Daily Papers

Large language models (LLMs) excel at answering pre-specified questions, yet their ability to navigate the open-ended, pre-conclusion stage of discovery remains largely unmeasured. We introduce Prospective Hypothesis Discovery (PHD), which asks models to autonomously construct grounded, discriminative, and testable hypothesis spaces from inconclusive evidence, including anomalous observations and fragmented records, to guide subsequent investigation. To evaluate this capability, we introduce HypoArena, comprising HypoData, a benchmark of 988 cases across six scientific and analytical domains, and HypoEval, an evaluation framework for open-ended hypothesis sets. To construct HypoData at scale, we propose Retrospective Context Regression, a Forge--Audit pipeline that reconstructs pre-conclusion contexts from completed expert documents by removing explicit conclusions, target hypotheses, and retrospective causal attributions while preserving the factual substrate. Because PHD admits multiple valid outputs, HypoEval combines bidirectional pairwise judgments with Bradley--Terry--Davidson aggregation for ranking and six-dimensional rubric scoring for diagnosis. Experiments on 15 frontier LLMs reveal clear capability stratification and model-dependent effects of structured analytical skills, with gains for several lower-performing models on HypoArena but regressions for other systems, including a top-performing model. Compared with absolute rubric scoring, arena evaluation resolves finer-grained differences among models, with aggregated rankings showing strong agreement with human experts and an independent judge. Together, these results support treating PHD as a distinct target for evaluating how LLMs formulate investigative directions when final conclusions are withheld. Our code and data are publicly available at github.com/SKYLENAGE-AI/HypoArena and github.com/SKYLENAGE-AI/HypoArena.

Scientific discovery requires developing worthwhile hypotheses into practical investigations, yet learning from this evolving research process remains challenging. We introduce an operational definition of valuable and testable research hypotheses: evidence-grounded claims about consequential uncertainties, coupled with feasible investigations, explicit decision criteria, and alternative explanations. Our DiscoveryRSI framework develops hypothesis trees through multi-agent evolutionary search, compiles selected investigations into executable Harbor tasks, and recursively learns through three mechanisms: hypothesis credit optimization attributes scientific assessments to documented research contributions; harness replay identifies productive strategies and recurring failures to refine research workflows; and rediscovery applies accepted improvements to new investigations, generating further experience for subsequent learning. We also introduce DFM-Bench, which provides comprehensive assessment of hypothesis quality and cumulative research progress at the levels of hypotheses, revisions, development paths and research runs. Across four life-science domains, automated evaluation shows that hypothesis quality rises from 4.86 for the base model to 5.39 after two rounds of self-improvement, with the large gains in falsifiability and data resolvability. We further validate hypothesis quality through expert review, comparing our DiscoveryRSI-27B with other research agents. Preliminary human assessments show that DiscoveryRSI-27B scores higher than GPT-6 Luna on hypothesis importance and whether claims are plausible and evidence-bounded. DiscoveryRSI-27B achieved a 6.3% rate of hypothesis correspondence with research published after the model cutoff, largely outperform GPT-6 with 2.5% and Claude Opus 5 with 2.3%, while delivering greater human-rated improvement along research paths.

Test-time scaling has enabled LLMs to solve increasingly complex reasoning, discovery, and optimization tasks. However, existing approaches often gather observations while seeking evidence for current hypotheses, then generate new hypotheses conditioned on those hypotheses and their associated evidence. This couples observation discovery to existing hypotheses, favoring local refinements over exploration of unknown hypotheses regions. Inspired by the hypothetico-deductive method (Hempel, 1945) and dual-space models of scientific discovery (Klahr & Dunbar, 1988), we introduce SHELDON, a scientific reasoning harness that separately represents and jointly explores hypothesis and observation spaces. By actively seeking new observations along with new hypotheses, SHELDON can discover observations that its current hypotheses do not explain. These unexplained observations expose gaps in its understanding, motivate new investigations, and guide the generation of hypotheses beyond refinements of existing ones. Across diagnosis, abstract reasoning, and optimization benchmarks, SHELDON outperforms evaluated baselines by up to 26.7 points. Additional analysis shows that SHELDON generates up to 4.5x more novel solutions.

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.

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.

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.

Open-ended scientific discovery with large language models (LLMs) increasingly operates as a long-horizon loop of hypothesis search and verification, where a reward signal guides which hypotheses to test next. A notable recent example is AutoDiscovery, which uses "Bayesian surprise" - the belief shift an LLM undergoes after observing evidence for a hypothesis - as both a discovery metric and a reward for search. We first observe that AutoDiscovery treats surprisal as a static quantity, while surprisal in human reasoning is non-stationary - it is defined relative to beliefs that evolve with experience, a prerequisite for continual scientific discovery. We address this mismatch with evidence-informed LLM beliefs: priors updated with evidence from previous hypotheses to compute non-stationary surprisal for new hypotheses. We compare in-context belief-updating mechanisms and find that embedding-based retrieval-augmented generation over prior discoveries best anticipates eventual posteriors, identifying 37.5% of static surprisals as spurious. We then modify search to avoid these spurious rewards and prioritize hypotheses that remain surprising under non-stationary beliefs. Concretely, we introduce two complementary changes to the original search procedure: belief-update filtering and diversity maximization. Across five discovery domains, our method increases accumulated non-stationary surprisal by 30.62% on average compared to the original search procedure, demonstrating that continual scientific discovery with LLMs requires not only better belief measurement but also search procedures that avoid redundancy and encourage diversity.

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.

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

Large language models (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.

Scientific discovery requires identifying the scientific principles underlying observed phenomena to guide further investigation. As these empirical principles are often unknown in complex discovery processes, they are constructed via a hypotheses-to-principle pipeline to obtain recurring causalities from progressively accumulated observations during test-time discovery. However, constructing this knowledge requires substantial domain expertise, time, and effort, making this translation stage a bottleneck for scientific discovery. To address this limitation, we propose Principia, an LLM-based framework that constructs and continually refines scientific principles at test time. Drawing on how human researchers develop principles, Principia forms comparative causal hypotheses from related inputs and their observed outcomes, then synthesizes recurring relationships across these hypotheses into inductive principles. By applying the constructed hypotheses and inductive principles to the task, it obtains new observations, revises the hypotheses used based on these new observations, and reconstructs principles from the updated hypotheses, allowing scientific knowledge to continuously evolve throughout test-time discovery. Across benchmarks spanning molecular optimization, protein engineering, gene perturbation, and molecular property prediction, Principia outperforms baselines relying on internal knowledge, external sources, or experience summaries, while generating principles that are plausible and consistent with the scientific literature, demonstrating its effectiveness in constructing and refining task-specific hypotheses and principles at test time for scientific discovery. Our code is available at https://github.com/DongkiKim95/Principia.

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.

Scientific discovery is an inherently creative and uncertain process, requiring reasoning beyond the recall of known knowledge. While many benchmarks have been proposed to evaluate large language model (LLM) performance on deep research tasks via multi-hop retrieval, their innovative reasoning abilities essential for true scientific discovery remain largely untested. We introduce a benchmark framework for evaluating model performance in scientific discovery and reasoning, building up from a raw problem to the classical null hypothesis test. In our framework, models initially receive only the topic and research question from a recent paper, with technical details progressively revealed. At each stage of information disclosure, the model is tasked with generating hypotheses that address the research question, which is compared with the conclusions from the original paper and evaluated via automated semantic similarity of constituent atomic claims. This progressive evaluation of semantic divergence from ground-truth conclusions enables assessment of a model's innovativeness (under minimal information) to grounded reasoning capabilities (under full experimental details), both critical for using LLMs for scientific discovery purposes. Our framework provides a foundation for systematically evaluating scientific reasoning and discovery capabilities in LLMs, crucial for advancing the development of next-generation AI scientist/co-scientist systems. Specifically, here we evaluate GPT-5, GPT-5.4, Gemini 2.5 pro, and Gemini 3.1 pro preview across 45 papers spanning bioactive materials, mechanical materials, and nanomaterials. We find that GPT-5.4 and Gemini 3.1 pro outperform their previous generation counterparts as expected, and GPT-5.4 in particular maintains 0.7 F1 score alignment with ground truth conclusions even under minimal context.

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

AI systems are increasingly capable of contributing to mathematical research. In research practice, frontier-model reasoning is a limited resource, and expert mathematical review is even more sharply constrained. Allocating these scarce resources well is therefore central to making AI-assisted mathematical discovery efficient. In most current AI-for-math workflows, human effort is concentrated at the beginning and end, in selecting suitable research problems and later reviewing the resulting artifacts. These two stages are becoming bottlenecks for research-level mathematics. We address them by proposing a new human-AI discovery paradigm. The human input is no longer a single problem selected in advance, but a research direction in which the experts have interest and expertise. The system then searches a broad literature corpus for candidate problems in that direction. Inspired by search and recommender systems, we build Find, Attempt, and Recommend (FAR), a literature-to-review cascade that automates the search for suitable problems and focuses human attention on artifacts that have passed several stages of filtering. In a combinatorics pilot, the pipeline starts from 5,245 combinatorics papers, recovers 6,453 candidate conjectures or open problems, and filters them to 4,717 apparently well-posed and still-open conjectures. Subsequent reasoning and automated triage stages surface 598 potential resolutions and select 77 items for author-team review. Among them, we identify many interesting discoveries, including results on conjectures and questions of Davies--Jenssen--Perkins--Roberts, Erdős--Straus, Ikenmeyer--Pak--Panova, and Lund--Saraf--Wolf. These results demonstrate the effectiveness of this new mode of human-AI collaboration for mathematical discovery.

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.

Scientific progress depends on sequences of enabling contributions, yet existing AI4Science benchmarks largely focus on citation prediction, literature retrieval, or idea generation rather than the dependencies that make progress possible. In this paper, we introduce discovery pathway forecasting: given a target scientific contribution and the prior literature available at a specified time, the task is to (1) identify the enabling contributions required to realize it and (2) ground each in prior work when such prior work exists. We present SciPaths, a benchmark of 262 expert-annotated gold pathways and 2,444 silver pathways constructed from machine learning and natural language processing papers, where each pathway records enabling contributions, roles, rationales, and prior-work groundings or unmapped decisions. Evaluating frontier and open-weight language models, we find that the best model reaches only 0.189 F1 under strict semantic matching, with core methodological dependencies hardest to recover. Prior-work grounding improves substantially when gold enabling contributions are provided, showing that decomposition quality is a major bottleneck for end-to-end pathway recovery. SciPaths therefore shifts evaluation toward a missing capability in scientific forecasting: reasoning backward from a target contribution to the enabling scientific building blocks and prior-work dependencies that make it feasible.

