Daily Papers

Systems that generate scientific research questions are evaluated today by expert scores, LLM-as-judge ratings, or curated case studies -- all subjective, none falsifiable. We formalize historical backtesting as an alternative: a system generates questions from a corpus frozen at a historical cutoff, the questions are frozen before any access to later literature, and a temporally isolated future corpus then determines whether each question was subsequently answered, partially addressed, independently posed, or ignored, and whether its underlying premise was supported or refuted. The protocol is model-agnostic: any system that emits frozen questions can be scored. We release reproducible astronomy instances with temporally isolated corpora, frozen questions, auditable labels, four reference baselines, and a submission interface. Two findings result. First, evidence-structure-first generation outperforms LLM-only prompting: across a generator decomposition crossed with a four-cutoff stress test (2010-2024, 798 judged questions) whose last window postdates model training, LLM-only generation shows memorized relevance without specific foresight, while a generator using no model weights at all finds questions whose premises the future refutes in every era. Second, a seven-rater agreement study (two blinded human annotators, five judge models, 90 items) indicts the outcome taxonomy rather than the judge: two careful humans agree at kappa = 0.17, every judge model agrees with the professional annotator as well or better (0.17-0.26), and frontier models agree with one another at 0.60 -- certifying an LLM judge by model-model agreement would have overstated its reliability threefold. A prospective instance -- 200 questions frozen 2026-08-17, scored 2027-2030 -- is released so the central claims become contamination-free tests that time itself will grade.

Knowledge Graph-based Question Answering (KGQA) plays a pivotal role in complex reasoning tasks but remains constrained by two persistent challenges: the structural heterogeneity of Knowledge Graphs(KGs) often leads to semantic mismatch during retrieval, while existing reasoning path retrieval methods lack a global structural perspective. To address these issues, we propose Structure-Tracing Evidence Mining (STEM), a novel framework that reframes multi-hop reasoning as a schema-guided graph search task. First, we design a Semantic-to-Structural Projection pipeline that leverages KG structural priors to decompose queries into atomic relational assertions and construct an adaptive query schema graph. Subsequently, we execute globally-aware node anchoring and subgraph retrieval to obtain the final evidence reasoning graph from KG. To more effectively integrate global structural information during the graph construction process, we design a Triple-Dependent GNN (Triple-GNN) to generate a Global Guidance Subgraph (Guidance Graph) that guides the construction. STEM significantly improves both the accuracy and evidence completeness of multi-hop reasoning graph retrieval, and achieves State-of-the-Art performance on multiple multi-hop benchmarks.

Alignment in LLMs is more brittle than commonly assumed: misalignment can be triggered by adversarial prompts, benign fine-tuning, emergent misalignment, and goal misgeneralization. Recent evidence suggests that some misalignment behaviors are encoded as linear structure in activation space, making it tractable via steering, while safety alignment has been shown to govern the first few output tokens primarily, leaving subsequent generation unguarded. These findings motivate activation steering as a lightweight runtime defense that continuously corrects misaligned activations throughout generation. We evaluate three methods: Steer-With-Fixed-Coeff (SwFC), which applies uniform additive steering, and two novel projection-aware methods, Steer-to-Target-Projection (StTP) and Steer-to-Mirror-Projection (StMP), that use a logistic regression decision boundary to selectively intervene only on tokens whose activations fall below distributional thresholds. Using malicious system prompts as a controlled proxy for misalignment, we evaluate under two threat models (dishonesty and dismissiveness) and two architectures (Llama-3.3-70B-Instruct, Qwen3-32B). All methods substantially recover target traits (honesty and compassion) while preserving coherence. StTP and StMP better maintain general capabilities (MMLU, MT-Bench, AlpacaEval) and produce less repetition in multi-turn conversations.

Multi-video event understanding demands models that can locate and attribute query-relevant evidence scattered across long, heterogeneous video corpora. Existing large vision-language models (LVLMs) often underperform in this regime because they quickly exhaust their context budget and struggle to precisely localize evidentially important segments, frequently missing dense informational cues such as broadcast graphics, subtitles, and scoreboards. We introduce TRACE, an evidence grounding-guided framework that follows a ground-before-reasoning strategy for multi-video event reasoning. Our approach first builds a structured, text-searchable timeline for each video using OCR and object detection. A text-only LLM then conducts query-aware evidence localization, selecting relevant moments prior to any downstream visual reasoning. The retrieved frames and their grounding summaries are subsequently used to steer LVLM-based claim generation and cross-video citation consolidation. Experiments on MAGMaR 2026 and WikiVideo demonstrate that structured grounding markedly boosts factual completeness and attribution fidelity. On the MAGMaR validation split, TRACE raises macro-average MiRAGE F1 from 0.705 to 0.811 compared to an unguided Qwen3-VL-30B baseline, with especially strong improvements in citation recall from 0.440 to 0.628. The method also attains state-of-the-art results on the official MAGMaR 2026 leaderboard. Code is released at https://github.com/pengyu965/TRACE.

Current automated pipelines for audio-visual Question Answering (QA) generally adopt a ``video-caption-QA'' paradigm. However, these methods typically segment videos into short clips and generate separate descriptions for audio and visual modalities. This decoupled processing severs inherent associations between sounds and their visual sources, while independent clip processing often causes inconsistent descriptions of the same entity across segments. Furthermore, coupling long-text comprehension and QA synthesis into a single step often restricts models to localized events, yielding questions lacking long-term temporal connections and deep cross-modal reasoning. To address these issues, we propose an automated data engine featuring two mechanisms: (1) Entity-Anchored Video Scripting transforms videos into structured scripts, comprising summaries, main entity lists, and segment-wise audio-visual descriptions. The entity list serves as a global prior to ensure cross-segment referential consistency and reconstruct audio-visual associations. (2) Clue-Guided QA Generation prompts models to first mine cross-segment, multimodal clues from the script, and subsequently generate QA pairs based on these high-value clues. Leveraging this pipeline, we construct the instruction-tuning dataset OmniVideo-100K and a human-verified test set, OmniVideo-Test. Fine-tuning VITA-1.5, Qwen2.5-Omni-7B and Qwen3-Omni-30B on OmniVideo-100K yields performance gains of up to 20.59% on OmniVideo-Test, demonstrating strong generalization (up to 12.64% improvements) across established benchmarks like Daily-Omni and JointAVBench.

Front-end web code has become a core product surface for every frontier LLM release, yet evaluating these interactive applications at development speed remains costly because human-judged leaderboards like Arena do not scale. Existing automated proxies typically lean on reference implementations, test suites, or rigid checklists, and tend to miss the reasoned synthesis a human reviewer performs over a live session. We articulate a new evaluation regime that is simultaneously reference-free, autonomously driven, and holistically reasoned, and instantiate it through two artifacts. \dataname is an 11-domain, 54-leaf, 1,000-query WebDev benchmark spanning both static-presentation and interactive-application tasks, balanced across three difficulty tiers and three target-language groups, with briefs rewritten to resist recall from circulated prompts. \framename, grounded in Flavell's metacognitive monitoring, separates evidence accumulation from judgment across three stages: Static Perception forms a first impression from passive observation; Agent-Driven Interaction explores the application autonomously while capturing continuous screen video, audio, and per-step screenshots; Dynamic Scoring issues holistic functionality and aesthetics verdicts with structured failure attribution only after the evidence chain is complete. On \dataname, \framename aligns closely with expert human ratings while surfacing substantial headroom across 13 frontier LLMs on interactive web generation. \noindenthttps://anonymous.4open.science/r/Cookie-3CE/

LLM-based coding agents have significantly advanced automated software issue resolution, yet they remain highly prone to factual errors caused by insufficient repository understanding. Recent methods attempt to mitigate this limitation through pre-repair repository exploration; however, their fix-driven strategies explore repositories without identifying the agent's knowledge gaps, often yielding imprecise context that fails to bridge the underlying understanding deficit. In this paper, we propose ACQUIRE, a QA-driven framework for software issue resolution. Mirroring how experienced developers first comprehend unfamiliar code before attempting a fix, ACQUIRE explicitly acquires repository knowledge prior to repair. The framework decouples knowledge acquisition from patch generation through two stages: in the first stage, a Questioner and an Answerer collaborate to acquire structured repository knowledge, where the Questioner poses targeted questions and the Answerer produces evidence-grounded answers through autonomous exploration; in the second stage, the Resolver leverages the resulting QA knowledge to generate informed patches. By transforming implicit knowledge gaps into explicit, factually reliable understanding, ACQUIRE accelerates knowledge-intensive repair stages and enables more accurate resolution. Experiments on SWE-bench Verified demonstrate that ACQUIRE consistently outperforms representative pre-repair methods, raising Pass@1 by up to 4.4 percentage points with modest additional cost and time.

Inverse materials design starts from target functionality and searches for structures that can realize it. Its value in closed-loop discovery depends not only on prediction performance, but also on whether expensive first-principles results are independently validated, provenance-recorded, and admitted as feedback only when evidence is sufficient. This is especially important for composite properties such as carrier mobility, where a final scalar value hides intermediate quantities, fit quality, convergence history, and workflow assumptions. Here we present InvDesMobility, a reliability-gated first-principles feedback framework that integrates multi-agent automated DFT, evidence stratification, generative structure proposal, acquisition ranking, and auditable release. Using 516 2DMatPedia-derived candidates, the workflow produced 280 QC-passed materials and 573 retained carrier-direction seed channels after channel-level reliability gating. These records were split into two feedback objects: relaxed structures updated the generative model, while retained mobility channels trained the acquisition model and set validation priority. Over multiple iterations, InvDesMobility screened 2.4 x 10^6 structures, submitted 102 candidates for DFT validation, and retained 86 reliability-gated generated channels across 41 formulas. Overall, the main contribution is not a fixed list of high-mobility materials, but a transferable feedback contract that makes closed-loop inverse design both useful and auditable when learning from expensive calculated properties. All source data, retained feedback records, and workflows are available at https://github.com/DreamLufei/invDesMobility, with an accompanying evidence website at https://dreamlufei.github.io/invDesMobility/.

Inferring causal structure poses a combinatorial search problem that typically involves evaluating structures with a score or independence test. The resulting search is costly, and designing suitable scores or tests that capture prior knowledge is difficult. In this work, we propose to amortize causal structure learning. Rather than searching over structures, we train a variational inference model to directly predict the causal structure from observational or interventional data. This allows our inference model to acquire domain-specific inductive biases for causal discovery solely from data generated by a simulator, bypassing both the hand-engineering of suitable score functions and the search over graphs. The architecture of our inference model emulates permutation invariances that are crucial for statistical efficiency in structure learning, which facilitates generalization to significantly larger problem instances than seen during training. On synthetic data and semisynthetic gene expression data, our models exhibit robust generalization capabilities when subject to substantial distribution shifts and significantly outperform existing algorithms, especially in the challenging genomics domain. Our code and models are publicly available at: https://github.com/larslorch/avici.

Strategies for the generation of periodic discrete structures with identical two-point correlation are developed. Starting from a pair of root structures, which are not related by translation, phase inversion or axis reflections, child structures of arbitrary resolution (i.e., pixel or voxel numbers) and number of phases (i.e., material phases/species) can be generated by means of trivial embedding based phase extension, application of kernels and/or phase coalescence, such that the generated structures inherit the two-point-correlation equivalence. Proofs of the inheritance property are provided by means of the Discrete Fourier Transform theory. A Python 3 implementation of the results is offered by the authors through the Github repository https://github.com/DataAnalyticsEngineering/EQ2PC in order to make the provided results reproducible and useful for all interested readers. Examples for the generation of structures are demonstrated, together with applications in the homogenization theory of periodic media.

Generative models trained at scale can now produce text, video, and more recently, scientific data such as crystal structures. In applications of generative approaches to materials science, and in particular to crystal structures, the guidance from the domain expert in the form of high-level instructions can be essential for an automated system to output candidate crystals that are viable for downstream research. In this work, we formulate end-to-end language-to-structure generation as a multi-objective optimization problem, and propose Generative Hierarchical Materials Search (GenMS) for controllable generation of crystal structures. GenMS consists of (1) a language model that takes high-level natural language as input and generates intermediate textual information about a crystal (e.g., chemical formulae), and (2) a diffusion model that takes intermediate information as input and generates low-level continuous value crystal structures. GenMS additionally uses a graph neural network to predict properties (e.g., formation energy) from the generated crystal structures. During inference, GenMS leverages all three components to conduct a forward tree search over the space of possible structures. Experiments show that GenMS outperforms other alternatives of directly using language models to generate structures both in satisfying user request and in generating low-energy structures. We confirm that GenMS is able to generate common crystal structures such as double perovskites, or spinels, solely from natural language input, and hence can form the foundation for more complex structure generation in near future.

Trustworthy Large Language Models (LLMs) must cite human-verifiable sources in high-stakes domains such as healthcare, law, academia, and finance, where even small errors can have severe consequences. Practitioners and researchers face a choice: let models generate citations during decoding, or let models draft answers first and then attach appropriate citations. To clarify this choice, we introduce two paradigms: Generation-Time Citation (G-Cite), which produces the answer and citations in one pass, and Post-hoc Citation (P-Cite), which adds or verifies citations after drafting. We conduct a comprehensive evaluation from zero-shot to advanced retrieval-augmented methods across four popular attribution datasets and provide evidence-based recommendations that weigh trade-offs across use cases. Our results show a consistent trade-off between coverage and citation correctness, with retrieval as the main driver of attribution quality in both paradigms. P-Cite methods achieve high coverage with competitive correctness and moderate latency, whereas G-Cite methods prioritize precision at the cost of coverage and speed. We recommend a retrieval-centric, P-Cite-first approach for high-stakes applications, reserving G-Cite for precision-critical settings such as strict claim verification. Our codes and human evaluation results are available at https://anonymous.4open.science/r/Citation_Paradigms-BBB5/

Multi-turn-to-single-turn (M2S) compresses iterative red-teaming into one structured prompt, but prior work relied on a handful of manually written templates. We present X-Teaming Evolutionary M2S, an automated framework that discovers and optimizes M2S templates through language-model-guided evolution. The system pairs smart sampling from 12 sources with an LLM-as-judge inspired by StrongREJECT and records fully auditable logs. Maintaining selection pressure by setting the success threshold to theta = 0.70, we obtain five evolutionary generations, two new template families, and 44.8% overall success (103/230) on GPT-4.1. A balanced cross-model panel of 2,500 trials (judge fixed) shows that structural gains transfer but vary by target; two models score zero at the same threshold. We also find a positive coupling between prompt length and score, motivating length-aware judging. Our results demonstrate that structure-level search is a reproducible route to stronger single-turn probes and underscore the importance of threshold calibration and cross-model evaluation. Code, configurations, and artifacts are available at https://github.com/hyunjun1121/M2S-x-teaming.

Epilepsy diagnosis and treatment require evidence-intensive reasoning across heterogeneous clinical knowledge, including biosignal patterns, genetic mechanisms, pharmacogenomics, treatment strategies, and patient outcomes. In this work, we present EpiGraph, a large-scale epilepsy knowledge graph and benchmark for evaluating knowledge-augmented clinical reasoning. EpiGraph integrates 48,166 peer-reviewed papers and seven clinical resources into a heterogeneous graph containing 24,324 entities and 32,009 evidence-grounded triplets across five clinical layers. Built upon this graph, EpiBench defines five clinically motivated tasks spanning clinical decision-making, EEG report generation, pharmacogenomic precision medicine, treatment recommendation, and deep research planning. We evaluate six LLMs under both standard and Graph-RAG settings. Results show that integrating EpiGraph consistently improves performance across all tasks, with the largest gains observed in pharmacogenomic reasoning (+30--41\%). Our findings demonstrate that structured epilepsy knowledge substantially enhances evidence-grounded clinical reasoning and provides a practical benchmark framework for evaluating knowledge-augmented LLMs in real-world neurological settings. Our code is available at: https://github.com/LabRAI/EEG-KG.

