Daily Papers

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

Recovering governing Ordinary Differential Equations (ODEs) from data is a central challenge in modeling dynamical systems across scientific domains. Existing approaches cast discovery as a static inference problem over fixed datasets, assuming that the observed trajectories are sufficiently informative. However, dynamical systems evolve over large state spaces, and limited data can make multiple equations observationally indistinguishable, leading to identifiability gaps and the recovery of incorrect governing equations. To address this, we introduce LLM-ACES, or LLM-guided Active Closed-loop Equation Search, a closed-loop framework that jointly optimizes symbolic hypothesis construction and adaptive data acquisition. In LLM-ACES, a large language model (LLM) proposes operator priors that partition the large search space into distinct regions, within which candidate equations are fit to the observed data. The disagreement among these candidates guides the acquisition of informative trajectories, creating a feedback loop that iteratively refines both the hypothesis space and the discovered dynamics. On 122 ODE systems spanning ODEBench and ODEBase, LLM-ACES achieves the lowest median NMSE, outperforming state-of-the-art baselines by several orders of magnitude while achieving a high symbolic accuracy of 46.2% and 52.4%, respectively. Our analysis further shows that LLM-ACES is sample-efficient, achieving better performance with one-tenth the data. Furthermore, LLM-ACES's feedback-driven data acquisition makes it robust to noise and recovers the correct symbolic structure, while baselines introduce spurious terms that fit the data locally but obscure the true governing relationships.

We propose agentic automata learning to evaluate the extent to which tool-calling LLM agents can uncover hidden environments through interaction. In our setup, an agent should uncover a hidden deterministic finite automaton (DFA) by interacting with an oracle through (1) membership queries ("Does this string belong to the target language?") and (2) equivalence queries ("Is this the target DFA?"). This yields a scalable testbed with controlled task complexity, measurable interaction efficiency, and strong baselines (classic automata-learning algorithms). Evaluating state-of-the-art LLMs, we find that performance drops sharply as DFA size increases. Reasoning models are markedly stronger than non-reasoning models, yet trajectory analyses reveal recurring failures in query planning, evidence integration, and hypothesis construction. Overall, our results show that current LLM agents can sometimes perform non-trivial interactive discovery, but remain far less robust and efficient than classic algorithms for the task.

Large language model-driven multi-agent systems (LLM-MAS) excel at complex tasks, yet unreliable agents remain a key bottleneck to system-level reliability. Automatic failure attribution is therefore critical, but existing approaches, such as direct prediction of agent-error pairs and agent-first failure attribution, rely on local logs of agents and miss global failures that only manifest over full interaction trajectories, such as cross-step inconsistencies and inter-agent coordination errors. Moreover, directly predicting failures induces a large combinatorial search space, hindering fine-grained attribution. To address these challenges, we propose VerifyMAS, a hypothesis verification framework for agent failure attribution. Instead of directly predicting faulty agents and error types, VerifyMAS formulates and verifies failure hypotheses against full trajectories. This verification-based approach decomposes attribution into trajectory-level error validation and fine-grained agent localization, providing an error-first attribution approach that captures global failure patterns while substantially reducing the search space. We further introduce a hypothesis-based data construction strategy grounded in a structured error taxonomy and fine-tune a specialized LLM verifier model for trajectory-level failure verification and agent attribution. Experiments on Aegis-Bench and Who&When show that VerifyMAS consistently improves diverse backbone models, including open-source Qwen and API-based GPT models, outperforming prior methods without sacrificing inference efficiency for long multi-agent trajectories.

While current deep learning systems excel at tasks such as object classification, language processing, and gameplay, few can construct or modify a complex system such as a tower of blocks. We hypothesize that what these systems lack is a "relational inductive bias": a capacity for reasoning about inter-object relations and making choices over a structured description of a scene. To test this hypothesis, we focus on a task that involves gluing pairs of blocks together to stabilize a tower, and quantify how well humans perform. We then introduce a deep reinforcement learning agent which uses object- and relation-centric scene and policy representations and apply it to the task. Our results show that these structured representations allow the agent to outperform both humans and more naive approaches, suggesting that relational inductive bias is an important component in solving structured reasoning problems and for building more intelligent, flexible machines.

Construction grammar posits that children acquire constructions (form-meaning pairings) from the statistics of their environment. Recent work supports this hypothesis by showing sensitivity to constructions in pretrained language models (PLMs), including one recent study (Rozner et al., 2025) demonstrating that constructions shape the PLM's output distribution. However, models under study have generally been trained on developmentally implausible amounts of data, casting doubt on their relevance to human language learning. Here we use Rozner et al.'s methods to evaluate constructional learning in models from the 2024 BabyLM challenge. Our results show that even when trained on developmentally plausible quantities of data, models represent diverse constructions, even hard cases that are superficially indistinguishable. We further find correlational evidence that constructional performance may be functionally relevant: models that better represent constructions perform better on the BabyLM benchmarks.

Informally, the 'linear representation hypothesis' is the idea that high-level concepts are represented linearly as directions in some representation space. In this paper, we address two closely related questions: What does "linear representation" actually mean? And, how do we make sense of geometric notions (e.g., cosine similarity or projection) in the representation space? To answer these, we use the language of counterfactuals to give two formalizations of "linear representation", one in the output (word) representation space, and one in the input (sentence) space. We then prove these connect to linear probing and model steering, respectively. To make sense of geometric notions, we use the formalization to identify a particular (non-Euclidean) inner product that respects language structure in a sense we make precise. Using this causal inner product, we show how to unify all notions of linear representation. In particular, this allows the construction of probes and steering vectors using counterfactual pairs. Experiments with LLaMA-2 demonstrate the existence of linear representations of concepts, the connection to interpretation and control, and the fundamental role of the choice of inner product.

Accelerating materials discovery requires AI systems that can generate scientifically valid hypotheses through multi-step, domain-grounded reasoning. Standard large language models often produce fluent but weakly traceable responses to open-ended materials design problems, making it difficult to determine whether final answers are supported by coherent intermediate reasoning. We develop Graph-PRefLexOR, a family of graph-native reasoning models fine-tuned with Group Relative Policy Optimization (GRPO) to organize reasoning into explicit phases for mechanism exploration, graph construction, pattern extraction, and hypothesis synthesis. This design links neural language generation with symbolic relational structure, enabling causal connections to be constructed, inspected, and reused. On 100 open-ended questions from materials science and mechanics literature, Graph-PRefLexOR achieves 40-65% improvements over corresponding base models, with the largest gains in reasoning traceability. Embedding analyses show broader semantic exploration and approximately 2-3 times greater semantic diversity than baselines. Semantic backtracking and layer-wise hidden-state analyses further show stronger alignment between structured reasoning and final answers. Finally, test-time graph expansion reveals that additional compute primarily increases long-range conceptual recombination within a bounded semantic space, rather than simply expanding semantic coverage. These results establish graph-native reinforcement learning as a pathway toward interpretable AI systems for scientific hypothesis generation in materials design and other scientific applications.

Immune therapies act across cell-intrinsic programs, tissue ecosystems, and patient-specific immune states, yet most predictors address these scales separately. We used a governed evolutionary AI Scientist to construct the Immune World Model, an action-conditioned model that learns how interventions move immune states across cellular, tissue, and individual levels. The Immune World Model--building Scientist searched candidate architectures and workflows, and the resulting world model was frozen before independent confirmation. The frozen model generalized to unseen interventions and biological contexts, recovered intervention-specific cellular programs, integrated cell and tissue information to improve ecosystem and patient-response prediction, and forecast unseen perturbation combinations. Immune World Model--guided analysis then combined measured perturbations with cross-axis inference to nominate IL-36γ plus SIRPα inhibition as a complementary-axis therapeutic hypothesis, whereas a governed self-correction audit rejected every screened cytokine pair. The Immune World Model provides a framework for multiscale immune simulation that connects AI Scientist-driven model construction, intervention forecasting, and the generation of prospectively testable therapeutic hypotheses.

Autonomous AI agents increasingly execute actions, invoke tools, and operate on protected resources with limited human oversight. Existing authentication and authorization mechanisms establish identity and delegate authority, but do not inherently provide cryptographic evidence that a concrete request issued by a specific agent satisfies the applicable policy in a specific execution context. This paper hypothesizes that agent authorization can be formalized as a cryptographically verifiable relation, denoted R_{CVA}, that jointly binds an agent principal, a concrete authorization request, an execution context, and the satisfaction of an applicable policy, while selectively preserving the confidentiality of private authorization attributes. We introduce a preliminary formal abstraction for Cryptographically Verifiable Agent Authorization (CVA), define a compact set of candidate security properties including authorization soundness, principal binding, request binding, policy binding, and replay resistance, and provide an executable zero-knowledge proof of concept that instantiates selected elements of the model over a Groth16 zk-SNARK construction. We further identify and formalize the structural separation among identity binding, authorization-request binding, and runtime execution binding as a central open problem in the design of secure agentic systems (a distinction {not explicitly addressed by} current agentic security frameworks) and present a falsifiable research agenda for its resolution.

