiple research domains, we reveal significant limitations in LLMs' ability to process complex scientific content. Our results demonstrate that closed-source models like GPT-4 and Claude consistently outperform open-source counterparts in precision and recall across claim-evidence identification tasks. Furthermore, strategically designed three-pass and one-by-one prompting approaches significantly improve LLMs' abilities to accurately link dispersed evidence with claims, although this comes at increased computational cost. CLAIM-BENCH sets a new standard for evaluating scientific comprehension in LLMs, offering both a diagnostic tool and a path forward for building systems capable of deeper, more reliable reasoning across full-length papers.

Whether the media faithfully communicate scientific information has long been a core issue to the science community. Automatically identifying paraphrased scientific findings could enable large-scale tracking and analysis of information changes in the science communication process, but this requires systems to understand the similarity between scientific information across multiple domains. To this end, we present the SCIENTIFIC PARAPHRASE AND INFORMATION CHANGE DATASET (SPICED), the first paraphrase dataset of scientific findings annotated for degree of information change. SPICED contains 6,000 scientific finding pairs extracted from news stories, social media discussions, and full texts of original papers. We demonstrate that SPICED poses a challenging task and that models trained on SPICED improve downstream performance on evidence retrieval for fact checking of real-world scientific claims. Finally, we show that models trained on SPICED can reveal large-scale trends in the degrees to which people and organizations faithfully communicate new scientific findings. Data, code, and pre-trained models are available at http://www.copenlu.com/publication/2022_emnlp_wright/.

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

Scientific reasoning, the process through which humans apply logic, evidence, and critical thinking to explore and interpret scientific phenomena, is essential in advancing knowledge reasoning across diverse fields. However, despite significant progress, current scientific reasoning models still struggle with generalization across domains and often fall short of multimodal perception. Multimodal Large Language Models (MLLMs), which integrate text, images, and other modalities, present an exciting opportunity to overcome these limitations and enhance scientific reasoning. Therefore, this position paper argues that MLLMs can significantly advance scientific reasoning across disciplines such as mathematics, physics, chemistry, and biology. First, we propose a four-stage research roadmap of scientific reasoning capabilities, and highlight the current state of MLLM applications in scientific reasoning, noting their ability to integrate and reason over diverse data types. Second, we summarize the key challenges that remain obstacles to achieving MLLM's full potential. To address these challenges, we propose actionable insights and suggestions for the future. Overall, our work offers a novel perspective on MLLM integration with scientific reasoning, providing the LLM community with a valuable vision for achieving Artificial General Intelligence (AGI).

In their recent Nature Human Behaviour paper, "Emergent analogical reasoning in large language models," (Webb, Holyoak, and Lu, 2023) the authors argue that "large language models such as GPT-3 have acquired an emergent ability to find zero-shot solutions to a broad range of analogy problems." In this response, we provide counterexamples of the letter string analogies. In our tests, GPT-3 fails to solve even the easiest variants of the problems presented in the original paper. Zero-shot reasoning is an extraordinary claim that requires extraordinary evidence. We do not see that evidence in our experiments. To strengthen claims of humanlike reasoning such as zero-shot reasoning, it is important that the field develop approaches that rule out data memorization.

In this paper, we present the current progress of the project Verif.ai, an open-source scientific generative question-answering system with referenced and verified answers. The components of the system are (1) an information retrieval system combining semantic and lexical search techniques over scientific papers (PubMed), (2) a fine-tuned generative model (Mistral 7B) taking top answers and generating answers with references to the papers from which the claim was derived, and (3) a verification engine that cross-checks the generated claim and the abstract or paper from which the claim was derived, verifying whether there may have been any hallucinations in generating the claim. We are reinforcing the generative model by providing the abstract in context, but in addition, an independent set of methods and models are verifying the answer and checking for hallucinations. Therefore, we believe that by using our method, we can make scientists more productive, while building trust in the use of generative language models in scientific environments, where hallucinations and misinformation cannot be tolerated.

Seeking health-related advice on the internet has become a common practice in the digital era. Determining the trustworthiness of medical claims found online and finding appropriate evidence for this information is increasingly challenging. Fact-checking has emerged as an approach to assess the veracity of factual claims using evidence from credible knowledge sources. To help advance the automation of this task, in this paper, we introduce a novel dataset of 750 health-related claims, labeled for veracity by medical experts and backed with evidence from appropriate clinical studies. We provide an analysis of the dataset, highlighting its characteristics and challenges. The dataset can be used for Machine Learning tasks related to automated fact-checking such as evidence retrieval, veracity prediction, and explanation generation. For this purpose, we provide baseline models based on different approaches, examine their performance, and discuss the findings.

Although much research has focused on AI explanations to support decisions in complex information-seeking tasks such as fact-checking, the role of evidence is surprisingly under-researched. In our study, we systematically varied explanation type, AI prediction certainty, and correctness of AI system advice for non-expert participants, who evaluated the veracity of claims and AI system predictions. Participants were provided the option of easily inspecting the underlying evidence. We found that participants consistently relied on evidence to validate AI claims across all experimental conditions. When participants were presented with natural language explanations, evidence was used less frequently although they relied on it when these explanations seemed insufficient or flawed. Qualitative data suggests that participants attempted to infer evidence source reliability, despite source identities being deliberately omitted. Our results demonstrate that evidence is a key ingredient in how people evaluate the reliability of information presented by an AI system and, in combination with natural language explanations, offers valuable support for decision-making. Further research is urgently needed to understand how evidence ought to be presented and how people engage with it in practice.

