Scientific Reasoning

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Latest papers 39

Sep 12, 2026cs.AI

Sci-MMR: Benchmarking Multi-Step Evidence-Grounded Scientific Reasoning in Multimodal Agents

Autonomous research agents are increasingly expected to search the literature, analyze experimental evidence, and generate scientific hypotheses. These capabilities require multi-step evidence grounded reasoning that progressively acquires, integrates, and verifies evidence before reaching a conclusion. Existing multimodal benchmarks, however, largely evaluate final-answer accuracy, leaving open whether predictions are actually supported by traceable scientific evidence. We introduce Sci-MMR, a benchmark for multi-step evidence-grounded scientific reasoning built on structured argument graphs linking scientific claims, citation-grounded knowledge, visual evidence, and supporting regions. Sci-MMR comprises 235 multi-hop reasoning tasks spanning four scientific disciplines, with an average of nine figure panels per task. Evaluating eight frontier multimodal models, we find that answer accuracy consistently exceeds complete-evidence recovery rate by more than 20%, revealing a substantial gap that answer-only evaluation is structurally unable to capture. Through controlled interventions, we identify two fundamental bottlenecks. First, evidence acquisition: models struggle to extract complete structured evidence from scientific figures, accounting for 57.2% of failures. While cropping tools yield modest gains (+4.5 points), providing gold evidence improves accuracy by up to 37.0 points, indicating difficulty in assembling complete multi-region evidence. Second, evidence integration: models struggle to translate available evidence into correct conclusions, accounting for 31.8% of failures, while even with gold evidence the strongest model achieves only 69.1% accuracy on the hardest tasks. These findings indicate that current answer-centric benchmarks substantially overestimate the evidence-grounded reasoning capabilities of multimodal research agents

Jiaqiang Li, Yajie Yang, Zhiheng Xi +15

Fudan NLP Lab · Fudan NLP Group

Evidence-Grounded Reasoning Scientific Reasoning Multimodal Agents Multimodal Model Evaluation

Aug 31, 2026cs.AI

ScienceArena: Benchmarking LLMs on Latest Scientific Olympiad Competitions

Benchmark saturation and data contamination increasingly obscure genuine scientific reasoning in frontier LLMs. We introduce \textsc{ScienceArena}, an olympiad-style benchmark from thirteen public science competitions in physics, chemistry, and biology, including IPhO and IChO 2025--2026, IBO 2023, USAPhO 2026, and USNCO 2025. Its open-ended, multi-step problems use process-credit rubrics, making faithful scoring difficult. We build ScienceArena through an expert-audited digitization pipeline that converts official exams, figures, solutions, and rubrics into structured items verified by olympiad medalists. To scale evaluation beyond costly human grading, we calibrate LLM-as-judge against medalist ground truth on archived answers from five models across IPhO and IChO; two strong judges stay within one point of expert total scores. Medalist notes show that failures often stem from visual grounding, structure fidelity, and global problem control rather than missing terminology. Evaluating fourteen recent LLMs with interleaved solving, we find that top models obtain medal-equivalent rubric scores on several public international exams, while chemistry and long-horizon consistency remain key bottlenecks. We provide an interactive demo.

Guangxiang Zhao, Qilong Shi, Xusen Xiao +13

1Qiyuan Tech · 2Tsinghua University · 3The University of Hong Kong +1

LLM Evaluation Scientific Reasoning

Aug 31, 2026cs.AI

SPARK: Skeleton-Guided Reasoning Synthesis from Large-Scale Scientific Literature

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

Yu Li, Wei Li, Xin Gao +4

Shanghai AI Laboratory · University of Science and Technology of China · 1Shanghai AI Laboratory 2University of Science and Technology of China +5

Evidence-Grounded Reasoning Scientific Reasoning Synthetic Data Generation for Language Models

Aug 25, 2026cs.AI

Memory Is Not Always Needed: Characterizing Conditional Memory in Scientific Reasoning

Scientific reasoning requires language models to retrieve specialized knowledge and incorporate it reliably into multi-step computation. Conditional memory provides an explicit lookup pathway that complements dense neural representations, but its usefulness is inherently input- and computation-dependent: retrieved information may repair missing scientific associations, yet it may also introduce distracting shortcuts or interfere with reasoning that the base model can already perform correctly. In this work, we systematically investigate when, where, and to what extent conditional memory should participate in scientific reasoning. We characterize the scientific knowledge boundary and controlled interventions on memory-enabled knowledge-circuit nodes. Based on these analyses, we propose a Knowledge Boundary-Aware Router that uses task-specific input proxies available before generation to determine whether memory is activated, which layer-stage nodes receive memory signals, and how strongly these signals contribute. Experiments on biological and chemical reasoning benchmarks, covering two backbone families and six task types, show that memory effects vary substantially across inputs, tasks, and injection locations. Compared with static and activation-rate-matched random routing, our approach more consistently preserves beneficial memory contributions while suppressing memory-induced regressions, establishing selective memory allocation as an important principle for reliable scientific reasoning.