The rise of Large Language Models (LLMs) has triggered legal and ethical concerns, especially regarding the unauthorized use of copyrighted materials in their training datasets. This has led to lawsuits against tech companies accused of using protected content without permission. Membership Inference Attacks (MIAs) aim to detect whether specific documents were used in a given LLM pretraining, but their effectiveness is undermined by biases such as time-shifts and n-gram overlaps. This paper addresses the evaluation of MIAs on LLMs with partially inferable training sets, under the ex-post hypothesis, which acknowledges inherent distributional biases between members and non-members datasets. We propose and validate algorithms to create ``non-biased'' and ``non-classifiable'' datasets for fairer MIA assessment. Experiments using the Gutenberg dataset on OpenLamma and Pythia show that neutralizing known biases alone is insufficient. Our methods produce non-biased ex-post datasets with AUC-ROC scores comparable to those previously obtained on genuinely random datasets, validating our approach. Globally, MIAs yield results close to random, with only one being effective on both random and our datasets, but its performance decreases when bias is removed.

Large language models (LLMs) have demonstrated impressive capabilities and are receiving increasing attention to enhance their reasoning through scaling test--time compute. However, their application in open--ended, knowledge--intensive, complex reasoning scenarios is still limited. Reasoning--oriented methods struggle to generalize to open--ended scenarios due to implicit assumptions of complete world knowledge. Meanwhile, knowledge--augmented reasoning (KAR) methods fail to address two core challenges: 1) error propagation, where errors in early steps cascade through the chain, and 2) verification bottleneck, where the explore--exploit tradeoff arises in multi--branch decision processes. To overcome these limitations, we introduce ARise, a novel framework that integrates risk assessment of intermediate reasoning states with dynamic retrieval--augmented generation (RAG) within a Monte Carlo tree search paradigm. This approach enables effective construction and optimization of reasoning plans across multiple maintained hypothesis branches. Experimental results show that ARise significantly outperforms the state--of--the--art KAR methods by up to 23.10%, and the latest RAG-equipped large reasoning models by up to 25.37%. Our project page is at https://opencausalab.github.io/ARise.

In this study, we investigate in-context learning (ICL) in document-level event argument extraction (EAE) to alleviate the dependency on large-scale labeled data for this task. We introduce the Heuristic-Driven Link-of-Analogy (HD-LoA) prompting to address the challenge of example selection and to develop a prompting strategy tailored for EAE. Specifically, we hypothesize and validate that LLMs learn task-specific heuristics from demonstrations via ICL. Building upon this hypothesis, we introduce an explicit heuristic-driven demonstration construction approach, which transforms the haphazard example selection process into a methodical method that emphasizes task heuristics. Additionally, inspired by the analogical reasoning of human, we propose the link-of-analogy prompting, which enables LLMs to process new situations by drawing analogies to known situations, enhancing their performance on unseen classes beyond limited ICL examples. Experiments show that our method outperforms existing prompting methods and few-shot supervised learning methods on document-level EAE datasets. Additionally, the HD-LoA prompting shows effectiveness in diverse tasks like sentiment analysis and natural language inference, demonstrating its broad adaptability.

Safety alignment incurs safety tax that perturbs a large reasoning model's (LRM) general reasoning ability. Existing datasets used for safety alignment for an LRM are usually constructed by distilling safety reasoning traces and answers from an external LRM or human labeler. However, such reasoning traces and answers exhibit a distributional gap with the target LRM that needs alignment, and we conjecture such distributional gap is the culprit leading to significant degradation of reasoning ability of the target LRM. Driven by this hypothesis, we propose a safety alignment dataset construction method, dubbed DGR. DGR transforms and refines an existing out-of-distributional safety reasoning dataset to be aligned with the target's LLM inner distribution. Experimental results demonstrate that i) DGR effectively mitigates the safety tax while maintaining safety performance across all baselines, i.e., achieving +30.2\% on DirectRefusal and +21.2\% on R1-ACT improvement in average reasoning accuracy compared to Vanilla SFT; ii) the degree of reasoning degradation correlates with the extent of distribution shift, suggesting that bridging this gap is central to preserving capabilities. Furthermore, we find that safety alignment in LRMs may primarily function as a mechanism to activate latent knowledge, as a mere 10 samples are sufficient for activating effective refusal behaviors. These findings not only emphasize the importance of distributional consistency but also provide insights into the activation mechanism of safety in reasoning models.

A rule-based logic solver resolves every instance in our benchmark in under 50 microseconds with 100% accuracy; the best frontier language model reaches 65% at best and drops to 23.5% under rendering-robust evaluation (worst case over four surface renderings). We introduce DeFAb (Defeasible Abduction Benchmark), a dataset and generation pipeline that converts four decades of publicly funded knowledge bases into formally grounded instances for defeasible abduction: constructing hypotheses that explain anomalies by overriding defaults while preserving unrelated expectations. Because every hypothesis must pass polynomial-time checks for valid derivation, conservativity, and minimality, DeFAb makes logical rigor the instrument for measuring creativity and theoretical reasoning, scoring the disciplined construction of theory revisions rather than fluent but theory-destroying prose. The pipeline pairs taxonomic hierarchies (OpenCyc, YAGO, Wikidata) with behavioral property graphs (ConceptNet, UMLS) to produce 372,648+ instances across 33.75M materialized rules from 18 sources, in three levels with polynomial-time verifiable gold standards. Four frontier models do not reliably internalize defeasible reasoning: rendering-robust Level 2 accuracy is 7.8-23.5%; chain-of-thought variance (~36 pp) exceeds any inter-model gap; and a matched contamination control isolates a +19.4 pp Level 3 gap. We further release DeFAb-Hard (a 235-instance Level 3 difficulty variant; best model 53.3% vs 100% symbolic) and CONJURE (a kernel-verified transformative-creativity variant of 560 Lean 4/Mathlib instances whose gold answers are definitions the proof kernel did not previously contain, judge-free verifier; a pilot finds zero novel concepts). The same verifier doubles as an exact reward for preference optimization (DPO, RLVR/GRPO). Released under MIT at https://huggingface.co/datasets/PatrickAllenCooper/DeFAb.

Scaling reinforcement learning for visual mathematical reasoning requires more than generating harder questions: as data volume grows, the reward labels themselves must remain reliable. Yet existing data pipelines scale supervision while trusting the labeller, and policy-side methods assume the underlying answers are already correct. We instead treat scaling as a verifiable data-construction problem and decouple two axes before any policy update: prompt difficulty, expanded by route-specific evolution operators, and answer reliability, enforced by offline hypothesis-test falsification. We instantiate this as VeriEvol, an iterative framework with two extensible components: a type-aware evolution module that rewrites low-difficulty image-question seeds into harder, image-grounded prompts; and HTV-Agent, a verifier that accepts an answer only after multi-source counter-evidence has failed to refute it. The resulting verified data scales in volume, extends by adding evolution routes or verifier channels, and plugs directly into existing GRPO-style RL recipes. On a five-benchmark visual-math suite, scaling evolved SFT data from 10K to 250K samples raises the mean accuracy from 35.42 to 54.73; then, with backbone, SFT initialization, and GRPO recipe held fixed, VeriEvol adds a cumulative +3.88 over an un-evolved RL baseline, of which +1.82 comes from evolved prompts and +2.06 from the HTV-Agent verifier. We release the prompts, data, models, code, and the full verifier trace of every sample, so that downstream work can scale and audit the pipeline rather than only inspect its outputs.

Despite their extensive pretraining knowledge and strong reasoning capabilities, large language models (LLMs) struggle to adaptively gather information in experimental design tasks. We study how to amortize sequential Bayesian experimental design (BED) into an LLM by explicitly training the reasoning that guides action selection using information-gain rewards. Our approach specifies the experimental generative model independently of the LLM's own beliefs, allowing us to optimize expected information gain under a model of our choosing. We investigate the design choices for amortization, including alternative generative-model constructions, reward estimation, hypothesis-space specification, multi-step objectives, and computational costs relative to training- and inference-time BED baselines. On Twenty Questions, the resulting policies improve information acquisition and task performance, outperform inference- and training-time BED baselines at substantially lower computational cost, and generalize to unseen categories. We further demonstrate positive transfer from Twenty Questions training to Medi-Q, a real-world clinical dialogue benchmark. These results suggest that information gathering can be learned as a generalizable reasoning skill in LLMs.

Unified multimodal models (UMMs) aim to integrate understanding and generation within a single architecture. However, it remains underexplored how to effectively coordinate these two capabilities for more effective and efficient reasoning. Existing coordination approaches either perform coupling during training, without explicit inference-time coordination, or impose a fixed coordination pattern for all inputs. In this work, we show that multimodal tasks exhibit substantial coordination-path diversity: different inputs favor different coordination paths. This suggests that exploiting such diversity is key to improving performance. We propose UniPath, a framework for adaptively modeling and exploiting coordination-path diversity. Instead of enforcing a single coordination pattern, we represent task solving as the selection and execution of a path, ranging from direct answering to textual inference, visual-thought construction, and hypothesis-based exploration. We construct role-aligned trajectories to train a path-conditioned executor and introduce a lightweight planner mechanism to enable input-dependent path selection. Experiments show that leveraging coordination-path diversity improves performance over fixed coordination strategies while providing interpretable intermediate behaviors. The code is available at:https://github.com/AIFrontierLab/TorchUMM/tree/main/src/umm/post_training/unipath.