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.

Causal discovery aims to uncover the underlying causal relationships given data generated from a system. The goal, however, is not merely to predict causal edges given data, but also to be able to interpret and explain either observed or hypothesized phenomena, such as a particularly large causal effect. We consider this task of conditional causal discovery and cast it as a Bayesian inference problem, in which we target the posterior over causal graphs and parameters conditional on an event such as a causal-effect constraint. Unfortunately, this poses a computational challenge: existing approaches to Bayesian causal discovery struggle when the event has small posterior mass. To address this, we adapt rare-event estimation techniques to perform inference the joint graph-parameter space. Our method gradually drives a particle population toward the constrained region while maintaining samples that approximate the conditional posterior. Empirical evaluation on synthetic graphs validates the accuracy of our approach at small and large scales, and we show in a case study on the Sachs protein dataset how our method can be used to aid scientific exploration by providing pathway-level summaries.

Autonomous scientific discovery systems offer the potential to accelerate research by automating the process of hypothesis generation and validation. However, current systems operate within constrained search spaces or require predefined research questions, limiting their capacity for true open-ended inquiry. Furthermore, while they generate hypotheses iteratively, they largely lack the ability to explicitly synthesize their own accumulated findings to uncover complex, interconnected phenomena. We introduce DiscoPER, an autonomous large language model-powered framework that conducts open-ended research by dynamically generating and executing code to explore datasets without pre-specified research objectives. To ensure rigorous scientific validity, every proposed discovery must pass statistical testing. To overcome the limitations of isolated search, our framework introduces a second-order reasoning mechanism that periodically analyzes its own accumulated discoveries. By treating prior discoveries as empirical data, DiscoPER identifies structural patterns, confounds, and epistemic gaps, actively redirecting hypothesis exploration toward uncharted regions of the search space. The search space is further expanded by incorporating tool use, enabling the system to explore hypotheses beyond structured metadata by seamlessly processing and extracting useful information from multimodal sources like images. Evaluated on iNatDisco, a new multimodal ecological knowledge benchmark with pattern-level ground truth obtained from peer-reviewed literature, DiscoPER recovers 8 of 9 known patterns with a 72.7% hypothesis support rate, outperforming both classical causal discovery and LLM-guided baselines. Ablations show that DiscoPER scales with more data, and confirms the benefits of second-order meta-reflection.

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.

Contemporary automated scientific discovery has focused on agents for generating scientific experiments, while systems that perform higher-level scientific activities such as theory building remain underexplored. In this work, we formulate the problem of synthesizing theories consisting of qualitative and quantitative laws from large corpora of scientific literature. We study theory generation at scale, using 13.7k source papers to synthesize 2.9k theories, examining how generation using literature-grounding versus parametric knowledge, and accuracy-focused versus novelty-focused generation objectives change theory properties. Our experiments show that, compared to using parametric LLM memory for generation, our literature-supported method creates theories that are significantly better at both matching existing evidence and at predicting future results from 4.6k subsequently-written papers

There has been a surge of interest in harnessing the reasoning capabilities of Large Language Models (LLMs) to accelerate scientific discovery. While existing approaches rely on grounding the discovery process within the relevant literature, effectiveness varies significantly with the quality and nature of the retrieved literature. We address the challenge of retrieving prior work whose concepts can inspire solutions for a given research problem, a task we define as Methodology Inspiration Retrieval (MIR). We construct a novel dataset tailored for training and evaluating retrievers on MIR, and establish baselines. To address MIR, we build the Methodology Adjacency Graph (MAG); capturing methodological lineage through citation relationships. We leverage MAG to embed an "intuitive prior" into dense retrievers for identifying patterns of methodological inspiration beyond superficial semantic similarity. This achieves significant gains of +5.4 in Recall@3 and +7.8 in Mean Average Precision (mAP) over strong baselines. Further, we adapt LLM-based re-ranking strategies to MIR, yielding additional improvements of +4.5 in Recall@3 and +4.8 in mAP. Through extensive ablation studies and qualitative analyses, we exhibit the promise of MIR in enhancing automated scientific discovery and outline avenues for advancing inspiration-driven retrieval.

Scientific contributions rarely develop in isolation, but instead build upon prior discoveries. We formulate the task of automated technological roadmapping as extracting scientific contributions from scholarly articles and linking them to their prerequisites. We present the Scientific Contribution Graph, a large-scale resource containing 6 million detailed scientific contributions extracted from 655k open-access papers spanning computer science, medicine, biology, physics, chemistry, and other sciences, and connected by 36 million prerequisite edges. We further introduce scientific prerequisite prediction, a scientific discovery task in which models predict which existing technologies can enable future discoveries, and show that contemporary models are rapidly improving on this task, reaching 0.48 MAP when evaluated using temporally-filtered backtesting. We anticipate technological roadmapping resources such as this will support scientific impact assessment and automated scientific discovery.

Agents are widely deployed as assistants over documents, tools, and code. However, they typically act only on explicit user requests, which surface only the problems the user has noticed, while many other important problems coexist, hidden in plain sight, within the broader user context, with their total number unknown in advance. We frame this as the task of discovering multiple hidden problems from context, in which coexisting problems should be uncovered, grounded in supporting evidence, and paired with concrete actions. To this end, we introduce TIDE, a template-guided iterative framework with two complementary mechanisms. Specifically, motivated by the observation that single-pass prediction anchors on the most salient cases and yields generic claims, we propose iterative discovery, which surfaces a small batch of candidates per round while conditioning on what has already been found, so subsequent rounds extend coverage; and thought templates, reusable schemas distilled from previously solved cases that specify what contextual signals to attend to and how to connect them, anchoring each prediction in a recognizable problem class. We validate TIDE on two realistic settings, personal workspaces and software repositories, across four model backbones, showing substantial gains over single-shot and parallel multi-agent baselines on task coverage, identification, and resolution.

As language models accelerate scientific research by automating hypothesis generation and implementation, a new bottleneck emerges: evaluating and filtering hundreds of AI-generated ideas without exhaustive experimentation. We ask whether LMs can learn to forecast the empirical success of research ideas before any experiments are run. We study comparative empirical forecasting: given a benchmark-specific research goal and two candidate ideas, predict which will achieve better benchmark performance. We construct a dataset of 11,488 idea pairs grounded in objective outcomes from PapersWithCode. While off-the-shelf 8B-parameter models struggle (30% acc.), SFT dramatically boosts performance to 77.1%, outperforming GPT-5 (61.1%). By framing evaluation as a reasoning task via Reinforcement Learning with Verifiable Rewards (RLVR), we train models to discover latent reasoning paths, achieving 71.35% acc. with interpretable justifications. Through additional ablations and out-of-distribution tests, we show robustness to surface-level heuristics and transfer to both a cross-domain time-split test set and an independently constructed test set. Our results demonstrate that compute-efficient small language models can serve as effective, objective verifiers, offering a scalable path for autonomous scientific discovery.

Foundation models have progressed from learning and reasoning over existing knowledge, to increasingly learning through action, tool use, and outcome feedback. We argue that the next frontier is a further transition: from solving and acting within problems specified by humans to participating in the process by which new problems, representations, explanations, and knowledge are created. We refer to this capability as Discovery Intelligence. We formulate Discovery Foundation Models (DFMs) as general-purpose model systems for open-ended discovery. A DFM operates over a revisable research state and supports seven coupled capabilities spanning problem discovery, formulation, representation construction, hypothesis formation, intervention, evidence-grounded revision, and continual discovery improvement. We instantiate this framework with Zetema, which couples explicit research-state dynamics, verification and experimental gating, external grounding, and cross-task Discovery Skill evolution. We further ground the framework with GALILEO, a real therapeutic-discovery system in which Dry-Lab reasoning, robotic and hands-on Wet-Lab experimentation, external biological evidence, and iterative hypothesis and design revision form a closed physical discovery loop. We then formulate a unified approach to capability formation and process-centered evaluation, enabling discovery behavior to be trained, improved, and measured beyond final-answer performance. Together, these components establish discovery as a learnable, executable, and evaluable capability of foundation-model systems. We view this shift as a broader progression in intelligence scaling: from learning over existing knowledge, to learning from action outcomes, and ultimately to participating in the construction, testing, and revision of the structures through which new knowledge is discovered. Code: https://github.com/Gen-Verse/DFM-Plans

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.

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.

Autonomous scientific discovery systems increasingly use large language models (LLMs) to propose new hypotheses, but many such systems condition primarily on experimental memory: archives of high-scoring candidates or heuristic summaries of recent trials. We argue that discovery agents should instead maintain explicit, uncertainty-aware beliefs about hypothesis quality. We introduce BayesEvolve, a belief-guided discovery framework that converts experimental evidence into a predictive belief state and uses this belief to guide future experimentation. As a controlled testbed for belief-guided discovery, we evaluate BayesEvolve on shifted BBOB-style black-box optimization tasks, leaving program and laboratory discovery domains to future work. BayesEvolve improves sample efficiency over memory- and archive-guided LLM baselines under a fixed evaluation budget. We further show that the belief state is predictive on held-out candidate pools, that controlled decision-rule ablations favor belief-guided selection with an annealed uncertainty bonus, and that BayesEvolve exhibits productive late-stage concentration rather than unfocused exploration.

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.