Universally modeling all typical information extraction tasks (UIE) with one generative language model (GLM) has revealed great potential by the latest study, where various IE predictions are unified into a linearized hierarchical expression under a GLM. Syntactic structure information, a type of effective feature which has been extensively utilized in IE community, should also be beneficial to UIE. In this work, we propose a novel structure-aware GLM, fully unleashing the power of syntactic knowledge for UIE. A heterogeneous structure inductor is explored to unsupervisedly induce rich heterogeneous structural representations by post-training an existing GLM. In particular, a structural broadcaster is devised to compact various latent trees into explicit high-order forests, helping to guide a better generation during decoding. We finally introduce a task-oriented structure fine-tuning mechanism, further adjusting the learned structures to most coincide with the end-task's need. Over 12 IE benchmarks across 7 tasks our system shows significant improvements over the baseline UIE system. Further in-depth analyses show that our GLM learns rich task-adaptive structural bias that greatly resolves the UIE crux, the long-range dependence issue and boundary identifying. Source codes are open at https://github.com/ChocoWu/LasUIE.

Studies of bias in LLM-as-judge systems typically build synthetic corpora by prompting an LLM to generate a hallucinated answer to pair with a factual one, then presenting both to a judge. We report a case in which this generation step silently failed, and use it to argue that the failure mode is structural rather than incidental. In a multilingual (Turkish/English) faithfulness-judgment corpus, a decoding-budget parameter shared between judging and generation calls truncated one producer's hallucinated answers to a few words. The resulting items produced a large, statistically robust effect: a 32-point cross-lingual collapse in one judge's selection accuracy, replicated from N=50 to N=500, explained by a three-layer mechanistic account, and confirmed by a controlled producer-swap experiment, none of which was real. The effect vanished to ceiling once the shared parameter was corrected, and only manual reading of the raw generations, not any aggregate statistical check, exposed the fault. A second measured bias (Markdown-formatting preference) was not fabricated but distorted by the same fault, its magnitude and in one case its sign shifting with stimulus length, a mode aggregate metrics cannot distinguish from the first. We frame the underlying vulnerability using the test oracle problem: corpora whose negative examples are LLM-generated carry no mechanical way to verify item integrity, while corpora built by deterministic perturbation of a gold answer carry an item-level oracle for free. A positive control supports this claim directly: an analogous fault injected into a minimal perturbation-based corpus is caught with 100% accuracy by a zero-cost, zero-human gold-to-negative string comparison. We close with a validation protocol, derived from our own case, for analysts working in the oracle-less regime that we argue describes most contemporary multilingual LLM-as-judge corpora.

Parallel thinking has enjoyed great success for boosting LLM performance on reasoning tasks without the need for any re-training. However, existing methods follow a think-first-then-decide paradigm, i.e., they first sample multiple reasoning paths, which inevitably leads to overgeneration, then prune or stop unnecessary paths to compensate. In contrast, decide-first-then-think, i.e., first identifying points that are likely to lead to desirable generations, has been underexplored so far. Following this paradigm, we propose Fork-think with confidence, that first identifies forking points using model confidence in a single seeding path, then triggers thinking, sampling multiple continuations and aggregating them for the final response. Our experiments across three models and three reasoning benchmarks show that Fork-think reduces the token consumption by up to 30% and run-time by up to 57%, while performing comparable to or better than parallel thinking. Our analysis reveals that Fork-think is able to identify forking points that are meaningful with respect to the downstream task and that sampling at later positions can lead to substantially better generations. Finally, we demonstrate how combining Fork-think with existing mechanisms such as early stopping and weighted voting can further boost the performance and perform comparably to existing state-of-the-art methods, without requiring any warm-up or offline training. Our results establish pre-determined forking as a promising research direction for efficient LLM reasoning.

Retrieval-augmented generation has gained significant attention due to its ability to integrate relevant external knowledge, enhancing the accuracy and reliability of the LLMs' responses. Most of the existing methods apply a dynamic multiple retrieval-generating process, to address multi-hop complex questions by decomposing them into sub-problems. However, these methods rely on an unidirectional forward reasoning paradigm, where errors from insufficient reasoning steps or inherent flaws in current retrieval systems are irreversible, potentially derailing the entire reasoning chain. For the first time, this work introduces Retroactive Retrieval-Augmented Generation (RetroRAG), a novel framework to build a retroactive reasoning paradigm. RetroRAG revises and updates the evidence, redirecting the reasoning chain to the correct direction. RetroRAG constructs an evidence-collation-discovery framework to search, generate, and refine credible evidence. It synthesizes inferential evidence related to the key entities in the question from the existing source knowledge and formulates search queries to uncover additional information. As new evidence is found, RetroRAG continually updates and organizes this information, enhancing its ability to locate further necessary evidence. Paired with an Answerer to generate and evaluate outputs, RetroRAG is capable of refining its reasoning process iteratively until a reliable answer is obtained. Empirical evaluations show that RetroRAG significantly outperforms existing methods.

Evidence-grounded reasoning requires more than attaching retrieved text to a prediction: a model should make decisions that depend on whether the provided evidence supports the target claim. In practice, this often fails because supervision is weak, evidence is only loosely tied to the claim, and evaluation does not test evidence dependence directly. We introduce case-grounded evidence verification, a general framework in which a model receives a local case context, external evidence, and a structured claim, and must decide whether the evidence supports the claim for that case. Our key contribution is a supervision construction procedure that generates explicit support examples together with semantically controlled non-support examples, including counterfactual wrong-state and topic-related negatives, without manual evidence annotation. We instantiate the framework in radiology and train a standard verifier on the resulting support task. The learned verifier substantially outperforms both case-only and evidence-only baselines, remains strong under correct evidence, and collapses when evidence is removed or swapped, indicating genuine evidence dependence. This behavior transfers across unseen evidence articles and an external case distribution, though performance degrades under evidence-source shift and remains sensitive to backbone choice. Overall, the results suggest that a major bottleneck in evidence grounding is not only model capacity, but the lack of supervision that encodes the causal role of evidence.

Recent years have seen significant advancements in foundation models through generative pre-training, yet algorithmic innovation in this space has largely stagnated around autoregressive models for discrete signals and diffusion models for continuous signals. This stagnation creates a bottleneck that prevents us from fully unlocking the potential of rich multi-modal data, which in turn limits the progress on multimodal intelligence. We argue that an inference-first perspective, which prioritizes scaling efficiency during inference time across sequence length and refinement steps, can inspire novel generative pre-training algorithms. Using Inductive Moment Matching (IMM) as a concrete example, we demonstrate how addressing limitations in diffusion models' inference process through targeted modifications yields a stable, single-stage algorithm that achieves superior sample quality with over an order of magnitude greater inference efficiency.

Assessing whether an article supports an assertion is essential for hallucination detection and claim verification. While large language models (LLMs) have the potential to automate this task, achieving strong performance requires frontier models such as GPT-5 that are prohibitively expensive to deploy at scale. To efficiently perform biomedical evidence attribution, we present Med-V1, a family of small language models with only three billion parameters. Trained on high-quality synthetic data newly developed in this study, Med-V1 substantially outperforms (+27.0% to +71.3%) its base models on five biomedical benchmarks unified into a verification format. Despite its smaller size, Med-V1 performs comparably to frontier LLMs such as GPT-5, along with high-quality explanations for its predictions. We use Med-V1 to conduct a first-of-its-kind use case study that quantifies hallucinations in LLM-generated answers under different citation instructions. Results show that the format instruction strongly affects citation validity and hallucination, with GPT-5 generating more claims but exhibiting hallucination rates similar to GPT-4o. Additionally, we present a second use case showing that Med-V1 can automatically identify high-stakes evidence misattributions in clinical practice guidelines, revealing potentially negative public health impacts that are otherwise challenging to identify at scale. Overall, Med-V1 provides an efficient and accurate lightweight alternative to frontier LLMs for practical and real-world applications in biomedical evidence attribution and verification tasks. Med-V1 is available at https://github.com/ncbi-nlp/Med-V1.

Recent advances in generative models, including large language models (LLMs), vision language models (VLMs), and diffusion models, have accelerated the field of natural language and image processing in medicine and marked a significant paradigm shift in how biomedical models can be developed and deployed. While these models are highly adaptable to new tasks, scaling and evaluating their usage presents new challenges not addressed in previous frameworks. In particular, the ability of these models to produce useful outputs with little to no specialized training data ("zero-" or "few-shot" approaches), as well as the open-ended nature of their outputs, necessitate the development of new guidelines for robust reporting of clinical generative model research. In response to gaps in standards and best practices for the development of clinical AI tools identified by US Executive Order 141103 and several emerging national networks for clinical AI evaluation, we begin to formalize some of these guidelines by building on the original MI-CLAIM checklist. The new checklist, MI-CLAIM-GEN (Table 1), aims to address differences in training, evaluation, interpretability, and reproducibility of new generative models compared to non-generative ("predictive") AI models. This MI-CLAIM-GEN checklist also seeks to clarify cohort selection reporting with unstructured clinical data and adds additional items on alignment with ethical standards for clinical AI research.

Large language models (LLMs) are transforming the landscape of medicine, yet two fundamental challenges persist: keeping up with rapidly evolving medical knowledge and providing verifiable, evidence-grounded reasoning. Retrieval-augmented generation (RAG) has been widely adopted to address these limitations by supplementing model outputs with retrieved evidence. However, whether RAG reliably achieves these goals remains unclear. Here, we present the most comprehensive expert evaluation of RAG in medicine to date. Eighteen medical experts contributed a total of 80,502 annotations, assessing 800 model outputs generated by GPT-4o and Llama-3.1-8B across 200 real-world patient and USMLE-style queries. We systematically decomposed the RAG pipeline into three components: (i) evidence retrieval (relevance of retrieved passages), (ii) evidence selection (accuracy of evidence usage), and (iii) response generation (factuality and completeness of outputs). Contrary to expectation, standard RAG often degraded performance: only 22% of top-16 passages were relevant, evidence selection remained weak (precision 41-43%, recall 27-49%), and factuality and completeness dropped by up to 6% and 5%, respectively, compared with non-RAG variants. Retrieval and evidence selection remain key failure points for the model, contributing to the overall performance drop. We further show that simple yet effective strategies, including evidence filtering and query reformulation, substantially mitigate these issues, improving performance on MedMCQA and MedXpertQA by up to 12% and 8.2%, respectively. These findings call for re-examining RAG's role in medicine and highlight the importance of stage-aware evaluation and deliberate system design for reliable medical LLM applications.

International Classification of Diseases (ICD) coding assigns diagnosis codes to clinical documents and is essential for healthcare billing and clinical analysis. Reliable coding requires that each predicted code be supported by explicit textual evidence. However, existing public datasets provide only code labels, without evidence annotations, limiting models' ability to learn evidence-grounded predictions. In this work, we argue that dense, document-level evidence annotation is not always necessary for learning evidence-based coding. Instead, models can learn code-specific evidence patterns from local spans and use these patterns to support document-level evidence-based coding. Based on this insight, we propose Span-Centric Learning (SCL), a training framework that strengthens LLMs' coding ability at the span level and transfers this capability to full clinical documents. Specifically, we use a small set of annotated documents to supervise evidence recognition, aggregation, and code assignment, while leveraging a large collection of lightweight evidence spans to reinforce span-level reasoning. Due to their compactness, span annotations are scalable and can be further augmented through synthesis. Under the same Llama3.1-8B backbone, our approach achieves an 8.2-point improvement in macro-F1 at only 20% of the training cost of standard SFT, and provides explicit supporting evidence for each predicted code, enabling human auditing and revision.

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

Modern multi-agent knowledge systems increasingly accumulate knowledge through chains of autonomous transformations rather than direct retrieval. Existing provenance work records what happened - execution traces, tool calls, evidence links - and source-reliability estimation is long established (truth discovery, reputation systems). What is missing is an operational framework that attaches graded, per-domain transmitter reliability to claim-level transmission chains, with completeness semantics, transformation-typed aggregation, decoupled content criticism, and serve/review/quarantine routing. Classical Islamic hadith science confronted a structurally similar problem: deciding whether knowledge transmitted through chains of human narrators should be accepted. Over centuries it developed a rigorous methodology - isnad (a complete transmission chain attached to every claim), rijal (systematic grading of each narrator's integrity and precision), weakest-link chain evaluation, corroboration through independent chains, and matn criticism (content evaluated independently of chain quality). This paper transfers that methodology to AI system design. We contribute a formal mapping from hadith-science concepts to multi-agent pipelines, a relational schema implementing claim chains and a graded narrator registry, a decision matrix combining chain grade with content criticism, and an evaluation on 20,000 claims from real physics textbooks. The evaluation validates weakest-link quarantine and independent-chain corroboration; reports a partial failure of the grade-recovery loop, which missed the highest-fault narrator; and reports two analyses as inconclusive, including a matched-coverage comparison the framework could not reach with the reference content critic. The paper is explicit throughout about which claims the evidence does and does not yet support.

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

Structural fidelity is essential to scientific methodology diagrams. To communicate research logic, these diagrams must faithfully render components, directional relations, and textual annotations. Since a single error, such as a reversed arrow or an unreadable equation, can invalidate the entire figure, structural fidelity is inherently conjunctive: correctness on one axis cannot compensate for failure on another. Current open-source models fail to satisfy this criterion. Supervised fine-tuning (SFT) learns plausible layouts but cannot reliably ensure structural correctness, while scalar reward-based post-training obscures which structural dimension has failed. To address this, we introduce SciForma, a framework for the structure faithful generation of scientific methodology diagrams. Specifically, SciForma decomposes diagram quality into three structural axes: Component, Arrow, and Text, guided by a structural inventory. Built on this foundation, we curate SciFormaData-700K for structured training and SciFormaBench-2K for logic-verified evaluation. To close the gap left by SFT, we develop Multi-Dimensional Conjunctive Preference Optimization (M-DPO), which enforces simultaneous correctness across all axes and adaptively routes gradients to the most deficient dimension in post-training. The same structural inventory also enables iterative editing at inference time to correct residual errors. This combination allows SciForma-9B to exceed all open-source baselines and GPT-Image-1.5 on both SciFormaBench-2K and AIBench, bringing open scientific diagram generation close to proprietary-level structural fidelity. Our code and data will be available at: https://github.com/microsoft/SciForma.

AI systems can now cheaply generate plausible scientific artifacts such as papers, reviews, and surveys. This creates a risk of epistemic pollution in our scientific systems, where unreliable but plausible-looking artifacts can accumulate faster than the system can filter them out. The problem is structural: the epistemic infrastructure of science was calibrated to a world where producing a plausible artifact required substantial expertise, labor, and time, so generation cost itself served as a rough filter; AI weakens that filter without comparably lowering verification cost. We argue that AI-era science should treat this as an engineering problem: redesigning epistemic infrastructure to rebalance the costs of generation and verification. The current paper-centered system makes verification expensive: papers compress long-context scientific logic into prose, forcing reviewers, human or AI, to reconstruct underlying argument structure before they can evaluate it. As one step in this direction, we propose blueprints as preliminary epistemic infrastructure: structured, decomposed research artifacts that represent claims, evidence, assumptions, and definitions as typed graph components. Blueprints are designed to trade an upfront generation cost for cheaper, more local, more distributed verification downstream. We have instantiated the proposal in a proof-of-concept prototype.