Zhen Bi, Xueshu Chen, Yan Wang +6

Huzhou Normal University · Alibaba Group · Bota Biosciences +1

Memory-Augmented Language Models Scientific Reasoning Adaptive Computation

Aug 11, 2026cs.CL

MUSE: A Full-Text Cross-Domain Knowledge Base of Scientific Problems, Solutions, and Rationales

Scientific papers contain fine-grained records of problem solving: authors mention technical obstacles and methods that were used to address them, often along with reasoning on why those methods were chosen. We introduce MUSE (Mining Underlying Scientific Explanations), a full-text, multi-domain resource of scientific Problem-Solution-Rationale (P-S-R) triplets. We curate 579 expert-annotated full-text paragraphs, with a rich annotation schema covering salient problem, solution, and rationale spans, solves and rationale_of links and conceptual coreference. A modular extraction pipeline scales this annotation to build a high-quality knowledge base of 37K source-grounded P-S-R triplets. We evaluate the extraction components and include a preliminary experiment training a rationale-supervised LLM for scientific problem solving. Interestingly, we find that rationale supervision improves performance on complex, multi-constraint problems but can harm performance on simpler ones.

Tsofia Cohen, Tom Hope

The Hebrew University of Jerusalem · Allen Institute for AI (Ai2)

Relation Extraction KG Construction Scientific Reasoning Document Information Extraction

Aug 7, 2026cs.AI

Science Edge Evaluation: SEE the Missing Step Toward Real Scientific Discovery

Large language models (LLMs) are increasingly involved in scientific discovery, yet it remains unclear whether they can support complex real laboratory science. Here we introduce Science Edge Evaluation (SEE), a multimodal benchmark of expert-curated questions grounded in peer-reviewed literature and experimental practice in chemistry, biology, and materials science. Evaluation of 19 multimodal large language models (MLLMs) shows that even the best-performing model reaches only 48.7% accuracy. Moreover, general-purpose models outperform science-specialized models on average. In the visual-agent evaluation, the use of tools increases the best accuracy to 52.7%. Tool use can expand the information available to models, but more information does not necessarily lead to reliable scientific reasoning. The key challenge is whether models can manage tool-derived information within the boundaries of the original experimental evidence. Together, these findings reveal that current MLLMs still cannot reliably make justified and evidence-bounded inferences from experimental results, which is an essential capability in real scientific discovery. Bridging this gap requires MLLMs to transition from explaining established scientific concepts to deriving novel and evidence-based insights from experimental data.

Taolin Han, Yuchen Zhang, Jinghang Wang +22

1Alibaba Group · University of Chinese Academy of Sciences · Taolin Han1,3* +28

Scientific Reasoning Scientific Discovery Scientific Reasoning in Language Models Multimodal Model Evaluation

Jul 23, 2026cs.CE

Chemical Chain-of-Thought Functions as a Hallucination-Prone Molecular Scratchpad

Chemical reasoning language models are expected to derive molecular answers through faithful chain-of-thought (CoT). However, across four reasoning model families and twelve chemistry tasks, hallucination is widespread and largely decoupled from answer correctness: correct answers often coexist with fabricated structural claims absent from the relevant molecules. Yet this does not make the reasoning trace computationally irrelevant. Attribution analyses suggest a shared scratchpad function expressed in model-specific forms: Chem-R and ether-0 rely on fragmented SMILES drafts, whereas ChemDFM-R emphasizes scaffold, positional, and naming cues. Notably, perturbing Chem-R's SMILES sketches degrades generation, showing that structural drafts can be causally load-bearing even when verbal structural claims are largely inert. Together, these results show that chemical CoT is neither a faithful explanation nor merely a post-hoc rationalization, but a hallucination-prone molecular scratchpad. This finding cautions against treating CoT as direct evidence of faithful reasoning and motivates process-level supervision beyond answer-only evaluation.

Jiatong Li, Yuxuan Ren, Weida Wang +2

Blue Whale Lab, National University of Singapore · Fudan University · Hong Kong Polytechnic University

CoT Faithfulness Scientific Reasoning Hallucination in Language Models Scientific Reasoning in Language Models

Jul 18, 2026cs.CL

Though Language Models Err While They Strive: Conformal Prediction for Self-Correcting Scientific Generation

Large language models frequently violate fundamental scientific principles when generating technical content, undermining their reliability in scientific applications. We introduce Scientific Feasibility Control SFC, a graph-structured conformal prediction framework that provides statistical guarantees for scientific reasoning validity through progressive absolute-coherent-factuality validation. Our approach decomposes scientific reasoning into atomic absolute-coherent-factuality units requiring both individual correctness against physical laws and logical substantiation from preceding context, addressing the cascade effect where early scientific errors contaminate subsequent reasoning steps. Unlike independence-based methods that treat claims in isolation, SFC models logical dependencies as approximate deducibility graphs and operates through real-time validation with dynamic branching when scientific violations are detected, the system branches to alternative generation paths using verified context as foundation. We demonstrate SFC across established scientific reasoning benchmarks including PhyX multimodal physics, MATH, ScienceQA, and ARC Challenge, achieving 50.1 percent accuracy on PhyX physics reasoning, substantially outperforming recent reasoning models including DeepSeek-R1 49.8 percent and GPT-4 45.8 percent while providing 91.7 percent scientific validity with formal conformal coverage guarantees at alpha equals 0.10 confidence level and reducing scientific law violations by 73 percent across multiple model architectures.