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

Negation is poorly captured by current language models, although the extent of this problem is not widely understood. We introduce a natural language inference (NLI) test suite to enable probing the capabilities of NLP methods, with the aim of understanding sub-clausal negation. The test suite contains premise--hypothesis pairs where the premise contains sub-clausal negation and the hypothesis is constructed by making minimal modifications to the premise in order to reflect different possible interpretations. Aside from adopting standard NLI labels, our test suite is systematically constructed under a rigorous linguistic framework. It includes annotation of negation types and constructions grounded in linguistic theory, as well as the operations used to construct hypotheses. This facilitates fine-grained analysis of model performance. We conduct experiments using pre-trained language models to demonstrate that our test suite is more challenging than existing benchmarks focused on negation, and show how our annotation supports a deeper understanding of the current NLI capabilities in terms of negation and quantification.

Recent advances in Large Reasoning Models (LRMs) trained with Long Chain-of-Thought (Long CoT) reasoning have demonstrated remarkable cross-domain generalization capabilities. However, the underlying mechanisms supporting such transfer remain poorly understood. We hypothesize that cross-domain generalization arises from shared abstract reasoning prototypes -- fundamental reasoning patterns that capture the essence of problems across domains. These prototypes minimize the nuances of the representation, revealing that seemingly diverse tasks are grounded in shared reasoning structures.Based on this hypothesis, we propose ProtoReasoning, a framework that enhances the reasoning ability of LLMs by leveraging scalable and verifiable prototypical representations (Prolog for logical reasoning, PDDL for planning).ProtoReasoning features: (1) an automated prototype construction pipeline that transforms problems into corresponding prototype representations; (2) a comprehensive verification system providing reliable feedback through Prolog/PDDL interpreters; (3) the scalability to synthesize problems arbitrarily within prototype space while ensuring correctness. Extensive experiments show that ProtoReasoning achieves 4.7% improvement over baseline models on logical reasoning (Enigmata-Eval), 6.3% improvement on planning tasks, 4.0% improvement on general reasoning (MMLU) and 1.0% on mathematics (AIME24). Significantly, our ablation studies confirm that learning in prototype space also demonstrates enhanced generalization to structurally similar problems compared to training solely on natural language representations, validating our hypothesis that reasoning prototypes serve as the foundation for generalizable reasoning in large language models.

Alpha mining, a critical component in quantitative investment, focuses on discovering predictive signals for future asset returns in increasingly complex financial markets. However, the pervasive issue of alpha decay, where factors lose their predictive power over time, poses a significant challenge for alpha mining. Traditional methods like genetic programming face rapid alpha decay from overfitting and complexity, while approaches driven by Large Language Models (LLMs), despite their promise, often rely too heavily on existing knowledge, creating homogeneous factors that worsen crowding and accelerate decay. To address this challenge, we propose AlphaAgent, an autonomous framework that effectively integrates LLM agents with ad hoc regularizations for mining decay-resistant alpha factors. AlphaAgent employs three key mechanisms: (i) originality enforcement through a similarity measure based on abstract syntax trees (ASTs) against existing alphas, (ii) hypothesis-factor alignment via LLM-evaluated semantic consistency between market hypotheses and generated factors, and (iii) complexity control via AST-based structural constraints, preventing over-engineered constructions that are prone to overfitting. These mechanisms collectively guide the alpha generation process to balance originality, financial rationale, and adaptability to evolving market conditions, mitigating the risk of alpha decay. Extensive evaluations show that AlphaAgent outperforms traditional and LLM-based methods in mitigating alpha decay across bull and bear markets, consistently delivering significant alpha in Chinese CSI 500 and US S&P 500 markets over the past four years. Notably, AlphaAgent showcases remarkable resistance to alpha decay, elevating the potential for yielding powerful factors.

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.

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.

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 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.

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

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

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.

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.

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.

The ability to derive underlying principles from a handful of observations and then generalize to novel situations -- known as inductive reasoning -- is central to human intelligence. Prior work suggests that language models (LMs) often fall short on inductive reasoning, despite achieving impressive success on research benchmarks. In this work, we conduct a systematic study of the inductive reasoning capabilities of LMs through iterative hypothesis refinement, a technique that more closely mirrors the human inductive process than standard input-output prompting. Iterative hypothesis refinement employs a three-step process: proposing, selecting, and refining hypotheses in the form of textual rules. By examining the intermediate rules, we observe that LMs are phenomenal hypothesis proposers (i.e., generating candidate rules), and when coupled with a (task-specific) symbolic interpreter that is able to systematically filter the proposed set of rules, this hybrid approach achieves strong results across inductive reasoning benchmarks that require inducing causal relations, language-like instructions, and symbolic concepts. However, they also behave as puzzling inductive reasoners, showing notable performance gaps between rule induction (i.e., identifying plausible rules) and rule application (i.e., applying proposed rules to instances), suggesting that LMs are proposing hypotheses without being able to actually apply the rules. Through empirical and human analyses, we further reveal several discrepancies between the inductive reasoning processes of LMs and humans, shedding light on both the potentials and limitations of using LMs in inductive reasoning tasks.

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

A key component of creativity is associative reasoning: the ability to draw novel yet meaningful connections between concepts. We introduce CREATE, a benchmark designed to evaluate models' capacity for creative associative reasoning. CREATE requires models to generate sets of paths connecting concepts in a model's parametric knowledge. Paths should have high specificity (distinctiveness and closeness of the concept connection) and high diversity (dissimilarity from other paths), and models are scored more highly if they produce a larger set of strong, diverse paths. This task shares demands of real creativity tasks like hypothesis generation, including an extremely large search space, but enables collection of a sizable benchmark with objective answer grading. Evaluation of frontier models shows that the strongest models achieve higher creative utility than others, with the high multiplicity of answers and complexity of the search making benchmark saturation difficult to achieve. Furthermore, our results illustrate that thinking models are not always more effective on our task, even with high token budgets. Recent approaches for creative prompting give some but limited additional improvement. CREATE provides a sandbox for developing new methods to improve models' capacity for associative creativity.

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.

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

We present a generic framework for creating differentially private versions of any hypothesis test in a black-box way. We analyze the resulting tests analytically and experimentally. Most crucially, we show good practical performance for small data sets, showing that at epsilon = 1 we only need 5-6 times as much data as in the fully public setting. We compare our work to the one existing framework of this type, as well as to several individually-designed private hypothesis tests. Our framework is higher power than other generic solutions and at least competitive with (and often better than) individually-designed tests.

Information accounting provides a better foundation for hypothesis testing than does uncertainty quantification. A quantitative account of science is derived under this perspective that alleviates the need for epistemic bridge principles, solves the problem of ad hoc falsification criteria, and deals with verisimilitude by facilitating a general approach to process-level diagnostics. Our argument is that the well-known inconsistencies of both Bayesian and classical statistical hypothesis tests are due to the fact that probability theory is an insufficient logic of science. Information theory, as an extension of probability theory, is required to provide a complete logic on which to base quantitative theories of empirical learning. The organizing question in this case becomes not whether our theories or models are more or less true, or about how much uncertainty is associated with a particular model, but instead whether there is any information available from experimental data that might allow us to improve the model. This becomes a formal hypothesis test, provides a theory of model diagnostics, and suggests a new approach to building dynamical systems models.

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.

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.

The reward hypothesis posits that, "all of what we mean by goals and purposes can be well thought of as maximization of the expected value of the cumulative sum of a received scalar signal (reward)." We aim to fully settle this hypothesis. This will not conclude with a simple affirmation or refutation, but rather specify completely the implicit requirements on goals and purposes under which the hypothesis holds.

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.

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.

Reliable hypothesis testing is the foundation of many empirical scientific claims. Large language model (LLM) agents are increasingly used to automate this process, as they can inspect datasets, generate code, and produce analyses end-to-end. However, we show that they frequently make subtle inferential errors that lead to incorrect conclusions despite correctly executed analyses. Existing benchmarks fail to capture this failure mode, as they rarely assess whether a reported p-value is statistically valid given the assumptions underlying the data. We address this gap by building P-Bench, a benchmark comprising 425 open-ended, realistic hypothesis-testing tasks spanning economics, biology, and medicine. Each task requires an agent to select a statistical method, compute a p-value, and draw a conclusion given only a scientific hypothesis and a dataset. We further introduce Fisher-R1, an open-weight LLM agent trained for rigorous hypothesis testing using synthetic tasks and reinforcement learning. On P-Bench, Fisher-R1-14B substantially improves over its backbone and outperforms strong proprietary and open-source baselines, including GPT-5.4 and DeepSeekV4-Pro, achieving a 21% average relative improvement in single-trial success over DeepSeek-V4-Pro, with gains up to 26% on the most challenging tasks. Our results demonstrate that current LLM agents lack reliable statistical reasoning for hypothesis testing and that reinforcement learning on tasks with verified statistical reward substantially improves reliability.

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

Scientific reasoning remains challenging for open-source models, largely due to the lack of high-quality scientific reasoning data. Existing datasets are often dominated by factual recall or formulaic problem solving, with limited emphasis on mechanism understanding, evidence-grounded reasoning, and hypothesis evaluation. To address this, we introduce SPARK (Scientific Paper Abstracted Reasoning sKeleton), a paper-oriented synthesis framework built on Sci-Base, a large-scale corpus of research papers spanning 10 scientific disciplines. Instead of directly converting papers into question-answer pairs, SPARK treats the claim-evidence-derivation structure of a paper as the fundamental unit of reasoning synthesis. Specifically, SPARK (1) distills each paper into a compact reasoning skeleton capturing its central claims and supporting evidence, enabling self-contained question generation, and (2) synthesizes reasoning tasks from four scientific perspectives: mechanistic reasoning, hypothesis falsification, quantitative derivation, and boundary calibration. A final consistency verification stage further removes unsupported or contradictory outputs. Using this framework, we construct Spark-234K, a scientific reasoning dataset with substantially higher difficulty and diversity than existing resources. Experiments show that Spark-234K consistently outperforms existing scientific reasoning datasets while achieving stronger performance with significantly fewer training samples.