Learning causal structure from observational data often assumes that we observe independent and identically distributed (i.\,i.\,d) data. The traditional approach aims to find a graphical representation that encodes the same set of conditional independence relationships as those present in the observed distribution. It is known that under i.\,i.\,d assumption, even with infinite data, there is a limit to how fine-grained a causal structure we can identify. To overcome this limitation, recent work has explored using data originating from different, related environments to learn richer causal structure. These approaches implicitly rely on the independent causal mechanisms (ICM) principle, which postulates that the mechanism giving rise to an effect given its causes and the mechanism which generates the causes do not inform or influence each other. Thus, components of the causal model can independently change from environment to environment. Despite its wide application in machine learning and causal inference, there is a lack of statistical formalization of the ICM principle and how it enables identification of richer causal structures from grouped data. Here we present new causal de Finetti theorems which offer a first statistical formalization of ICM principle and show how causal structure identification is possible from exchangeable data. Our work provides theoretical justification for a broad range of techniques leveraging multi-environment data to learn causal structure.

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.

The increasing adoption of large language models (LLMs) has been accompanied by growing concerns regarding their reliability and trustworthiness. As a result, a growing body of research focuses on evidence-based text generation with LLMs, aiming to link model outputs to supporting evidence to ensure traceability and verifiability. However, the field is fragmented due to inconsistent terminology, isolated evaluation practices, and a lack of unified benchmarks. To bridge this gap, we systematically analyze 134 papers, introduce a unified taxonomy of evidence-based text generation with LLMs, and investigate 300 evaluation metrics across seven key dimensions. Thereby, we focus on approaches that use citations, attribution, or quotations for evidence-based text generation. Building on this, we examine the distinctive characteristics and representative methods in the field. Finally, we highlight open challenges and outline promising directions for future work.

Generative modeling has emerged as a promising approach for crystal structure discovery. However, existing LLM-based generative models struggle with low-level atomic precision, while diffusion-based methods fall short in integrating high-level scientific knowledge. As a result, generated structures are often invalid, unstable, or do not possess desirable properties. To address this gap, we propose CrystalReasoner (\method), an end-to-end LLM framework that generates crystal structures from natural language instructions through reasoning and alignment. \method introduces physical priors as thinking tokens, which include crystallographic symmetry, local coordination environments and predicted physical properties before generating atomic coordinates. This bridges the gap between natural language and 3D structures. \method then employs reinforcement learning (RL) with a multi-objective, dense reward function to align generation with physical validity, chemical consistency, and thermodynamic stability. For property-conditioned tasks, we design task-specific reward functions and train specialized models for discrete constraints (e.g., space group) and continuous properties (e.g., elasticity, thermal expansion). Empirical results demonstrate that compared to prior works and baselines without thinking traces or RL, \method obtains better performance on diverse metrics, triples S.U.N. ratio, and achieves better performance for property conditioned generation. \method also exhibits adaptive reasoning, increasing reasoning lengths as the number of atoms increases. Our work demonstrates the potential of leveraging thinking traces and RL for generating valid, stable, and property-conditioned crystal structures. Please see our work at https://crystalreasoner.github.io/ .

Reliable epidemiological reasoning requires synthesizing study evidence to infer disease burden, transmission dynamics, and intervention effects at the population level. Existing medical question answering benchmarks primarily emphasize clinical knowledge or patient-level reasoning, yet few systematically evaluate evidence-grounded epidemiological inference. We present EpiQAL, the first diagnostic benchmark for epidemiological question answering across diverse diseases, comprising three subsets built from open-access literature. The subsets respectively evaluate text-grounded factual recall, multi-step inference linking document evidence with epidemiological principles, and conclusion reconstruction with the Discussion section withheld. Construction combines expert-designed taxonomy guidance, multi-model verification, and retrieval-based difficulty control. Experiments on ten open models reveal that current LLMs show limited performance on epidemiological reasoning, with multi-step inference posing the greatest challenge. Model rankings shift across subsets, and scale alone does not predict success. Chain-of-Thought prompting benefits multi-step inference but yields mixed results elsewhere. EpiQAL provides fine-grained diagnostic signals for evidence grounding, inferential reasoning, and conclusion reconstruction.

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

Scientific research follows multi-turn, multi-step workflows that require proactively searching the literature, consulting figures and tables, and integrating evidence across papers to align experimental settings and support reproducible conclusions. This joint capability is not systematically assessed in existing benchmarks, which largely under-evaluate proactive search, multi-evidence integration and sustained evidence use over time. In this work, we introduce EpiBench, an episodic multi-turn multimodal benchmark that instantiates short research workflows. Given a research task, agents must navigate across papers over multiple turns, align evidence from figures and tables, and use the accumulated evidence in the memory to answer objective questions that require cross paper comparisons and multi-figure integration. EpiBench introduces a process-level evaluation framework for fine-grained testing and diagnosis of research agents. Our experiments show that even the leading model achieves an accuracy of only 29.23% on the hard split, indicating substantial room for improvement in multi-turn, multi-evidence research workflows, providing an evaluation platform for verifiable and reproducible research agents.

Retrieval-Augmented Generation (RAG) has become a powerful and widely used approach for improving large language models by grounding generation in retrieved evidence. However, RAG systems still produce incorrect answers in many cases. Why RAG fails despite having access to external information remains poorly understood. We present a model-internal study of retrieval-augmented generation that examines how retrieved evidence influences answer generation. Using circuit tracing, we construct attribution graphs that model the flow of information through transformer layers during decoding. These graphs represent interactions among retrieved context, intermediate model activations, and generated tokens, providing a graph, circuit-level view of how external evidence is integrated into the model's reasoning process across multiple question answering benchmarks, we observe consistent structural differences: correct predictions exhibit deeper reasoning paths, more distributed evidence flow, and a more structured pattern of local connectivity, while failed predictions show shallower, fragmented, and overly concentrated evidence flow. Building on these findings, we develop a graph-based error detection framework that uses attribution-graph topology features. Furthermore, we show that attribution graphs enable targeted interventions. By reinforcing question-constrained evidence grounding, we reshape internal routing so that answer generation remains guided by the question, leading to more effective integration of retrieved information and fewer errors.

Deep Research Agents are a prominent category of LLM-based agents. By autonomously orchestrating multistep web exploration, targeted retrieval, and higher-order synthesis, they transform vast amounts of online information into analyst-grade, citation-rich reports--compressing hours of manual desk research into minutes. However, a comprehensive benchmark for systematically evaluating the capabilities of these agents remains absent. To bridge this gap, we present DeepResearch Bench, a benchmark consisting of 100 PhD-level research tasks, each meticulously crafted by domain experts across 22 distinct fields. Evaluating DRAs is inherently complex and labor-intensive. We therefore propose two novel methodologies that achieve strong alignment with human judgment. The first is a reference-based method with adaptive criteria to assess the quality of generated research reports. The other framework is introduced to evaluate DRA's information retrieval and collection capabilities by assessing its effective citation count and overall citation accuracy. We have open-sourced DeepResearch Bench and key components of these frameworks at https://github.com/Ayanami0730/deep_research_bench to accelerate the development of practical LLM-based agents.

Despite remarkable advances in the field, LLMs remain unreliable in distinguishing causation from correlation. Recent results from the Corr2Cause dataset benchmark reveal that state-of-the-art LLMs -- such as GPT-4 (F1 score: 29.08) -- only marginally outperform random baselines (Random Uniform, F1 score: 20.38), indicating limited capacity of generalization. To tackle this limitation, we propose a novel structured approach: rather than directly answering causal queries, we provide the model with the capability to structure its thinking by guiding the model to build a structured knowledge graph, systematically encoding the provided correlational premises, to answer the causal queries. This intermediate representation significantly enhances the model's causal capabilities. Experiments on the test subset of the Corr2Cause dataset benchmark with Qwen3-32B model (reasoning model) show substantial gains over standard direct prompting methods, improving F1 scores from 32.71 to 48.26 (over 47.5% relative increase), along with notable improvements in precision and recall. These results underscore the effectiveness of providing the model with the capability to structure its thinking and highlight its promising potential for broader generalization across diverse causal inference tasks.

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

Heterogeneous tabular data poses unique challenges in generative modelling due to its fundamentally different underlying data structure compared to homogeneous modalities, such as images and text. Although previous research has sought to adapt the successes of generative modelling in homogeneous modalities to the tabular domain, defining an effective generator for tabular data remains an open problem. One major reason is that the evaluation criteria inherited from other modalities often fail to adequately assess whether tabular generative models effectively capture or utilise the unique structural information encoded in tabular data. In this paper, we carefully examine the limitations of the prevailing evaluation framework and introduce TabStruct, a novel evaluation benchmark that positions structural fidelity as a core evaluation dimension. Specifically, TabStruct evaluates the alignment of causal structures in real and synthetic data, providing a direct measure of how effectively tabular generative models learn the structure of tabular data. Through extensive experiments using generators from eight categories on seven datasets with expert-validated causal graphical structures, we show that structural fidelity offers a task-independent, domain-agnostic evaluation dimension. Our findings highlight the importance of tabular data structure and offer practical guidance for developing more effective and robust tabular generative models. Code is available at https://github.com/SilenceX12138/TabStruct.

How do we most effectively treat a disease or condition? Ideally, we could consult a database of evidence gleaned from clinical trials to answer such questions. Unfortunately, no such database exists; clinical trial results are instead disseminated primarily via lengthy natural language articles. Perusing all such articles would be prohibitively time-consuming for healthcare practitioners; they instead tend to depend on manually compiled systematic reviews of medical literature to inform care. NLP may speed this process up, and eventually facilitate immediate consult of published evidence. The Evidence Inference dataset was recently released to facilitate research toward this end. This task entails inferring the comparative performance of two treatments, with respect to a given outcome, from a particular article (describing a clinical trial) and identifying supporting evidence. For instance: Does this article report that chemotherapy performed better than surgery for five-year survival rates of operable cancers? In this paper, we collect additional annotations to expand the Evidence Inference dataset by 25\%, provide stronger baseline models, systematically inspect the errors that these make, and probe dataset quality. We also release an abstract only (as opposed to full-texts) version of the task for rapid model prototyping. The updated corpus, documentation, and code for new baselines and evaluations are available at http://evidence-inference.ebm-nlp.com/.

Observational studies can yield clinically actionable evidence at scale, but executing them on real-world databases is open-ended and requires coherent decisions across cohort construction, analysis, and reporting. Prior evaluations of LLM agents emphasize isolated steps or single answers, missing the integrity and internal structure of the resulting evidence bundle. To address this gap, we introduce RWE-bench, a benchmark grounded in MIMIC-IV and derived from peer-reviewed observational studies. Each task provides the corresponding study protocol as the reference standard, requiring agents to execute experiments in a real database and iteratively generate tree-structured evidence bundles. We evaluate six LLMs (three open-source, three closed-source) under three agent scaffolds using both question-level correctness and end-to-end task metrics. Across 162 tasks, task success is low: the best agent reaches 39.9%, and the best open-source model reaches 30.4%. Agent scaffolds also matter substantially, causing over 30% variation in performance metrics. Furthermore, we implement an automated cohort evaluation method to rapidly localize errors and identify agent failure modes. Overall, the results highlight persistent limitations in agents' ability to produce end-to-end evidence bundles, and efficient validation remains an important direction for future work. Code and data are available at https://github.com/somewordstoolate/RWE-bench.

We present a complete theoretical characterization of Latent Posterior Factors (LPF), a principled framework for aggregating multiple heterogeneous evidence items in probabilistic prediction tasks. Multi-evidence reasoning arises pervasively in high-stakes domains including healthcare diagnosis, financial risk assessment, legal case analysis, and regulatory compliance, yet existing approaches either lack formal guarantees or fail to handle multi-evidence scenarios architecturally. LPF encodes each evidence item into a Gaussian latent posterior via a variational autoencoder, converting posteriors to soft factors through Monte Carlo marginalization, and aggregating factors via exact Sum-Product Network inference (LPF-SPN) or a learned neural aggregator (LPF-Learned). We prove seven formal guarantees spanning the key desiderata for trustworthy AI: Calibration Preservation (ECE <= epsilon + C/sqrt(K_eff)); Monte Carlo Error decaying as O(1/sqrt(M)); a non-vacuous PAC-Bayes bound with train-test gap of 0.0085 at N=4200; operation within 1.12x of the information-theoretic lower bound; graceful degradation as O(epsilon*delta*sqrt(K)) under corruption, maintaining 88% performance with half of evidence adversarially replaced; O(1/sqrt(K)) calibration decay with R^2=0.849; and exact epistemic-aleatoric uncertainty decomposition with error below 0.002%. All theorems are empirically validated on controlled datasets spanning up to 4,200 training examples. Our theoretical framework establishes LPF as a foundation for trustworthy multi-evidence AI in safety-critical applications.

Model cards describe model behavior through a mixture of textual descriptions and structured artifacts, including performance, configuration, and dataset tables. Existing model search systems rely predominantly on semantic similarity over text, which can produce homogeneous result sets and limit exploration of alternatives. We argue that model search is inherently comparative: users want models that are task-aligned yet differentiated in measurable ways. We hypothesize that this balance requires retrieval over condensed, high-quality evidence rather than verbose descriptions, and much of that evidence is concentrated in structured tables. We present StructuredSemanticSearch, a table-driven model search framework built on the ModelTables benchmark. Given a query, StructuredSemanticSearch combines a semantic baseline for task alignment with a structure-aware pipeline that discovers query-related model-card tables using table discovery operators such as unionability, joinability, and keyword search. Retrieved tables are mapped back to model cards under a controlled top-k budget, enabling fair comparison between text-based and table-based retrieval. Beyond retrieval, StructuredSemanticSearch adapts table integration to the model-table domain through orientation-aware integration, producing compact integrated views of tables from partially overlapping and sometimes transposed evidence tables. For evaluation, we introduce a nugget-based, auditable protocol that extracts compact evidence items from model cards, matches queries to condition- or intent-specific nuggets, and measures evidence coverage and diversity over retrieved model-card candidate sets. This protocol also provides a scalable path toward approximate, evidence-based labeling in dynamic model lakes. Experiments on 597 model-recommendation queries show improved nugget coverage for the structure-aware pipeline than semantic baseline

Causal discovery, the process of recovering underlying causal structures from observational data, is a fundamental pursuit across scientific disciplines. Over the past decades, numerous algorithms have been developed to tackle this challenge through workflows tailored to the specific causal mechanisms underlying each type of dataset, demonstrating effectiveness across a wide range of applications. However, as the volume and heterogeneity of real-world data continue to grow, this dataset-specific approach inevitably leads to a fragmented, test-driven paradigm that struggles to scale to the demands of modern scientific discovery. To address this, we formulate the Causal Discovery Foundation Model (CDFM) as a unified, general-purpose framework for zero-shot structural inference. To ensure reliable generalization across unknown domains, we first investigate the theoretical boundaries of causal identifiability, revealing the indispensable role of causal prior mechanisms in this process. Building on these insights, we formulate a principled variational framework that treats unknown causal mechanisms as latent variables and mathematically decomposes the intractable marginal likelihood into distinct, tractable learning modules. The variational decomposition provides a conceptual design principle for the architecture design of CDFM, while comprehensive causal knowledge guides the large-scale synthesis of our pretraining data. By pretraining on a massive, highly diverse space of synthetic structural causal models, CDFM successfully internalizes complex statistical asymmetries. Extensive experiments demonstrate that CDFM consistently outperforms traditional algorithms, driving a paradigm shift toward a general-purpose causal discovery foundation model.