Mingqiao Mo, Yunlong Tan, Hao Zhang

University of Chinese Academy of Sciences

LLM Self-Correction Scientific Reasoning Conformal Prediction LLM Reliability Scientific Reasoning in Language Models Scientific Claim Verification

Jul 13, 2026cs.AI

Are LLMs Ready for Scientific Discovery? A Capability-Oriented Benchmark for AI Scientists

Existing benchmarks for scientific data analysis evaluate LLMs primarily on code execution or workflow completion, overlooking that scientific analysis serves to support distinct types of scientific claims: hypothesis exploration, statistical inference, mechanistic explanation, each with different assumptions and validity criteria. We introduce SDABench, a benchmark that reorganizes evaluation around six capabilities (descriptive, exploratory, inferential, predictive, causal, and mechanistic) across five domains (Biology, Chemistry, Environment, Geography, Physics). SDABench comprises 527 real-data instances (SDA-Real) and 6000 synthetic instances (SDA-Synth), each in both multiple-choice and open-ended formats, constructed through an automated pipeline. Evaluating 15 representative LLMs, we find that models handle descriptive analysis well but degrade sharply on tasks requiring assumption selection, latent-process modeling, or mechanistic reasoning. SDABench further provides a five-stage error analysis framework that locates where LLMs fail: more advanced models more reliably identify the relevant scope and variables, but still struggle to select appropriate analytical procedures, model variable relationships, and draw valid conclusions.

Chuhan Shi, Xiaoquan Ren, Sicheng Song +3

Southeast University · East China Normal University · Hong Kong University of Science and Technology

AI for Science LLM Evaluation Scientific Reasoning

Jul 9, 2026cs.AI

Ideas Have Genomes: Benchmarking Scientific Lineage Reasoning and Lineage-Grounded Idea Generation

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.

Yifan Zhou, Qihao Yang, Yan Li +14

Shanghai Jiao Tong University · Carnegie Mellon University · University of Chinese Academy of Sciences +4

Scientific Reasoning Scientific Hypothesis Generation AI Agent Benchmarks Research Idea Generation

Jul 9, 2026cs.AI

A safety-oriented hypothetico-deductive framework for AI-assisted differential diagnosis

Diagnostic error is a major threat to patient safety, yet current large language model (LLM) systems often treat diagnosis as a one-shot prediction task, lacking safeguards against missed high-risk alternatives or rigorous verification of their reasoning. Here, we present AegisDx, a safety-oriented framework for hypothetico-deductive clinical reasoning. AegisDx coordinates specialized LLM components through role-specific contracts, structured intermediate outputs, evidence-retrieval interfaces, and verification gates to generate broad differential diagnoses, enforce explicit screening for dangerous "must-not-miss" conditions, verify reasoning against grounded medical evidence, and structure actionable next steps. We evaluated AegisDx across three layers. On literature-derived case reports from NEJM and JAMA, with GPT-oss-120B as the shared backbone, Top-3 diagnostic accuracy was 59.9% versus 52.1% for the standalone LLM on JAMA cases and 62.7% versus 51.4% on NEJM cases. On cases from Annals of Emergency Medicine, Top-3 accuracy was 85.7% versus 68.6%; against physician-consensus must-not-miss diagnosis sets, AegisDx captured at least one such condition among its top three diagnoses in 78.0% of cases versus 52.0%. In a blinded physician evaluation of 43 real-world emergency department notes from the Yale New Haven Health System compared against GPT-5, AegisDx improved the physician-rated composite safety score from 4.31 to 4.55 on a 5-point scale (adjusted p = 2.1x10^-4), with qualitative gains in must-not-miss identification and reasoning safety. Our findings suggest that engineering diagnostic AI as a safety-oriented reasoning framework, rather than optimizing raw predictive accuracy alone, can provide a safer, more transparent, and clinically meaningful layer of bedside decision support for acute care workflows.

Fan Ma, Mauro Giuffrè, Donald Wright +12

Department of Biomedical Informatics and Data Science, Yale School of Medicine, Yale University, New Haven, USA · Department of Medical, Surgical and Health Sciences, Università degli Studi di Trieste, Trieste, Italy · Department of Emergency Medicine, Yale School of Medicine, Yale University, New Haven, USA +3

Scientific Reasoning Medical Diagnosis Clinical Decision Support LLM Safety Clinical Reasoning Differential Diagnosis+1

Jul 8, 2026cs.CL

Accurate, Interdisciplinary and Transparent Structure-property Understanding with Deep Native Structural Reasoning

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.

Chen Tang, Yizhou Wang, Jianyu Wu +26

Shanghai Artificial Intelligence Laboratory, China. · The Chinese University of Hong Kong, Hong Kong. · Shanghai Jiao Tong University, China. +8

Scientific Reasoning Materials Property Prediction Multimodal Reasoning Protein Representation Learning Molecular Representation Learning

Jul 1, 2026cs.CL

IsoSci: A Benchmark of Isomorphic Cross-Domain Science Problems for Evaluating Reasoning versus Knowledge Retrieval in LLMs