The rapid advancements in large language models (LLMs) have demonstrated their potential to accelerate scientific discovery, particularly in automating the process of research ideation. LLM-based systems have shown promise in generating hypotheses and research ideas. However, current approaches predominantly rely on prompting-based pre-trained models, limiting their ability to optimize generated content effectively. Moreover, they also lack the capability to deal with the complex interdependence and inherent restrictions among novelty, feasibility, and effectiveness, which remains challenging due to the inherent trade-offs among these dimensions, such as the innovation-feasibility conflict. To address these limitations, we for the first time propose fine-tuning LLMs to be better idea proposers and introduce a novel framework that employs a two-stage approach combining Supervised Fine-Tuning (SFT) and controllable Reinforcement Learning (RL). In the SFT stage, the model learns foundational patterns from pairs of research papers and follow-up ideas. In the RL stage, multi-dimensional reward modeling, guided by fine-grained feedback, evaluates and optimizes the generated ideas across key metrics. Dimensional controllers enable dynamic adjustment of generation, while a sentence-level decoder ensures context-aware emphasis during inference. Our framework provides a balanced approach to research ideation, achieving high-quality outcomes by dynamically navigating the trade-offs among novelty, feasibility, and effectiveness.

Large language models (LLMs) are on the rise for accelerating scientific discovery, most recently in advanced tasks such as generating valid scientific hypotheses. Yet in many discovery settings, the goal is not to identify a single best hypothesis since validation can be noisy and expensive, and scientists benefit from a set of high-quality alternative hypotheses that hedge against downstream uncertainty for the best solutions. Nevertheless, commonly used evolutionary search recipes tend to prioritize optimization over exploration in hypothesis generation, and the resulting selection pressure during the search process leads to diversity collapse. Motivated by these limitations, we formulate hypothesis search as a sampling problem, where the objective is to efficiently produce diverse, high-quality hypotheses under a fixed validation budget. Building on this perspective, we propose \ours, an evolutionary framework inspired by the classical parallel tempering algorithm that searches hypotheses at multiple temperature levels and enables principled information exchange across temperatures to improve exploration without disrupting convergence. Across domains including molecular discovery, equation discovery, and algorithm discovery, our approach consistently improves both hypothesis quality and diversity under the same validation budget, and produces candidates that remain robust under more expensive downstream computational validations.

"An idea is nothing more nor less than a new combination of old elements" (Young, J.W.). The widespread adoption of Large Language Models (LLMs) and publicly available ChatGPT have marked a significant turning point in the integration of Artificial Intelligence (AI) into people's everyday lives. This study explores the capability of LLMs in generating novel research ideas based on information from research papers. We conduct a thorough examination of 4 LLMs in five domains (e.g., Chemistry, Computer, Economics, Medical, and Physics). We found that the future research ideas generated by Claude-2 and GPT-4 are more aligned with the author's perspective than GPT-3.5 and Gemini. We also found that Claude-2 generates more diverse future research ideas than GPT-4, GPT-3.5, and Gemini 1.0. We further performed a human evaluation of the novelty, relevancy, and feasibility of the generated future research ideas. This investigation offers insights into the evolving role of LLMs in idea generation, highlighting both its capability and limitations. Our work contributes to the ongoing efforts in evaluating and utilizing language models for generating future research ideas. We make our datasets and codes publicly available.

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.

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.

Large-scale datasets for natural language inference are created by presenting crowd workers with a sentence (premise), and asking them to generate three new sentences (hypotheses) that it entails, contradicts, or is logically neutral with respect to. We show that, in a significant portion of such data, this protocol leaves clues that make it possible to identify the label by looking only at the hypothesis, without observing the premise. Specifically, we show that a simple text categorization model can correctly classify the hypothesis alone in about 67% of SNLI (Bowman et. al, 2015) and 53% of MultiNLI (Williams et. al, 2017). Our analysis reveals that specific linguistic phenomena such as negation and vagueness are highly correlated with certain inference classes. Our findings suggest that the success of natural language inference models to date has been overestimated, and that the task remains a hard open problem.

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.

Current AI systems are optimized for answering questions; the scientific enterprise is bottlenecked earlier, at discovering the questions worth investigating. We present a framework that turns a traceable, reproducible, scope controlled research corpus into ranked, falsifiable research questions: evidence is represented as provenance carrying claims; cross paper tensions are detected, typed, and human adjudicated; surviving signals are refined into questions and ranked by a two stage protocol separating scientific priority from execution priority. We instantiate the framework on exoplanet atmospheres, a domain that uniquely combines literature, structured catalogs, and space telescope archives. In a historical backtest, all questions generated from evidence available before 2021 were substantively engaged by the 2021 to 2026 literature the sys?tem never saw: two were answered, including one whose premise the community later explicitly refuted and the top ranked question is independently posed and still open. These results sug?gest that systematic question discovery from evidence tensions surfaces the questions working scientists subsequently invest in.

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.

We automate deep step-by step reasoning in an LLM dialog thread by recursively exploring alternatives (OR-nodes) and expanding details (AND-nodes) up to a given depth. Starting from a single succinct task-specific initiator we steer the automated dialog thread to stay focussed on the task by synthesizing a prompt that summarizes the depth-first steps taken so far. Our algorithm is derived from a simple recursive descent implementation of a Horn Clause interpreter, except that we accommodate our logic engine to fit the natural language reasoning patterns LLMs have been trained on. Semantic similarity to ground-truth facts or oracle advice from another LLM instance is used to restrict the search space and validate the traces of justification steps returned as answers. At the end, the unique minimal model of a generated Horn Clause program collects the results of the reasoning process. As applications, we sketch implementations of consequence predictions, causal explanations, recommendation systems and topic-focussed exploration of scientific literature.

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.

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.

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.

This paper proposes a research direction to advance AI which draws inspiration from cognitive theories of human decision making. The premise is that if we gain insights about the causes of some human capabilities that are still lacking in AI (for instance, adaptability, generalizability, common sense, and causal reasoning), we may obtain similar capabilities in an AI system by embedding these causal components. We hope that the high-level description of our vision included in this paper, as well as the several research questions that we propose to consider, can stimulate the AI research community to define, try and evaluate new methodologies, frameworks, and evaluation metrics, in the spirit of achieving a better understanding of both human and machine intelligence.

This paper introduces PRobELM (Plausibility Ranking Evaluation for Language Models), a benchmark designed to assess language models' ability to discern more plausible from less plausible scenarios through their parametric knowledge. While benchmarks such as TruthfulQA emphasise factual accuracy or truthfulness, and others such as COPA explore plausible scenarios without explicitly incorporating world knowledge, PRobELM seeks to bridge this gap by evaluating models' capabilities to prioritise plausible scenarios that leverage world knowledge over less plausible alternatives. This design allows us to assess the potential of language models for downstream use cases such as literature-based discovery where the focus is on identifying information that is likely but not yet known. Our benchmark is constructed from a dataset curated from Wikidata edit histories, tailored to align the temporal bounds of the training data for the evaluated models. PRobELM facilitates the evaluation of language models across multiple prompting types, including statement, text completion, and question-answering. Experiments with 10 models of various sizes and architectures on the relationship between model scales, training recency, and plausibility performance, reveal that factual accuracy does not directly correlate with plausibility performance and that up-to-date training data enhances plausibility assessment across different model architectures.

A core goal of computational social science is to discover interpretable differences in how language varies across outcomes of interest, such as political affiliation or instructional quality. Recent LLM-based hypothesis generation methods describe such differences in natural language, but select for globally discriminative patterns without accounting for covariates that shape the data based on researchers' domain knowledge. When covariates are ignored, selected patterns can reflect confounds rather than differences of substantive interest. We introduce conditional hypothesis generation, a framework that incorporates researcher-specified covariates to steer hypothesis discovery toward differences that hold within relevant subgroups. Two challenges arise: the target subgroup may be underrepresented (stratum imbalance), and the direction of a difference may reverse across subgroups (sign reversal). We propose two econometrics-inspired methods: one introduces feature--covariate interactions to detect sign reversals, and the other applies within-stratum demeaning and inverse-frequency reweighting to equalize underrepresented strata. Synthetic experiments show each method outperforms global baselines in its targeted setting, and expert evaluation on two real-world datasets confirms that covariate-aware generation surfaces more useful hypotheses within relevant subgroups.

Recent advancements in large language models (LLMs) have sparked optimism about their potential to accelerate scientific discovery, with a growing number of works proposing research agents that autonomously generate and validate new ideas. Despite this, no evaluations have shown that LLM systems can take the very first step of producing novel, expert-level ideas, let alone perform the entire research process. We address this by establishing an experimental design that evaluates research idea generation while controlling for confounders and performs the first head-to-head comparison between expert NLP researchers and an LLM ideation agent. By recruiting over 100 NLP researchers to write novel ideas and blind reviews of both LLM and human ideas, we obtain the first statistically significant conclusion on current LLM capabilities for research ideation: we find LLM-generated ideas are judged as more novel (p < 0.05) than human expert ideas while being judged slightly weaker on feasibility. Studying our agent baselines closely, we identify open problems in building and evaluating research agents, including failures of LLM self-evaluation and their lack of diversity in generation. Finally, we acknowledge that human judgements of novelty can be difficult, even by experts, and propose an end-to-end study design which recruits researchers to execute these ideas into full projects, enabling us to study whether these novelty and feasibility judgements result in meaningful differences in research outcome.

This paper demonstrates that artificial intelligence can accelerate mathematical discovery by autonomously solving an open problem in theoretical physics. We present a neuro-symbolic system, combining the Gemini Deep Think large language model with a systematic Tree Search (TS) framework and automated numerical feedback, that successfully derived novel, exact analytical solutions for the power spectrum of gravitational radiation emitted by cosmic strings. Specifically, the agent evaluated the core integral I(N,α) for arbitrary loop geometries, directly improving upon recent AI-assisted attempts BCE+25 that only yielded partial asymptotic solutions. To substantiate our methodological claims regarding AI-accelerated discovery and to ensure transparency, we detail system prompts, search constraints, and intermittent feedback loops that guided the model. The agent identified a suite of 6 different analytical methods, the most elegant of which expands the kernel in Gegenbauer polynomials C_l^{(3/2)} to naturally absorb the integrand's singularities. The methods lead to an asymptotic result for I(N,α) at large N that both agrees with numerical results and also connects to the continuous Feynman parameterization of Quantum Field Theory. We detail both the algorithmic methodology that enabled this discovery and the resulting mathematical derivations.