Scientific ideas rarely start from a blank page. They inherit mechanisms, repair known limitations, and recombine pieces of earlier work, much like biological genomes. Current benchmarks still say little about whether AI systems can follow this inheritance structure. We present IdeaGene-Bench (IG-Bench), a benchmark for scientific lineage reasoning and lineage-grounded idea generation. IG-Bench is organized around the IdeaGene framework: each paper or proposal is represented as a set of minimal, typed, evidence-grounded Idea Genome objects, and a GenomeDiff aligns these objects to record inheritance, mutation, loss, external import, and novel insertion under six operational evolutionary dynamics. The benchmark contains 1,961 golden lineage traces, 1,085 curated Idea Genome objects, and 920 pairwise GenomeDiff records across 10 scientific domains. It supports two evaluations. IG-Exam (42 task types, 1,029 instances) tests closed-form lineage reasoning across Idea Genome abstraction, inheritance tracing, evolutionary reasoning, and lineage verification. IG-Arena evaluates generation with a lineage-conditioned Population-Evolution Score(PES), asking whether a proposal can be inserted as a coherent descendant of a given lineage population: it should inherit the right Idea Genome objects, vary meaningfully from nearby work, and offer selection value for future research. Experiments on 14 LLM-based scientists expose a compositional bottleneck. The strongest system reaches only 27.3% exact accuracy on lineage reasoning, and structured lineage context reshuffles system rankings rather than helping every participant uniformly.

Traditional ontologies describe domain structure but cannot generate novel artifacts. Large language models generate fluently but produce outputs lacking structural validity, hallucinating mechanisms without components, goals without end conditions. We introduce Generative Ontology, a framework synthesizing these complementary strengths: ontology provides the grammar; the LLM provides the creativity. Generative Ontology encodes domain knowledge as executable Pydantic schemas constraining LLM generation via DSPy signatures. A multi-agent pipeline assigns specialized roles: a Mechanics Architect designs game systems, a Theme Weaver integrates narrative, a Balance Critic identifies exploits, each carrying a professional "anxiety" that prevents shallow outputs. Retrieval-augmented generation grounds designs in precedents from existing exemplars. We demonstrate the framework through GameGrammar, generating complete tabletop game designs, and present three empirical studies. An ablation study (120 designs, 4 conditions) shows multi-agent specialization produces the largest quality gains (fun d=1.12, depth d=1.59; p<.001), while schema validation eliminates structural errors (d=4.78). A benchmark against 20 published board games reveals structural parity but a bounded creative gap (fun d=1.86): generated designs score 7-8 while published games score 8-9. A test-retest study (50 evaluations) validates the LLM-based evaluator, with 7/9 metrics achieving Good-to-Excellent reliability (ICC 0.836-0.989). The pattern generalizes beyond games. Any domain with expert vocabulary, validity constraints, and accumulated exemplars is a candidate for Generative Ontology.

While large language models (LLMs) like GPT-4 have recently demonstrated astonishing zero-shot capabilities in general domain tasks, they often generate content with hallucinations in specific domains such as Chinese law, hindering their application in these areas. This is typically due to the absence of training data that encompasses such a specific domain, preventing GPT-4 from acquiring in-domain knowledge. A pressing challenge is that it's not plausible to continue training LLMs of such scale on in-domain data. This paper introduces a simple and effective domain adaptation framework for GPT-4 by reformulating generation as an adapt-retrieve-revise process. The initial step is to adapt an affordable 7B LLM to the target domain by continuing learning on in-domain data. When solving a task, we leverage the adapted LLM to generate a draft answer given a task query. Then, the draft answer will be used to retrieve supporting evidence candidates from an external in-domain knowledge base. Finally, the draft answer and retrieved evidence are concatenated into a whole prompt to let GPT-4 assess the evidence and revise the draft answer to generate the final answer. Our proposal combines the advantages of the efficiency of adapting a smaller 7B model with the evidence-assessing capability of GPT-4 and effectively prevents GPT-4 from generating hallucinatory content. In the zero-shot setting of four Chinese legal tasks, our method improves accuracy by 33.3\% compared to the direct generation by GPT-4. When compared to two stronger retrieval-based baselines, our method outperforms them by 15.4\% and 23.9\%. Our code will be released

Large language models produce fluent text but struggle with systematic reasoning, often hallucinating confident but unfounded claims. When Apple researchers added irrelevant context to mathematical problems, LLM performance degraded by 65% Apple Machine Learning Research, exposing brittle pattern-matching beneath apparent reasoning. This epistemic gap, the inability to ground claims in traceable evidence, limits AI reliability in domains requiring justification. We introduce Pramana, a novel approach that teaches LLMs explicit epistemological methodology by fine-tuning on Navya-Nyaya logic, a 2,500-year-old Indian reasoning framework. Unlike generic chain-of-thought prompting, Navya-Nyaya enforces structured 6-phase reasoning: SAMSHAYA (doubt analysis), PRAMANA (evidence source identification), PANCHA AVAYAVA (5-member syllogism with universal rules), TARKA (counterfactual verification), HETVABHASA (fallacy detection), and NIRNAYA (ascertainment distinguishing knowledge from hypothesis). This integration of logic and epistemology provides cognitive scaffolding absent from standard reasoning approaches. We fine-tune Llama 3.2-3B and DeepSeek-R1-Distill-Llama-8B on 55 Nyaya-structured logical problems (constraint satisfaction, Boolean SAT, multi-step deduction). Stage 1 achieves 100% semantic correctness on held-out evaluation despite only 40% strict format adherence revealing that models internalize reasoning content even when structural enforcement is imperfect. Ablation studies show format prompting and temperature critically affect performance, with optimal configurations differing by stage. We release all models, datasets, and training infrastructure on Hugging Face to enable further research on epistemic frameworks for AI reasoning.

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.

AI research often requires decisions before future evidence exists: which bottleneck to attack, which direction to pursue, or where a project should be positioned. We introduce ForeSci, a temporally controlled benchmark for evaluating whether LLM agents can make such forward-looking research judgements from historical evidence. ForeSci contains 500 tasks across four fast-moving AI domains and four decision families. Each task is paired with a cutoff-aligned offline knowledge base; post-cutoff papers are hidden during generation and used only for validation. To avoid random future-event prediction, tasks are derived from pre-cutoff taxonomy branches and evidence signals, and answer-generation backbones are selected to precede the task cutoffs. We evaluate native LLMs, Hybrid RAG, and three research-agent adaptations across four backbones. Results show that explicit evidence organization improves traceability and factual support, but gains depend strongly on the decision family. Diagnostics reveal a recurring evidence-decision decoupling: agents may cite relevant evidence while forecasting the wrong research object. ForeSci turns forward-looking AI research judgement into a controlled benchmark for evaluating research agents as decision-making systems.

Large-taxonomy retrieval often assumes that the input already expresses the target concept. In many settings, however, the input is indirect evidence, such as a table cell whose meaning depends on its row, column, datatype, and context. We call this mismatch the retrieval readiness gap. Our analysis shows that the current index retrieves the target reliably when its semantics are explicit, while raw evidence often leaves it deep in the ranking. We propose Factorized Hypothesis Search (FHS), which maintains multiple partial interpretations over named semantic dimensions. These hypotheses support structured query rendering, multi-hypothesis retrieval, and dimension-level candidate verification. On both financial taxonomy tagging and CodiEsp clinical coding tasks, FHS achieves the best Recall@1, MRR, and final accuracy among the non-oracle methods. Replacing the factorized hypothesis path with a free-text ensemble causes the largest drop in head-ranking performance, while sequential refinement provides no additional gain over FHS's strong parallel first round.

Generative Foundation Models (GenFMs) have emerged as transformative tools. However, their widespread adoption raises critical concerns regarding trustworthiness across dimensions. This paper presents a comprehensive framework to address these challenges through three key contributions. First, we systematically review global AI governance laws and policies from governments and regulatory bodies, as well as industry practices and standards. Based on this analysis, we propose a set of guiding principles for GenFMs, developed through extensive multidisciplinary collaboration that integrates technical, ethical, legal, and societal perspectives. Second, we introduce TrustGen, the first dynamic benchmarking platform designed to evaluate trustworthiness across multiple dimensions and model types, including text-to-image, large language, and vision-language models. TrustGen leverages modular components--metadata curation, test case generation, and contextual variation--to enable adaptive and iterative assessments, overcoming the limitations of static evaluation methods. Using TrustGen, we reveal significant progress in trustworthiness while identifying persistent challenges. Finally, we provide an in-depth discussion of the challenges and future directions for trustworthy GenFMs, which reveals the complex, evolving nature of trustworthiness, highlighting the nuanced trade-offs between utility and trustworthiness, and consideration for various downstream applications, identifying persistent challenges and providing a strategic roadmap for future research. This work establishes a holistic framework for advancing trustworthiness in GenAI, paving the way for safer and more responsible integration of GenFMs into critical applications. To facilitate advancement in the community, we release the toolkit for dynamic evaluation.

While Retrieval-Augmented Generation (RAG) mitigates hallucination and knowledge staleness in Large Language Models (LLMs), existing frameworks often falter on complex, multi-hop queries that require synthesizing information from disparate sources. Current advanced RAG methods, employing iterative or adaptive strategies, lack a robust mechanism to systematically identify and fill evidence gaps, often propagating noise or failing to gather a comprehensive context. We introduce FAIR-RAG, a novel agentic framework that transforms the standard RAG pipeline into a dynamic, evidence-driven reasoning process. At its core is an Iterative Refinement Cycle governed by a module we term Structured Evidence Assessment (SEA). The SEA acts as an analytical gating mechanism: it deconstructs the initial query into a checklist of required findings and audits the aggregated evidence to identify confirmed facts and, critically, explicit informational gaps. These gaps provide a precise signal to an Adaptive Query Refinement agent, which generates new, targeted sub-queries to retrieve missing information. This cycle repeats until the evidence is verified as sufficient, ensuring a comprehensive context for a final, strictly faithful generation. We conducted experiments on challenging multi-hop QA benchmarks, including HotpotQA, 2WikiMultiHopQA, and MusiQue. In a unified experimental setup, FAIR-RAG significantly outperforms strong baselines. On HotpotQA, it achieves an F1-score of 0.453 -- an absolute improvement of 8.3 points over the strongest iterative baseline -- establishing a new state-of-the-art for this class of methods on these benchmarks. Our work demonstrates that a structured, evidence-driven refinement process with explicit gap analysis is crucial for unlocking reliable and accurate reasoning in advanced RAG systems for complex, knowledge-intensive tasks.

Scientific surveys require not only summarizing large bodies of literature, but also organizing them into clear and coherent conceptual structures. Existing automatic survey generation methods typically focus on linear text generation and struggle to explicitly model hierarchical relations among research topics and structured methodological comparisons, resulting in gaps in structural organization compared to expert-written surveys. We propose MVSS, a multi-view structured survey generation framework that jointly generates and aligns citation-grounded hierarchical trees, structured comparison tables, and survey text. MVSS follows a structure-first paradigm: it first constructs a conceptual tree of the research domain, then generates comparison tables constrained by the tree, and finally uses both as structural constraints for text generation. This enables complementary multi-view representations across structure, comparison, and narrative. We introduce an evaluation framework assessing structural quality, comparative completeness, and citation fidelity. Experiments on 76 computer science topics show MVSS outperforms existing methods in organization and evidence grounding, achieving performance comparable to expert surveys.

We propose a novel hierarchical Bayesian model for learning with a large (possibly infinite) number of tasks/episodes, which suits well the few-shot meta learning problem. We consider episode-wise random variables to model episode-specific target generative processes, where these local random variables are governed by a higher-level global random variate. The global variable helps memorize the important information from historic episodes while controlling how much the model needs to be adapted to new episodes in a principled Bayesian manner. Within our model framework, the prediction on a novel episode/task can be seen as a Bayesian inference problem. However, a main obstacle in learning with a large/infinite number of local random variables in online nature, is that one is not allowed to store the posterior distribution of the current local random variable for frequent future updates, typical in conventional variational inference. We need to be able to treat each local variable as a one-time iterate in the optimization. We propose a Normal-Inverse-Wishart model, for which we show that this one-time iterate optimization becomes feasible due to the approximate closed-form solutions for the local posterior distributions. The resulting algorithm is more attractive than the MAML in that it is not required to maintain computational graphs for the whole gradient optimization steps per episode. Our approach is also different from existing Bayesian meta learning methods in that unlike dealing with a single random variable for the whole episodes, our approach has a hierarchical structure that allows one-time episodic optimization, desirable for principled Bayesian learning with many/infinite tasks. The code is available at https://github.com/minyoungkim21/niwmeta.

We establish a fundamental connection between optimal structure learning and optimal conditional independence testing by showing that the minimax optimal rate for structure learning problems is determined by the minimax rate for conditional independence testing in these problems. This is accomplished by establishing a general reduction between these two problems in the case of poly-forests, and demonstrated by deriving optimal rates for several examples, including Bernoulli, Gaussian and nonparametric models. Furthermore, we show that the optimal algorithm in these settings is a suitable modification of the PC algorithm. This theoretical finding provides a unified framework for analyzing the statistical complexity of structure learning through the lens of minimax testing.

Autonomous research systems increasingly make the scientific workflow executable: agents can propose ideas, run code, inspect results, and draft papers. But executable workflows do not by themselves produce research judgment. We analyze where current systems lose trial experience: weak evidence becomes prose, pilot signals become broad claims, memory remains textual, and recurring process failures do not change later behavior. We introduce Sibyl-AutoResearch, a self-evolving AutoResearch framework built around Scientific Trial-and-Error Harnesses. A harness lets agents run bounded trials, preserve positive and negative outcomes, and route lessons into later planning, validation, claim scope, scheduling, critique, writing, and harness repair. We formalize this through two auditable conversion units: trial-to-behavior conversion, which links trial signals to later research actions, and trial-to-harness-behavior conversion, which links recurring process failures to system updates. We implement the framework in SIBYL, a file-backed autonomous research system that exposes the state, roles, memory, gates, and artifact traces needed to inspect these conversion paths. A retrospective audit identifies eight high-confidence conversion events, with a median latency of one iteration and a maximum latency of three iterations. A recovered-failure registry further shows how five naturally occurring failure classes, including duplicate results, stale numbers, and unsupported statistics, were blocked, downgraded, or routed into later repair. These traces do not establish a comparative performance claim; they show that the proposed conversion units are recoverable from realistic autonomous-research workspaces. The SIBYL framework and system are available at https://github.com/Sibyl-Research-Team/AutoResearch-SibylSystem.

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

Schema-guided reasoning pipelines ask LLMs to produce explicit intermediate structures -- rubrics, checklists, verification queries -- before committing to a final decision. But do these structures causally determine the output, or merely accompany it? We introduce a causal evaluation protocol that makes this directly measurable: by selecting tasks where a deterministic function maps intermediate structures to decisions, every controlled edit implies a unique correct output. Across eight models and three benchmarks, models appear self-consistent with their own intermediate structures but fail to update predictions after intervention in up to 60% of cases -- revealing that apparent faithfulness is fragile once the intermediate structure changes. When derivation of the final decision from the structure is delegated to an external tool, this fragility largely disappears; however, prompts which ask to prioritize the intermediate structure over the original input do not materially close the gap. Overall, intermediate structures in schema-guided pipelines function as influential context rather than stable causal mediators.