We introduce ISOSCI, a benchmark of isomorphic cross-domain science problem pairs that separates reasoning ability from domain knowledge retrieval in LLM evaluation. Each pair shares identical logical structure but requires different domain-specific knowledge, enabling controlled attribution of reasoning-mode gains. Across five model pairs spanning four model families, we find that 91.3% of reasoning-mode gains are knowledge-dependent rather than structure-invariant (63/69 gains; Wilson 95% CI [82.3%, 96.0%]), directly challenging the assumption that chain-of-thought reasoning improves short-horizon procedural scientific problem-solving. Reasoning toggles on highly capable models provide less than 5 percentage points accuracy gain across all domains, and a reasoning-specialized model (o3-mini) that outperforms its standard counterpart on GPQA Diamond (+19.2 percentage points) underperforms on ISOSCI (-24.7 percentage points), showing that benchmark choice determines conclusions about reasoning utility. We release ISOSCI at https://huggingface.co/datasets/isosci/isosci

Samir Abdaljalil, Erchin Serpedin, Hasan Kurban

Electrical and Computer Engineering Texas A&M University College Station, TX USA · College of Science and Engineering Hamad Bin Khalifa University Doha, Qatar

LLM Evaluation Scientific Reasoning Factual Knowledge in Language Models LLM Reasoning

Jun 24, 2026cs.AI

Accelerating Returns and the Qualitative Engine for Science

Ray Kurzweil described a thesis of accelerating returns, which is the most influential narratives in discussions of technological progress. Its central claim is that advances in multiple technological fields, especially compute, artificial intelligence, brain science, and biotechnology, interact in such a way that progress becomes self-amplifying and approximately exponential. This paper gives a simple mathematical interpretation of that claim and then argues that, even if such acceleration is real, it does not by itself resolve the central problem of scientific discovery. The reason is that accelerating returns apply most naturally to executional and infrastructural capability, whereas genuine discovery often depends on a different capacity: qualitative reasoning about when a current framework is structurally inadequate and what conceptual move is needed next. Recent ARC-AGI-3 results sharpen this distinction: humans solve the benchmark at ceiling, whereas frontier AI systems remain below 1%, indicating that the gap between current AI and human flexible reasoning is still very large. At the same time, Demis Hassabis has emphasized that humans must retain their sense of meaning and what they choose to focus their lives on, a reminder that the future of AI is not only a technical forecast but also a question of what forms of human understanding are worth preserving and transmitting. This paper positions the Qualitative Engine for Science (QES) [3] as a response to that missing capacity. In this view, the Kurzweil theory helps explain why quantitative capability may accelerate, while QES addresses the central problem in scientific discovery that acceleration alone does not solve. Its value does not depend on when AGI arrives, but on the fact that the processes of scientific discovery themselves constitute a form of human wisdom worth preserving, organizing, and making accessible.

Guojun Liao

Department of Mathematics, The University of Texas at Arlington · Department of Mathematics, University of Texas at Arlington

AI for Science Scientific Reasoning Scientific Discovery

Jun 18, 2026cs.CL

SciLens: Multi-modal Scientific Claim Verification with Agentic Entailment and Grounding

Scientific discovery increasingly relies on automated systems that generate hypotheses, inspect multimodal evidence, and validate claims at scale. Yet scientific claim verification is not well served by asking a vision-language model for a direct binary judgment: claims often combine numerical results, comparisons, scope qualifiers, and explanatory context, while evidence is encoded in tables and figures with distinct grounding structures. We present SciLens, an evidence-conditioned atomic entailment framework for multimodal scientific claim verification. SciLens decomposes each claim into central empirical atoms and background atoms, grounds the central atoms to modality-specific evidence witnesses, and predicts the final label with an atom-level entailment rule. For tables, atoms are grounded to rows, columns, cells, arithmetic relations, and table scope; for figures, they are grounded through panels, axes, legends, visual encodings, categories, trends, ranks, and qualifier checks. This yields a unified validation procedure in which a claim is supported only if every central empirical atom is entailed by the current evidence. On the SciClaimEval development set, SciLens achieves 79.2% macro-F1 and 63.1% pair accuracy, showing that structured agentic validation improves both evidence sensitivity and interpretability.

Yueming Wang, Tianshi Zheng, Jiaxin Bai +3

The Hong Kong University of Science and Technology Hong Kong SAR, China · NVIDIA AI Technology Center Santa Clara, USA

Multimodal Grounding AI for Science Evidence-Grounded Reasoning Scientific Reasoning Scientific Claim Verification

Jun 11, 2026cs.AI

A Three-Layer Framework for AI in Scientific Discovery

Current discussions of AI in scientific discovery are often dominated by two visible capabilities: search over existing knowledge and execution through optimization, simulation, and automation. Both are important, but neither fully captures the central act of discovery: the formation and evolution of models. This paper proposes a three-layer view of AI in discovery. Layer 1 is search and retrieval by large language models. Layer 2, as the main innovation of this paper, is model formation through qualitative reasoning: the capacity to recognize when a current framework is structurally inadequate and to understand the problem within a broader representational space, not through trial and error, but through structural insight into what is missing and where it can be found. Layer 3 is execution, optimization, and refinement. The main claim is that Layer 2 is both the most important and the least developed. Search without model formation remains confined to inherited frameworks, while execution without conceptual revision only amplifies an existing formulation. We illustrate Layer 2 reasoning through three case studies: S. S. Chern's intrinsic proof of the Gauss-Bonnet theorem, the resolution of the Nesterov Accelerated Gradient convergence problem via Lyapunov functions, and the autonomous disproof of the Erdos unit distance conjecture by OpenAI in 2026. Each case exhibits the same structural signature: a framework that had become inadequate, a missing conceptual object, and a resolution found in an unexpected neighboring field.