Keeping track of scientific challenges, advances and emerging directions is a fundamental part of research. However, researchers face a flood of papers that hinders discovery of important knowledge. In biomedicine, this directly impacts human lives. To address this problem, we present a novel task of extraction and search of scientific challenges and directions, to facilitate rapid knowledge discovery. We construct and release an expert-annotated corpus of texts sampled from full-length papers, labeled with novel semantic categories that generalize across many types of challenges and directions. We focus on a large corpus of interdisciplinary work relating to the COVID-19 pandemic, ranging from biomedicine to areas such as AI and economics. We apply a model trained on our data to identify challenges and directions across the corpus and build a dedicated search engine. In experiments with 19 researchers and clinicians using our system, we outperform a popular scientific search engine in assisting knowledge discovery. Finally, we show that models trained on our resource generalize to the wider biomedical domain and to AI papers, highlighting its broad utility. We make our data, model and search engine publicly available. https://challenges.apps.allenai.org/

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.

Machine learning has achieved remarkable success in many applications. However, existing studies are largely based on the closed-world assumption, which assumes that the environment is stationary, and the model is fixed once deployed. In many real-world applications, this fundamental and rather naive assumption may not hold because an open environment is complex, dynamic, and full of unknowns. In such cases, rejecting unknowns, discovering novelties, and then incrementally learning them, could enable models to be safe and evolve continually as biological systems do. This paper provides a holistic view of open-world machine learning by investigating unknown rejection, novel class discovery, and class-incremental learning in a unified paradigm. The challenges, principles, and limitations of current methodologies are discussed in detail. Finally, we discuss several potential directions for future research. This paper aims to provide a comprehensive introduction to the emerging open-world machine learning paradigm, to help researchers build more powerful AI systems in their respective fields, and to promote the development of artificial general intelligence.

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.

Reasoning, a crucial ability for complex problem-solving, plays a pivotal role in various real-world settings such as negotiation, medical diagnosis, and criminal investigation. It serves as a fundamental methodology in the field of Artificial General Intelligence (AGI). With the ongoing development of foundation models, e.g., Large Language Models (LLMs), there is a growing interest in exploring their abilities in reasoning tasks. In this paper, we introduce seminal foundation models proposed or adaptable for reasoning, highlighting the latest advancements in various reasoning tasks, methods, and benchmarks. We then delve into the potential future directions behind the emergence of reasoning abilities within foundation models. We also discuss the relevance of multimodal learning, autonomous agents, and super alignment in the context of reasoning. By discussing these future research directions, we hope to inspire researchers in their exploration of this field, stimulate further advancements in reasoning with foundation models, and contribute to the development of AGI.

Commonsense causality reasoning (CCR) aims at identifying plausible causes and effects in natural language descriptions that are deemed reasonable by an average person. Although being of great academic and practical interest, this problem is still shadowed by the lack of a well-posed theoretical framework; existing work usually relies on deep language models wholeheartedly, and is potentially susceptible to confounding co-occurrences. Motivated by classical causal principles, we articulate the central question of CCR and draw parallels between human subjects in observational studies and natural languages to adopt CCR to the potential-outcomes framework, which is the first such attempt for commonsense tasks. We propose a novel framework, ROCK, to Reason O(A)bout Commonsense K(C)ausality, which utilizes temporal signals as incidental supervision, and balances confounding effects using temporal propensities that are analogous to propensity scores. The ROCK implementation is modular and zero-shot, and demonstrates good CCR capabilities.

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

Thinking about the future is one of the important activities that people do in daily life. Futurists also pay a lot of effort into figuring out possible scenarios for the future. We argue that the exploration of this direction is still in an early stage in the NLP research. To this end, we propose three argument generation tasks in the financial application scenario. Our experimental results show these tasks are still big challenges for representative generation models. Based on our empirical results, we further point out several unresolved issues and challenges in this research direction.

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.

In an era of exponential scientific growth, identifying novel research ideas is crucial and challenging in academia. Despite potential, the lack of an appropriate benchmark dataset hinders the research of novelty detection. More importantly, simply adopting existing NLP technologies, e.g., retrieving and then cross-checking, is not a one-size-fits-all solution due to the gap between textual similarity and idea conception. In this paper, we propose to harness large language models (LLMs) for scientific novelty detection (ND), associated with two new datasets in marketing and NLP domains. To construct the considerate datasets for ND, we propose to extract closure sets of papers based on their relationship, and then summarize their main ideas based on LLMs. To capture idea conception, we propose to train a lightweight retriever by distilling the idea-level knowledge from LLMs to align ideas with similar conception, enabling efficient and accurate idea retrieval for LLM novelty detection. Experiments show our method consistently outperforms others on the proposed benchmark datasets for idea retrieval and ND tasks. Codes and data are available at https://anonymous.4open.science/r/NoveltyDetection-10FB/.

Recent advances in LLMs have made automated scientific research the next frontline in the path to artificial superintelligence. However, these systems are bound either to tasks of narrow scope or the limited creative capabilities of LLMs. We propose Spacer, a scientific discovery system that develops creative and factually grounded concepts without external intervention. Spacer attempts to achieve this via 'deliberate decontextualization,' an approach that disassembles information into atomic units - keywords - and draws creativity from unexplored connections between them. Spacer consists of (i) Nuri, an inspiration engine that builds keyword sets, and (ii) the Manifesting Pipeline that refines these sets into elaborate scientific statements. Nuri extracts novel, high-potential keyword sets from a keyword graph built with 180,000 academic publications in biological fields. The Manifesting Pipeline finds links between keywords, analyzes their logical structure, validates their plausibility, and ultimately drafts original scientific concepts. According to our experiments, the evaluation metric of Nuri accurately classifies high-impact publications with an AUROC score of 0.737. Our Manifesting Pipeline also successfully reconstructs core concepts from the latest top-journal articles solely from their keyword sets. An LLM-based scoring system estimates that this reconstruction was sound for over 85% of the cases. Finally, our embedding space analysis shows that outputs from Spacer are significantly more similar to leading publications compared with those from SOTA LLMs.

Scientific discovery begins where known problems end. There, AI systems must engage in exploration: framing hypotheses, designing experiments, and iterating on the results. However, evaluating this ability is difficult: (1) how to verify whether a genuinely new hypothesis holds, and (2) how to determine whether a system has discovered it through exploration or merely recalled related knowledge from pre-training data. To this end, we introduce ExplorationBench, which turns the wicked problem of evaluating scientific exploration into a concrete and tractable framework built on verifiable Alien Worlds: their rules are executable, so every answer can be checked exactly, and they conflict with familiar knowledge, so recall alone cannot solve the tasks. The benchmark contains two sandboxes, AlienCode (31 discovery targets, 70 tasks) and AlienLogic (24 discovery targets, 70 tasks). Each sandbox provides a flawed manual, task-specific environmental feedback, and a dedicated tool-call schema. Systems use these resources to explore the sandbox, then solve held-out tasks. We evaluate 10 AI systems and find that the strongest systems can acquire and apply unfamiliar rules, while performance varies substantially across trajectories and continued exploration can stall or reverse earlier gains. ExplorationBench represents a step towards AI systems that can acquire and apply genuinely new knowledge through exploration in unknown environments.

Predicting the answer to interventional ``what if'' questions --- the outcome of an action never taken --- requires a mechanistic, causal model, not a curve fit; and learning such a model requires experiments, because passive data leaves its mechanisms unidentified. Experiments are expensive, so the central problem is data efficiency. We present the Model Discovery Agent (MDA), which couples a large language model (LLM), used as a proposer of candidate structures, with standard Bayesian machinery --- sequential Monte Carlo (SMC) for parameter and structure posteriors, simulation-based inference (SBI) for intractable likelihoods, and value-of-information (VoI) for experiment design --- to discover latent mechanistic world models from few interventions. MDA operates in the M-open setting: when the truth lies outside the current hypothesis class, a predictive check flags the inadequacy and the proposer expands the hypothesis space with a new model whose parameters are then identified by designed experiments. We show that discovery and design reinforce: the design step identifies the mechanism the discovery step proposes, and the identified mechanism improves predictions, enabling further discoveries from the remaining unexplained residuals. On three different benchmarks --- covering physics (\DPbench, wiemann2026discoverphysics), chemistry (\CHEMbench, kabra2026autoscilab) and biology (\HHbench, a new partially observed single-neuron electrophysiology benchmark we create) --- we show that MDA sets a new SOTA in terms of data-efficient model learning and reliable interventional prediction ability.

Recent advances in foundation models have enabled AI scientists to automate increasingly complete research workflows, from hypothesis generation and code execution to manuscript preparation. Yet workflow coverage alone does not provide access to the full evidence on which scientific discovery depends. Existing systems typically reason over text, code, labels, or precomputed summaries, leaving scientifically decisive spatial, temporal, cross-channel, and procedural relations unavailable to the agent. We introduce OmniScientist, an end-to-end, omni-modal AI scientist that conducts multidisciplinary research directly from heterogeneous raw evidence. A perception layer and 3 autonomous agents for ideation, experiment, and writeup operate within a deterministic pipeline, allowing observations to shape research questions, experimental decisions, and final claims throughout the research lifecycle. By running idea, rigour, and claim checks in code, the system enforces novelty screening, statistical validity, execution provenance, and numerical traceability. We evaluate OmniScientist on 36 real-data cases spanning 5 discipline families, 4 families of scientific evidence, and modalities including images, signals, audio, video, 3-D structures, trajectories, tables, formulae, and graphs. The system completes the full path from raw data to a compiled manuscript in all 36 cases and achieves a mean overall paper score of 6.3 with the reference reasoning backbone. In paired comparisons against a blind variant that receives only precomputed scalar features, direct perception improves all 7 evaluation dimensions and wins 85% of head-to-head judgments. These results show that lifecycle-wide perception is essential for evidence-grounded scientific discovery and provides a practical path toward broadly capable AI scientists.

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.