In October 2007, a Research Proposal for the University of Sydney, Australia, the author suggested that biovie-physical phenomenon as `electrodynamic dependant biological vision', is governed by relativistic quantum laws and biovision. The phenomenon on the basis of `biovielectroluminescence', satisfies man/microbio/megabio/computer vision (MMMCV), as a robust candidate for physical and visual sciences. The general aim of this addendum is to present a refined text of Sections 1-3 of that proposal and highlighting the contents of its Appendix in form of a `Mechanisms' Section. We then briefly remind in an article aimed for December 2007, by appending two more equations into Section 3, a theoretical II-time scenario as a time model well-proposed for the phenomenon. The time model within the core of the proposal, plays a significant role in emphasizing the principle points on Objectives no. 1-8, Sub-hypothesis 3.1.2, mentioned in Article [arXiv:0710.0410]. It also expresses the time concept in terms of causing quantized energy f(|E|) of time |t|, emit in regard to shortening the probability of particle loci as predictable patterns of particle's un-occurred motion, a solution to Heisenberg's uncertainty principle (HUP) into a simplistic manner. We conclude that, practical frames via a time algorithm to this model, fixates such predictable patterns of motion of scenery bodies onto recordable observation points of a MMMCV system. It even suppresses/predicts superposition phenomena coming from a human subject and/or other bio-subjects for any decision making event, e.g., brainwave quantum patterns based on vision. Maintaining the existential probability of Riemann surfaces of II-time scenarios in the context of biovielectroluminescence, makes motion-prediction a possibility.

We present a novel method for symbolic regression (SR), the task of searching for compact programmatic hypotheses that best explain a dataset. The problem is commonly solved using genetic algorithms; we show that we can enhance such methods by inducing a library of abstract textual concepts. Our algorithm, called LaSR, uses zero-shot queries to a large language model (LLM) to discover and evolve concepts occurring in known high-performing hypotheses. We discover new hypotheses using a mix of standard evolutionary steps and LLM-guided steps (obtained through zero-shot LLM queries) conditioned on discovered concepts. Once discovered, hypotheses are used in a new round of concept abstraction and evolution. We validate LaSR on the Feynman equations, a popular SR benchmark, as well as a set of synthetic tasks. On these benchmarks, LaSR substantially outperforms a variety of state-of-the-art SR approaches based on deep learning and evolutionary algorithms. Moreover, we show that LaSR can be used to discover a novel and powerful scaling law for LLMs.

Reasoning is a core capability in artificial intelligence systems, for which large language models (LLMs) have recently shown remarkable progress. However, most work focuses exclusively on deductive reasoning, which is problematic since other types of reasoning are also essential in solving real-world problems, and they are less explored. This work focuses on evaluating LLMs' inductive and abductive reasoning capabilities. We introduce a programmable and synthetic dataset, InAbHyD (pronounced in-a-bid), where each reasoning example consists of an incomplete world model and a set of observations. The task for the intelligent agent is to produce hypotheses to explain observations under the incomplete world model to solve each reasoning example. We propose a new metric to evaluate the quality of hypotheses based on Occam's Razor. We evaluate and analyze some state-of-the-art LLMs. Our analysis shows that LLMs can perform inductive and abductive reasoning in simple scenarios, but struggle with complex world models and producing high-quality hypotheses, even with popular reasoning-enhancing techniques such as in-context learning and RLVR.

Finding relevant literature underpins the practice of evidence-based medicine. From 2014 to 2016, TREC conducted a clinical decision support track, wherein participants were tasked with finding articles relevant to clinical questions posed by physicians. In total, 87 teams have participated over the past three years, generating 395 runs. During this period, each team has trialled a variety of methods. While there was significant overlap in the methods employed by different teams, the results were varied. Due to the diversity of the platforms used, the results arising from the different techniques are not directly comparable, reducing the ability to build on previous work. By using a stable platform, we have been able to compare different document and query processing techniques, allowing us to experiment with different search parameters. We have used our system to reproduce leading teams runs, and compare the results obtained. By benchmarking our indexing and search techniques, we can statistically test a variety of hypotheses, paving the way for further research.

Earthquakes are evaluated among the most destructive disasters for human beings, as also experienced for Turkiye region. Data science has the property of discovering hidden patterns in case a sufficient volume of data is supplied. Time dependency of events, specifically being defined by co-occurrence in a specific time window, may be handled as an associate rule mining task such as a market-basket analysis application. In this regard, we assumed each day's seismic activity as a single basket of events, leading to discovering the association patterns between these events. Consequently, this study presents the most prominent association rules for the earthquakes recorded in Turkiye region in the last 5 years, each year presented separately. Results indicate statistical inference with events recorded from regions of various distances, which could be further verified with geologic evidence from the field. As a result, we believe that the current study may form a statistical basis for the future works with the aid of machine learning algorithm performed for associate rule mining.