Data-driven social science research is inherently slow, relying on iterative cycles of observation, hypothesis generation, and experimental validation. While recent data-driven methods promise to accelerate parts of this process, they largely fail to support end-to-end scientific discovery. To address this gap, we introduce EXPERIGEN, an agentic framework that operationalizes end-to-end discovery through a Bayesian optimization inspired two-phase search, in which a Generator proposes candidate hypotheses and an Experimenter evaluates them empirically. Across multiple domains, EXPERIGEN consistently discovers 2-4x more statistically significant hypotheses that are 7-17 percent more predictive than prior approaches, and naturally extends to complex data regimes including multimodal and relational datasets. Beyond statistical performance, hypotheses must be novel, empirically grounded, and actionable to drive real scientific progress. To evaluate these qualities, we conduct an expert review of machine-generated hypotheses, collecting feedback from senior faculty. Among 25 reviewed hypotheses, 88 percent were rated moderately or strongly novel, 70 percent were deemed impactful and worth pursuing, and most demonstrated rigor comparable to senior graduate-level research. Finally, recognizing that ultimate validation requires real-world evidence, we conduct the first A/B test of LLM-generated hypotheses, observing statistically significant results with p less than 1e-6 and a large effect size of 344 percent.

First-order logic (FOL) reasoning, which involves sequential deduction, is pivotal for intelligent systems and serves as a valuable task for evaluating reasoning capabilities, particularly in chain-of-thought (CoT) contexts. Existing benchmarks often rely on extensive human annotation or handcrafted templates, making it difficult to achieve the necessary complexity, scalability, and diversity for robust evaluation. To address these limitations, we propose a novel framework called ProverGen that synergizes the generative strengths of Large Language Models (LLMs) with the rigor and precision of symbolic provers, enabling the creation of a scalable, diverse, and high-quality FOL reasoning dataset, ProverQA. ProverQA is also distinguished by its inclusion of accessible and logically coherent intermediate reasoning steps for each problem. Our evaluation shows that state-of-the-art LLMs struggle to solve ProverQA problems, even with CoT prompting, highlighting the dataset's challenging nature. We also finetune Llama3.1-8B-Instruct on a separate training set generated by our framework. The finetuned model demonstrates consistent improvements on both in-distribution and out-of-distribution test sets, suggesting the value of our proposed data generation framework. Code available at: https://github.com/opendatalab/ProverGen

Practitioners inferring causality from observational data usually rely on a single method and treat its output as causal truth. Recent tools select an optimal method for a dataset, and recent ensembles aggregate multiple causal-discovery algorithms into one graph, but little work pools evidence across different mathematical traditions, including non-causal ones. We present Multi-Method Causal Evidence Synthesis (MCES), a framework that ranks which candidate drivers in an observational system are most likely relevant to a set of outcomes, and with what strength of evidence. MCES runs eleven methods across eight mathematical traditions on observational panel data and pools their outputs into a Convergent Evidence Score (CES), a linear opinion pool. CES quantifies convergence of evidence across analytical lenses: the degree to which methods with different assumptions point to the same driver-outcome relationship. It does not claim causal identification in the interventionist sense; it supports hypothesis prioritization, not a transferable probability of causation. MCES first applies Structural-Behavioral Decomposition to remove definitional (algebraic) relationships, then runs all methods, normalizes outputs to [0,1], and pools them. We distinguish MCES from method selection, structural ensembles, prediction ensembles, and literature synthesis. Using synthetic data with embedded ground truth, the Sachs protein-signaling benchmark, six Bayesian-network structure benchmarks, and two further synthetic domains, we show MCES ranks true edges near the top (Precision@5 = 1.0, Precision@10 = 0.96 on the primary scenario), with a low empirical rate of null pairs reaching Moderate-or-higher convergence. Our central point is not that the pool beats every individual method, but that no single method is uniformly best across the evaluated scenarios, so MCES offers a method-agnostic default.

As Retrieval-Augmented Generation (RAG) shifts toward diverse portfolio generation, it is stymied by two critical bottlenecks: flawed measurement of evidence utilization, and suboptimal context budget allocation. We resolve both sequentially. To resolve measurement, we expose a pervasive ``diagnostic illusion'': standard relevance proxies fail catastrophically on hard negatives. We replace them with an efficient causal leave-one-out probe that accurately isolates generative reliance and formally calibrates the structural dilution of LLM attention. To resolve allocation, we deploy this causal probe in a deconfounded factorial grid. We prove that the prevailing strategy of monolithic context widening is an architectural trap penalized by relevance decay. Instead, allocating compute iteratively across multiple sequential generations drives transformative portfolio recall gains of 16.7--20.5 absolute percentage points, scaling robustly up to 32B models. Finally, we unify these solutions into a deployable closed-loop submodular scheduler. Augmented by an attribution-steered contrastive decoder to override LLM attention inertia, our architecture systematically forces fresh evidence integration. By dominating classical open-loop baselines, we establish sequential, feedback-driven orchestration as the definitive paradigm for generative search. Our code, data, and causal measurement instruments are available at https://github.com/PeiYangLiu/ascp.

While chain-of-thought (CoT) prompting has revolutionized how LLMs perform reasoning tasks, its current methods and variations (e.g, Self-consistency, ReACT, Reflexion, Tree-of-Thoughts (ToT), Cumulative Reasoning (CR)) suffer from limitations like slowness, limited context grounding, hallucination and inconsistent outputs. To overcome these challenges, we introduce Evidence to Generate (E2G), a novel single-agent, two-step prompting framework. Instead of unverified reasoning claims, this innovative approach leverages the power of "evidence for decision making" by first focusing exclusively on the thought sequences (the series of intermediate steps) explicitly mentioned in the context which then serve as extracted evidence, guiding the LLM's output generation process with greater precision and efficiency. This simple yet powerful approach unlocks the true potential of chain-of-thought like prompting, paving the way for faster, more reliable, and more contextually aware reasoning in LLMs. \tool achieves remarkable results robustly across a wide range of knowledge-intensive reasoning and generation tasks, surpassing baseline approaches with state-of-the-art LLMs. For example, (i) on LogiQA benchmark using GPT-4 as backbone model, \tool achieves a new state-of-the Accuracy of 53.8% exceeding CoT by 18%, ToT by 11%, CR by 9% (ii) a variant of E2G with PaLM2 outperforms the variable-shot performance of Gemini Ultra by 0.9 F1 points, reaching an F1 score of 83.3 on a subset of DROP.

Structure reasoning is a fundamental capability of large language models (LLMs), enabling them to reason about structured commonsense and answer multi-hop questions. However, existing benchmarks for structure reasoning mainly focus on horizontal and coordinate structures (e.g. graphs), overlooking the hierarchical relationships within them. Hierarchical structure reasoning is crucial for human cognition, particularly in memory organization and problem-solving. It also plays a key role in various real-world tasks, such as information extraction and decision-making. To address this gap, we propose HiBench, the first framework spanning from initial structure generation to final proficiency assessment, designed to benchmark the hierarchical reasoning capabilities of LLMs systematically. HiBench encompasses six representative scenarios, covering both fundamental and practical aspects, and consists of 30 tasks with varying hierarchical complexity, totaling 39,519 queries. To evaluate LLMs comprehensively, we develop five capability dimensions that depict different facets of hierarchical structure understanding. Through extensive evaluation of 20 LLMs from 10 model families, we reveal key insights into their capabilities and limitations: 1) existing LLMs show proficiency in basic hierarchical reasoning tasks; 2) they still struggle with more complex structures and implicit hierarchical representations, especially in structural modification and textual reasoning. Based on these findings, we create a small yet well-designed instruction dataset, which enhances LLMs' performance on HiBench by an average of 88.84\% (Llama-3.1-8B) and 31.38\% (Qwen2.5-7B) across all tasks. The HiBench dataset and toolkit are available here, https://github.com/jzzzzh/HiBench, to encourage evaluation.

As economics scales, a key bottleneck is representing what papers claim in a comparable, aggregable form. We introduce evidence-annotated claim graphs that map each paper into a directed network of standardized economic concepts (nodes) and stated relationships (edges), with each edge labeled by evidentiary basis, including whether it is supported by causal inference designs or by non-causal evidence. Using a structured multi-stage AI workflow, we construct claim graphs for 44,852 economics papers from 1980-2023. The share of causal edges rises from 7.7% in 1990 to 31.7% in 2020. Measures of causal narrative structure and causal novelty are positively associated with top-five publication and long-run citations, whereas non-causal counterparts are weakly related or negative.

Answering complex questions over long documents frequently requires integrating evidence that the source itself disperses naturally across distant passages. In an incident report, the operating condition, design flaw, and missed safety check that jointly explain a disaster may appear dozens of sections apart; in a novel, a character's true motive may surface only through scenes far removed from the moment it becomes relevant. This source-internal evidence integration is central to real-world long-document analysis, yet existing benchmarks largely sidestep it. Needle probes, planted facts, and reverse-engineered multi-hop chains embed evidence that may differ from the host text in distribution, placement, or register, making it unclear whether strong performance reflects genuine source reasoning or distributional artifacts. We introduce WILDTRACE, a benchmark of 481 tasks over 214 naturally occurring long-form sources such as technical incident reports and lesser-known literary narratives, where all evidence trails arise from the document's own causal, temporal, and narrative logic. Drawing on Pearl's causal hierarchy and prior multi-hop reasoning typologies, we define seven source-internal evidence geometries that characterize the distinct relational demands of analytical reading in long documents. A source-first construction pipeline mines candidate trails from document structure before writing questions; each item then undergoes multi-stage validation covering clue necessity, answer groundedness, rubric fidelity, contamination resistance and answerability. As models are increasingly entrusted with real-world high-stakes analytical tasks, this gap between accessing information and reasoning over naturally dispersed evidence emerges as a defining challenge for the next stage of long-context research.

Teaching large language models (LLMs) to generate text with citations to evidence sources can mitigate hallucinations and enhance verifiability in information-seeking systems. However, improving this capability requires high-quality attribution data, which is costly and labor-intensive. Inspired by recent advances in self-improvement that enhance LLMs without manual annotation, we present START, a Self-Taught AttRibuTion framework for iteratively improving the attribution capability of LLMs. First, to prevent models from stagnating due to initially insufficient supervision signals, START leverages the model to self-construct synthetic training data for warming up. To further self-improve the model's attribution ability, START iteratively utilizes fine-grained preference supervision signals constructed from its sampled responses to encourage robust, comprehensive, and attributable generation. Experiments on three open-domain question-answering datasets, covering long-form QA and multi-step reasoning, demonstrate significant performance gains of 25.13% on average without relying on human annotations and more advanced models. Further analysis reveals that START excels in aggregating information across multiple sources.

Large language models (LLMs) are capable of generating coherent summaries from very long contexts given a user query. Extracting and properly citing evidence spans could help improve the transparency and reliability of these summaries. At the same time, LLMs suffer from positional biases in terms of which information they understand and attend to, which could affect evidence citation. Whereas previous work has focused on evidence citation with predefined levels of granularity (e.g. sentence, paragraph, document, etc.), we propose the task of long-context query focused summarization with unstructured evidence citation. We show how existing systems struggle to generate and properly cite unstructured evidence from their context, and that evidence tends to be "lost-in-the-middle". To help mitigate this, we create the Summaries with Unstructured Evidence Text dataset (SUnsET), a synthetic dataset generated using a novel domain-agnostic pipeline which can be used as supervision to adapt LLMs to this task. We demonstrate across 5 LLMs of different sizes and 4 datasets with varying document types and lengths that LLMs adapted with SUnsET data generate more relevant and factually consistent evidence than their base models, extract evidence from more diverse locations in their context, and can generate more relevant and consistent summaries.

Can we learn more from data than existed in the generating process itself? Can new and useful information be constructed from merely applying deterministic transformations to existing data? Can the learnable content in data be evaluated without considering a downstream task? On these questions, Shannon information and Kolmogorov complexity come up nearly empty-handed, in part because they assume observers with unlimited computational capacity and fail to target the useful information content. In this work, we identify and exemplify three seeming paradoxes in information theory: (1) information cannot be increased by deterministic transformations; (2) information is independent of the order of data; (3) likelihood modeling is merely distribution matching. To shed light on the tension between these results and modern practice, and to quantify the value of data, we introduce epiplexity, a formalization of information capturing what computationally bounded observers can learn from data. Epiplexity captures the structural content in data while excluding time-bounded entropy, the random unpredictable content exemplified by pseudorandom number generators and chaotic dynamical systems. With these concepts, we demonstrate how information can be created with computation, how it depends on the ordering of the data, and how likelihood modeling can produce more complex programs than present in the data generating process itself. We also present practical procedures to estimate epiplexity which we show capture differences across data sources, track with downstream performance, and highlight dataset interventions that improve out-of-distribution generalization. In contrast to principles of model selection, epiplexity provides a theoretical foundation for data selection, guiding how to select, generate, or transform data for learning systems.

Retrieval-Augmented Generation (RAG) helps large language models (LLMs) answer knowledge-intensive and time-sensitive questions by conditioning generation on external evidence. However, most RAG systems still retrieve unstructured chunks and rely on one-shot generation, which often yields redundant context, low information density, and brittle multi-hop reasoning. While structured RAG pipelines can improve grounding, they typically require costly and error-prone graph construction or impose rigid entity-centric structures that do not align with the query's reasoning chain. We propose TaSR-RAG, a taxonomy-guided structured reasoning framework for evidence selection. We represent both queries and documents as relational triples, and constrain entity semantics with a lightweight two-level taxonomy to balance generalization and precision. Given a complex question, TaSR-RAG decomposes it into an ordered sequence of triple sub-queries with explicit latent variables, then performs step-wise evidence selection via hybrid triple matching that combines semantic similarity over raw triples with structural consistency over typed triples. By maintaining an explicit entity binding table across steps, TaSR-RAG resolves intermediate variables and reduces entity conflation without explicit graph construction or exhaustive search. Experiments on multiple multi-hop question answering benchmarks show that TaSR-RAG consistently outperforms strong RAG and structured-RAG baselines by up to 14\%, while producing clearer evidence attribution and more faithful reasoning traces.

Literature reviews are an essential component of scientific research, but they remain time-intensive and challenging to write, especially due to the recent influx of research papers. This paper explores the zero-shot abilities of recent Large Language Models (LLMs) in assisting with the writing of literature reviews based on an abstract. We decompose the task into two components: 1. Retrieving related works given a query abstract, and 2. Writing a literature review based on the retrieved results. We analyze how effective LLMs are for both components. For retrieval, we introduce a novel two-step search strategy that first uses an LLM to extract meaningful keywords from the abstract of a paper and then retrieves potentially relevant papers by querying an external knowledge base. Additionally, we study a prompting-based re-ranking mechanism with attribution and show that re-ranking doubles the normalized recall compared to naive search methods, while providing insights into the LLM's decision-making process. In the generation phase, we propose a two-step approach that first outlines a plan for the review and then executes steps in the plan to generate the actual review. To evaluate different LLM-based literature review methods, we create test sets from arXiv papers using a protocol designed for rolling use with newly released LLMs to avoid test set contamination in zero-shot evaluations. We release this evaluation protocol to promote additional research and development in this regard. Our empirical results suggest that LLMs show promising potential for writing literature reviews when the task is decomposed into smaller components of retrieval and planning. Our project page including a demonstration system and toolkit can be accessed here: https://litllm.github.io.