Autonomous agents can increasingly propose ideas, modify code, and run experiments, creating an opportunity to accelerate scientific discovery using teams of collaborative AI researchers. To escape local minima in the discovery, we propose to encourage orthogonal exploration by constructing the team using agents with varying expertise. However, realizing this design requires more than diverse backgrounds. When experiments are costly, a team can test only a limited number of ideas, thereby creating the need to balance exploration and exploitation when selecting a subset of researchers to propose and execute new experiments. Furthermore, each result should shape what the team tries next. We therefore ask how AI researchers with different scientific backgrounds can build on one another's findings and sustain progress under a limited experimental budget. To address these challenges, we build a team of persistent AI researchers, each grounded in a different discipline, who keep private research histories, share experimental evidence, and receive research opportunities through adaptive allocation. We demonstrate the effectiveness of this design by deploying the team to search for linear attention architectures, where it outperforms GDN2 at 1.3B scale on language modeling, common-sense reasoning, and synthetic and real-world retrieval tasks. In controlled comparisons, removing any single organizational component from our design yields markedly weaker discoveries: without disciplinary backgrounds, the search plateaus early; without private histories, researchers make less progress despite identical shared evidence; and uniform selection falls short of adaptive allocation within the same budget. These results suggest that sustained autonomous discovery depends not only on stronger agents, but also on who explores, what they remember, and how research effort is allocated.

Public funding plays a central role in driving scientific discovery. To better understand the link between research inputs and outputs, we introduce FIND (Funding-Impact NSF Database), an open-access dataset that systematically links NSF grant proposals to their downstream research outputs, including publication metadata and abstracts. The primary contribution of this project is the creation of a large-scale, structured dataset that enables transparency, impact evaluation, and metascience research on the returns to public funding. To illustrate the potential of FIND, we present two proof-of-concept NLP applications. First, we analyze whether the language of grant proposals can predict the subsequent citation impact of funded research. Second, we leverage large language models to extract scientific claims from both proposals and resulting publications, allowing us to measure the extent to which funded projects deliver on their stated goals. Together, these applications highlight the utility of FIND for advancing metascience, informing funding policy, and enabling novel AI-driven analyses of the scientific process.

Large Language Models (LLMs) have been used for novel discovery of algorithms, theorems, drugs, and other tasks through the use of harnesses that prompt an LLM to iteratively optimize an objective. In this work, we study the relationship between the population of previous iterates and eventual discovery success. We generalize past work on harness design to develop a suite of 12 harnesses called 'Modular' and characterize their performance across 5 diverse discovery tasks, finding that discovery success is brittle and sensitive to harness design. We uncover mode collapse, characterized by a dramatic drop in the diversity of iterates, as a common failure mode. We find that popular state-of-the-art harnesses and diversity-inducing harness interventions, which aim to prolong this collapse, yield inconsistent gains. Our results instead uncover that the performance of early discoveries is predictive of eventual success. We therefore propose a universally applicable intervention that performs an initial stage of parallel exploration in order to initialize subsequent iterative optimization. Our method provides consistent gains across many harnesses and target applications, confirming the importance of initialization in LLM-driven discovery.

Scientific equation discovery has long been central to scientific progress, proceeding through iterative cycles of hypothesis generation, observational testing, and refinement under scientific constraints. As LLM capabilities advance and their role in AI for Science expands, it remains an open problem whether they can genuinely discover scientific laws and how this ability should be evaluated. Existing evaluations, however, often either simplify discovery through synthetic settings or reuse published targets that may already be familiar to LLMs. We therefore introduce SCILAWS-BENCH, a benchmark for scientific law discovery built from published research and real scientific data. It comprises 118 problems drawn from 381 scientific papers, covering 291 candidate laws and roughly 8M real data points across six scientific disciplines. Each problem is instantiated in two complementary settings: (1) SCILAWS-REAL asks models to propose laws from fixed real observations and evaluates held-out predictive fit and scientific validity derived from the source literature, and (2) SCILAWS-PARALLEL asks models to actively query residual-calibrated worlds and recover synthesized hidden laws derived from published forms. This two-setting task design preserves each problem's scientific context while separately evaluating fixed-record law discovery and active recovery of a newly synthesized hidden law. We find that predictive fit can diverge from scientific validity, memorization shapes whether models reproduce or move beyond published formulas, and our best-of-N study reveals a selection bottleneck. Our work provides a paper-grounded benchmark and new empirical perspectives for evaluating AI for scientific discovery. Project page: https://yiyihum.github.io/SciLaws-Bench

The extraction of a small number of relevant insights from vast amounts of data is a crucial component of data-driven decision-making. However, accomplishing this task requires considerable technical skills, domain expertise, and human labor. This study explores the potential of using Large Language Models (LLMs) to automate the discovery of insights in data, leveraging recent advances in reasoning and code generation techniques. We propose a new evaluation methodology based on a "capture the flag" principle, measuring the ability of such models to recognize meaningful and pertinent information (flags) in a dataset. We further propose two proof-of-concept agents, with different inner workings, and compare their ability to capture such flags in a real-world sales dataset. While the work reported here is preliminary, our results are sufficiently interesting to mandate future exploration by the community.

With recent Nobel Prizes recognising AI contributions to science, Large Language Models (LLMs) are transforming scientific research by enhancing productivity and reshaping the scientific method. LLMs are now involved in experimental design, data analysis, and workflows, particularly in chemistry and biology. However, challenges such as hallucinations and reliability persist. In this contribution, we review how Large Language Models (LLMs) are redefining the scientific method and explore their potential applications across different stages of the scientific cycle, from hypothesis testing to discovery. We conclude that, for LLMs to serve as relevant and effective creative engines and productivity enhancers, their deep integration into all steps of the scientific process should be pursued in collaboration and alignment with human scientific goals, with clear evaluation metrics. The transition to AI-driven science raises ethical questions about creativity, oversight, and responsibility. With careful guidance, LLMs could evolve into creative engines, driving transformative breakthroughs across scientific disciplines responsibly and effectively. However, the scientific community must also decide how much it leaves to LLMs to drive science, even when associations with 'reasoning', mostly currently undeserved, are made in exchange for the potential to explore hypothesis and solution regions that might otherwise remain unexplored by human exploration alone.

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.

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.

Physics is a field of science that has traditionally used the scientific method to answer questions about why natural phenomena occur and to make testable models that explain the phenomena. Discovering equations, laws and principles that are invariant, robust and causal explanations of the world has been fundamental in physical sciences throughout the centuries. Discoveries emerge from observing the world and, when possible, performing interventional studies in the system under study. With the advent of big data and the use of data-driven methods, causal and equation discovery fields have grown and made progress in computer science, physics, statistics, philosophy, and many applied fields. All these domains are intertwined and can be used to discover causal relations, physical laws, and equations from observational data. This paper reviews the concepts, methods, and relevant works on causal and equation discovery in the broad field of Physics and outlines the most important challenges and promising future lines of research. We also provide a taxonomy for observational causal and equation discovery, point out connections, and showcase a complete set of case studies in Earth and climate sciences, fluid dynamics and mechanics, and the neurosciences. This review demonstrates that discovering fundamental laws and causal relations by observing natural phenomena is being revolutionised with the efficient exploitation of observational data, modern machine learning algorithms and the interaction with domain knowledge. Exciting times are ahead with many challenges and opportunities to improve our understanding of complex systems.

Scientific discovery has advanced through successive transformations in the organization of knowledge. Observation and experimentation established the empirical foundations of science. Theory made it possible to derive general principles from particular phenomena. Computation extended inquiry into systems beyond direct observation, while data-intensive methods opened new spaces of pattern and prediction. Science now confronts a different frontier. The central challenge is no longer simply to produce more information, but to organize expanding knowledge, reasoning, and evidence into a coherent process of discovery. Here, we introduce Bridging Literature, Agents, and Zero-gap Experimentation (BLAZE), a paradigm of socialized scientific intelligence. BLAZE conceives AI not as an assistant for isolated research tasks, but as an organizational infrastructure for scientific discovery. It connects persistent knowledge, collective reasoning, empirical validation, and human judgment within a continuous research lifecycle, transforming fragmented activities into a cumulative process of inquiry, criticism, and revision. The central premise of BLAZE is that scientific intelligence does not arise from computation alone. It emerges from the sustained interaction among knowledge, hypotheses, experiments, and collective verification. By organizing humans and machines within a shared scientific process, BLAZE makes discovery more traceable, reproducible, and cumulative while preserving human creativity, judgment, and responsibility. Socialized scientific intelligence may provide a foundation for the next era of science. Its purpose is not to replace human discovery, but to extend the scale, depth, and continuity of collective scientific inquiry.

Large language models (LLMs) excel at structured, verifiable tasks, but their low-entropy bias can produce homogeneous and predictable outputs, limiting their utility for open-ended scientific ideation. Effective discovery, however, spans a broader creative spectrum: from structured day science to loosely structured, serendipitous night science that reaches ideas beyond those typically considered. We introduce AI Night-Scientist, an agentic framework that uses reinforcement learning to teach models when and how to depart from predictable reasoning. Grounded in cognitive science, we model creativity along three axes: action (what to do and how creatively), process (when to explore versus exploit), and outcome (the novelty and usefulness of the resulting idea). We use these axes to train models with GRPO, exposing them to varying degrees and forms of creativity throughout training. This produces substantially more diverse scientific proposals, expanding the range of research directions by 27.8% and contribution types by 14.9% over the base model. It also improves predicted citation impact by up to 32.0 percentage points and originality by 66.2 points. These gains cannot be reproduced by simply increasing decoding temperature; instead, we find that semantic guidance specifying what kind of creativity to pursue is critical. Overall, our results suggest that creativity is a learnable, multi-level ability that can be shaped to help researchers reach ideas beyond those typically explored by LLMs.

Scientific discoveries often hinge on synthesizing decades of research, a task that potentially outstrips human information processing capacities. Large language models (LLMs) offer a solution. LLMs trained on the vast scientific literature could potentially integrate noisy yet interrelated findings to forecast novel results better than human experts. To evaluate this possibility, we created BrainBench, a forward-looking benchmark for predicting neuroscience results. We find that LLMs surpass experts in predicting experimental outcomes. BrainGPT, an LLM we tuned on the neuroscience literature, performed better yet. Like human experts, when LLMs were confident in their predictions, they were more likely to be correct, which presages a future where humans and LLMs team together to make discoveries. Our approach is not neuroscience-specific and is transferable to other knowledge-intensive endeavors.