Accelerating scientific discovery requires the identification of which experiments would yield the best outcomes before committing resources to costly physical validation. While existing benchmarks evaluate LLMs on scientific knowledge and reasoning, their ability to predict experimental outcomes - a task where AI could significantly exceed human capabilities - remains largely underexplored. We introduce SciPredict, a benchmark comprising 405 tasks derived from recent empirical studies in 33 specialized sub-fields of physics, biology, and chemistry. SciPredict addresses two critical questions: (a) can LLMs predict the outcome of scientific experiments with sufficient accuracy? and (b) can such predictions be reliably used in the scientific research process? Evaluations reveal fundamental limitations on both fronts. Model accuracies are 14-26% and human expert performance is approx20%. Although some frontier models exceed human performance model accuracy is still far below what would enable reliable experimental guidance. Even within the limited performance, models fail to distinguish reliable predictions from unreliable ones, achieving only approx20% accuracy regardless of their confidence or whether they judge outcomes as predictable without physical experimentation. Human experts, in contrast, demonstrate strong calibration: their accuracy increases from approx5% to approx80% as they deem outcomes more predictable without conducting the experiment. SciPredict establishes a rigorous framework demonstrating that superhuman performance in experimental science requires not just better predictions, but better awareness of prediction reliability. For reproducibility all our data and code are provided at https://github.com/scaleapi/scipredict

Retrieval-enhanced methods have become a primary approach in fact verification (FV); it requires reasoning over multiple retrieved pieces of evidence to verify the integrity of a claim. To retrieve evidence, existing work often employs off-the-shelf retrieval models whose design is based on the probability ranking principle. We argue that, rather than relevance, for FV we need to focus on the utility that a claim verifier derives from the retrieved evidence. We introduce the feedback-based evidence retriever(FER) that optimizes the evidence retrieval process by incorporating feedback from the claim verifier. As a feedback signal we use the divergence in utility between how effectively the verifier utilizes the retrieved evidence and the ground-truth evidence to produce the final claim label. Empirical studies demonstrate the superiority of FER over prevailing baselines.

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.

Earth remains the only known example of a planet with technology, and future projections of Earth's trajectory provide a basis and motivation for approaching the search for extraterrestrial technospheres. Conventional approaches toward projecting Earth's technosphere include applications of the Kardashev scale, which suggest the possibility that energy-intensive civilizations may expand to harness the entire energy output available to their planet, host star, or even the entire galaxy. In this study, we argue that the Kardashev scale is better understood as a "luminosity limit" that describes the maximum capacity for a civilization to harvest luminous stellar energy across a given spatial domain, and we note that thermodynamic efficiency will always keep a luminosity-limited technosphere from actually reaching this theoretical limit. We suggest the possibility that an advanced technosphere might evolve beyond this luminosity limit to draw its energy directly from harvesting stellar mass, and we also discuss possible trajectories that could exist between Earth today and such hypothetical "stellivores." We develop a framework to describe trajectories for long-lived technospheres that optimize their growth strategies between exploration and exploitation, unlike Earth today. We note that analyses of compact accreting stars could provide ways to test the stellivore hypothesis, and we more broadly suggest an expansion of technosignature search strategies beyond those that reside exactly at the luminosity limit.

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.

Foundation models (FMs), such as GPT-4 and AlphaFold, are reshaping the landscape of scientific research. Beyond accelerating tasks such as hypothesis generation, experimental design, and result interpretation, they prompt a more fundamental question: Are FMs merely enhancing existing scientific methodologies, or are they redefining the way science is conducted? In this paper, we argue that FMs are catalyzing a transition toward a new scientific paradigm. We introduce a three-stage framework to describe this evolution: (1) Meta-Scientific Integration, where FMs enhance workflows within traditional paradigms; (2) Hybrid Human-AI Co-Creation, where FMs become active collaborators in problem formulation, reasoning, and discovery; and (3) Autonomous Scientific Discovery, where FMs operate as independent agents capable of generating new scientific knowledge with minimal human intervention. Through this lens, we review current applications and emerging capabilities of FMs across existing scientific paradigms. We further identify risks and future directions for FM-enabled scientific discovery. This position paper aims to support the scientific community in understanding the transformative role of FMs and to foster reflection on the future of scientific discovery. Our project is available at https://github.com/usail-hkust/Awesome-Foundation-Models-for-Scientific-Discovery.

Scientific reasoning is critical for developing AI scientists and supporting human researchers in advancing the frontiers of natural science discovery. However, the open-source community has primarily focused on mathematics and coding while neglecting the scientific domain, largely due to the absence of open, large-scale, high-quality, verifiable scientific reasoning datasets. To bridge this gap, we first present TextbookReasoning, an open dataset featuring truthful reference answers extracted from 12k university-level scientific textbooks, comprising 650k reasoning questions spanning 7 scientific disciplines. We further introduce MegaScience, a large-scale mixture of high-quality open-source datasets totaling 1.25 million instances, developed through systematic ablation studies that evaluate various data selection methodologies to identify the optimal subset for each publicly available scientific dataset. Meanwhile, we build a comprehensive evaluation system covering diverse subjects and question types across 15 benchmarks, incorporating comprehensive answer extraction strategies to ensure accurate evaluation metrics. Our experiments demonstrate that our datasets achieve superior performance and training efficiency with more concise response lengths compared to existing open-source scientific datasets. Furthermore, we train Llama3.1, Qwen2.5, and Qwen3 series base models on MegaScience, which significantly outperform the corresponding official instruct models in average performance. In addition, MegaScience exhibits greater effectiveness for larger and stronger models, suggesting a scaling benefit for scientific tuning. We release our data curation pipeline, evaluation system, datasets, and seven trained models to the community to advance scientific reasoning research.