Structure-property relationships are foundational to biology, chemistry and materials science, where function, reactivity and physical response emerge from spatial, chemical and periodic organization. Mechanistically explaining these relationships requires interpreting structural evidence through scientific principles and physical constraints, from stereochemistry and bonding to symmetry, energetics and periodic order. However, applying artificial intelligence to this process presents a joint challenge of representation and reasoning: models must preserve domain-native structural information while showing how specific evidence supports predictions under these constraints. Here we introduce SciReasoner, a multimodal scientific foundation model for native structural reasoning across proteins, small molecules and inorganic crystals. SciReasoner discretizes coordinates, topologies and periodic connectivities into a unified structure-aware vocabulary, treating structural tokens as addressable evidence units during reasoning. In homology-controlled Gene Ontology prediction, SciReasoner improves Cellular Component annotation for low-homology and orphan-like proteins, increasing F_{max} from 0.42 to 0.55. In chemistry, it raises single-step retrosynthesis accuracy from 0.63 to 0.72 while generating fragment-level disconnection and precursor-verification traces. In materials science, its representations separate elemental and compound phases and resolve high- and low-band-gap regimes. Across 86 benchmarks, SciReasoner achieves state-of-the-art performance on 67 tasks. Double-blind expert evaluation rates its reasoning traces as preferred or at least comparable to those of a frontier large language model in 98% of cases. By making structure an inspectable substrate for reasoning under scientific constraints, SciReasoner connects accurate prediction with interpretable scientific inference.

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

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.

Deep research agents have attracted increasing attention for their ability to collect large-scale online information to acquire target knowledge, with recent efforts shifting from purely text-based information seeking to multimodal settings. However, existing agentic workflows are largely aligned with evidence accumulation models, which linearly aggregate evidence and lack principled mechanisms for handling contradictory information across heterogeneous modalities. Towards this end, we propose Struct-Searcher, a structural agentic workflow grounded in belief revision theory that explicitly maintains an evolving multimodal structural graph throughout the reasoning process, enabling effective conflict-aware multimodal deep information seeking. Extensive experiments across multiple benchmark datasets and backbone models demonstrate that Struct-Searcher is (1) plug-and-play and model-agnostic, yielding an average relative accuracy improvement of 17.2% on BrowseComp-VL across five different backbones. (2) top-performing, consistently outperforming state-of-the-art vision-language models (VLMs) and deep research agents, with relative accuracy improvements of 3.7% on MM-BrowseComp, 1.5% on HLE-VL, and 0.7% on BrowseComp-VL over the second-best competing approach.

Scientific research based on multimodal clinical data (including medical imaging) requires coordinating clinical, radiological, programming, and biostatistical expertise, a fragmented process that bottlenecks discovery. We present VERITAS (Verifiable Epistemic Reasoning for Image-Derived Hypothesis Testing via Agentic Systems), a clinical co-scientist: a multi-agent system that autonomously tests natural-language hypotheses and produces a fully auditable evidence trail, tracing every conclusion through executable outputs from analysis plan to segmentation masks to statistical code to final verdict. Unlike prior AI-scientist systems, which mainly operate on tabular or text data, VERITAS grounds autonomous discovery directly in medical images. It decomposes the workflow into four phases handled by role-specialized agents, and introduces an epistemic evidence label framework that mechanically classifies outcomes as Supported, Refuted, Underpowered, or Invalid by jointly evaluating significance, effect direction, and study power. This distinction is critical in medical imaging, where non-significant results often reflect insufficient sample size rather than absent effects. We construct a tiered benchmark of 64 hypotheses spanning six complexity levels across cardiac and brain glioma MRI datasets. VERITAS reaches 81.4% verdict accuracy with frontier models and 71.2% with locally-hosted open-weight models (8-30B), outperforming all single-model baselines in both classes. It also produces the highest rate of independently verifiable statistical outputs (86.6%), so even its failures remain diagnosable through artifact inspection. Structured multi-agent decomposition thus substitutes for model scale while preserving the verifiability that scientific discovery demands. We release code, hypothesis bank, and evaluation pipeline at https://github.com/LucZot/veritas.

The foundational pretraining phase determines a model's capability ceiling, as post-training struggles to overcome capability foundations established during pretraining, yet it remains critically under-explored. This stems from a structural paradox: organizations with computational resources operate under commercial pressures that inhibit transparent disclosure, while academic institutions possess research freedom but lack pretraining-scale computational resources. daVinci-LLM occupies this unexplored intersection, combining industrial-scale resources with full research freedom to advance the science of pretraining. We adopt a fully-open paradigm that treats openness as scientific methodology, releasing complete data processing pipelines, full training processes, and systematic exploration results. Recognizing that the field lacks systematic methodology for data processing, we employ the Data Darwinism framework, a principled L0-L9 taxonomy from filtering to synthesis. We train a 3B-parameter model from random initialization across 8T tokens using a two-stage adaptive curriculum that progressively shifts from foundational capabilities to reasoning-intensive enhancement. Through 200+ controlled ablations, we establish that: processing depth systematically enhances capabilities, establishing it as a critical dimension alongside volume scaling; different domains exhibit distinct saturation dynamics, necessitating adaptive strategies from proportion adjustments to format shifts; compositional balance enables targeted intensification while preventing performance collapse; how evaluation protocol choices shape our understanding of pretraining progress. By releasing the complete exploration process, we enable the community to build upon our findings and systematic methodologies to form accumulative scientific knowledge in pretraining.

Root cause analysis (RCA) in complex systems is challenging due to error propagation across multiple variables, the need for structural causal knowledge, and the computational cost of inference at test time. We introduce PRIM (Prior-fitted Root cause Identification with Meta-learning), a causal meta-learning approach that frames RCA as a Bayesian inference task over a synthetic prior of causal models. By marginalising out structural uncertainty, PRIM implicitly identifies changes in the data-generating mechanism between baseline and anomalous periods. In doing so, PRIM infers distributional differences without explicit statistical testing, and implicitly learns causal structure without model fitting at test time. Following the simulation-based meta-learning paradigm of prior-fitted networks, PRIM uses a Model-Averaged Causal Estimation (MACE) transformer neural process that jointly attends over observational and anomalous samples and the causal structure of nodes, enabling zero-shot inference in 17,ms for systems with up to 100 variables. Across synthetic benchmarks and two realistic benchmark datasets, PetShop and CausRCA, PRIM is competitive with methods that are aware of the system's causal graphical structure a priori while outperforming graph-unaware methods on several tasks. Lightweight fine-tuning to specific domains and data dynamics improves performance further.

The field of natural language processing (NLP) has witnessed significant progress in recent years, with a notable focus on improving large language models' (LLM) performance through innovative prompting techniques. Among these, prompt engineering coupled with structures has emerged as a promising paradigm, with designs such as Chain-of-Thought, Tree of Thoughts, or Graph of Thoughts, in which the overall LLM reasoning is guided by a structure such as a graph. As illustrated with numerous examples, this paradigm significantly enhances the LLM's capability to solve numerous tasks, ranging from logical or mathematical reasoning to planning or creative writing. To facilitate the understanding of this growing field and pave the way for future developments, we devise a general blueprint for effective and efficient LLM reasoning schemes. For this, we conduct an in-depth analysis of the prompt execution pipeline, clarifying and clearly defining different concepts. We then build the first taxonomy of structure-enhanced LLM reasoning schemes. We focus on identifying fundamental classes of harnessed structures, and we analyze the representations of these structures, algorithms executed with these structures, and many others. We refer to these structures as reasoning topologies, because their representation becomes to a degree spatial, as they are contained within the LLM context. Our study compares existing prompting schemes using the proposed taxonomy, discussing how certain design choices lead to different patterns in performance and cost. We also outline theoretical underpinnings, relationships between prompting and others parts of the LLM ecosystem such as knowledge bases, and the associated research challenges. Our work will help to advance future prompt engineering techniques.

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

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

Access to the right evidence does not guarantee that large language models (LLMs) will reason with it correctly. This gap between retrieval and reasoning is especially concerning in clinical settings, where outputs must align with structured protocols. We study this gap using Written Exposure Therapy (WET) guidelines as a testbed. In evaluating model responses to curated clinician-vetted questions, we find that errors persist even when authoritative passages are provided. To address this, we propose an evaluation framework that measures accuracy, consistency, and fidelity of reasoning. Our results highlight both the potential and the risks: retrieval-augmented generation (RAG) can constrain outputs, but safe deployment requires assessing reasoning as rigorously as retrieval.

Retrieval-augmented generation (RAG) improves large language models (LMs) by incorporating non-parametric knowledge through evidence retrieved from external sources. However, it often struggles to cope with inconsistent and irrelevant information that can distract the LM from its tasks, especially when multiple evidence pieces are required. While compressing the retrieved evidence with a compression model aims to address this issue, the compressed evidence may still be unfamiliar to the target model used for downstream tasks, potentially failing to utilize the evidence effectively. We propose FaviComp (Familarity-Aware Evidence Compression), a novel training-free evidence compression technique that makes retrieved evidence more familiar to the target model, while seamlessly integrating parametric knowledge from the model. Experimental results show that FaviComp consistently outperforms most recent evidence compression baselines across multiple open-domain QA datasets, improving accuracy by up to 28.1% while achieving high compression rates. Additionally, we demonstrate the effective integration of both parametric and non-parametric knowledge during evidence compression.

Causal discovery is fundamental to scientific understanding and reliable decision-making. Existing approaches face critical limitations: purely data-driven methods suffer from statistical indistinguishability and modeling assumptions, while recent LLM-based methods either ignore statistical evidence or incorporate unverified priors that can mislead result. To this end, we propose CauScientist, a collaborative framework that synergizes LLMs as hypothesis-generating "data scientists" with probabilistic statistics as rigorous "verifiers". CauScientist employs hybrid initialization to select superior starting graphs, iteratively refines structures through LLM-proposed modifications validated by statistical criteria, and maintains error memory to guide efficient search space. Experiments demonstrate that CauScientist substantially outperforms purely data-driven baselines, achieving up to 53.8% F1 score improvement and enhancing recall from 35.0% to 100.0%. Notably, while standalone LLM performance degrades with graph complexity, CauScientist reduces structural hamming distance (SHD) by 44.0% compared to Qwen3-32B on 37-node graphs. Our project page is at https://github.com/OpenCausaLab/CauScientist.

Geometric Attention (GA) specifies an attention layer by four independent inputs: a finite carrier (what indices are addressable), an evidence-kernel rule (how masked proto-scores and a link induce nonnegative weights), a probe family (which observables are treated as admissible), and an anchor/update rule (which representative kernel is selected and how it is applied). Probe families induce an operational equivalence relation on kernels and therefore a gauge; anchors select representatives relative to that probe. Under a scalar relational-work representation and a multiplicative compositionality law for evidence, the admissible link family is exponential, yielding Gibbs weights; with row anchoring this includes the softmax kernel family as a subregime. After quotienting unary row/column score fields, the remaining interaction component admits a canonical rank-r normal form (Eckart-Young/SVD); dot-product score charts implement the corresponding low-rank interaction regime. Fixing the carrier and extensionalizing the update yields the standard fixed-token Transformer attention operator; allowing carrier updates yields adaptive-carrier and staged-depth regimes. The operator language also supports multihead/mixed kernels, plan-based anchors (e.g., entropic OT/Sinkhorn), and unary operators (e.g., FFN-style fields) as explicit regime choices. This separates invariant structure from modeling choice, enabling principled comparison and extension of attention mechanisms, and attention-based architectures.

Professional-document review is a constraint-checking problem in which decisions depend on relations among text, geometry, pages, and document revisions. We present an evidence-grounded pipeline that normalizes extracted facts, executes four-state rules deterministically, retains source spans, and escalates unresolved cases. We evaluate its PDF evidence allocator on 160 reference-based tasks from 29 construction projects using a repeated four-system test and a disjoint two-system breadth extension. In the repeated test, reallocating a four-image budget from retrieved page overviews to one overview and three overlapping tiles improves project-family standardized decision accuracy by 10.6 percentage points (95% project-cluster bootstrap CI: 4.3 to 18.0; exact p = 0.031). This effect does not persist in the broader block: Region-RAG changes accuracy by -4.1 points (95% CI: -10.2 to 1.9; exact p = 0.209), while an equal-image sensitivity favors page breadth. Exact finding-set recovery remains low, false passes remain common, and repeated-run agreement is poorly calibrated. The results identify a resolution-breadth trade-off rather than a universal advantage for region-focused evidence, motivating rule-aware evidence routing and expert review.

Proving theorems in Lean 4 often requires identifying a scattered set of library lemmas whose joint use enables a concise proof -- a task we call global premise retrieval. Existing tools address adjacent problems: semantic search engines find individual declarations matching a query, while premise-selection systems predict useful lemmas one tactic step at a time. Neither recovers the full premise set an entire theorem requires. We present LeanSearch v2, a two-mode retrieval system for this task. Its standard mode applies a hierarchy-informalized Mathlib corpus with an embedding-reranker pipeline, achieving state-of-the-art single-query retrieval without domain-specific fine-tuning (nDCG@10 of 0.62 vs. 0.53 for the next-best system). Its reasoning mode builds on standard mode as its retrieval substrate, targeting global premise retrieval through iterative sketch-retrieve-reflect cycles. On a 69-query benchmark of research-level Mathlib theorems, reasoning mode recovers 46.1% of ground-truth premise groups within 10 retrieved candidates, outperforming strong reasoning retrieval systems (38.0%) and premise-selection baselines (9.3%) on the same benchmark. In a controlled downstream evaluation with a fixed prover loop, replacing alternative retrievers with LeanSearch v2 yields the highest proof success (20% vs. 16% for the next-best system and 4% without retrieval), confirming that retrieval quality propagates to proof generation. We have open-sourced all code, data, and benchmarks. Code and data: https://github.com/frenzymath/LeanSearch-v2 . The standard mode is publicly available with API access at https://leansearch.net/ .

Pre-trained Language Models (PLMs) have achieved great success on Machine Reading Comprehension (MRC) over the past few years. Although the general language representation learned from large-scale corpora does benefit MRC, the poor support in evidence extraction which requires reasoning across multiple sentences hinders PLMs from further advancing MRC. To bridge the gap between general PLMs and MRC, we present REPT, a REtrieval-based Pre-Training approach. In particular, we introduce two self-supervised tasks to strengthen evidence extraction during pre-training, which is further inherited by downstream MRC tasks through the consistent retrieval operation and model architecture. To evaluate our proposed method, we conduct extensive experiments on five MRC datasets that require collecting evidence from and reasoning across multiple sentences. Experimental results demonstrate the effectiveness of our pre-training approach. Moreover, further analysis shows that our approach is able to enhance the capacity of evidence extraction without explicit supervision.