When prompted with a few examples and intermediate steps, large language models (LLMs) have demonstrated impressive performance in various reasoning tasks. However, prompting methods that rely on implicit knowledge in an LLM often generate incorrect answers when the implicit knowledge is wrong or inconsistent with the task. To tackle this problem, we present Hypotheses-to-Theories (HtT), a framework that learns a rule library for reasoning with LLMs. HtT contains two stages, an induction stage and a deduction stage. In the induction stage, an LLM is first asked to generate and verify rules over a set of training examples. Rules that appear and lead to correct answers sufficiently often are collected to form a rule library. In the deduction stage, the LLM is then prompted to employ the learned rule library to perform reasoning to answer test questions. Experiments on relational reasoning, numerical reasoning and concept learning problems show that HtT improves existing prompting methods, with an absolute gain of 10-30% in accuracy. The learned rules are also transferable to different models and to different forms of the same problem.

Large language models (LLMs) have enabled agent-based systems that aim to automate scientific research workflows. Most existing approaches focus on fully autonomous discovery, where AI systems generate research ideas, conduct analyses, and produce manuscripts with minimal human involvement. However, empirical research in economics and the social sciences poses additional constraints: research questions must be grounded in available datasets, identification strategies require careful design, and human judgment remains essential for evaluating economic significance. We introduce HLER (Human-in-the-Loop Economic Research), a multi-agent architecture that supports empirical research automation while preserving critical human oversight. The system orchestrates specialized agents for data auditing, data profiling, hypothesis generation, econometric analysis, manuscript drafting, and automated review. A key design principle is dataset-aware hypothesis generation, where candidate research questions are constrained by dataset structure, variable availability, and distributional diagnostics, reducing infeasible or hallucinated hypotheses. HLER further implements a two-loop architecture: a question quality loop that screens and selects feasible hypotheses, and a research revision loop where automated review triggers re-analysis and manuscript revision. Human decision gates are embedded at key stages, allowing researchers to guide the automated pipeline. Experiments on three empirical datasets show that dataset-aware hypothesis generation produces feasible research questions in 87% of cases (versus 41% under unconstrained generation), while complete empirical manuscripts can be produced at an average API cost of 0.8-1.5 per run. These results suggest that Human-AI collaborative pipelines may provide a practical path toward scalable empirical research.

Chain-of-Thought (CoT) prompting has become the de facto method to elicit reasoning capabilities from large language models (LLMs). However, to mitigate hallucinations in CoT that are notoriously difficult to detect, current methods such as process reward models (PRMs) or self-consistency operate as opaque boxes and do not provide checkable evidence for their judgments, possibly limiting their effectiveness. To address this issue, we draw inspiration from the idea that "the gold standard for supporting a mathematical claim is to provide a proof". We propose a retrospective, step-aware formal verification framework Safe. Rather than assigning arbitrary scores, we strive to articulate mathematical claims in formal mathematical language Lean 4 at each reasoning step and provide formal proofs to identify hallucinations. We evaluate our framework Safe across multiple language models and various mathematical datasets, demonstrating a significant performance improvement while offering interpretable and verifiable evidence. We also propose FormalStep as a benchmark for step correctness theorem proving with 30,809 formal statements. To the best of our knowledge, our work represents the first endeavor to utilize formal mathematical language Lean 4 for verifying natural language content generated by LLMs, aligning with the reason why formal mathematical languages were created in the first place: to provide a robust foundation for hallucination-prone human-written proofs.

Humans have a powerful and mysterious capacity to reason. By working through a series of purely mental steps, we can make inferences we would not be capable of making directly -- despite the fact that we get no additional data from the world. Similarly, when large language models generate a series of intermediate steps (a chain of thought) before answering a question, they often produce better answers than they otherwise would. We investigate why and how chain-of-thought reasoning is useful in language models, testing the hypothesis that reasoning is effective when training data consists of local clusters of variables that influence each other strongly. These training conditions enable the chaining of accurate local inferences in order to estimate relationships between variables that were not seen together in training. We prove that there will exist a "reasoning gap", where reasoning through intermediate variables improves inference, for the simple case of an autoregressive density estimator trained on local samples from a chain-structured probabilistic model. We then test our hypothesis empirically in more complex models, training an autoregressive language model on samples from Bayes nets but only including a subset of variables in each sample. We test language models' ability to match conditional probabilities with and without intermediate reasoning steps, finding that intermediate steps are only helpful when the training data is locally structured with respect to dependencies between variables and that the combination of locally-structured observations and reasoning is much more data-efficient than training on all variables. Our results illustrate how the effectiveness of reasoning step by step is rooted in the local statistical structure of the training data.

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.

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

Large language models (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.

Reasoning models have demonstrated remarkable progress in solving complex and logic-intensive tasks by generating extended Chain-of-Thoughts (CoTs) prior to arriving at a final answer. Yet, the emergence of this "slow-thinking" paradigm, with numerous tokens generated in sequence, inevitably introduces substantial computational overhead. To this end, it highlights an urgent need for effective acceleration. This survey aims to provide a comprehensive overview of recent advances in efficient reasoning. It categorizes existing works into three key directions: (1) shorter - compressing lengthy CoTs into concise yet effective reasoning chains; (2) smaller - developing compact language models with strong reasoning capabilities through techniques such as knowledge distillation, other model compression techniques, and reinforcement learning; and (3) faster - designing efficient decoding strategies to accelerate inference. A curated collection of papers discussed in this survey is available in our GitHub repository.

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.

Suppose Alice trains an open-weight language model and Bob uses a blackbox derivative of Alice's model to produce text. Can Alice prove that Bob is using her model, either by querying Bob's derivative model (query setting) or from the text alone (observational setting)? We formulate this question as an independence testing problem--in which the null hypothesis is that Bob's model or text is independent of Alice's randomized training run--and investigate it through the lens of palimpsestic memorization in language models: models are more likely to memorize data seen later in training, so we can test whether Bob is using Alice's model using test statistics that capture correlation between Bob's model or text and the ordering of training examples in Alice's training run. If Alice has randomly shuffled her training data, then any significant correlation amounts to exactly quantifiable statistical evidence against the null hypothesis, regardless of the composition of Alice's training data. In the query setting, we directly estimate (via prompting) the likelihood Bob's model gives to Alice's training examples and order; we correlate the likelihoods of over 40 fine-tunes of various Pythia and OLMo base models ranging from 1B to 12B parameters with the base model's training data order, achieving a p-value on the order of at most 1e-8 in all but six cases. In the observational setting, we try two approaches based on estimating 1) the likelihood of Bob's text overlapping with spans of Alice's training examples and 2) the likelihood of Bob's text with respect to different versions of Alice's model we obtain by repeating the last phase (e.g., 1%) of her training run on reshuffled data. The second approach can reliably distinguish Bob's text from as little as a few hundred tokens; the first does not involve any retraining but requires many more tokens (several hundred thousand) to achieve high power.

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.

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.

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.

Post-training has become a primary driver of recent progress in large reasoning models, and reasoning data are often the key variable determining whether this stage succeeds. Work on post-training reasoning data has grown rapidly, yet this literature remains scattered across dataset papers, reinforcement-learning recipes, reward-model studies, benchmarks, and frontier system reports. This paper is the first primer to synthesize over 150 key public studies and system reports on post-training reasoning data. We organize the field around four questions: what data objects exist, what makes them useful, how they are constructed, and how they scale. Together, this organization provides an attribution framework for future reasoning-data releases and post-training recipes.

We propose a hypothesis only baseline for diagnosing Natural Language Inference (NLI). Especially when an NLI dataset assumes inference is occurring based purely on the relationship between a context and a hypothesis, it follows that assessing entailment relations while ignoring the provided context is a degenerate solution. Yet, through experiments on ten distinct NLI datasets, we find that this approach, which we refer to as a hypothesis-only model, is able to significantly outperform a majority class baseline across a number of NLI datasets. Our analysis suggests that statistical irregularities may allow a model to perform NLI in some datasets beyond what should be achievable without access to the context.

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

Exploiting large language models (LLMs) to tackle deductive reasoning has garnered growing attention. It still remains highly challenging to achieve satisfactory results in complex deductive problems, characterized by plenty of premises (i.e., facts or rules) entailing intricate relationships among entities and requiring multi-hop reasoning. One intuitive solution is to decompose the original task into smaller sub-tasks, and then chain the multiple casual reasoning steps together in a forward (e.g., Selection-Inference) or backward (e.g., LAMBADA) direction. However, these techniques inevitably necessitate a large number of overall stages, leading to computationally expensive operations and a higher possibility of making misleading steps. In addition to stage-by-stage decomposition, we draw inspiration from another aspect of human problem-solving. Humans tend to distill the most relevant information and organize their thoughts systematically (e.g., creating mind maps), which assists them in answering questions or drawing conclusions precisely and quickly. In light of this, we propose a novel reasoning approach named Concise and Organized Perception (COP). COP carefully analyzes the given statements to efficiently identify the most pertinent information while eliminating redundancy. It then prompts the LLMs in a more organized form that adapts to the model's inference process. By perceiving concise and organized proofs, the deductive reasoning abilities of LLMs can be better elicited, and the risk of acquiring errors caused by excessive reasoning stages is mitigated. Furthermore, our approach can be combined with the aforementioned ones to further boost their performance. Extensive experimental results on three popular deductive benchmarks (i.e., ProofWriter, PrOntoQA and PrOntoQA-OOD) show that COP significantly outperforms previous state-of-the-art methods.