Materials discovery and design are essential for advancing technology across various industries by enabling the development of application-specific materials. Recent research has leveraged Large Language Models (LLMs) to accelerate this process. We explore the potential of LLMs to generate viable hypotheses that, once validated, can expedite materials discovery. Collaborating with materials science experts, we curated a novel dataset from recent journal publications, featuring real-world goals, constraints, and methods for designing real-world applications. Using this dataset, we test LLM-based agents that generate hypotheses for achieving given goals under specific constraints. To assess the relevance and quality of these hypotheses, we propose a novel scalable evaluation metric that emulates the process a materials scientist would use to evaluate a hypothesis critically. Our curated dataset, proposed method, and evaluation framework aim to advance future research in accelerating materials discovery and design with LLMs.

Humanities scholars commonly provide evidence for claims that they make about a work of literature (e.g., a novel) in the form of quotations from the work. We collect a large-scale dataset (RELiC) of 78K literary quotations and surrounding critical analysis and use it to formulate the novel task of literary evidence retrieval, in which models are given an excerpt of literary analysis surrounding a masked quotation and asked to retrieve the quoted passage from the set of all passages in the work. Solving this retrieval task requires a deep understanding of complex literary and linguistic phenomena, which proves challenging to methods that overwhelmingly rely on lexical and semantic similarity matching. We implement a RoBERTa-based dense passage retriever for this task that outperforms existing pretrained information retrieval baselines; however, experiments and analysis by human domain experts indicate that there is substantial room for improvement over our dense retriever.

Words of estimative probability (WEP) are expressions of a statement's plausibility (probably, maybe, likely, doubt, likely, unlikely, impossible...). Multiple surveys demonstrate the agreement of human evaluators when assigning numerical probability levels to WEP. For example, highly likely corresponds to a median chance of 0.90+-0.08 in Fagen-Ulmschneider (2015)'s survey. In this work, we measure the ability of neural language processing models to capture the consensual probability level associated to each WEP. Firstly, we use the UNLI dataset (Chen et al., 2020) which associates premises and hypotheses with their perceived joint probability p, to construct prompts, e.g. "[PREMISE]. [WEP], [HYPOTHESIS]." and assess whether language models can predict whether the WEP consensual probability level is close to p. Secondly, we construct a dataset of WEP-based probabilistic reasoning, to test whether language models can reason with WEP compositions. When prompted "[EVENTA] is likely. [EVENTB] is impossible.", a causal language model should not express that [EVENTA&B] is likely. We show that both tasks are unsolved by off-the-shelf English language models, but that fine-tuning leads to transferable improvement.

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.

The history of science is punctuated by serendipitous discoveries, where unexpected observations, rather than targeted hypotheses, opened new fields of inquiry. While modern autonomous laboratories excel at accelerating hypothesis testing, their optimization for efficiency risks overlooking these crucial, unplanned findings. To address this gap, we introduce SciLink, an open-source, multi-agent artificial intelligence framework designed to operationalize serendipity in materials research by creating a direct, automated link between experimental observation, novelty assessment, and theoretical simulations. The framework employs a hybrid AI strategy where specialized machine learning models perform quantitative analysis of experimental data, while large language models handle higher-level reasoning. These agents autonomously convert raw data from materials characterization techniques into falsifiable scientific claims, which are then quantitatively scored for novelty against the published literature. We demonstrate the framework's versatility across diverse research scenarios, showcasing its application to atomic-resolution and hyperspectral data, its capacity to integrate real-time human expert guidance, and its ability to close the research loop by proposing targeted follow-up experiments. By systematically analyzing all observations and contextualizing them, SciLink provides a practical framework for AI-driven materials research that not only enhances efficiency but also actively cultivates an environment ripe for serendipitous discoveries, thereby bridging the gap between automated experimentation and open-ended scientific exploration.

We consider the problem of automatically generating a narrative biomedical evidence summary from multiple trial reports. We evaluate modern neural models for abstractive summarization of relevant article abstracts from systematic reviews previously conducted by members of the Cochrane collaboration, using the authors conclusions section of the review abstract as our target. We enlist medical professionals to evaluate generated summaries, and we find that modern summarization systems yield consistently fluent and relevant synopses, but that they are not always factual. We propose new approaches that capitalize on domain-specific models to inform summarization, e.g., by explicitly demarcating snippets of inputs that convey key findings, and emphasizing the reports of large and high-quality trials. We find that these strategies modestly improve the factual accuracy of generated summaries. Finally, we propose a new method for automatically evaluating the factuality of generated narrative evidence syntheses using models that infer the directionality of reported findings.

We present SciClaimEval, a new scientific dataset for the claim verification task. Unlike existing resources, SciClaimEval features authentic claims, including refuted ones, directly extracted from published papers. To create refuted claims, we introduce a novel approach that modifies the supporting evidence (figures and tables), rather than altering the claims or relying on large language models (LLMs) to fabricate contradictions. The dataset provides cross-modal evidence with diverse representations: figures are available as images, while tables are provided in multiple formats, including images, LaTeX source, HTML, and JSON. SciClaimEval contains 1,664 annotated samples from 180 papers across three domains, machine learning, natural language processing, and medicine, validated through expert annotation. We benchmark 11 multimodal foundation models, both open-source and proprietary, across the dataset. Results show that figure-based verification remains particularly challenging for all models, as a substantial performance gap remains between the best system and human baseline.