Guojun Liao

Department of Mathematics, University of Texas at Arlington

AI for Science Scientific Reasoning Scientific Discovery

Jun 11, 2026cs.AI

TerraBench: Can Agents Reason Over Heterogeneous Earth-System Data?

Climate and environmental decision-making increasingly requires reasoning across heterogeneous inputs, including gridded physical data, satellite imagery, geospatial context, and simulator outputs. Weather and climate foundation models can forecast well, but do not reason interactively in language, while large language models (LLMs) reason in language but cannot operate directly on high-dimensional Earth-system data. As a result, real scientific workflows in Earth-science remain underserved. We introduce TerraBench, a benchmark for grounded Earth-science reasoning, built on TerraAgent, a ReAct-style executable framework that interleaves reasoning, tool calls, and observations to couple LLM planning with scientific tools for environmental retrieval, geospatial processing, simulation, and artifact-backed computation. TerraBench unifies analysis of Earth observation imagery, gridded data, GIS reasoning and simulation in a single executable interface, whereas prior benchmarks isolate these capabilities into narrow individual tasks. It is also the first in this space to pair process-level tool-use metrics with tolerance-aware numeric scoring. The benchmark comprises 403 extensive agentic tasks across three tracks (Fundamentals, Simulator-Grounded, and Document-Grounded Verification) and eight application domains with 24,500 verified execution steps. These results indicate that reliable Earth-science agents must go beyond tool access to coordinate heterogeneous workflows, parameterize tools precisely, and preserve artifact provenance.

Dat Tien Nguyen, Thao Nguyen, Fadillah Adamsyah Maani +5

Mohamed bin Zayed University of Artificial Intelligence, Abu Dhabi, UAE · ADIA Lab, Abu Dhabi, UAE

AI Agents for Scientific Discovery Scientific Reasoning LLM Agent Evaluation Geospatial Reasoning AI Agent Benchmarks LLM Agents+1

Jun 11, 2026cs.AI

SciR: A Controllable Benchmark for Scientific Reasoning in LLMs

Three paradigmatic forms of inference recur across scientific reasoning: deduction, induction, and causal abduction. Reliably evaluating LLMs on these in scientific settings is currently out of reach: scientific benchmarks built on human annotations are costly and lack mechanistic ground truth, while synthetic logical-reasoning benchmarks do not resemble real scientific documents. We introduce SciR, a benchmark that combines multi-paradigm reasoning with controllable scientific rendering, anchored on three paradigmatic scientific problems. Tasks are generated from formal objects (deduction tree, inductive rule hypothesis, causal graph) to guarantee verifiable answers, then rendered into multi-document scientific discourse via per-track domain-tuned genres. The construction lets us independently vary two difficulty axes: how hard it is to extract the key information needed for inference, and how hard the principled inference itself is. We test six models. Both axes hurt every model, and their effects compound. The rendering even hurts neurosymbolic pipelines, which hand inference to a verified solver. The two axes yield a per-model extraction-vs-inference profile: for instance, reasoning models like deepseek-r1 mostly surpass non-reasoning instruct models on the inference axis. To our knowledge, SciR is the first multi-paradigm scientific-reasoning benchmark with parametric control on both extraction and inference difficulty.

Pierre Beckmann, Marco Valentino, Andre Freitas

Idiap Research Institute, Switzerland · EPFL, Switzerland · School of Computer Science, University of Sheffield, UK +2

LLM Evaluation Scientific Reasoning Synthetic Benchmark Generation Structured Reasoning Scientific Reasoning in Language Models

Jun 7, 2026cs.AI

DN-Hypo-Pipeline: An AI-Driven Workflow for Generating Hypotheses using Large Language Models and Scientific Explanations

Modern artificial intelligence excels at prediction but cannot explain. From large language models to AI-for-science systems, today's machines answer what by recombining patterns already present in the human literature, yet they cannot reason out why a phenomenon must arise from underlying principles even though explanation, not prediction, lies at the heart of scientific discovery. Here we ask whether the structure of scientific explanation can be operationalized to guide how a machine generates hypotheses. We introduce DN-Hypo-Pipeline, a hypothesis-generation framework that adopts a layered, explanation-theoretic scaffold: Hempel's deductive-nomological (DN) model supplies the output form and deductive validity of a hypothesis, Salmon's causal-process account supplies an organizing constraint on where to search for the governing laws, and Armstrong's view of laws as relations between universals supplies the bridge from a phenomenon's constituent processes to the laws that may be associated with it. Rather than searching the space of what has been written, the framework searches the space of what principles govern a phenomenon: given an explanandum, it abstracts the universals instantiated in the phenomenon's formation process, retrieves the laws relating those universals, and deductively reconstructs a new, testable explanation. Evaluated in data-science modeling and judged by both LLMs and human experts, hypotheses generated through this principled reasoning significantly outperform those from direct prompting. Crucially, we translated the two highest-scoring hypotheses into novel algorithms one that reduces the Transformer's theoretical complexity with only minimal performance loss, and another that achieves competitive accuracy with substantially fewer parameters.