Logical reading comprehension is a challenging task that entails grasping the underlying semantics of text and applying reasoning to deduce the correct answer. Prior researches have primarily focused on enhancing logical reasoning capabilities through Chain-of-Thought (CoT) or data augmentation. However, previous work constructing chain-of-thought rationales concentrates solely on analyzing correct options, neglecting the incorrect alternatives. Addtionally, earlier efforts on data augmentation by altering contexts rely on rule-based methods, which result in generated contexts that lack diversity and coherence. To address these issues, we propose a Premise-Oriented Data Augmentation (PODA) framework. This framework can generate CoT rationales including analyses for both correct and incorrect options, while constructing diverse and high-quality counterfactual contexts from incorrect candidate options. We integrate summarizing premises and identifying premises for each option into rationales. Subsequently, we employ multi-step prompts with identified premises to construct counterfactual context. To facilitate the model's capabilities to better differentiate the reasoning process associated with each option, we introduce a novel thought-path contrastive learning method that compares reasoning paths between the original and counterfactual samples. Experimental results on three representative LLMs demonstrate that our method can improve the baselines substantially across two challenging logical reasoning benchmarks (ReClor and LogiQA 2.0). The data and code are released at https://github.com/lalalamdbf/TPReasoner.

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

Chain-of-thought reasoning, a cognitive process fundamental to human intelligence, has garnered significant attention in the realm of artificial intelligence and natural language processing. However, there still remains a lack of a comprehensive survey for this arena. To this end, we take the first step and present a thorough survey of this research field carefully and widely. We use X-of-Thought to refer to Chain-of-Thought in a broad sense. In detail, we systematically organize the current research according to the taxonomies of methods, including XoT construction, XoT structure variants, and enhanced XoT. Additionally, we describe XoT with frontier applications, covering planning, tool use, and distillation. Furthermore, we address challenges and discuss some future directions, including faithfulness, multi-modal, and theory. We hope this survey serves as a valuable resource for researchers seeking to innovate within the domain of chain-of-thought reasoning.

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.

Our goal, in the context of open-domain textual question-answering (QA), is to explain answers by showing the line of reasoning from what is known to the answer, rather than simply showing a fragment of textual evidence (a "rationale'"). If this could be done, new opportunities for understanding and debugging the system's reasoning become possible. Our approach is to generate explanations in the form of entailment trees, namely a tree of multipremise entailment steps from facts that are known, through intermediate conclusions, to the hypothesis of interest (namely the question + answer). To train a model with this skill, we created ENTAILMENTBANK, the first dataset to contain multistep entailment trees. Given a hypothesis (question + answer), we define three increasingly difficult explanation tasks: generate a valid entailment tree given (a) all relevant sentences (b) all relevant and some irrelevant sentences, or (c) a corpus. We show that a strong language model can partially solve these tasks, in particular when the relevant sentences are included in the input (e.g., 35% of trees for (a) are perfect), and with indications of generalization to other domains. This work is significant as it provides a new type of dataset (multistep entailments) and baselines, offering a new avenue for the community to generate richer, more systematic explanations.

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.

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.

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.

Logical reasoning is central to complex human activities, such as thinking, debating, and planning; it is also a central component of many AI systems as well. In this paper, we investigate the extent to which encoder-only transformer language models (LMs) can reason according to logical rules. We ask whether those LMs can deduce theorems in propositional calculus and first-order logic; if their relative success in these problems reflects general logical capabilities; and which layers contribute the most to the task. First, we show for several encoder-only LMs that they can be trained, to a reasonable degree, to determine logical validity on various datasets. Next, by cross-probing fine-tuned models on these datasets, we show that LMs have difficulty in transferring their putative logical reasoning ability, which suggests that they may have learned dataset-specific features, instead of a general capability. Finally, we conduct a layerwise probing experiment, which shows that the hypothesis classification task is mostly solved through higher layers.

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 show that there is a general, informative and reliable procedure for discovering causal relations when, for all the investigator knows, both latent variables and selection bias may be at work. Given information about conditional independence and dependence relations between measured variables, even when latent variables and selection bias may be present, there are sufficient conditions for reliably concluding that there is a causal path from one variable to another, and sufficient conditions for reliably concluding when no such causal path exists.

As automated reasoning systems advance rapidly, there is a growing need for research-level formal mathematical problems to accurately evaluate their capabilities. To address this, we present Formal Conjectures, an evolving benchmark of currently 2615 mathematical problem statements formalized in Lean 4. Sourced from areas of active mathematical research, the dataset features 1029 open research conjectures providing a zero-contamination benchmark for mathematical proof discovery, and 836 solved problems for proof autoformalization. Notably, the repository provides a structured interface connecting mathematicians who formalize and clarify problems with the AI systems and humans attempting to solve them. Demonstrating its immediate utility, the benchmark has already been leveraged to make new mathematical discoveries, including the resolution of open research conjectures. We describe our approach to ensuring the correctness of these formalizations in a collaborative open-source project where contributions stem from an active community. In this framework, AI-generated proofs and disproofs serve as a valuable auditing mechanism to iteratively improve the fidelity of the benchmark. Finally, we provide a standardized evaluation setup and report baseline results on frozen evaluation subsets, demonstrating a climbable signal that measures the current frontier of automated reasoning on research-level mathematics.

Unitary quantum theory, having no Born Rule, is non-probabilistic. Hence the notorious problem of reconciling it with the unpredictability and appearance of stochasticity in quantum measurements. Generalising and improving upon the so-called 'decision-theoretic approach' (Deutsch, 1999; Wallace, 2003, 2007, 2012), I shall recast that problem in the recently proposed constructor theory of information - where quantum theory is represented as one of a class of superinformation theories, which are local, non-probabilistic theories conforming to certain constructor-theoretic conditions. I prove that the unpredictability of measurement outcomes (to which I give an exact meaning via constructor theory), necessarily arises in superinformation theories. Then I explain how the appearance of stochasticity in (finitely many) repeated measurements can arise under superinformation theories. And I establish sufficient conditions for a superinformation theory to inform decisions (made under it) as if it were probabilistic, via a Deutsch-Wallace-type argument - thus defining a class of decision-supporting superinformation theories. This broadens the domain of applicability of that argument to cover constructor-theory compliant theories. In addition, in this version some of the argument's assumptions, previously construed as merely decision-theoretic, follow from physical properties expressed by constructor-theoretic principles.

Combinatorics is central to Olympiad-level mathematical problem solving, requiring deep discrete reasoning, creative constructions, and rigorous structural insight. Recent evidence suggests that even today's strongest frontier models remain uneven on Olympiad combinatorics, revealing a gap in creative mathematical reasoning. We introduce ComBench, an Olympiad-level combinatorics benchmark for evaluating and diagnosing the combinatorial reasoning capabilities of large language models. ComBench contains 100 human-annotated competition-level problems organized around two complementary settings: analysis-centric problems, which primarily require rigorous mathematical arguments, and construction-centric problems, which require explicit constructions in addition to correctness justifications. The evaluation protocol combines rubric-guided proof grading with deterministic construction verification, exposing cases where proof quality and construction validity diverge. Experiments on frontier open- and closed-source models show that ComBench is far from saturated: the strongest model reaches 65.4% overall Avg. and 75.3% overall Best@4. We further find that Rigorous Proof Reasoning and Constructive Realization are distinct capabilities: Kimi-K2.6 trails GPT-5.5 on analysis-centric proof grading but surpasses it on construction-centric Best@4, while Existence and Construction problems remain consistently hardest across representative frontier models.

Mathematical reasoning lies at the heart of artificial intelligence, underpinning applications in education, program verification, and research-level mathematical discovery. Mathematical competitions, in particular, present two challenging problem types: theorem proving, which requires rigorous proofs of stated conclusions, and answer construction, which involves hypothesizing and formally verifying mathematical objects. Large Language Models (LLMs) effectively generate creative candidate answers but struggle with formal verification, while symbolic provers ensure rigor but cannot efficiently handle creative conjecture generation. We introduce the Enumerate-Conjecture-Prove (ECP) framework, a modular neuro-symbolic method integrating LLM-based enumeration and pattern-driven conjecturing with formal theorem proving. We present ConstructiveBench, a dataset of 3,431 answer-construction problems in various math competitions with verified Lean formalizations. On the ConstructiveBench dataset, ECP improves the accuracy of answer construction from a Chain-of-Thought (CoT) baseline of 14.54% to 45.06% with the gpt-4.1-mini model. Moreover, combined with ECP's constructed answers, the state-of-the-art DeepSeek-Prover-V2-7B model generates correct proofs for 858 of the 3,431 constructive problems in Lean, achieving 25.01% accuracy compared to 9.86% for symbolic-only baselines. Our code and dataset are publicly available at https://github.com/JackSun200312/ECP.