There has been a lot of recent interest in adopting machine learning methods for scientific and engineering applications. This has in large part been inspired by recent successes and advances in the domains of Natural Language Processing (NLP) and Image Classification (IC). However, scientific and engineering problems have their own unique characteristics and requirements raising new challenges for effective design and deployment of machine learning approaches. There is a strong need for further mathematical developments on the foundations of machine learning methods to increase the level of rigor of employed methods and to ensure more reliable and interpretable results. Also as reported in the recent literature on state-of-the-art results and indicated by the No Free Lunch Theorems of statistical learning theory incorporating some form of inductive bias and domain knowledge is essential to success. Consequently, even for existing and widely used methods there is a strong need for further mathematical work to facilitate ways to incorporate prior scientific knowledge and related inductive biases into learning frameworks and algorithms. We briefly discuss these topics and discuss some ideas proceeding in this direction.

Despite improvements in performances on different natural language generation tasks, deep neural models are prone to hallucinating facts that are incorrect or nonexistent. Different hypotheses are proposed and examined separately for different tasks, but no systematic explanations are available across these tasks. In this study, we draw connections between hallucinations and predictive uncertainty in conditional language generation. We investigate their relationship in both image captioning and data-to-text generation and propose a simple extension to beam search to reduce hallucination. Our analysis shows that higher predictive uncertainty corresponds to a higher chance of hallucination. Epistemic uncertainty is more indicative of hallucination than aleatoric or total uncertainties. It helps to achieve better results of trading performance in standard metric for less hallucination with the proposed beam search variant.

Despite interdisciplinary research leading to larger and longer-term impact, most work remains confined to single-domain academic silos. Recent AI-based approaches to scientific discovery show promise for interdisciplinary research, but many prioritize rapidly designing experiments and solutions, bypassing the exploratory, collaborative reasoning processes that drive creative interdisciplinary breakthroughs. As a result, prior efforts largely prioritize automating scientific discovery rather than augmenting the reasoning processes that underlie scientific disruption. We present Idea-Catalyst, a novel framework that systematically identifies interdisciplinary insights to support creative reasoning in both humans and large language models. Starting from an abstract research goal, Idea-Catalyst is designed to assist the brainstorming stage, explicitly avoiding premature anchoring on specific solutions. The framework embodies key metacognitive features of interdisciplinary reasoning: (a) defining and assessing research goals, (b) awareness of a domain's opportunities and unresolved challenges, and (c) strategic exploration of interdisciplinary ideas based on impact potential. Concretely, Idea-Catalyst decomposes an abstract goal (e.g., improving human-AI collaboration) into core target-domain research questions that guide the analysis of progress and open challenges within that domain. These challenges are reformulated as domain-agnostic conceptual problems, enabling retrieval from external disciplines (e.g., Psychology, Sociology) that address analogous issues. By synthesizing and recontextualizing insights from these domains back into the target domain, Idea-Catalyst ranks source domains by their interdisciplinary potential. Empirically, this targeted integration improves average novelty by 21% and insightfulness by 16%, while remaining grounded in the original research problem.

Climate change poses an urgent global threat, needing the rapid identification and deployment of innovative solutions. We hypothesise that many of these solutions already exist within scientific literature but remain underutilised. To address this gap, this study employs a curated dataset sourced from OpenAlex, a comprehensive repository of scientific papers. Utilising Large Language Models (LLMs), such as GPT4-o from OpenAI, we evaluate title-abstract pairs from scientific papers on seven dimensions, covering climate change mitigation potential, stage of technological development, and readiness for deployment. The outputs of the language models are then compared with human evaluations to assess their effectiveness in identifying promising yet overlooked climate innovations. Our findings suggest that these LLM-based models can effectively augment human expertise, uncovering climate solutions that are potentially impactful but with far greater speed, throughput and consistency. Here, we focused on UK-based solutions, but the workflow is region-agnostic. This work contributes to the discovery of neglected innovations in scientific literature and demonstrates the potential of AI in enhancing climate action strategies.

Recent advances in mechanistic interpretability have revealed that large language models (LLMs) develop internal representations corresponding not only to concrete entities but also distinct, human-understandable abstract concepts and behaviour. Moreover, these hidden features can be directly manipulated to steer model behaviour. However, it remains an open question whether this phenomenon is unique to models trained on inherently structured data (ie. language, images) or if it is a general property of foundation models. In this work, we investigate the internal representations of a large physics-focused foundation model. Inspired by recent work identifying single directions in activation space for complex behaviours in LLMs, we extract activation vectors from the model during forward passes over simulation datasets for different physical regimes. We then compute "delta" representations between the two regimes. These delta tensors act as concept directions in activation space, encoding specific physical features. By injecting these concept directions back into the model during inference, we can steer its predictions, demonstrating causal control over physical behaviours, such as inducing or removing some particular physical feature from a simulation. These results suggest that scientific foundation models learn generalised representations of physical principles. They do not merely rely on superficial correlations and patterns in the simulations. Our findings open new avenues for understanding and controlling scientific foundation models and has implications for AI-enabled 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.

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.

In the last year or so and going back many decades there has been extensive claims by major computational scientists, engineers, and others that AGI, artificial general intelligence, is five or ten years away, but without a scintilla of scientific evidence, for a broad body of these claims. Computers will become conscious, have a theory of mind, think and reason, will become more intelligent than humans, and so on. But the claims are science fiction, not science. This article reviews evidence for the following three propositions using extensive body of scientific research and related sources from the cognitive and neurosciences, evolutionary evidence, linguistics, data science, comparative psychology, self-driving cars, robotics. and the learning sciences. (1) Do computing machines think or reason? (2) Are computing machines sentient or conscious? (3) Do computing machines have a theory of mind?