Scientific innovation is pivotal for humanity, and harnessing large language models (LLMs) to generate research ideas could transform discovery. However, existing LLMs often produce simplistic and repetitive suggestions due to their limited ability in acquiring external knowledge for innovation. To address this problem, we introduce an enhanced planning and search methodology designed to boost the creative potential of LLM-based systems. Our approach involves an iterative process to purposely plan the retrieval of external knowledge, progressively enriching the idea generation with broader and deeper insights. Validation through automated and human assessments indicates that our framework substantially elevates the quality of generated ideas, particularly in novelty and diversity. The number of unique novel ideas produced by our framework is 3.4 times higher than without it. Moreover, our method outperforms the current state-of-the-art, generating at least 2.5 times more top-rated ideas based on 170 seed papers in a Swiss Tournament evaluation.

Collectively, machine learning (ML) researchers are engaged in the creation and dissemination of knowledge about data-driven algorithms. In a given paper, researchers might aspire to any subset of the following goals, among others: to theoretically characterize what is learnable, to obtain understanding through empirically rigorous experiments, or to build a working system that has high predictive accuracy. While determining which knowledge warrants inquiry may be subjective, once the topic is fixed, papers are most valuable to the community when they act in service of the reader, creating foundational knowledge and communicating as clearly as possible. Recent progress in machine learning comes despite frequent departures from these ideals. In this paper, we focus on the following four patterns that appear to us to be trending in ML scholarship: (i) failure to distinguish between explanation and speculation; (ii) failure to identify the sources of empirical gains, e.g., emphasizing unnecessary modifications to neural architectures when gains actually stem from hyper-parameter tuning; (iii) mathiness: the use of mathematics that obfuscates or impresses rather than clarifies, e.g., by confusing technical and non-technical concepts; and (iv) misuse of language, e.g., by choosing terms of art with colloquial connotations or by overloading established technical terms. While the causes behind these patterns are uncertain, possibilities include the rapid expansion of the community, the consequent thinness of the reviewer pool, and the often-misaligned incentives between scholarship and short-term measures of success (e.g., bibliometrics, attention, and entrepreneurial opportunity). While each pattern offers a corresponding remedy (don't do it), we also discuss some speculative suggestions for how the community might combat these trends.

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.

Recently, slow-thinking reasoning systems, such as o1, have demonstrated remarkable capabilities in solving complex reasoning tasks. These systems typically engage in an extended thinking process before responding to a query, allowing them to generate more thorough, accurate, and well-reasoned solutions. These systems are primarily developed and maintained by industry, with their core techniques not publicly disclosed. In response, an increasing number of studies from the research community aim to explore the technical foundations underlying these powerful reasoning systems. Building on these prior efforts, this paper presents a reproduction report on implementing o1-like reasoning systems. We introduce an "imitate, explore, and self-improve" framework as our primary technical approach to train the reasoning model. In the initial phase, we use distilled long-form thought data to fine-tune the reasoning model, enabling it to invoke a slow-thinking mode. The model is then encouraged to explore challenging problems by generating multiple rollouts, which can result in increasingly more high-quality trajectories that lead to correct answers. Furthermore, the model undergoes self-improvement by iteratively refining its training dataset. To verify the effectiveness of this approach, we conduct extensive experiments on three challenging benchmarks. The experimental results demonstrate that our approach achieves competitive performance compared to industry-level reasoning systems on these benchmarks.

We present an online method for estimating the cost of solving SAT problems. Modern SAT solvers present several challenges to estimate search cost including non-chronological backtracking, learning and restarts. Our method uses a linear model trained on data gathered at the start of search. We show the effectiveness of this method using random and structured problems. We demonstrate that predictions made in early restarts can be used to improve later predictions. We also show that we can use such cost estimations to select a solver from a portfolio.

Bold claims about AI's role in science-from "AGI will cure all diseases" to promises of radically accelerated discovery-raise a central epistemic question: do large language models (LLMs) truly generate new knowledge, or do they merely remix memorized fragments? We propose unlearning-as-ablation as a falsifiable probe of constructive scientific discovery. The idea is to systematically remove a target result together with its forget-closure (supporting lemmas, paraphrases, and multi-hop entailments) and then evaluate whether the model can re-derive the result from only permitted axioms and tools. Success would indicate generative capability beyond recall; failure would expose current limits. Unlike prevailing motivations for unlearning-privacy, copyright, or safety-our framing repositions it as an epistemic probe for AI-for-Science. We outline a minimal pilot in mathematics and algorithms to illustrate feasibility, and sketch how the same approach could later be extended to domains such as physics or chemistry. This is a position paper: our contribution is conceptual and methodological, not empirical. We aim to stimulate discussion on how principled ablation tests could help distinguish models that reconstruct knowledge from those that merely retrieve it, and how such probes might guide the next generation of AI-for-Science benchmarks.

Scientific agents contribute to hypothesis discovery by synthesizing evidence, assessing proposals, and developing new explanations. Recent systems combine scientific agents with evolutionary search through critique, comparison, and revision. However, how different forms of agent collaboration affect hypothesis quality remains an open question. Answering this question requires separating the effects of agents' scientific capabilities from those of their collaboration. A framework must therefore preserve agents' scientific roles and support rules for combining, revising, and retaining hypotheses. Building on this view, we introduce HypoEvolve, which makes collaboration explicit through successive updates to a hypothesis population. Specifically, we propose a generational genetic algorithm to coordinate specialized large language model (LLM) agents that integrate mechanistic arguments, reconsider assumptions, and assess evidence and testability. Each generation specifies how scientific judgments and new proposals reshape the population, making collaboration effects on hypothesis quality directly testable. Moreover, we design our evaluation around scientifically meaningful hypotheses that explain how a proposed intervention could work. Drug repurposing links these explanations to target-level biological claims assessed against external evidence. Specifically, we adapt DepMap and Open Targets into complementary external measures grounded in experimental, genetic, and clinical evidence. Across 34 cancer types, HypoEvolve achieves the highest scores against six baselines on both measures. DepMap selectivity reaches 0.171, versus 0.115 for the strongest baseline. Gains over single-pass generation also generalize to held-out cancer types. HypoEvolve advances a vision of autonomous science in which AI research teams achieve a capacity for discovery beyond that of individual models.

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.

Traditionally, a debate usually requires a manual preparation process, including reading plenty of articles, selecting the claims, identifying the stances of the claims, seeking the evidence for the claims, etc. As the AI debate attracts more attention these years, it is worth exploring the methods to automate the tedious process involved in the debating system. In this work, we introduce a comprehensive and large dataset named IAM, which can be applied to a series of argument mining tasks, including claim extraction, stance classification, evidence extraction, etc. Our dataset is collected from over 1k articles related to 123 topics. Near 70k sentences in the dataset are fully annotated based on their argument properties (e.g., claims, stances, evidence, etc.). We further propose two new integrated argument mining tasks associated with the debate preparation process: (1) claim extraction with stance classification (CESC) and (2) claim-evidence pair extraction (CEPE). We adopt a pipeline approach and an end-to-end method for each integrated task separately. Promising experimental results are reported to show the values and challenges of our proposed tasks, and motivate future research on argument mining.

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

Artificial Intelligence (AI) algorithms frequently learn creative and unexpected solutions, surprising even expert researchers who develop and study them. They often astonish practitioners by discovering unanticipated behavior, exploiting loopholes in reward signals, or spontaneously uncovering previously unknown scientific phenomena. However, accounts of such unconventional behavior across machine learning are seldom formally documented. This work presents 26 curated firsthand anecdotes from various machine learning subfields representing the work of over 100 researchers. These anecdotes showcase the capability of modern AI systems to circumvent human-imposed design limitations and discover unexpected solutions to the tasks we train them on. Furthermore, these accounts are particularly important for the safety of future AI systems. They illustrate the fundamental challenge of aligning models with human values without diminishing their creativity, so they can make surprising discoveries without producing surprising, potentially harmful outcomes. The paper first details AI achieving superhuman success through reinforcement learning across many challenging domains. However, reward-driven optimization can fail when the model learns to hack an underspecified reward or unarticulated constraint. We then present case studies suggesting that harnessing internet-scale foundation models (FMs) has not resolved these fundamental challenges and, in fact, can supercharge them. Nevertheless, we argue that these same learning dynamics can be harnessed to accelerate scientific discovery. Finally, we hope this work provides a consolidated resource to inform future research and demonstrates that the tendency toward unexpected behaviors is commonplace in modern AI, highlighting the need to anticipate and manage AI's capacity for innovative, yet unpredictable, solutions. (abstract abridged)

Large language models (LLMs) increasingly act as research agents, yet their ability to track shifts in research attention is difficult to evaluate because reviews and research ideas lack uniquely verifiable outcomes. We introduce Research Attention Prediction (RAP), a rolling benchmark covering 278 AI/ML fields and 1,390 episodes. At each cut-off, an LLM agent searches a temporally restricted arXiv corpus and predicts the next six months' paper shares across eight frozen research directions. Search generally helps, but all four diagnostic models perform worse than an exact-count exponentially weighted moving average (EWMA) baseline in compositional accuracy. We identify two linked bottlenecks. Under cumulative-history access, State carry-forward outperforms direct Forecast for all four diagnostic models; frozen-evidence replay links a shared component of this reversal to Forecast-oriented policies retrieving a smaller share of recent evidence. Even with exact historical activity, future-specific updating remains limited, with only GPT-5.5 plus reopened Search slightly surpassing EWMA. Fine-tuning on realised outcomes improves Qwen3-4B's forecast Spearman correlation by 0.105 on held-out fields at later origins, with gains also on change-rich episodes.

Large language models (LLMs) have rapidly evolved from text generators into powerful problem solvers. Yet, many open tasks demand critical thinking, multi-source, and verifiable outputs, which are beyond single-shot prompting or standard retrieval-augmented generation. Recently, numerous studies have explored Deep Research (DR), which aims to combine the reasoning capabilities of LLMs with external tools, such as search engines, thereby empowering LLMs to act as research agents capable of completing complex, open-ended tasks. This survey presents a comprehensive and systematic overview of deep research systems, including a clear roadmap, foundational components, practical implementation techniques, important challenges, and future directions. Specifically, our main contributions are as follows: (i) we formalize a three-stage roadmap and distinguish deep research from related paradigms; (ii) we introduce four key components: query planning, information acquisition, memory management, and answer generation, each paired with fine-grained sub-taxonomies; (iii) we summarize optimization techniques, including prompting, supervised fine-tuning, and agentic reinforcement learning; and (iv) we consolidate evaluation criteria and open challenges, aiming to guide and facilitate future development. As the field of deep research continues to evolve rapidly, we are committed to continuously updating this survey to reflect the latest progress in this area.