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.

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.

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.

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

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.

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.

While Large Reasoning Models (LRMs) generate extensive chain-of-thought reasoning, we lack a principled framework for understanding how these thoughts are structured. In this paper, we introduce a novel approach by applying Schoenfeld's Episode Theory, a classic cognitive framework for human mathematical problem-solving, to analyze the reasoning traces of LRMs. We annotated thousands of sentences and paragraphs from model-generated solutions to math problems using seven cognitive labels (e.g., Plan, Implement, Verify). The result is the first publicly available benchmark for the fine-grained analysis of machine reasoning, including a large annotated corpus and detailed annotation guidebooks. Our preliminary analysis reveals distinct patterns in LRM reasoning, such as the transition dynamics between cognitive states. This framework provides a theoretically grounded methodology for interpreting LRM cognition and enables future work on more controllable and transparent reasoning systems.

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.

In this paper, we present a novel framework for the analysis of Riemann Hypothesis [27], which is composed of three key components: a) probabilistic modeling with cross entropy optimization and reasoning; b) the application of the law of large numbers; c) the application of mathematical inductions. The analysis is mainly conducted by virtue of probabilistic modeling of cross entropy optimization and reasoning with rare event simulation techniques. The application of the law of large numbers [2, 3, 6] and the application of mathematical inductions make the analysis of Riemann Hypothesis self-contained and complete to make sure that the whole complex plane is covered as conjectured in Riemann Hypothesis. We also discuss the method of enhanced top-p sampling with large language models (LLMs) for reasoning, where next token prediction is not just based on the estimated probabilities of each possible token in the current round but also based on accumulated path probabilities among multiple top-k chain of thoughts (CoTs) paths. The probabilistic modeling of cross entropy optimization and reasoning may suit well with the analysis of Riemann Hypothesis as Riemann Zeta functions are inherently dealing with the sums of infinite components of a complex number series. We hope that our analysis in this paper could shed some light on some of the insights of Riemann Hypothesis. The framework and techniques presented in this paper, coupled with recent developments with chain of thought (CoT) or diagram of thought (DoT) reasoning in large language models (LLMs) with reinforcement learning (RL) [1, 7, 18, 21, 24, 34, 39-41], could pave the way for eventual proof of Riemann Hypothesis [27].

Large Language Models (LLMs) have emerged as powerful sources of evidence for linguists seeking to develop theories of syntax. In this paper, we argue that causal interpretability methods, applied to LLMs, can greatly enhance the value of such evidence by helping us characterize the abstract mechanisms that LLMs learn to use. Our empirical focus is a set of English filler-gap dependency constructions (e.g., questions, relative clauses). Linguistic theories largely agree that these constructions share many properties. Using experiments based in Distributed Interchange Interventions, we show that LLMs converge on similar abstract analyses of these constructions. These analyses also reveal previously overlooked factors -- relating to frequency, filler type, and surrounding context -- that could motivate changes to standard linguistic theory. Overall, these results suggest that mechanistic, internal analyses of LLMs can push linguistic theory forward.

Clinical diagnosis is critical in medical practice, typically requiring a continuous and evolving process that includes primary diagnosis, differential diagnosis, and final diagnosis. However, most existing clinical diagnostic tasks are single-step processes, which does not align with the complex multi-step diagnostic procedures found in real-world clinical settings. In this paper, we propose a multi-step diagnostic task and annotate a clinical diagnostic dataset (MSDiagnosis). This dataset includes primary diagnosis, differential diagnosis, and final diagnosis questions. Additionally, we propose a novel and effective framework. This framework combines forward inference, backward inference, reflection, and refinement, enabling the LLM to self-evaluate and adjust its diagnostic results. To assess the effectiveness of our proposed method, we design and conduct extensive experiments. The experimental results demonstrate the effectiveness of the proposed method. We also provide a comprehensive experimental analysis and suggest future research directions for this task.

The development of state-of-the-art (SOTA) Natural Language Processing (NLP) systems has steadily been establishing new techniques to absorb the statistics of linguistic data. These techniques often trace well-known constructs from traditional theories, and we study these connections to close gaps around key NLP methods as a means to orient future work. For this, we introduce an analytic model of the statistics learned by seminal algorithms (including GloVe and Word2Vec), and derive insights for systems that use these algorithms and the statistics of co-occurrence, in general. In this work, we derive -- to the best of our knowledge -- the first known solution to Word2Vec's softmax-optimized, skip-gram algorithm. This result presents exciting potential for future development as a direct solution to a deep learning (DL) language model's (LM's) matrix factorization. However, we use the solution to demonstrate a seemingly-universal existence of a property that word vectors exhibit and which allows for the prophylactic discernment of biases in data -- prior to their absorption by DL models. To qualify our work, we conduct an analysis of independence, i.e., on the density of statistical dependencies in co-occurrence models, which in turn renders insights on the distributional hypothesis' partial fulfillment by co-occurrence statistics.

While reasoning in LLMs plays a natural role in math, code generation, and multi-hop factual questions, its effect on simple, single-hop factual questions remains unclear. Such questions do not require step-by-step logical decomposition, making the utility of reasoning highly counterintuitive. Nevertheless, we find that enabling reasoning substantially expands the capability boundary of the model's parametric knowledge recall, unlocking correct answers that are otherwise effectively unreachable. Why does reasoning aid parametric knowledge recall when there are no complex reasoning steps to be done? To answer this, we design a series of hypothesis-driven controlled experiments, and identify two key driving mechanisms: (1) a computational buffer effect, where the model uses the generated reasoning tokens to perform latent computation independent of their semantic content; and (2) factual priming, where generating topically related facts acts as a semantic bridge that facilitates correct answer retrieval. Importantly, this latter generative self-retrieval mechanism carries inherent risks: we demonstrate that hallucinating intermediate facts during reasoning increases the likelihood of hallucinations in the final answer. Finally, we show that our insights can be harnessed to directly improve model accuracy by prioritizing reasoning trajectories that contain hallucination-free factual statements.

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.

Test-time compute allocation in large reasoning models (LRMs) is widely used and has applications in mathematical problem solving, code synthesis, and planning. Recent work has addressed this problem by scaling self-consistency and parallel thinking, adding generic ``thinking tokens'' and prompting models to re-read the question before answering. Unfortunately, these approaches either inject task-agnostic tokens or mandate heuristics that do not explain -- and often ignore -- the spontaneous repetition that many LRMs exhibit at the head of their internal chains. In contrast, we analyze and harness the model's tendency to restate the question, which we term the Echo of Prompt (EOP), as a front-loaded, compute-shaping mechanism. We formalize its probabilistic cost by casting echo removal as rejection-based conditioning and defining the Echo Likelihood Gap ΔL as a computable proxy. This provides the missing theoretical link that links early repetition to likelihood gains and downstream accuracy. However, it does not by itself specify how to exploit EOP. Consequently, we develop Echo-Distilled SFT (ED-SFT) to instill an ``echo-then-reason'' pattern through supervised finetuning, and Echoic Prompting (EP) to re-ground the model mid-trace without training. While promising, quantifying benefits beyond verbosity is non-trivial. Therefore, we conduct length and suffix-controlled likelihood analyses together with layer-wise attention studies, showing that EOP increases answer to answer-prefix attention in middle layers, consistent with an attention refocusing mechanism. We evaluate on GSM8K, MathQA, Hendrycks-MATH, AIME24, and MATH-500 under identical decoding settings and budgets, and find consistent gains over baselines. Code is available at https://github.com/hhh2210/echoes-as-anchors.

Traditional language model-based theorem proving assumes that by training on a sufficient amount of formal proof data, a model will learn to prove theorems. Our key observation is that a wealth of informal information that is not present in formal proofs can be useful for learning to prove theorems. For instance, humans think through steps of a proof, but this thought process is not visible in the resulting code. We present Lean-STaR, a framework for training language models to produce informal thoughts prior to each step of a proof, thereby boosting the model's theorem-proving capabilities. Lean-STaR uses retrospective ground-truth tactics to generate synthetic thoughts for training the language model. At inference time, the trained model directly generates the thoughts prior to the prediction of the tactics in each proof step. Building on the self-taught reasoner framework, we then apply expert iteration to further fine-tune the model on the correct proofs it samples and verifies using the Lean solver. Lean-STaR achieves state-of-the-art results on the miniF2F-test benchmark within the Lean theorem proving environment, significantly outperforming base models (43.4% rightarrow 46.3%, Pass@64). We also analyze the impact of the augmented thoughts on various aspects of the theorem proving process, providing insights into their effectiveness.

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.

To make claims about representations that generalize beyond a particular trained model, we need to specify when two representations should count as equivalent. The Linear Representation Hypothesis is often discussed without making this equivalence explicit. Different notions of equivalence preserve different structures, so metrics, probes, and interventions that appear to study the same representation may in fact correspond to different hypotheses. We therefore argue that the Linear Representation Hypothesis is not one hypothesis but a family of claims distinguished by representation equivalence. We formalize this idea using group actions, specifying the representation object, the procedure that produces it, and the property ultimately asserted, while accounting for equivalences imposed by the model architecture. This framework clarifies how assumptions can change across metrics, reading points, and analysis stages, and we use it to audit common representation quantities and recent interpretability analyses.