Lei Lin, Ronghao Wang, Chunbao Zhou +2

Computer Network Information Center, Chinese Academy of Sciences, China

Scientific Reasoning Scientific Hypothesis Generation Research Idea Generation Scientific Reasoning in Language Models Large Language Model-Guided Scientific Discovery

Jun 6, 2026cs.CY

Contemporary AI lacks the imagination to diverge or negate in science

Bold projections that artificial intelligence will accelerate scientific discovery have raced ahead of evidence from working scientists, and the field still lacks large-scale, scientist-in-the-loop tests of these claims. Here we mount the largest such evaluation to date and map what AI cannot yet do for science. We invited authors of 121,640 recent preprints across biology, medicine, chemistry, and the social sciences to judge ideas that large language models (LLMs) generated from the context and puzzles of their own papers. 6,749 scientists returned 25,139 sets of ratings on novelty, empirical feasibility, probability of being true, and favorability of adoption. Three patterns emerge. First, non-reasoning LLMs collapse into a narrow "hivemind" of similar ideas; reasoning models roam a wider hypothesis space, yet no model class spontaneously proposes null hypotheses -- a move humans make more freely. Second, scientists reward ideas that resemble their own and prize probability over novelty, though social scientists tolerate risk more readily than life scientists. Senior social scientists are the harshest critics, and their skepticism is well-earned: LLMs falter most in pluralistic fields like the social sciences that demand context-aware interpretation and evolving theories. Third, automated evaluators on which the community currently relies -- LLM-as-a-judge, artificial metrics, and even state-of-the-art (SOTA) models -- agree only weakly with expert judgment, and retrieval augmentation and scientist persona prompting yield only marginal gains. A Qwen3-14B reward model we post-trained on human ratings captures field taste nuances, beats SOTA models by up to 27%, and closes the gap to the inter-rater consistency of independent peer reviewers. For all the hype, today's scientific AI still represents a collaborator whose imagination, outputs and judgment benefit from human grounding.

Honglin Bao, Siyang Wu, Xiao Liu +3

Data Science Institute, University of Chicago · Knowledge Lab, University of Chicago

LLM-as-a-Judge Scientific Reasoning Scientific Hypothesis Generation Human-in-the-Loop Evaluation

Jun 3, 2026cs.AI

SCI-PRM: A Tool Aware Process Reward Model for Scientific Reasoning Verification

While Process Reward Models (PRMs) have achieved remarkable success in mathematical reasoning, their application in complex scientific domains-such as biology, chemistry, and physics remains largely unexplored. Scientific problems demand not only logical rigor but also factual consistency and the precise usage of domain-specific tools, areas where current models often suffer from hallucinations and lack of verification. In this paper, we first construct SCIPRM70K, a large-scale dataset featuring Chain-of-Tool trajectories that explicitly interleave reasoning with the execution of scientific tools. Building upon this, we train an efficient reward model called Sci-PRM to provide fine-grained supervision on tool selection, execution accuracy, and result interpretation at each step in one inference. Experiments demonstrate that Sci-PRM significantly enhances foundation models in two key aspects: (1) it enables effective test-time scaling via Best-of-N selection; and (2) when integrated into Reinforcement Learning, it serves as a dense reward signal that mitigates the critical issue of advantage disappearance, allowing the model to break through existing performance ceilings.

Xiangyu Zhao, Henry Hengyuan Zhao, Yiheng Wang +7

The Hong Kong Polytechnic University · National University of Singapore · Shanghai AI Lab +3

Process Reward Models Scientific Reasoning Reinforcement Learning with Verifiable Rewards RL for Tool Use

Jun 2, 2026cs.CV

NewtPhys: Do Foundation Models Understand Newtonian Physics?

Previous work has evaluated physics reasoning in foundation models using synthetic or semi-synthetic scenes and visual question-answering tasks. However, these benchmarks emphasize high-level events and lack the visual fidelity required to assess true low-level Newtonian understanding. We introduce NewtPhys, a 4D physically annotated dataset built from multiview images of real-world scenes with physics-grounded simulations. The dataset provides dense, fine-grained annotations across timesteps -- including 3D forces and amodal per-pixel quantities covering physics, tracking, semantics and geometry -- bridging the gap between simplistic synthetic setups and realistic visual complexity. Using NewtPhys, we systematically evaluate 56 VLMs, including 54 open-weight models and 2 closed-source frontier models, and 10 VFMs and reveal limitations in low-level physics reasoning. Beyond benchmarking, our dataset enables future research in physics-grounded vision and the development of next-generation physics-aware evaluations. Code and datasets are available at https://astra-vision.github.io/NewtPhys.

Sebastian Cavada, Soumava Paul, Tuan-Hung Vu +2

MBZUAI · Inria

VLM Evaluation Scientific Reasoning Visual Reasoning Physical Reasoning in Video

May 31, 2026cs.AI

Science Earth: Towards A Planet-Scale Operating System for AI-Native Scientific Discovery

Scientific discovery demands intelligence, perseverance, and serendipity across vast search spaces. Today, top scientific capabilities remain siloed--one AI system for biological analysis, another for clinical reasoning, mathematical derivation, or materials simulation--and no pre-designed team can anticipate every skill a question will need. Science Earth is a planet-scale scientific runtime in which any capability--a simulation cluster, a wet-lab robot, a proof engine, a single-cell pipeline--can connect to any other, with collaboration structure emerging from the question itself. Its underlying EACN protocol lets capabilities discover one another, negotiate task ownership, and adjudicate across incompatible evidentiary standards without prior knowledge of who will meet whom. This shifts the organizing challenge from workflow design to open-ended connectivity. Two runs validate this under structurally distinct conditions. In a trans-Pacific higher-order Kuramoto synchronization study, agents identified and corrected a closure-ratio assumption in Ott-Antonsen analytic theory that fails outside the Lorentzian limit, within thirty minutes. In an eight-agent single-cell run on the 4.88M-cell Kang 2024 pan-cancer atlas, heterogeneous capabilities coupled over a 64.9-hour window with one structural external instruction, producing three new result layers and anchoring findings against an independent wet-lab study on an adjacent CCR8- TIGIT+ Treg subset. These cases are a first empirical reading, not a benchmark sweep. They show that when AI capabilities are truly connectable and coordination emerges from the problem, scientific reasoning becomes a distributed, self-correcting process--a step towards scaling AI-native discovery to the planet.