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

Modern large language models (LLMs) employ various forms of logical inference, both implicitly and explicitly, when addressing reasoning tasks. Understanding how to optimally leverage these inference paradigms is critical for advancing LLMs' reasoning capabilities. This paper adopts an exploratory approach by introducing a controlled evaluation environment for analogical reasoning -- a fundamental cognitive task -- that is systematically parameterized across three dimensions: modality (textual, visual, symbolic), difficulty (easy, medium, hard), and task format (multiple-choice or free-text generation). We analyze the comparative dynamics of inductive, abductive, and deductive inference pipelines across these dimensions, and demonstrate that our findings generalize to broader in-context learning tasks. Additionally, we investigate advanced paradigms such as hypothesis selection, verification, and refinement, revealing their potential to scale up logical inference in LLM reasoning. This exploratory study provides a foundation for future research in enhancing LLM reasoning through systematic logical inference strategies.

Language models (LMs) can make a correct prediction based on many possible signals in a prompt, not all corresponding to recall of factual associations. However, current interpretations of LMs fail to take this into account. For example, given the query "Astrid Lindgren was born in" with the corresponding completion "Sweden", no difference is made between whether the prediction was based on knowing where the author was born or assuming that a person with a Swedish-sounding name was born in Sweden. In this paper, we present a model-specific recipe - PrISM - for constructing datasets with examples of four different prediction scenarios: generic language modeling, guesswork, heuristics recall and exact fact recall. We apply two popular interpretability methods to the scenarios: causal tracing (CT) and information flow analysis. We find that both yield distinct results for each scenario. Results for exact fact recall and generic language modeling scenarios confirm previous conclusions about the importance of mid-range MLP sublayers for fact recall, while results for guesswork and heuristics indicate a critical role of late last token position MLP sublayers. In summary, we contribute resources for a more extensive and granular study of fact completion in LMs, together with analyses that provide a more nuanced understanding of how LMs process fact-related queries.

Despite rapid progress in automating scientific research, generating promising and well grounded research solutions remains a central challenge. We isolate research ideation as a standalone task and build our solution on the intuition that a challenge in one field can often be addressed by a mechanism that solved an analogous challenge in another. Accordingly, we introduce IdeaScientist, which decomposes ideation into gap finding, innovation, and report writing, and trains each role with reinforcement learning. These roles identify limitations in related work, draw solution intuitions from analogous problem settings, and develop those intuitions into complete research proposals. To facilitate discovery of insights across domains, we construct the Svalbard Idea Vault, a corpus of 2.77M decomposed research ideas for retrieval, training, and temporally controlled evaluation. Our evaluation restricts access to literature available before a cutoff date and assesses how closely proposed directions align with those later explored in 15K papers authored by human researchers. On Qwen3.6-27B, IdeaScientist outperforms the strongest open-source autoresearch baseline by 14.0%, driven mainly by gains in novelty. On this 27B open backbone, IdeaScientist even outperforms Claude Code SDK with Claude-4.8-Opus and Codex SDK with GPT-5.4, by up to 5.9%.

Recent attempts to combine large language models (LLMs) with causal discovery ask models to infer pairwise directions, propose graph structures, or inject language-model outputs as priors and constraints. These approaches promise faster analysis, but they also obscure whether a causal evidence is supported by data and assumptions or by textual associations, prompt artifacts and hallucinated mechanisms. We argue for a different role for agents in causal discovery. Agents should inspect data, retrieve context, explain method assumptions and clarify graph outputs, but they should not supply edges, orientations, priors, constraints or causal conclusions. We propose the principle that agents assist the workflow, while causal claims remain grounded in data, explicit assumptions, formal algorithms, diagnostics and user or domain-expert decisions. We instantiate this principle in causal-learn+, an online platform that coordinates data analysis, preprocessing, method recommendation, expert-knowledge incorporation, formal discovery and interpretation around the algorithmic ecosystem of causal-learn. A case study on Big Five personality data illustrates agent-assisted pipeline of causal discovery without turning language-model unreliability into causal evidence. The platform is available at causallearn.com.

Identifying and predicting the factors that contribute to the success of interdisciplinary research is crucial for advancing scientific discovery. However, there is a lack of methods to quantify the integration of new ideas and technological advancements in astronomical research and how these new technologies drive further scientific breakthroughs. Large language models, with their ability to extract key concepts from vast literature beyond keyword searches, provide a new tool to quantify such processes. In this study, we extracted concepts in astronomical research from 297,807 publications between 1993 and 2024 using large language models, resulting in a set of 24,939 concepts. These concepts were then used to form a knowledge graph, where the link strength between any two concepts was determined by their relevance through the citation-reference relationships. By calculating this relevance across different time periods, we quantified the impact of numerical simulations and machine learning on astronomical research. The knowledge graph demonstrates two phases of development: a phase where the technology was integrated and another where the technology was explored in scientific discovery. The knowledge graph reveals that despite machine learning has made much inroad in astronomy, there is currently a lack of new concept development at the intersection of AI and Astronomy, which may be the current bottleneck preventing machine learning from further transforming the field of astronomy.

Higher-level cognition depends on the ability to learn models of the world. We can characterize this at the computational level as a structure-learning problem with the goal of best identifying the prevailing causal relationships among a set of relata. However, the computational cost of performing exact Bayesian inference over causal models grows rapidly as the number of relata increases. This implies that the cognitive processes underlying causal learning must be substantially approximate. A powerful class of approximations that focuses on the sequential absorption of successive inputs is captured by the Neurath's ship metaphor in philosophy of science, where theory change is cast as a stochastic and gradual process shaped as much by people's limited willingness to abandon their current theory when considering alternatives as by the ground truth they hope to approach. Inspired by this metaphor and by algorithms for approximating Bayesian inference in machine learning, we propose an algorithmic-level model of causal structure learning under which learners represent only a single global hypothesis that they update locally as they gather evidence. We propose a related scheme for understanding how, under these limitations, learners choose informative interventions that manipulate the causal system to help elucidate its workings. We find support for our approach in the analysis of four experiments.

Recently, large language models (LLMs) have shown promising abilities to generate novel research ideas in science, a direction which coincides with many foundational principles in computational creativity (CC). In light of these developments, we present an idea generation system named Spark that couples retrieval-augmented idea generation using LLMs with a reviewer model named Judge trained on 600K scientific reviews from OpenReview. Our work is both a system demonstration and intended to inspire other CC researchers to explore grounding the generation and evaluation of scientific ideas within foundational CC principles. To this end, we release the annotated dataset used to train Judge, inviting other researchers to explore the use of LLMs for idea generation and creative evaluations.

This paper provides an introductory survey to GPT-3. We cover some of the historical development behind this technology, some of the key features of GPT-3, and discuss the machine learning model and the datasets used. We survey both academic and commercial efforts applying GPT-3 in diverse domains such as developing conversational AI chatbots, software development, creative work, domain knowledge, and business productivity. We discuss some of the challenges that GPT-3 faces such as the problems of training complexity, bias, and hallucination/incorrect answers. We also discuss the future research opportunities in this area.

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.

Large Language Models (LLMs) have gained popularity in time series forecasting, but their potential for anomaly detection remains largely unexplored. Our study investigates whether LLMs can understand and detect anomalies in time series data, focusing on zero-shot and few-shot scenarios. Inspired by conjectures about LLMs' behavior from time series forecasting research, we formulate key hypotheses about LLMs' capabilities in time series anomaly detection. We design and conduct principled experiments to test each of these hypotheses. Our investigation reveals several surprising findings about LLMs for time series: 1. LLMs understand time series better as images rather than as text 2. LLMs did not demonstrate enhanced performance when prompted to engage in explicit reasoning about time series analysis 3. Contrary to common beliefs, LLM's understanding of time series do not stem from their repetition biases or arithmetic abilities 4. LLMs' behaviors and performance in time series analysis vary significantly across different model architectures This study provides the first comprehensive analysis of contemporary LLM capabilities in time series anomaly detection. Our results suggest that while LLMs can understand time series anomalies, many common conjectures based on their reasoning capabilities do not hold. Our code and data are available at `https://github.com/Rose-STL-Lab/AnomLLM/`.

Recent advances in large language models (LLMs) have opened new avenues for accelerating scientific research. While models are increasingly capable of assisting with routine tasks, their ability to contribute to novel, expert-level mathematical discovery is less understood. We present a collection of case studies demonstrating how researchers have successfully collaborated with advanced AI models, specifically Google's Gemini-based models (in particular Gemini Deep Think and its advanced variants), to solve open problems, refute conjectures, and generate new proofs across diverse areas in theoretical computer science, as well as other areas such as economics, optimization, and physics. Based on these experiences, we extract common techniques for effective human-AI collaboration in theoretical research, such as iterative refinement, problem decomposition, and cross-disciplinary knowledge transfer. While the majority of our results stem from this interactive, conversational methodology, we also highlight specific instances that push beyond standard chat interfaces. These include deploying the model as a rigorous adversarial reviewer to detect subtle flaws in existing proofs, and embedding it within a "neuro-symbolic" loop that autonomously writes and executes code to verify complex derivations. Together, these examples highlight the potential of AI not just as a tool for automation, but as a versatile, genuine partner in the creative process of scientific discovery.

Autonomous research agents must acquire and reason over evidence within a limited budget. Yet relevant sources can remain uninspected or unused, leaving a gap between retrieval coverage and the evidence that informs research. The challenge is to align fast local judgments with changing evidence needs and feed their findings back into research decisions. We introduce JevGPT, a dual-system architecture for autonomous research that couples fast evidence processing with deliberative research planning. System Two sets evidence objectives and integrates findings, while System One locates support, assesses relevance, and guides further inspection. Independent source judgments run in parallel; selected original passages inform the next research step. Experiments on fixed-corpus question answering and document ranking show that JevGPT achieves leading task performance, with faster completion and lower cost than comparably effective research agents. Evidence analysis shows broader source inspection and greater coverage of supporting documents in the research loop, highlighting efficient evidence processing as a route to more capable autonomous research.