Scientific machine learning papers typically make computational claims, e.g., that the relative mean square error is less than 5% or that the 95% predictive credible interval covers the test data. A coding agent can be prompted to replicate those claims from paper materials alone, but the prompt does not by itself reliably preserve progress or check whether generated evidence supports the paper's claims. We introduce Paper-replication, a workflow that makes each selected paper claim a target with recorded evidence, and implement it as a coding-agent skill. The workflow makes the agent record those targets, reconstruct the paper's method, run computational experiments, link generated outputs to provenance and comparisons with the paper's claims, record where matched evidence appears in the replication report, and pass validation checks before completion. We evaluate Paper-replication on twelve independent runs across four scientific machine learning papers. All twelve workspaces pass the completion gate, and all 158 recorded targets are matched with report coverage. Even in this completed workspace state, repeated runs differ in how papers are divided into targets, in numerical fidelity to the source papers, in elapsed replication time, in the number of intermediate executions replaced before final evidence is accepted, and in the rules used to accept evidence. Paper-replication makes completion depend on workspace evidence and validation checks rather than on the agent's final message.

Recent methods have demonstrated that Large Language Models (LLMs) can solve reasoning tasks better when they are encouraged to solve subtasks of the main task first. In this paper we devise a similar strategy that breaks down reasoning tasks into a problem decomposition phase and a problem solving phase and show that the strategy is able to outperform a single stage solution. Further, we hypothesize that the decomposition should be easier to distill into a smaller model compared to the problem solving because the latter requires large amounts of domain knowledge while the former only requires learning general problem solving strategies. We propose methods to distill these two capabilities and evaluate their impact on reasoning outcomes and inference cost. We find that we can distill the problem decomposition phase and at the same time achieve good generalization across tasks, datasets, and models. However, it is harder to distill the problem solving capability without losing performance and the resulting distilled model struggles with generalization. These results indicate that by using smaller, distilled problem decomposition models in combination with problem solving LLMs we can achieve reasoning with cost-efficient inference and local adaptation.

In this paper, we present and implement a multi-dimensional, modular framework for performing deep argument analysis (DeepA2) using current pre-trained language models (PTLMs). ArgumentAnalyst -- a T5 model (Raffel et al. 2020) set up and trained within DeepA2 -- reconstructs argumentative texts, which advance an informal argumentation, as valid arguments: It inserts, e.g., missing premises and conclusions, formalizes inferences, and coherently links the logical reconstruction to the source text. We create a synthetic corpus for deep argument analysis, and evaluate ArgumentAnalyst on this new dataset as well as on existing data, specifically EntailmentBank (Dalvi et al. 2021). Our empirical findings vindicate the overall framework and highlight the advantages of a modular design, in particular its ability to emulate established heuristics (such as hermeneutic cycles), to explore the model's uncertainty, to cope with the plurality of correct solutions (underdetermination), and to exploit higher-order evidence.

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

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.

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.

In Reinforcement Learning with Verifiable Rewards (RLVR), constructing a robust advantage baseline is critical for policy gradients, effectively guiding the policy model to reinforce desired behaviors. Recent research has introduced Generalist Value Models (such as V_0), which achieve pre-trained value estimation by explicitly encoding model capabilities in-context, eliminating the need to synchronously update the value model alongside the policy model. In this paper, we propose V_{0.5}, which adaptively fuses the baseline predicted by such value model (acting as a prior) with the empirical mean derived from sparse rollouts. This constructs a robust baseline that balances computational efficiency with extremely low variance. Specifically, we introduce a real-time statistical testing and dynamic budget allocation. This balances the high variance caused by sparse sampling against the systematic bias (or hallucinations) inherent in the value model's prior. By constructing a hypothesis test to evaluate the prior's reliability in real-time, the system dynamically allocates additional rollout budget on demand. This mechanism minimizes the baseline estimator's Mean Squared Error (MSE), guaranteeing stable policy gradients, even under extreme sparsity with a group size of 4. Extensive evaluations across six mathematical reasoning benchmarks demonstrate that V_{0.5} significantly outperforms GRPO and DAPO, achieving faster convergence and over some 10% performance improvement.

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

The research idea in a published paper is rarely the project's initial idea. Between the two lies a closed-loop process in which researchers run experiments, derive insights, identify challenges, explore the literature, and revise the idea, with each step motivated by evidence and reasoning they can articulate. We call the path one idea takes through this process, with the evidence and reasoning behind each step, its authentic research trajectory. Although it underlies every scientific contribution, it is rarely recorded. Existing LLM-based research agents generate an idea once, refine it against reviews, literature, or their own experimental results, or search over candidate ideas and experiments. In all of them the text of the idea evolves, while the evidence and reasoning that connected one version to the next are discarded. We propose the Research Progress Graph (RPG), a representation of authentic and complete research trajectories. An RPG records the evolution of an idea as typed research states connected by cognitive transitions, each annotated with a temporal index and the reasoning behind it, which makes this evolution an explicit object of study. We ground the representation in authentic trajectories whose steps their authors justify in annotations and papers. Comparing the representations of thirty-five research agents with the RPG, we find that each is an incomplete RPG; none keeps the state that changed, the evidence that changed it, and the reasoning connecting them as one evolving record. Modeling ideation with the RPG changes how research agents should be designed, evaluated, and trained. Agents predict the next research state instead of a complete idea, ideas are evaluated as trajectories instead of final texts, and authentic trajectories serve as training data. These directions shift research agents from generating static ideas to modeling how ideas evolve.

Scientific research often begins by synthesizing ideas from a set of related papers to identify gaps and formulate new directions. However, training language models to perform this form of literature-grounded ideation remains challenging, as existing approaches based on prompting or feedback lack structured supervision for how papers should be synthesized. We introduce IdeaAnchor, a paradigm for training LLMs to perform research ideation using structured specifications as privileged signals. Each IdeaAnchor instance encodes how each input paper should be synthesized into a successful idea, including their functional roles, relationships, and target synthesis criteria. We build this paradigm by mining instances from published papers, capturing how real ideas emerge from prior literature. We then train models via demonstration, self-distillation, and reinforcement learning, and further enhance generation with retrieval at inference time. Experiments show consistent improvements in ideation quality. Our analysis reveals a functional decomposition: anchor-based training strengthens creative synthesis, retrieval enhances detail elaboration, and combining both yields the best performance.

Recent advances leverage post-training to enhance model reasoning performance, which typically requires costly training pipelines and still suffers from inefficient, overly lengthy outputs. We introduce Speculative Thinking, a training-free framework that enables large reasoning models to guide smaller ones during inference at the reasoning level, distinct from speculative decoding, which operates at the token level. Our approach is based on two observations: (1) reasoning-supportive tokens such as "wait" frequently appear after structural delimiters like "\n\n", serving as signals for reflection or continuation; and (2) larger models exhibit stronger control over reflective behavior, reducing unnecessary backtracking while improving reasoning quality. By strategically delegating reflective steps to a more capable model, our method significantly boosts the reasoning accuracy of reasoning models while shortening their output. With the assistance of the 32B reasoning model, the 1.5B model's accuracy on MATH500 increases from 83.2% to 89.4%, marking a substantial improvement of 6.2%. Simultaneously, the average output length is reduced from 5439 tokens to 4583 tokens, representing a 15.7% decrease. Moreover, when applied to a non-reasoning model (Qwen-2.5-7B-Instruct), our framework boosts its accuracy from 74.0% to 81.8% on the same benchmark, achieving a relative improvement of 7.8%.

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.

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

Large Language Models (LLMs) have recently showcased remarkable reasoning abilities. However, larger models often surpass their smaller counterparts in reasoning tasks, posing the challenge of effectively transferring these capabilities from larger models. Existing approaches heavily rely on extensive fine-tuning data or continuous interactions with a superior teacher LLM during inference. We introduce a principle-based teacher-student framework called ``Teaching via Principle Discovery'' (TPD) to address these limitations. Inspired by human learning mechanisms, TPD mimics the interaction between a teacher and a student using a principle-based approach. The teacher LLM generates problem-solving instructions and corrective principles based on the student LLM's errors. These principles guide the refinement of instructions and the selection of instructive examples from a validation set. This enables the student model to learn from both the teacher's guidance and its own mistakes. Once the student model begins making inferences, TPD requires no further intervention from the teacher LLM or humans. Through extensive experiments across eight reasoning tasks, we demonstrate the effectiveness of TPD. Compared to standard chain-of-thought prompting, TPD significantly improves the student model's performance, achieving 6.2% improvement on average.

We study the interpretability issue of task-oriented dialogue systems in this paper. Previously, most neural-based task-oriented dialogue systems employ an implicit reasoning strategy that makes the model predictions uninterpretable to humans. To obtain a transparent reasoning process, we introduce neuro-symbolic to perform explicit reasoning that justifies model decisions by reasoning chains. Since deriving reasoning chains requires multi-hop reasoning for task-oriented dialogues, existing neuro-symbolic approaches would induce error propagation due to the one-phase design. To overcome this, we propose a two-phase approach that consists of a hypothesis generator and a reasoner. We first obtain multiple hypotheses, i.e., potential operations to perform the desired task, through the hypothesis generator. Each hypothesis is then verified by the reasoner, and the valid one is selected to conduct the final prediction. The whole system is trained by exploiting raw textual dialogues without using any reasoning chain annotations. Experimental studies on two public benchmark datasets demonstrate that the proposed approach not only achieves better results, but also introduces an interpretable decision process.