Zhe Zhao, Haibin Wen, Yingcheng Wu +10

Department of Pathology, Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA · Scripps Research, La Jolla, CA, USA · Division of Biostatistics, Department of Population Health, New York University Grossman School of Medicine, New York, NY, USA +4

Multi-Agent Coordination Multi-Agent Orchestration Agent Communication Protocols Scientific Reasoning Autonomous Scientific Discovery

May 31, 2026cs.AI

Reasoning4Sciences: Bridging Reasoning Language Models to All Scientific Branches

While Reasoning Language Models (RLMs) are rapidly emerging as powerful tools for scientific research, their impact is primarily concentrated in "hard science" fields. The slow -- or lack of -- adoption of RLMs in other branches of science is causing a widening gap in research productivity. In this survey, we provide the first comprehensive analysis of RLM adoption across 28 scientific disciplines following the classification used by the European Research Council (ERC), spanning the Social Sciences and Humanities, Physical Sciences and Engineering, and Life Sciences. We examine how RLMs are developed, evaluated, and applied across disciplines. Furthermore, we introduce a maturity-oriented assessment framework based on available domain-specific development and evaluation resources, revealing substantial disparities in RLM maturity that become even more pronounced when only publicly available resources are considered. Finally, we highlight current implementation paradigms that are gaining popularity across disciplines, current challenges, and future directions in enabling RLM adoption across science.

Teddy Ferdinan, Bartłomiej Koptyra, Mikołaj Langner +42

AI for Science Scientific Reasoning Scientific Reasoning in Language Models Large Language Model-Guided Scientific Discovery Large Reasoning Models

May 28, 2026cs.AI

ProjectionBench: Evaluating Scientific Hypothesis Generation in LLMs Under Progressive Information Disclosure

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

A. J. Lew, Y. Cao, M. J. Buehler

Unreasonable Labs · Unreasonable Labs Mountain View, CA 94043, USA

LLM Evaluation Scientific Reasoning Scientific Hypothesis Generation Research Idea Generation Scientific Reasoning in Language Models Large Language Model-Guided Scientific Discovery

May 26, 2026cs.AI

On the evolution of the concept of probability as a mirror of the evolution of reason

Over the centuries, probability theory has grown from the calculus of games of chance into a central framework for reasoning under uncertainty. This article interprets that evolution not merely as a mathematical history, but as a transformation of rationality itself. From Pascal and Fermat's combinatorial symmetry to the inductive logic of Bayes and Laplace, from Poisson's statistics of events to Kolmogorov's axiomatic formalization, probability progressively incorporated uncertainty, time, and coherence into scientific judgment. This trajectory reaches a mature epistemological form in modern Bayesian inference, especially in Tarantola's view of probability as a logic of information, where prior knowledge and data are combined coherently. Yet this framework also exposes a limit: probability quantifies uncertainty about well-defined propositions, but does not by itself formalize the vagueness of the concepts used to describe them. The article therefore examines how rationality extends beyond probability. Fuzzy logic is presented as a rigorous language for graded meaning and qualitative judgment, while deep learning is analyzed as a distinct, powerful mode of prediction based on geometric interpolation and optimization rather than explicit inference. By situating probability, fuzzy logic, and deep learning in a common historical and epistemological perspective, the article clarifies their roles and limits. It argues that contemporary scientific rationality cannot be reduced to data-driven performance alone, but requires the explicit articulation of uncertainty, vagueness, and inference.

Jean-Louis Le Mouël, Vincent Courtillot, Dominique Gibert +6

Acad´emie des Sciences, Institut de France, Paris, France · DeepField Sensing, France · Institute of Earthquake Prediction Theory and Mathematical Geophysics, Russian Academy of Sciences, Moscow, Russia +4

Scientific Reasoning Epistemic Uncertainty

May 24, 2026cs.AI

Geo-Expert: Towards Expert-Level Geological Reasoning via Parameter-Efficient Fine-Tuning

While general-purpose Large Language Models (LLMs) applied to Geology often hallucinate when reasoning about subsurface structures and deep-time evolution, current AI in Earth sciences predominantly targets surface remote sensing and GIS. To bridge this gap, we introduce Geo-Expert, a family of parameter-efficient geological LLMs fine-tuned on a custom-curated, high-quality instruction dataset processed using our custom instruction synthesis pipeline. We investigate the impact of model scaling and architecture by fine-tuning three base models: Qwen3-8B, Qwen3-32B, and Gemma-3-27B, with Low-Rank Adaptation (LoRA) method. Our extensive evaluation on a novel domain-specific benchmark, Geo-Eval, reveals that a domain-aligned 8B model can outperform open-weight 70B generalists and proprietary GPT-4o on specialized geological reasoning, while a 32B variant approaches frontier reasoning models. The optimized 8B model further offers a competitive cost-performance ratio for deployment. This work provides a reproducible recipe for democratizing scientific LLMs and establishes a baseline for geological artificial intelligence.