Many modern AI question-answering systems convert text into vectors and retrieve the closest matches to a user question. While effective for topical similarity, similarity scores alone do not explain why some retrieved text can serve as evidence while other equally similar text cannot. When many candidates receive similar scores, systems may select sentences that are redundant, incomplete, or address different conditions than the question requires. This paper presents a deterministic evidence selection framework for retrieval-augmented question answering. The approach introduces Meaning-Utility Estimation (MUE) and Diversity-Utility Estimation (DUE), fixed scoring and redundancy-control procedures that determine evidence admissibility prior to answer generation. Each sentence or record is evaluated independently using explicit signals for semantic relatedness, term coverage, conceptual distinctiveness, and redundancy. No training or fine-tuning is required. In the prototype, a unit is accepted only if it explicitly states the fact, rule, or condition required by the task. Units are not merged or expanded. If no unit independently satisfies the requirement, the system returns no answer. This deterministic gating produces compact, auditable evidence sets and establishes a clear boundary between relevant text and usable evidence.

Clinical trial matching is a key process in health delivery and discovery. In practice, it is plagued by overwhelming unstructured data and unscalable manual processing. In this paper, we conduct a systematic study on scaling clinical trial matching using large language models (LLMs), with oncology as the focus area. Our study is grounded in a clinical trial matching system currently in test deployment at a large U.S. health network. Initial findings are promising: out of box, cutting-edge LLMs, such as GPT-4, can already structure elaborate eligibility criteria of clinical trials and extract complex matching logic (e.g., nested AND/OR/NOT). While still far from perfect, LLMs substantially outperform prior strong baselines and may serve as a preliminary solution to help triage patient-trial candidates with humans in the loop. Our study also reveals a few significant growth areas for applying LLMs to end-to-end clinical trial matching, such as context limitation and accuracy, especially in structuring patient information from longitudinal medical records.

We formalize constraint-based structure learning of the "true" causal graph from observed data when unobserved variables are also existent. We provide conditions for a "natural" family of constraint-based structure-learning algorithms that output graphs that are Markov equivalent to the causal graph. Under the faithfulness assumption, this natural family contains all exact structure-learning algorithms. We also provide a set of assumptions, under which any natural structure-learning algorithm outputs Markov equivalent graphs to the causal graph. These assumptions can be thought of as a relaxation of faithfulness, and most of them can be directly tested from (the underlying distribution) of the data, particularly when one focuses on structural causal models. We specialize the definitions and results for structural causal models.

Modern Lean theorem provers achieve strong performance only with substantial training and inference compute, driven in part by scarce verified proof data and the long reasoning traces of formal proof search, making both supervised fine-tuning (SFT) and sampling expensive. We introduce Pythagoras-Prover, a compute-efficient open-source family of Lean theorem provers built for practical compute budgets. The family spans two generation paradigms: autoregressive models at 4B and 32B parameters, and a first proof-of-concept diffusion-based prover (4B) that iteratively refines Lean proofs at inference time. For training efficiency, we build a Lean-verified corpus stratified into easy, medium, and hard problems for curriculum SFT, so models acquire proof skills progressively from shorter, simpler proofs to longer, harder ones. During SFT, a dynamic proof-reasoning filtering scheme preserves informative proof traces while keeping each instance within an 8k-token context budget. We also introduce Augmented Lean Formalisation (ALF), which expands scarce verified corpora into variants of formal statements, populated via self-distillation for extra training signal without formally verifying every mutated instance. By perturbing known problems while preserving their formal character, ALF reduces reliance on any statement's surface form. Empirically, Pythagoras-Prover-4B surpasses DeepSeek-Prover-V2-671B at pass@32 on MiniF2F-Test (86.1% vs 82.4%) with ~167x fewer parameters, while Pythagoras-Prover-32B sets the open-source state of the art at 93.0% on MiniF2F-Test and solves 93 of 672 PutnamBench problems. We release MiniF2F-ALF, an ALF-mutated contamination-sensitive benchmark on which every evaluated model loses accuracy; here our 32B remains strongest and our 4B matches the prior state of the art, Goedel-Prover-V2-32B.

Large language models achieve strong scores on medical benchmarks, yet these benchmarks evaluate each question in isolation, providing no measure of whether a system can distinguish clinically similar presentations requiring different interventions. We introduce MamaBench, the first counterfactual benchmark for maternal and paediatric AI: 434 expert-authored clinical narratives in 217 pairs across 371 pathologies, evaluated via the Bias Trap Rate (BTR), the conditional probability that a model fails the counterfactual given success on the base case. We propose Evidence-Anchored RAG (EA-RAG), a three-stage retrieval method that replaces aggregate similarity with an evidence coverage objective through clinical parameter extraction, coverage auditing, and contrastive sub-queries. Across eight configurations of four frontier LLMs, base accuracy overstates robust accuracy by 16-28 percentage points in every model. EA-RAG achieves 20.3% BTR and 65.0% robust accuracy on Claude Sonnet 4.6, a 5.5 percentage point BTR reduction without degrading base accuracy. The residual 20% BTR confirms that counterfactual robustness in clinical AI remains an open challenge. Keywords: counterfactual evaluation, clinical AI, maternal healthcare, retrieval-augmented generation, diagnostic robustness

Large language models (LLM) often hallucinate, and while adding citations is a common solution, it is frequently insufficient for accountability as users struggle to verify how a cited source supports a generated claim. Existing methods are typically coarse-grained and fail to distinguish between direct quotes and complex reasoning. In this paper, we introduce Generation-time Fine-grained Provenance, a task where models must generate fluent answers while simultaneously producing structured, sentence-level provenance triples. To enable this, we present ReFInE (Relation-aware Fine-grained Interpretability & Evidence), a dataset featuring expert verified annotations that distinguish between Quotation, Compression, and Inference. Building on ReFInE, we propose GenProve, a framework that combines Supervised Fine-Tuning (SFT) with Group Relative Policy Optimization (GRPO). By optimizing a composite reward for answer fidelity and provenance correctness, GenProve significantly outperforms 14 strong LLMs in joint evaluation. Crucially, our analysis uncovers a reasoning gap where models excel at surface-level quotation but struggle significantly with inference-based provenance, suggesting that verifiable reasoning remains a frontier challenge distinct from surface-level citation.

LLM-based autonomous agents lack persistent procedural memory: they re-derive solutions from scratch even when structurally identical tasks have been solved before. We present APEX-EM, a non-parametric online learning framework that accumulates, retrieves, and reuses structured procedural plans without modifying model weights. APEX-EM introduces: (1) a structured experience representation encoding the full procedural-episodic trace of each execution -- planning steps, artifacts, iteration history with error analysis, and quality scores; (2) a Plan-Retrieve-Generate-Iterate-Ingest (PRGII) workflow with Task Verifiers providing multi-dimensional reward signals; and (3) a dual-outcome Experience Memory with hybrid retrieval combining semantic search, structural signature matching, and plan DAG traversal -- enabling cross-domain transfer between tasks sharing no lexical overlap but analogous operational structure. Successful experiences serve as positive in-context examples; failures as negative examples with structured error annotations. We evaluate on BigCodeBench, KGQAGen-10k, and Humanity's Last Exam using Claude Sonnet 4.5 and Opus 4.5. On KGQAGen-10k, APEX-EM achieves 89.6% accuracy versus 41.3% without memory (+48.3pp), surpassing the oracle-retrieval upper bound (84.9%). On BigCodeBench, it reaches 83.3% SR from a 53.9% baseline (+29.4pp), exceeding MemRL's +11.0pp gain under comparable frozen-backbone conditions (noting backbone differences controlled for in our analysis). On HLE, entity graph retrieval reaches 48.0% from 25.2% (+22.8pp). Ablations show component value is task-dependent: rich judge feedback is negligible for code generation but critical for structured queries (+10.3pp), while binary-signal iteration partially compensates for weaker feedback.

Across medical specialties, clinical practice is anchored in evidence-based guidelines that codify best studied diagnostic and treatment pathways. These pathways routinely fall short for the long tail of real-world care not covered by guidelines. Most medical large language models (LLMs), however, are trained to encode common, guideline-focused medical knowledge in their parameters. Current evaluations test models primarily on recalling and reasoning with this memorized content, often in multiple-choice settings. Given the fundamental importance of evidence-based reasoning in medicine, it is neither feasible nor reliable to depend on memorization in practice. To address this gap, we introduce OGCaReBench, a free-form retrieval-focused benchmark aimed at evaluating LLMs at answering clinical questions that require going beyond typical guidelines. Extracted from published medical case reports and validated by medical experts, OGCaReBench contains long-form clinical questions requiring free-text answers, providing a systematic framework for assessing open-ended medical reasoning in rare, case-based scenarios. Our experiments reveal that even the best-performing baseline (GPT-5.2) correctly answers only 56% of our benchmark with specialized models only reaching 42%. Augmenting models with retrieved medical articles improves this performance to up to 82% (using GPT-5.2) highlighting the importance of evidence-grounding for real-world medical reasoning tasks. This work thus establishes a foundation for benchmarking and advancing both general-purpose and medical LLMs to produce reliable answers in challenging clinical contexts.

Large language models (LLMs) exhibit remarkable generative capabilities but often suffer from hallucinations. Retrieval-augmented generation (RAG) offers an effective solution by incorporating external knowledge, but existing methods still face several limitations: additional deployment costs of separate retrievers, redundant input tokens from retrieved text chunks, and the lack of joint optimization of retrieval and generation. To address these issues, we propose RetroLLM, a unified framework that integrates retrieval and generation into a single, cohesive process, enabling LLMs to directly generate fine-grained evidence from the corpus with constrained decoding. Moreover, to mitigate false pruning in the process of constrained evidence generation, we introduce (1) hierarchical FM-Index constraints, which generate corpus-constrained clues to identify a subset of relevant documents before evidence generation, reducing irrelevant decoding space; and (2) a forward-looking constrained decoding strategy, which considers the relevance of future sequences to improve evidence accuracy. Extensive experiments on five open-domain QA datasets demonstrate RetroLLM's superior performance across both in-domain and out-of-domain tasks. The code is available at https://github.com/sunnynexus/RetroLLM.

Retrieval-augmented generation (RAG) is typically optimized for topical relevance, yet its success ultimately depends on whether retrieved passages are useful for a large language model (LLM) to generate correct and complete answers. We argue that such utility is often LLM-specific rather than universal, due to differences in models' knowledge, reasoning, and ability to leverage evidence. We formalize LLM-specific utility as the performance improvement of a target LLM when a passage is provided, compared to answering without evidence. To systematically study LLM-specific utility, we construct a benchmark of LLM-specific gold utilitarian passages for four LLMs (Qwen3-8B/14B/32B and Llama3.1-8B) on three QA datasets (Natural Questions, TriviaQA, and MS MARCO-FQA). Our analysis shows that utilitarian passages are model-dependent and non-transferable: each LLM performs best with its own utilitarian evidence, while evidence optimized for other LLMs is consistently suboptimal. Human-annotated evidence remains a strong general baseline but does not fully match individual LLM utility needs. We further introduce the LLM-specific utility judgment task and find that existing utility-aware selection and scoring methods largely capture model-agnostic usefulness and struggle to reliably estimate LLM-specific utility. Overall, our findings highlight the limitations of current utility-aware retrieval and motivate generator-tailored evidence selection for improving RAG.

Despite the potential of Large Language Models (LLMs) in medicine, they may generate responses lacking supporting evidence or based on hallucinated evidence. While Retrieval Augment Generation (RAG) is popular to address this issue, few studies implemented and evaluated RAG in downstream domain-specific applications. We developed a RAG pipeline with 70,000 ophthalmology-specific documents that retrieve relevant documents to augment LLMs during inference time. In a case study on long-form consumer health questions, we systematically evaluated the responses including over 500 references of LLMs with and without RAG on 100 questions with 10 healthcare professionals. The evaluation focuses on factuality of evidence, selection and ranking of evidence, attribution of evidence, and answer accuracy and completeness. LLMs without RAG provided 252 references in total. Of which, 45.3% hallucinated, 34.1% consisted of minor errors, and 20.6% were correct. In contrast, LLMs with RAG significantly improved accuracy (54.5% being correct) and reduced error rates (18.8% with minor hallucinations and 26.7% with errors). 62.5% of the top 10 documents retrieved by RAG were selected as the top references in the LLM response, with an average ranking of 4.9. The use of RAG also improved evidence attribution (increasing from 1.85 to 2.49 on a 5-point scale, P<0.001), albeit with slight decreases in accuracy (from 3.52 to 3.23, P=0.03) and completeness (from 3.47 to 3.27, P=0.17). The results demonstrate that LLMs frequently exhibited hallucinated and erroneous evidence in the responses, raising concerns for downstream applications in the medical domain. RAG substantially reduced the proportion of such evidence but encountered challenges.

Evaluation conclusions depend on evaluator-controlled semantics: legal references, scoreability, and aggregation. We call an artifact-defined endpoint Q(s) evaluation-semantically identified when it is invariant over a declared family. A frozen 217-row analysis appears stable within its restricted contract family. In TraceElephant, F_asym yields precise task-disjoint adoption effects from -40.76 to -43.03 percentage points, whereas both jointly frozen contrast-comparable treatments in F_cc yield exactly zero with [0, 0] intervals. Their union F_audit therefore does not identify T, even though F_cc identifies T = 0. A factorial audit attributes 100 percent of the disagreement to one-sided terminal deletion, with zero nonterminal contribution. Rankings remain specification-dependent across the symmetric treatments. This is a localized non-implication witness and reusable family-indexed audit, not a prevalence estimate, exhaustive semantic taxonomy, or independent replication.

Large-scale language models (LLMs) have achieved remarkable success across various language tasks but suffer from hallucinations and temporal misalignment. To mitigate these shortcomings, Retrieval-augmented generation (RAG) has been utilized to provide external knowledge to facilitate the answer generation. However, applying such models to the medical domain faces several challenges due to the lack of domain-specific knowledge and the intricacy of real-world scenarios. In this study, we explore LLMs with RAG framework for knowledge-intensive tasks in the medical field. To evaluate the capabilities of LLMs, we introduce MedicineQA, a multi-round dialogue benchmark that simulates the real-world medication consultation scenario and requires LLMs to answer with retrieved evidence from the medicine database. MedicineQA contains 300 multi-round question-answering pairs, each embedded within a detailed dialogue history, highlighting the challenge posed by this knowledge-intensive task to current LLMs. We further propose a new Distill-Retrieve-Read framework instead of the previous Retrieve-then-Read. Specifically, the distillation and retrieval process utilizes a tool calling mechanism to formulate search queries that emulate the keyword-based inquiries used by search engines. With experimental results, we show that our framework brings notable performance improvements and surpasses the previous counterparts in the evidence retrieval process in terms of evidence retrieval accuracy. This advancement sheds light on applying RAG to the medical domain.

Large Language Models (LLMs) have impressive capabilities, but are prone to outputting falsehoods. Recent work has developed techniques for inferring whether a LLM is telling the truth by training probes on the LLM's internal activations. However, this line of work is controversial, with some authors pointing out failures of these probes to generalize in basic ways, among other conceptual issues. In this work, we use high-quality datasets of simple true/false statements to study in detail the structure of LLM representations of truth, drawing on three lines of evidence: 1. Visualizations of LLM true/false statement representations, which reveal clear linear structure. 2. Transfer experiments in which probes trained on one dataset generalize to different datasets. 3. Causal evidence obtained by surgically intervening in a LLM's forward pass, causing it to treat false statements as true and vice versa. Overall, we present evidence that at sufficient scale, LLMs linearly represent the truth or falsehood of factual statements. We also show that simple difference-in-mean probes generalize as well as other probing techniques while identifying directions which are more causally implicated in model outputs.