Existing reasoning evaluations typically provide task-relevant information to models as available premises, rarely examining concurrently how models discover evidence autonomously and how information presentation within narratives guides or obscures judgment. This paper proposes the WORTH Benchmark: models read original mystery narratives without clue annotations, autonomously select key clue sentences, identify case participants, and explain their reasoning process. The narrative materials are designed by professional authors such that evidence facilitating reasoning coexists with narrative arrangements that delay the revelation of truth. We report a pilot experiment under full-story conditions across two episodes, conducting a total of 70 formal runs on models, of which 67 runs are content-scorable. Scoring separately records hits on author-designated key clue sentences and participant selections; natural language explanations are used for case diagnosis and are not scored independently. The results show that clue hits and participant judgments are not synchronized; across 37 content-scorable runs in Episode 02, 31 runs simultaneously selected the same set of incorrect participants, while adjacent suspicion-oriented and exoneration-oriented sentences were selected 25 times and 0 times, respectively. These phenomena illustrate the diagnostic value of component-wise analysis and suggest that not-fully-cooperative informational relationships may influence evidence selection and judgment. This study only implements full-story conditions for two episodes, and does not establish stable model rankings or infer general mechanisms on this basis; human player records have not yet been cleaned, and this version does not report human-model comparisons.

Recent Large Reasoning Models (LRMs), such as DeepSeek-R1 and OpenAI o1, have demonstrated strong performance gains by scaling up the length of Chain-of-Thought (CoT) reasoning during inference. However, a growing concern lies in their tendency to produce excessively long reasoning traces, which are often filled with redundant content (e.g., repeated definitions), over-analysis of simple problems, and superficial exploration of multiple reasoning paths for harder tasks. This inefficiency introduces significant challenges for training, inference, and real-world deployment (e.g., in agent-based systems), where token economy is critical. In this survey, we provide a comprehensive overview of recent efforts aimed at improving reasoning efficiency in LRMs, with a particular focus on the unique challenges that arise in this new paradigm. We identify common patterns of inefficiency, examine methods proposed across the LRM lifecycle, i.e., from pretraining to inference, and discuss promising future directions for research. To support ongoing development, we also maintain a real-time GitHub repository tracking recent progress in the field. We hope this survey serves as a foundation for further exploration and inspires innovation in this rapidly evolving area.

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.

Deductive reasoning plays a pivotal role in the formulation of sound and cohesive arguments. It allows individuals to draw conclusions that logically follow, given the truth value of the information provided. Recent progress in the domain of large language models (LLMs) has showcased their capability in executing deductive reasoning tasks. Nonetheless, a significant portion of research primarily assesses the accuracy of LLMs in solving such tasks, often overlooking a deeper analysis of their reasoning behavior. In this study, we draw upon principles from cognitive psychology to examine inferential strategies employed by LLMs, through a detailed evaluation of their responses to propositional logic problems. Our findings indicate that LLMs display reasoning patterns akin to those observed in humans, including strategies like supposition following or chain construction. Moreover, our research demonstrates that the architecture and scale of the model significantly affect its preferred method of reasoning, with more advanced models tending to adopt strategies more frequently than less sophisticated ones. Importantly, we assert that a model's accuracy, that is the correctness of its final conclusion, does not necessarily reflect the validity of its reasoning process. This distinction underscores the necessity for more nuanced evaluation procedures in the field.

Inductive reasoning is a core problem-solving capacity: humans can identify underlying principles from a few examples, which can then be robustly generalized to novel scenarios. Recent work has evaluated large language models (LLMs) on inductive reasoning tasks by directly prompting them yielding "in context learning." This can work well for straightforward inductive tasks, but performs very poorly on more complex tasks such as the Abstraction and Reasoning Corpus (ARC). In this work, we propose to improve the inductive reasoning ability of LLMs by generating explicit hypotheses at multiple levels of abstraction: we prompt the LLM to propose multiple abstract hypotheses about the problem, in natural language, then implement the natural language hypotheses as concrete Python programs. These programs can be directly verified by running on the observed examples and generalized to novel inputs. Because of the prohibitive cost of generation with state-of-the-art LLMs, we consider a middle step to filter the set of hypotheses that will be implemented into programs: we either ask the LLM to summarize into a smaller set of hypotheses, or ask human annotators to select a subset of the hypotheses. We verify our pipeline's effectiveness on the ARC visual inductive reasoning benchmark, its variant 1D-ARC, and string transformation dataset SyGuS. On a random 40-problem subset of ARC, our automated pipeline using LLM summaries achieves 27.5% accuracy, significantly outperforming the direct prompting baseline (accuracy of 12.5%). With the minimal human input of selecting from LLM-generated candidates, the performance is boosted to 37.5%. (And we argue this is a lower bound on the performance of our approach without filtering.) Our ablation studies show that abstract hypothesis generation and concrete program representations are both beneficial for LLMs to perform inductive reasoning tasks.

Autoformalisation, the task of expressing informal mathematical statements in formal language, is often viewed as a direct translation process. This, however, disregards a critical preceding step: conjecturing. Many mathematical problems cannot be formalised directly without first conjecturing a conclusion such as an explicit answer, or a specific bound. Since Large Language Models (LLMs) already struggle with autoformalisation, and the evaluation of their conjecturing ability is limited and often entangled within autoformalisation or proof, it is particularly challenging to understand its effect. To address this gap, we augment existing datasets to create ConjectureBench, and redesign the evaluation framework and metric specifically to measure the conjecturing capabilities of LLMs both as a distinct task and within the autoformalisation pipeline. Our evaluation of foundational models, including GPT-4.1 and DeepSeek-V3.1, reveals that their autoformalisation performance is substantially overestimated when the conjecture is accounted for during evaluation. However, the conjecture should not be assumed to be provided. We design an inference-time method, Lean-FIRe to improve conjecturing and autoformalisation, which, to the best of our knowledge, achieves the first successful end-to-end autoformalisation of 13 PutnamBench problems with GPT-4.1 and 7 with DeepSeek-V3.1. We demonstrate that while LLMs possess the requisite knowledge to generate accurate conjectures, improving autoformalisation performance requires treating conjecturing as an independent task, and investigating further how to correctly integrate it within autoformalisation. Finally, we provide forward-looking guidance to steer future research toward improving conjecturing, an overlooked step of formal mathematical reasoning.

Studies have underscored how, regardless of the recent breakthrough and swift advances in AI research, even state-of-the-art Large Language models (LLMs) continue to struggle when performing logical and mathematical reasoning. The results seem to suggest that LLMs still work as (highly advanced) data pattern identifiers, scoring poorly when attempting to generalise and solve reasoning problems the models have never previously seen or that are not close to samples presented in their training data. To address this compelling concern, this paper makes use of the notion of critical questions from the literature on argumentation theory, focusing in particular on Toulmin's model of argumentation. We show that employing these critical questions can improve the reasoning capabilities of LLMs. By probing the rationale behind the models' reasoning process, the LLM can assess whether some logical mistake is occurring and correct it before providing the final reply to the user prompt. The underlying idea is drawn from the gold standard of any valid argumentative procedure: the conclusion is valid if it is entailed by accepted premises. Or, to paraphrase such Aristotelian principle in a real-world approximation, characterised by incomplete information and presumptive logic, the conclusion is valid if not proved otherwise. This approach successfully steers the models' output through a reasoning pipeline, resulting in better performance against the baseline and its Chain-of-Thought (CoT) implementation. To this end, an extensive evaluation of the proposed approach on the MT-Bench Reasoning and Math tasks across a range of LLMs is provided.

We present the first comprehensive Lean 4 formalization of statistical learning theory (SLT) grounded in empirical process theory. Our end-to-end formal infrastructure implement the missing contents in latest Lean 4 Mathlib library, including a complete development of Gaussian Lipschitz concentration, the first formalization of Dudley's entropy integral theorem for sub-Gaussian processes, and an application to least-squares (sparse) regression with a sharp rate. The project was carried out using a human-AI collaborative workflow, in which humans design proof strategies and AI agents execute tactical proof construction, leading to the human-verified Lean 4 toolbox for SLT. Beyond implementation, the formalization process exposes and resolves implicit assumptions and missing details in standard SLT textbooks, enforcing a granular, line-by-line understanding of the theory. This work establishes a reusable formal foundation and opens the door for future developments in machine learning theory. The code is available at https://github.com/YuanheZ/lean-stat-learning-theory

We study the problem of detecting the correlation between two Gaussian databases XinR^{ntimes d} and Y^{ntimes d}, each composed of n users with d features. This problem is relevant in the analysis of social media, computational biology, etc. We formulate this as a hypothesis testing problem: under the null hypothesis, these two databases are statistically independent. Under the alternative, however, there exists an unknown permutation sigma over the set of n users (or, row permutation), such that X is rho-correlated with Y^sigma, a permuted version of Y. We determine sharp thresholds at which optimal testing exhibits a phase transition, depending on the asymptotic regime of n and d. Specifically, we prove that if rho^2dto0, as dtoinfty, then weak detection (performing slightly better than random guessing) is statistically impossible, irrespectively of the value of n. This compliments the performance of a simple test that thresholds the sum all entries of X^TY. Furthermore, when d is fixed, we prove that strong detection (vanishing error probability) is impossible for any rho<rho^star, where rho^star is an explicit function of d, while weak detection is again impossible as long as rho^2dto0. These results close significant gaps in current recent related studies.