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.

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.

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.

As scientific research becomes increasingly complex, innovative tools are needed to manage vast data, facilitate interdisciplinary collaboration, and accelerate discovery. Large language models (LLMs) are now evolving into LLM-based scientific agents that automate critical tasks, ranging from hypothesis generation and experiment design to data analysis and simulation. Unlike general-purpose LLMs, these specialized agents integrate domain-specific knowledge, advanced tool sets, and robust validation mechanisms, enabling them to handle complex data types, ensure reproducibility, and drive scientific breakthroughs. This survey provides a focused review of the architectures, design, benchmarks, applications, and ethical considerations surrounding LLM-based scientific agents. We highlight why they differ from general agents and the ways in which they advance research across various scientific fields. By examining their development and challenges, this survey offers a comprehensive roadmap for researchers and practitioners to harness these agents for more efficient, reliable, and ethically sound scientific discovery.

Scientific problem solving poses unique challenges for LLMs, requiring both deep domain knowledge and the ability to apply such knowledge through complex reasoning. While automated scientific reasoners hold great promise for assisting human scientists, there is currently no widely adopted holistic benchmark for evaluating scientific reasoning, and few approaches systematically disentangle the distinct roles of knowledge and reasoning in these tasks. To address these gaps, we introduce SciReas, a diverse suite of existing benchmarks for scientific reasoning tasks, and SciReas-Pro, a selective subset that requires more complex reasoning. Our holistic evaluation surfaces insights about scientific reasoning performance that remain hidden when relying on individual benchmarks alone. We then propose KRUX, a probing framework for studying the distinct roles of reasoning and knowledge in scientific tasks. Combining the two, we conduct an in-depth analysis that yields several key findings: (1) Retrieving task-relevant knowledge from model parameters is a critical bottleneck for LLMs in scientific reasoning; (2) Reasoning models consistently benefit from external knowledge added in-context on top of the reasoning enhancement; (3) Enhancing verbalized reasoning improves LLMs' ability to surface task-relevant knowledge. Finally, we conduct a lightweight analysis, comparing our science-focused data composition with concurrent efforts on long CoT SFT, and release SciLit01, a strong 8B baseline for scientific reasoning.

Building language models (LMs), especially small and medium ones, remains more art than science. While large LMs often improve by sheer scale, it is still unclear why many design choices work. For small LMs, this uncertainty is more limiting: tight parameter budgets make each decision critical, yet researchers still lack systematic, scientific ways to test and refine new ideas. We introduce Pico, a lightweight, modular framework that enables systematic, hypothesis-driven research for small and medium-scale language model development. Pico consists of two libraries that together provide a practical sandbox where researchers can make targeted changes to a model's architecture or training procedures and directly observe their effects on the model's behavior. To support reproducible experimentation, we also release a suite of baseline models, pico-decoder, trained under standardized conditions and open-sourced for the community. Case studies highlight how Pico can support iterative small LM design and analysis.

Mathematical equations have been unreasonably effective in describing complex natural phenomena across various scientific disciplines. However, discovering such insightful equations from data presents significant challenges due to the necessity of navigating extremely high-dimensional combinatorial and nonlinear hypothesis spaces. Traditional methods of equation discovery largely focus on extracting equations from data alone, often neglecting the rich domain-specific prior knowledge that scientists typically depend on. To bridge this gap, we introduce LLM-SR, a novel approach that leverages the extensive scientific knowledge and robust code generation capabilities of Large Language Models (LLMs) to discover scientific equations from data in an efficient manner. Specifically, LLM-SR treats equations as programs with mathematical operators and combines LLMs' scientific priors with evolutionary search over equation programs. The LLM iteratively proposes new equation skeletons, drawing from its physical understanding, which are then optimized against data to estimate skeleton parameters. We demonstrate LLM-SR's effectiveness across three diverse scientific domains, where it discovers physically accurate equations that provide significantly better fits to in-domain and out-of-domain data compared to the well-established equation discovery baselines

Interpretability research on large language models (LLMs) has yielded important insights into model behaviour, yet recurring pitfalls persist: findings that do not generalise, and causal interpretations that outrun the evidence. Our position is that causal inference specifies what constitutes a valid mapping from model activations to invariant high-level structures, the data or assumptions needed to achieve it, and the inferences it can support. Specifically, Pearl's causal hierarchy clarifies what an interpretability study can justify. Observations establish associations between model behaviour and internal components. Interventions (e.g., ablations or activation patching) support claims how these edits affect a behavioural metric (e.g., average change in token probabilities) over a set of prompts. However, counterfactual claims -- i.e., asking what the model output would have been for the same prompt under an unobserved intervention -- remain largely unverifiable without controlled supervision. We show how causal representation learning (CRL) operationalises this hierarchy, specifying which variables are recoverable from activations and under what assumptions. Together, these motivate a diagnostic framework that helps practitioners select methods and evaluations matching claims to evidence such that findings generalise.