Automated radiology report generation holds immense potential to alleviate the heavy workload of radiologists. Despite the formidable vision-language capabilities of recent Multimodal Large Language Models (MLLMs), their clinical deployment is severely constrained by inherent limitations: their "black-box" decision-making renders the generated reports untraceable due to the lack of explicit visual evidence to support the diagnosis, and they struggle to access external domain knowledge. To address these challenges, we propose the Evidence-driven Radiology Report Generation Agent (EviAgent). Unlike opaque end-to-end paradigms, EviAgent coordinates a transparent reasoning trajectory by breaking down the complex generation process into granular operational units. We integrate multi-dimensional visual experts and retrieval mechanisms as external support modules, endowing the system with explicit visual evidence and high-quality clinical priors. Extensive experiments on MIMIC-CXR, CheXpert Plus, and IU-Xray datasets demonstrate that EviAgent outperforms both large-scale generalist models and specialized medical models, providing a robust and trustworthy solution for automated radiology report generation.

Retrieval-Augmented Generation (RAG) is the prevailing paradigm for grounding Large Language Models (LLMs), yet the mechanisms governing how models integrate groups of conflicting retrieved evidence remain opaque. Does an LLM answer a certain way because the evidence is factually strong, because of a prior belief, or merely because it is repeated frequently? To answer this, we introduce GroupQA, a curated dataset of 1,635 controversial questions paired with 15,058 diversely-sourced evidence documents, annotated for stance and qualitative strength. Through controlled experiments, we characterize group-level evidence aggregation dynamics: Paraphrasing an argument can be more persuasive than providing distinct independent support; Models favor evidence presented first rather than last, and Larger models are increasingly resistant to adapt to presented evidence. Additionally, we find that LLM explanations to group-based answers are unfaithful. Together, we show that LLMs behave consistently as vulnerable heuristic followers, with direct implications for improving RAG system design.

Retrieval-Augmented Generation (RAG) integrates non-parametric knowledge into Large Language Models (LLMs), typically from unstructured texts and structured graphs. While recent progress has advanced text-based RAG to multi-turn reasoning through Reinforcement Learning (RL), extending these advances to hybrid retrieval introduces additional challenges. Existing graph-based or hybrid systems typically depend on fixed or handcrafted retrieval pipelines, lacking the ability to integrate supplementary evidence as reasoning unfolds. Besides, while graph evidence provides relational structures crucial for multi-hop reasoning, it is substantially more expensive to retrieve. To address these limitations, we introduce , an RL-based framework that enables LLMs to perform multi-turn and adaptive graph-text hybrid RAG. jointly optimizes the entire generation process via RL, allowing the model to learn when to reason, what to retrieve from either texts or graphs, and when to produce final answers, all within a unified generation policy. To guide this learning process, we design a two-stage training framework that accounts for both task outcome and retrieval efficiency, enabling the model to exploit hybrid evidence while avoiding unnecessary retrieval overhead. Experimental results across five question answering benchmarks demonstrate that significantly outperforms existing RAG baselines, highlighting the benefits of end-to-end RL in supporting adaptive and efficient retrieval for complex reasoning.

Large language models (LLMs) are widely used in retrieval-augmented generation (RAG) to incorporate external knowledge at inference time. However, when retrieved contexts are noisy, incomplete, or heterogeneous, a single generation process often struggles to reconcile evidence effectively. We propose MASS-RAG, a multi-agent synthesis approach to retrieval-augmented generation that structures evidence processing into multiple role-specialized agents. MASS-RAG applies distinct agents for evidence summarization, evidence extraction, and reasoning over retrieved documents, and combines their outputs through a dedicated synthesis stage to produce the final answer. This design exposes multiple intermediate evidence views, allowing the model to compare and integrate complementary information before answer generation. Experiments on four benchmarks show that MASS-RAG consistently improves performance over strong RAG baselines, particularly in settings where relevant evidence is distributed across retrieved contexts.

Large reasoning models (LRMs) spend substantial test-time compute on long chain-of-thought (CoT) traces, but what *characterizes* an effective CoT remains unclear. While prior work reports gains from lengthening CoTs and increasing review (revisiting earlier steps) via appended *wait* tokens, recent studies suggest that shorter thinking can outperform longer traces. We therefore conduct a systematic evaluation across ten LRMs on math and scientific reasoning. Contrary to the "longer-is-better" narrative, we find that both naive CoT lengthening and increased review are associated with *lower* accuracy. As CoT unfolds step by step, token-level metrics can conflate verbosity with process quality. We introduce a graph view of CoT to extract structure and identify a single statistic-the *Failed-Step Fraction (FSF)*, the fraction of steps in abandoned branches-that consistently outpredicts length and review ratio for correctness across models. To probe causality, we design two interventions. First, we rank candidate CoTs by each metric at test time, where FSF yields the largest pass@1 gains; second, we edit CoTs to remove failed branches, which significantly improves accuracy, indicating that failed branches bias subsequent reasoning. Taken together, these results characterize effective CoTs as those that *fail less* and support *structure-aware* test-time scaling over indiscriminately generating long CoT.

Meta-analysis is a demanding form of evidence synthesis that combines literature retrieval, PI/ECO-guided study selection, and statistical aggregation. Its structured, verifiable workflow makes it an ideal substrate for evaluating systematic scientific reasoning, yet existing benchmarks lack ground truth across the full retrieval-screening-synthesis pipeline. We introduce MetaSyn, a dataset of 442 expert-curated meta-analyses from Nature Portfolio journals. Each entry pairs a research question with PI/ECO criteria, a retrieval corpus of 140k PubMed articles, verified positive studies, hard negatives that are topically similar but PI/ECO-ineligible, and complete search strategies and date bounds. Benchmarking twelve pipeline configurations (nine RAG variants and a protocol-driven agent) reveals a critical screening bottleneck: despite a retrieval ceiling of 90.9% recall at K=200, no system recovers more than 52.7% of ground-truth included literature. Current LLMs fail to reliably separate eligible studies from PI/ECO-failing distractors in pools of comparable topical relevance. Stage-attributed metrics capture where systems succeed and fail; a single end-to-end score does not.

Corruption studies, the primary tool for evaluating chain-of-thought (CoT) faithfulness, identify which chain positions are "computationally important" by measuring accuracy when steps are replaced with errors. We identify a systematic confound: for chains with explicit terminal answer statements, the dominant format in standard benchmarks, corruption studies detect where the answer text appears, not where computation occurs. A within-dataset format ablation provides the key evidence: on standard GSM8K chains ending with "the answer is X," removing only the answer statement, preserving all reasoning, collapses suffix sensitivity ~19x at 3B (N=300, p=0.022). Conflicting-answer experiments quantify the causal mechanism: at 7B, CC accuracy drops to near-zero (<=0.02) across five architecture families; the followed-wrong rate spans 0.63-1.00 at 3B-7B and attenuates at larger scales (0.300 at Phi-4-14B, ~0.01 at 32B). A within-stable 7B replication (9.3x attenuation, N=76, p=7.8e-3; Qwen3-8B N=299, p=0.004) provides converging evidence, and the pattern replicates on MATH (DeepSeek-R1-7B: 10.9x suffix-survival recovery). On chains without answer suffixes the same protocol identifies the prefix as load-bearing (Delta=-0.77, p<10^-12). Generation-time probes confirm a dissociation: the answer is not early-determined during generation (early commitment <5%), yet at consumption time model outputs systematically follow the explicit answer text. The format-determination effect persists through 14B (8.5x ratio, p=0.001) and converges toward zero at 32B. We propose a three-prerequisite protocol (question-only control, format characterization, all-position sweep) as a minimum standard for corruption-based faithfulness studies.

Modern generative search engines enhance the reliability of large language model (LLM) responses by providing cited evidence. However, evaluating the answer's attribution, i.e., whether every claim within the generated responses is fully supported by its cited evidence, remains an open problem. This verification, traditionally dependent on costly human evaluation, underscores the urgent need for automatic attribution evaluation methods. To bridge the gap in the absence of standardized benchmarks for these methods, we present AttributionBench, a comprehensive benchmark compiled from various existing attribution datasets. Our extensive experiments on AttributionBench reveal the challenges of automatic attribution evaluation, even for state-of-the-art LLMs. Specifically, our findings show that even a fine-tuned GPT-3.5 only achieves around 80% macro-F1 under a binary classification formulation. A detailed analysis of more than 300 error cases indicates that a majority of failures stem from the model's inability to process nuanced information, and the discrepancy between the information the model has access to and that human annotators do.

Neural models have achieved great success on machine reading comprehension (MRC), many of which typically consist of two components: an evidence extractor and an answer predictor. The former seeks the most relevant information from a reference text, while the latter is to locate or generate answers from the extracted evidence. Despite the importance of evidence labels for training the evidence extractor, they are not cheaply accessible, particularly in many non-extractive MRC tasks such as YES/NO question answering and multi-choice MRC. To address this problem, we present a Self-Training method (STM), which supervises the evidence extractor with auto-generated evidence labels in an iterative process. At each iteration, a base MRC model is trained with golden answers and noisy evidence labels. The trained model will predict pseudo evidence labels as extra supervision in the next iteration. We evaluate STM on seven datasets over three MRC tasks. Experimental results demonstrate the improvement on existing MRC models, and we also analyze how and why such a self-training method works in MRC. The source code can be obtained from https://github.com/SparkJiao/Self-Training-MRC

Scientific archives now contain hundreds of petabytes of data across genomics, ecology, climate, and molecular biology that could reveal undiscovered patterns if systematically analyzed at scale. Large-scale, weakly-supervised datasets in language and vision have driven the development of foundation models whose internal representations encode structure (patterns, co-occurrences and statistical regularities) beyond their training objectives. Most existing methods extract structure only for pre-specified targets; they excel at confirmation but do not support open-ended discovery of unknown patterns. We ask whether sparse autoencoders (SAEs) can enable open-ended feature discovery from foundation model representations. We evaluate this question in controlled rediscovery studies, where the learned SAE features are tested for alignment with semantic concepts on a standard segmentation benchmark and compared against strong label-free alternatives on concept-alignment metrics. Applied to ecological imagery, the same procedure surfaces fine-grained anatomical structure without access to segmentation or part labels, providing a scientific case study with ground-truth validation. While our experiments focus on vision with an ecology case study, the method is domain-agnostic and applicable to models in other sciences (e.g., proteins, genomics, weather). Our results indicate that sparse decomposition provides a practical instrument for exploring what scientific foundation models have learned, an important prerequisite for moving from confirmation to genuine discovery.

Large language models (LLMs) have majorly advanced NLP and AI, and next to their ability to perform a wide range of procedural tasks, a major success factor is their internalized factual knowledge. Since Petroni et al. (2019), analyzing this knowledge has gained attention. However, most approaches investigate one question at a time via modest-sized pre-defined samples, introducing an ``availability bias'' (Tversky&Kahnemann, 1973) that prevents the analysis of knowledge (or beliefs) of LLMs beyond the experimenter's predisposition. To address this challenge, we propose a novel methodology to comprehensively materialize an LLM's factual knowledge through recursive querying and result consolidation. Our approach is a milestone for LLM research, for the first time providing constructive insights into the scope and structure of LLM knowledge (or beliefs). As a prototype, we build GPTKB, a knowledge base (KB) comprising 101 million relational triples for over 2.9 million entities from GPT-4o-mini. We use GPTKB to exemplarily analyze GPT-4o-mini's factual knowledge in terms of scale, accuracy, bias, cutoff and consistency, at the same time. GPTKB is accessible at https://gptkb.org

As language models shift from single-shot answer generation toward multi-step reasoning that retrieves and consumes evidence mid-inference, evaluating the role of individual retrieved items becomes more important. Existing RAG evaluation typically targets final-answer quality, citation faithfulness, or answer-level attribution, but none of these directly targets the intervention-based, per-evidence-item utility view we study here. We introduce CUE-R, a lightweight intervention-based framework for measuring per-evidence-item operational utility in single-shot RAG using shallow observable retrieval-use traces. CUE-R perturbs individual evidence items via REMOVE, REPLACE, and DUPLICATE operators, then measures changes along three utility axes (correctness, proxy-based grounding faithfulness, and confidence error) plus a trace-divergence signal. We also outline an operational evidence-role taxonomy for interpreting intervention outcomes. Experiments on HotpotQA and 2WikiMultihopQA with Qwen-3 8B and GPT-5.2 reveal a consistent pattern: REMOVE and REPLACE substantially harm correctness and grounding while producing large trace shifts, whereas DUPLICATE is often answer-redundant yet not fully behaviorally neutral. A zero-retrieval control confirms that these effects arise from degradation of meaningful retrieval. A two-support ablation further shows that multi-hop evidence items can interact non-additively: removing both supports harms performance far more than either single removal. Our results suggest that answer-only evaluation misses important evidence effects and that intervention-based utility analysis is a practical complement for RAG evaluation.

Large language models (LLMs) excel at function calling, but inference scaling has been explored mainly for unstructured generation. We propose an inference-scaling framework for structured outputs that combines fine-grained beam search with ToolPRM, a process reward model scoring each intra-call decision (function name and argument filling). We build the first fine-grained intra-call supervision dataset via function masking, rollout collection, and step-level annotation. ToolPRM outperforms outcome and coarse-grained reward models in predictive accuracy and yields consistent test-time gains on multiple function-calling benchmarks. We further show that structured generation follows ``explore more but retain less'', since early JSON errors are unrecoverable.

Deep research agents are increasingly evaluated on their ability to search for evidence, reason over retrieved sources, and produce grounded answers. Existing browsing benchmarks, however, largely assume that the user's query and the supporting evidence are written in the same language, leaving open whether agentic search systems can operate when relevant evidence appears in another language. We introduce XBCP (Cross-lingual BrowseComp-Plus), a controlled benchmark that preserves the English question-and-answer space of BrowseComp-Plus but varies the languages of the supporting documents. XBCP instantiates two complementary settings: in the cross-lingual setting, each query is paired with evidence in a single assigned language. In the multilingual setting, the full evidence corpus is distributed equally and randomly across 12 languages spanning high-resource and low-resource regimes. We evaluate four deep research agents using sparse and dense multilingual retrievers, measuring answer accuracy, evidence recall, search behavior, calibration, citation fidelity, and oracle retrieval. Results reveal substantial degradation when evidence is translated. Even strong, dense retrievers lose evidence recall, and agents become less calibrated and cite evidence less reliably. Notably, accuracy remains lower even when all gold evidence is supplied directly. These findings suggest that cross-lingual deep research exposes both retrieval failures and an independent, agent-side difficulty in integrating language-mismatched evidence.

Loss Given Default (LGD) modeling faces a fundamental data quality constraint: 90% of available training data consists of proxy estimates based on pre-distress balance sheets rather than actual recovery outcomes from completed bankruptcy proceedings. We demonstrate that this mixture-contaminated training structure causes systematic failure of recursive partitioning methods, with Random Forest achieving negative r-squared (-0.664, worse than predicting the mean) on held-out test data. Information-theoretic approaches based on Shannon entropy and mutual information provide superior generalization, achieving r-squared of 0.191 and RMSE of 0.284 on 1,218 corporate bankruptcies (1980-2023). Analysis reveals that leverage-based features contain 1.510 bits of mutual information while size effects contribute only 0.086 bits, contradicting regulatory assumptions about scale-dependent recovery. These results establish practical guidance for financial institutions deploying LGD models under Basel III requirements when representative outcome data is unavailable at sufficient scale. The findings generalize to medical outcomes research, climate forecasting, and technology reliability-domains where extended observation periods create unavoidable mixture structure in training data.