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 breakthroughs often emerge from synthesizing prior ideas into novel contributions. While language models (LMs) show promise in scientific discovery, their ability to perform this targeted, literature-grounded synthesis remains underexplored. We introduce insight anticipation, a generation task in which a model predicts a downstream paper's core insight from its foundational parent papers. To evaluate this capability, we develop GiantsBench, a benchmark of 17k examples across eight scientific domains, where each example consists of a set of parent papers paired with the core insight of a downstream paper. We evaluate models using an LM judge that scores similarity between generated and ground-truth insights, and show that these similarity scores correlate with expert human ratings. Finally, we present GIANTS-4B, an LM trained via reinforcement learning (RL) to optimize insight anticipation using these similarity scores as a proxy reward. Despite its smaller open-source architecture, GIANTS-4B outperforms proprietary baselines and generalizes to unseen domains, achieving a 34% relative improvement in similarity score over gemini-3-pro. Human evaluations further show that GIANTS-4B produces insights that are more conceptually clear than those of the base model. In addition, SciJudge-30B, a third-party model trained to compare research abstracts by likely citation impact, predicts that insights generated by GIANTS-4B are more likely to lead to higher citations, preferring them over the base model in 68% of pairwise comparisons. We release our code, benchmark, and model to support future research in automated scientific discovery.

Scaling up language models to billions of parameters has opened up possibilities for in-context learning, allowing instruction tuning and few-shot learning on tasks that the model was not specifically trained for. This has achieved breakthrough performance on language tasks such as translation, summarization, and question-answering. Furthermore, in addition to these associative "System 1" tasks, recent advances in Chain-of-thought prompt learning have demonstrated strong "System 2" reasoning abilities, answering a question in the field of artificial general intelligence whether LLMs can reason. The field started with the question whether LLMs can solve grade school math word problems. This paper reviews the rapidly expanding field of prompt-based reasoning with LLMs. Our taxonomy identifies different ways to generate, evaluate, and control multi-step reasoning. We provide an in-depth coverage of core approaches and open problems, and we propose a research agenda for the near future. Finally, we highlight the relation between reasoning and prompt-based learning, and we discuss the relation between reasoning, sequential decision processes, and reinforcement learning. We find that self-improvement, self-reflection, and some metacognitive abilities of the reasoning processes are possible through the judicious use of prompts. True self-improvement and self-reasoning, to go from reasoning with LLMs to reasoning by LLMs, remains future work.

Deployed large reasoning models (LRMs) often behave unexpectedly. Test-time steering controls LRM outputs by intervening on their hidden representations, but it can degrade output quality. We argue that prior steering work implicitly relies on internal features that detect behavior in already generated text. We show that these detection features are poor predictors of future behavioral outcomes, and thus not the natural intervention target. Instead, we train activation probes to predict future behavior likelihoods from intermediate reasoning steps. These probes predict the most likely behavior with 64%-91% accuracy, revealing a separate type of internal prediction features. Building on these prediction features, we introduce a text-level steering method, Future Probe Controlled Generation. FPCG samples multiple candidate sentences and chooses the best one according to a probe predicting the future behavior likelihood. This enables steering with almost no output quality degradation. FPCG also enables steering in several evaluations where activation steering fails. These results show that distinguishing detection and prediction features enables a more nuanced approach to controlling LRM behaviors.

We argue that progress toward AGI is theory limited rather than data or scale limited. Building on the critical rationalism of Popper and Deutsch, we challenge the Platonic Representation Hypothesis. Observationally equivalent worlds can diverge under interventions, so observational adequacy alone cannot guarantee interventional competence. We begin by laying foundations, definitions of knowledge, learning, intelligence, counterfactual competence and AGI, and then analyze the limits of observational learning that motivate an error centric shift. We recast the problem as three questions about how explicit and implicit errors evolve under an agent's actions, which errors are unreachable within a fixed hypothesis space, and how conjecture and criticism expand that space. From these questions we propose Causal Mechanics, a mechanisms first program in which hypothesis space change is a first class operation and probabilistic structure is used when useful rather than presumed. We advance structural principles that make error discovery and correction tractable, including a differential Locality and Autonomy Principle for modular interventions, a gauge invariant form of Independent Causal Mechanisms for separability, and the Compositional Autonomy Principle for analogy preservation, together with actionable diagnostics. The aim is a scaffold for systems that can convert unreachable errors into reachable ones and correct them.

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.

Recent work has shown promising results in causal discovery by leveraging interventional data with gradient-based methods, even when the intervened variables are unknown. However, previous work assumes that the correspondence between samples and interventions is known, which is often unrealistic. We envision a scenario with an extensive dataset sampled from multiple intervention distributions and one observation distribution, but where we do not know which distribution originated each sample and how the intervention affected the system, i.e., interventions are entirely latent. We propose a method based on neural networks and variational inference that addresses this scenario by framing it as learning a shared causal graph among an infinite mixture (under a Dirichlet process prior) of intervention structural causal models. Experiments with synthetic and real data show that our approach and its semi-supervised variant are able to discover causal relations in this challenging scenario.

Scientific discovery often involves optimising expensive-to-evaluate objectives over vast, structured, and open-ended hypothesis spaces, such as molecules, protein sequences, and computer programs. Generative models such as large language models (LLMs) provide expressive priors over such spaces, but their likelihoods and self-assessments are unreliable proxies for the objectives and calibrated epistemic uncertainty, especially for novel candidates outside the observed data distribution. We introduce the Large Discovery Model (LDM), an empirically grounded recurrent architecture that couples a generative model with a Bayesian non-parametric reward surrogate model. The generative model proposes and refines candidate designs, while the surrogate predicts their performance and quantifies uncertainty, yielding an uncertainty-aware value that guides candidate generation, refinement, and selection. The discovery memory and the surrogate model are continually updated as each new experimental observation arrives. We evaluate LDM on three scenarios spanning different design modalities and objectives, including neural-network training, antibody design, and molecular optimisation. Compared to LLM-only reflection or traditional statistical search across these domains, LDM achieves a 2.4times greater reduction in validation BPB, an 18.2% relative decrease in binding energy, and more than 60% relative gains in molecular multi-objective performance. These results suggests that LDM could serve as a general-purpose discovery engine for effective search over open-ended hypothesis spaces.

AI research agents can now generate research ideas, design experiments, run code, and draft papers, raising the possibility of large-scale AI-assisted scientific discovery. Many current agent frameworks explicitly encourage the generation of novel and high-impact ideas. Yet it remains unclear whether AI-assisted ideation broadens scientific exploration or mainly concentrates around existing work. We study AI research agents as scientific search systems. Using four AI research-agent frameworks and six large language models, we generate 37,802 scientific ideas from shared seed literature across citation-defined research areas in AI and machine learning. We then compare the resulting AI ideas against human-authored papers from the same research areas, follow-on human research emerging from the same seed literature, and the seed literature itself. Across experiments, four consistent patterns emerge. First, AI-generated ideas are substantially more concentrated than human-authored papers from the same research areas. Second, AI-generated ideas remain much closer to their starting literature than later human follow-on work does. Third, papers most similar to AI-generated ideas tend to receive lower subsequent citations. Fourth, when AI-generated ideas differ from prior work, the differences arise primarily from recombining existing technical methods rather than introducing fundamentally new research questions. Overall, current AI research agents appear better suited to local elaboration than to broadening scientific exploration.

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.

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/.

This paper introduces the Manifold Probe, a supervised method for discovering representation manifolds in superposition. The method generalizes linear regression probes by learning the space of features of a concept that can be linearly predicted from the representations, and then learning the directions used to encode them. We demonstrate the probe on representations of time and space in Llama 2-7b, finding manifolds which linearly represent an interpretable set of features in each case. In the case of time, we show that by steering along the manifold, we can influence the model's completions about the years in which famous songs, movies and books were released, providing evidence that the Manifold Probe can discover manifolds which are causally involved in model behaviour.

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

Finding evidence for human opinion and behavior at scale is a challenging task, often requiring an understanding of sophisticated thought patterns among vast online communities found on social media. For example, studying how gun ownership is related to the perception of Freedom, requires a retrieval system that can operate at scale over social media posts, while dealing with two key challenges: (1) identifying abstract concept instances, (2) which can be instantiated differently across different communities. To address these, we introduce ConceptCarve, an evidence retrieval framework that utilizes traditional retrievers and LLMs to dynamically characterize the search space during retrieval. Our experiments show that ConceptCarve surpasses traditional retrieval systems in finding evidence within a social media community. It also produces an interpretable representation of the evidence for that community, which we use to qualitatively analyze complex thought patterns that manifest differently across the communities.

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.

A growing body of work makes use of probing to investigate the working of neural models, often considered black boxes. Recently, an ongoing debate emerged surrounding the limitations of the probing paradigm. In this work, we point out the inability to infer behavioral conclusions from probing results and offer an alternative method that focuses on how the information is being used, rather than on what information is encoded. Our method, Amnesic Probing, follows the intuition that the utility of a property for a given task can be assessed by measuring the influence of a causal intervention that removes it from the representation. Equipped with this new analysis tool, we can ask questions that were not possible before, e.g. is part-of-speech information important for word prediction? We perform a series of analyses on BERT to answer these types of questions. Our findings demonstrate that conventional probing performance is not correlated to task importance, and we call for increased scrutiny of claims that draw behavioral or causal conclusions from probing results.

Being able to provide explanations for a model's decision has become a central requirement for the development, deployment, and adoption of machine learning models. However, we are yet to understand what explanation methods can and cannot do. How do upstream factors such as data, model prediction, hyperparameters, and random initialization influence downstream explanations? While previous work raised concerns that explanations (E) may have little relationship with the prediction (Y), there is a lack of conclusive study to quantify this relationship. Our work borrows tools from causal inference to systematically assay this relationship. More specifically, we study the relationship between E and Y by measuring the treatment effect when intervening on their causal ancestors, i.e., on hyperparameters and inputs used to generate saliency-based Es or Ys. Our results suggest that the relationships between E and Y is far from ideal. In fact, the gap between 'ideal' case only increase in higher-performing models -- models that are likely to be deployed. Our work is a promising first step towards providing a quantitative measure of the relationship between E and Y, which could also inform the future development of methods for E with a quantitative metric.

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.