While large language models (LLMs) show promise in scientific discovery, existing research focuses on inference or feedback-driven training, leaving the direct modeling of the generative reasoning process, P(hypothesis|background) (P(h|b)), unexplored. We demonstrate that directly training P(h|b) is mathematically intractable due to the combinatorial complexity (O(N^k)) inherent in retrieving and composing inspirations from a vast knowledge base. To break this barrier, we introduce MOOSE-Star, a unified framework enabling tractable training and scalable inference. In the best case, MOOSE-Star reduces complexity from exponential to logarithmic (O(log N)) by (1) training on decomposed subtasks derived from the probabilistic equation of discovery, (2) employing motivation-guided hierarchical search to enable logarithmic retrieval and prune irrelevant subspaces, and (3) utilizing bounded composition for robustness against retrieval noise. To facilitate this, we release TOMATO-Star, a dataset of 108,717 decomposed papers (38,400 GPU hours) for training. Furthermore, we show that while brute-force sampling hits a ''complexity wall,'' MOOSE-Star exhibits continuous test-time scaling.

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.

Foundation models are increasingly used in scientific research, but evaluating AI-generated scientific work remains challenging. While expert reviews are costly, large language models (LLMs) as proxy reviewers have proven to be unreliable. To address this, we investigate two automatic evaluation metrics, specifically citation count prediction and review score prediction. We parse all papers of OpenReview and augment each submission with its citation count, reference, and research hypothesis. Our findings reveal that citation count prediction is more viable than review score prediction, and predicting scores is more difficult purely from the research hypothesis than from the full paper. Furthermore, we show that a simple prediction model based solely on title and abstract outperforms LLM-based reviewers, though it still falls short of human-level consistency.

We introduce CLIMATE-FEVER, a new publicly available dataset for verification of climate change-related claims. By providing a dataset for the research community, we aim to facilitate and encourage work on improving algorithms for retrieving evidential support for climate-specific claims, addressing the underlying language understanding challenges, and ultimately help alleviate the impact of misinformation on climate change. We adapt the methodology of FEVER [1], the largest dataset of artificially designed claims, to real-life claims collected from the Internet. While during this process, we could rely on the expertise of renowned climate scientists, it turned out to be no easy task. We discuss the surprising, subtle complexity of modeling real-world climate-related claims within the fever framework, which we believe provides a valuable challenge for general natural language understanding. We hope that our work will mark the beginning of a new exciting long-term joint effort by the climate science and AI community.

We introduce SciEvalKit, a unified benchmarking toolkit designed to evaluate AI models for science across a broad range of scientific disciplines and task capabilities. Unlike general-purpose evaluation platforms, SciEvalKit focuses on the core competencies of scientific intelligence, including Scientific Multimodal Perception, Scientific Multimodal Reasoning, Scientific Multimodal Understanding, Scientific Symbolic Reasoning, Scientific Code Generation, Science Hypothesis Generation and Scientific Knowledge Understanding. It supports six major scientific domains, spanning from physics and chemistry to astronomy and materials science. SciEvalKit builds a foundation of expert-grade scientific benchmarks, curated from real-world, domain-specific datasets, ensuring that tasks reflect authentic scientific challenges. The toolkit features a flexible, extensible evaluation pipeline that enables batch evaluation across models and datasets, supports custom model and dataset integration, and provides transparent, reproducible, and comparable results. By bridging capability-based evaluation and disciplinary diversity, SciEvalKit offers a standardized yet customizable infrastructure to benchmark the next generation of scientific foundation models and intelligent agents. The toolkit is open-sourced and actively maintained to foster community-driven development and progress in AI4Science.

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

Scientific research demands sophisticated reasoning over multimodal data, a challenge especially prevalent in biology. Despite recent advances in multimodal large language models (MLLMs) for AI-assisted research, existing multimodal reasoning benchmarks only target up to college-level difficulty, while research-level benchmarks emphasize lower-level perception, falling short of the complex multimodal reasoning needed for scientific discovery. To bridge this gap, we introduce MicroVQA, a visual-question answering (VQA) benchmark designed to assess three reasoning capabilities vital in research workflows: expert image understanding, hypothesis generation, and experiment proposal. MicroVQA consists of 1,042 multiple-choice questions (MCQs) curated by biology experts across diverse microscopy modalities, ensuring VQA samples represent real scientific practice. In constructing the benchmark, we find that standard MCQ generation methods induce language shortcuts, motivating a new two-stage pipeline: an optimized LLM prompt structures question-answer pairs into MCQs; then, an agent-based `RefineBot' updates them to remove shortcuts. Benchmarking on state-of-the-art MLLMs reveal a peak performance of 53\%; models with smaller LLMs only slightly underperform top models, suggesting that language-based reasoning is less challenging than multimodal reasoning; and tuning with scientific articles enhances performance. Expert analysis of chain-of-thought responses shows that perception errors are the most frequent, followed by knowledge errors and then overgeneralization errors. These insights highlight the challenges in multimodal scientific reasoning, showing MicroVQA is a valuable resource advancing AI-driven biomedical research. MicroVQA is available at https://huggingface.co/datasets/jmhb/microvqa, and project page at https://jmhb0.github.io/microvqa.