Chenyou Guo, Zongqi Liu, Yizhou Zhang +2

Ocean University of China · Peking University · Monash University

Scientific Reasoning LLM Fine-Tuning Language Modeling

May 21, 2026cs.AI

Cross-domain benchmarks reveal when coordinated AI agents improve scientific inference from partial evidence

Scientific evidence often spans instruments, databases, and disciplines, so no single source records the full phenomenon. This makes it difficult to determine when coordinated AI agents add value over simpler scientific workflows. We evaluate this question with a cross-domain benchmark spanning four scientific tasks: mapping molecular structure into musical representations, detecting historical paradigm shifts in science, identifying vector-borne disease emergence, and vetting transiting-exoplanet candidates. Each case uses a frozen evaluation panel, predefined scoring protocols, explicit baselines, ablations or null controls, and stated limitations. The results define three operating regimes. When different disciplines each capture only part of the phenomenon, cross-channel composites improve over single-channel baselines: climate-vector emergence reaches AUROC 0.944 and exoplanet vetting reaches AUROC 0.955. However, the exoplanet workflow is effectively tied with a strong combined-summary baseline, showing that decomposition does not always improve top-line performance. When one signal dominates, as in paradigm-shift detection, coordination mainly improves interpretation and traceability. For molecular sonification, the gain is representational rather than predictive. ScienceClaw x Infinite provides the auditable artifact and provenance layer for this evaluation. The benchmark therefore assigns value to coordination only when the corresponding performance, provenance, or representation claim is supported by explicit comparators.

Fiona Y. Wong, Markus J. Buehler

Laboratory for Atomistic and Molecular Mechanics (LAMM) · Department of Biological Engineering · Department of Mechanical Engineering +2

AI for Science Multi-Agent Coordination Scientific Reasoning AI Agent Benchmarks

May 16, 2026cs.AI

Scientific Logicality Enriched Methodology for LLM Reasoning: A Practice in Physics

With the continuous advancement of reasoning abilities in Large Language Models (LLMs), their application to scientific reasoning tasks has gained significant research attention. Current research primarily emphasizes boosting LLMs' performance on scientific QA benchmarks by training on larger, more comprehensive datasets with extended reasoning chains. However, these approaches neglect the essence of the scientific reasoning process -- logicality, which is the rational foundation to ensure the validity of reasoning steps leading to reliable conclusions. In this work, we make the first systematic investigation into the internal logicality underlying LLM scientific reasoning, and develop a scientific logicality-enriched methodology, including a set of assessment criteria and data sampling methods for logicality-guided training, to improve the logical faithfulness as well as task performance. Further, we take physics, characterized by its diverse logical structures and formalisms, as an exemplar discipline to practise the above methodology. For data construction, we extract scientific problems from academic literature and sample a high-quality dataset exhibiting strong logicality. Experiments based on three different backbone LLMs reveal that: 1) the training data we constructed can effectively improve the scientific logicality in LLM reasoning; and 2) the enriched scientific logicality plays a critical role in solving scientific problems. Code is available at https://github.com/ScienceOne-AI/PhysLogic.

Zhaoxin Yu, Nan Xu, Kun Chen +3

State Key Laboratory of Multimodal Artificial Intelligence Systems, Institute of Automation, Chinese Academy of Sciences, Beijing, China · School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, China · Beijing Wenge Technology Co., Ltd, Beijing, China

Scientific Reasoning Scientific QA LLM Reasoning

May 14, 2026cs.AI

XDomainBench: Diagnosing Reasoning Collapse in High-Dimensional Scientific Knowledge Composition

Large Language Models (LLMs) are increasingly deployed for knowledge synthesis, yet their capacity for compositional generalization in scientific knowledge remains under-characterized. Existing benchmarks primarily focus on single-turn restricted scenarios, failing to capture the capability boundaries exposed by real-world interactive scientific workflows. To address this, we introduce XDomainBench, a diagnostic benchmark for interactive interdisciplinary scientific reasoning. We formalize the composition order and mixture structure to enable systematic stress-testing from single-discipline to inter-disciplinary, comprising 8,598 interactive sessions across 20 domains and 4 task categories, with 8 realistic trajectory patterns covering difficulty and domain-mixture dynamics, simulating real AI4S scenarios. Large-scale evaluation of LLMs reveals a systematic reasoning collapse as composition order increases, stemming from two root causes: (i) direct difficulty increases induced by domain composition, and (ii) indirect interaction-amplified failures where trajectory patterns trigger error accumulation, reasoning breaks, and domain confusion, ultimately leading to session collapse.

Gong Zhiren, Tiantong Wu, Jiaming Zhang +9

College of Computing and Data Science, Nanyang Technological University, Singapore · Interdisciplinary Graduate Programme, Nanyang Technological University, Singapore · Department of Mathematics and Mathematical Statistics, Umeå University, Sweden +2

AI for Science LLM Evaluation Scientific Reasoning AI Agent Benchmarks Compositional Generalization