The current landscape of AI for Science (AI4S) is predominantly anchored in large-scale textual corpora, where generative AI systems excel at hypothesis generation, literature search, and multi-modal reasoning. However, a critical bottleneck for accelerating closed-loop scientific discovery remains the utilization of raw experimental data. Characterized by extreme heterogeneity, high specificity, and deep domain expertise requirements, raw data possess neither direct semantic alignment with linguistic representations nor structural homogeneity suitable for a unified embedding space. The disconnect prevents the emerging class of Artificial General Intelligence for Science (AGI4S) from effectively interfacing with the physical reality of experimentation. In this work, we extend the text-centric AI-Ready concept to Scientific AI-Ready data paradigm, explicitly formalizing how scientific data is specified, structured, and composed within a computational workflow. To operationalize this idea, we propose SciDataCopilot, an autonomous agentic framework designed to handle data ingestion, scientific intent parsing, and multi-modal integration in a end-to-end manner. By positioning data readiness as a core operational primitive, the framework provides a principled foundation for reusable, transferable systems, enabling the transition toward experiment-driven scientific general intelligence. Extensive evaluations across three heterogeneous scientific domains show that SciDataCopilot improves efficiency, scalability, and consistency over manual pipelines, with up to 30times speedup in data preparation.

Evaluating whether multimodal large language models truly understand long-form scientific papers remains challenging: answer-only metrics and synthetic "Needle-In-A-Haystack" tests often reward answer matching without requiring a causal, evidence-linked reasoning trace in the document. We propose the "Fish-in-the-Ocean" (FITO) paradigm, which requires models to construct explicit cross-modal evidence chains within native scientific documents. To operationalize FITO, we build SIN-Data, a scientific interleaved corpus that preserves the native interleaving of text and figures. On top of it, we construct SIN-Bench with four progressive tasks covering evidence discovery (SIN-Find), hypothesis verification (SIN-Verify), grounded QA (SIN-QA), and evidence-anchored synthesis (SIN-Summary). We further introduce "No Evidence, No Score", scoring predictions when grounded to verifiable anchors and diagnosing evidence quality via matching, relevance, and logic. Experiments on eight MLLMs show that grounding is the primary bottleneck: Gemini-3-pro achieves the best average overall score (0.573), while GPT-5 attains the highest SIN-QA answer accuracy (0.767) but underperforms on evidence-aligned overall scores, exposing a gap between correctness and traceable support.

Autonomous agents powered by large language models (LLMs) promise to accelerate scientific discovery end-to-end, but rigorously evaluating their capacity for verifiable discovery remains a central challenge. Existing benchmarks face a trade-off: they either heavily rely on LLM-as-judge evaluations of automatically generated research outputs or optimize convenient yet isolated performance metrics that provide coarse proxies for scientific insight. To address this gap, we introduce FIRE-Bench (Full-cycle Insight Rediscovery Evaluation), a benchmark that evaluates agents through the rediscovery of established findings from recent, high-impact machine learning research. Agents are given only a high-level research question extracted from a published, verified study and must autonomously explore ideas, design experiments, implement code, execute their plans, and derive conclusions supported by empirical evidence. We evaluate a range of state-of-the-art agents with frontier LLMs backbones like gpt-5 on FIRE-Bench. Our results show that full-cycle scientific research remains challenging for current agent systems: even the strongest agents achieve limited rediscovery success (<50 F1), exhibit high variance across runs, and display recurring failure modes in experimental design, execution, and evidence-based reasoning. FIRE-Bench provides a rigorous and diagnostic framework for measuring progress toward reliable agent-driven scientific discovery.

Retrieval-Augmented Generation (RAG) extends large language models (LLMs) beyond parametric knowledge, yet it is unclear when iterative retrieval-reasoning loops meaningfully outperform static RAG, particularly in scientific domains with multi-hop reasoning, sparse domain knowledge, and heterogeneous evidence. We provide the first controlled, mechanism-level diagnostic study of whether synchronized iterative retrieval and reasoning can surpass an idealized static upper bound (Gold Context) RAG. We benchmark eleven state-of-the-art LLMs under three regimes: (i) No Context, measuring reliance on parametric memory; (ii) Gold Context, where all oracle evidence is supplied at once; and (iii) Iterative RAG, a training-free controller that alternates retrieval, hypothesis refinement, and evidence-aware stopping. Using the chemistry-focused ChemKGMultiHopQA dataset, we isolate questions requiring genuine retrieval and analyze behavior with diagnostics spanning retrieval coverage gaps, anchor-carry drop, query quality, composition fidelity, and control calibration. Across models, Iterative RAG consistently outperforms Gold Context, with gains up to 25.6 percentage points, especially for non-reasoning fine-tuned models. Staged retrieval reduces late-hop failures, mitigates context overload, and enables dynamic correction of early hypothesis drift, but remaining failure modes include incomplete hop coverage, distractor latch trajectories, early stopping miscalibration, and high composition failure rates even with perfect retrieval. Overall, staged retrieval is often more influential than the mere presence of ideal evidence; we provide practical guidance for deploying and diagnosing RAG systems in specialized scientific settings and a foundation for more reliable, controllable iterative retrieval-reasoning frameworks.

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.

Despite its simplicity and efficacy, the high token expenditure of self-consistency can limit its practical utility. Here we investigate if self-consistency can be made more token-efficient for long chain-of-thought reasoning tasks, while preserving its parallelism, through early hypothesis pruning. Concretely, we generate all solutions in parallel, but periodically prune intermediate hypotheses that are deemed unnecessary based on two lightweight indicators: (a) the model's own confidence in individual hypotheses, and (b) lexical coverage of all current hypotheses by candidate subsets that are under consideration for continued retention. We design a fast weighted set cover algorithm that utilizes the two indicators; our evaluation of five LLMs on three math benchmarks shows that this method can improve token efficiency for all models, by 10-35% in many cases.