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 \href{https://science-arena.onrender.com/}{demo}.
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.
While tool-augmented Large Language Models have significantly improved multi-step reasoning in quantitative STEM tasks, a critical residual failure mode remains: intermediate reasoning steps that are syntactically well-formed, mathematically executable, and unit-consistent, yet contextually ungrounded. Current approaches either rely on formal verifiers that cannot assess semantic intent, or burden Process Reward Models (PRMs) with the dual task of checking both arithmetic and logic. In this paper, we propose a neuro-symbolic framework that cleanly decouples reasoning into two formal dimensions: Symbolic Validity ($V$) and Semantic Groundedness ($G$). We guarantee $V$ by construction using a deterministic symbolic verifier acting as a hard filter. To assess $G$, we train a PRM conditionally on the verifier-accepted manifold. To train this PRM efficiently, we introduce Counterfactual Symbolic Perturbation (CSP), a novel data synthesis strategy that algorithmically generates constraint-preserving hard negatives (steps that perfectly pass the verifier but are logically flawed). At inference, we deploy a verifier-first constrained search that guarantees execution consistency for verifier-covered operations while relying on the PRM solely to rank semantic grounding. By targeting the exact residual error class of strong tool-using LLMs, our method significantly improves reasoning reliability without the sprawling heuristics of prior frameworks.
Zhen Bi, Xueshu Chen, Yan Wang +6cs.AI cs.CL cs.LG
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.
Joint-embedding predictive architectures are selected almost universally by linear probing and effective rank. We report a case where both read healthily while the representation carries zero usable instance information. We repair it, and a second failure appears: the repaired metric saturates on a target carrying no structural information. Our corpus is a scientific-reasoning graph over 57,903 articles, each a subgraph. A Graph-JEPA predicts one masked aspect from a subgraph's remaining aspects, attaining linear-probe accuracy 0.871 and effective rank 18-47, yet retrieval recovers 0.00 of 14.4 bits (MRR 1.9e-4 vs chance 1.99e-4, p=0.98). Three upper bounds on the same pool and code recover nearly everything (+14.28, +14.34, +14.22 bits), ruling out corpus, masking, pool, and metric as causes. We trace this to variance allocation - frozen inputs place 86.05% of variance on subgraph identity and 0.40% on aspect identity, while trained latents place 0.39% and 99.61%. This is a property of the objective's optimum: the degenerate solution is a global minimum of the coupled predictor/EMA-target objective, present already at init. A repaired configuration reaches 14.377 of 14.379 bits, above the 13.865-bit oracle; reverting the loss to regression drops it to 0.307 bits, confirming it. Yet the repair licenses nothing about reasoning: the target is reducible, since intra-subgraph edges are a deterministic function of node census. The oracle reaches 96.4% of the ceiling, and our largest effect is the learning-rate schedule, not architecture. Bits and a reasoning probe show no relation across ten cells. A data-derived target fails a quality gate - 25.96% of nodes are duplicate placeholders, and the rest is more generic than supporting evidence. Rank, probes, and metrics can all saturate on an unsupportive evaluation. We release a harness with a reducibility audit and target gate.
Group Relative Policy Optimization (GRPO) learns from reward differences within a rollout group, but receives no useful relative signal when every sampled response is incorrect. Privileged self-distillation can fill this gap with dense token supervision, yet applying it throughout training creates a different failure mode: the teacher is a biased, low-variance surrogate for the reward objective, so persistent imitation can oppose reward-improving updates after the policy becomes capable of producing successful trajectories. We introduce I-SDPO (Instance-Level Adaptive Self-Distillation Policy Optimization), which treats teacher reliance as capability-dependent. I-SDPO makes one routing decision per input instance and shares it across that instance's rollout group: all-incorrect groups use a privileged self-distillation objective, whereas any-success groups remain intact for GRPO. This design uses imitation only where group-relative rewards are uninformative. A local analysis characterizes when teacher and reward directions align and shows that a non-vanishing biased distillation weight induces an optimization bias floor. The routing rule automatically reduces the expected distillation rate as success probability rises, withdrawing teacher influence without a hand-designed schedule. On SciKnowEval, I-SDPO obtains the best result in all four scientific domains and improves average mean@16 accuracy from 56.67% with GRPO to 70.31%, with a maximum domain gain of 18.24 points.
Large language models are being proposed as agents in scientific workflows, in domains where no downstream verifier exists. Such deployment assumes the model can distinguish reliable scientific literature from unreliable literature, a capability that has not yet been directly measured. Existing benchmarks evaluate factuality on questions with known answers; the failure mode we target here is different. We introduce a probe corpus of 42 retracted, fraudulent, and pseudoscientific papers, paired with a methodology for eliciting and scoring single-shot model engagement with each paper's framing. Each probe pairs a preamble extracted near-verbatim from the target paper with a scientifically plausible study-design request. The probes span five claim types: fabricated observation, pseudophysical mechanism, magical premise, legitimization bridge, and cargo-cult experiment. Two complementary scores measure whether a model rejects the flawed premise outright (IFR-a) and whether it recognizes the unreliability while still engaging (IFR-i). A depth score, the Engagement Depth Index (EDI), quantifies reproduction of paper- or field-specific withheld details. Across 30 models and 10 repeated runs, aggregate IFR-a is 0.93 $\pm$ 0.004 and aggregate IFR-i is 0.809 $\pm$ 0.009. Models engaged with untenable premises in 95% of all non-empty responses. Every evaluated model fails more than 71% of agentic probes, and 22 of 30 models fail more than 90% of the time. Rejections are concentrated on a small number of high-notoriety topics and specific probes, and disappear under matched-structure controls. These results are consistent with topic-keyed safety behavior rather than robust epistemic competence, and indicate an urgent need for guardrail infrastructure for scientific deployment of language models.
We introduce Sci-VBench, a comprehensive benchmark for evaluating knowledge- and reasoning-intensive video generation across scientific domains. It contains 1,253 expert-annotated examples spanning 60 subjects across four core disciplines: Natural Science, Healthcare, Humanities & Social Sciences, and Engineering. Each example requires models to generate temporally rich videos that demand scientific reasoning and knowledge-grounded synthesis, going beyond surface-level visual plausibility. We further establish a rubric-based evaluation protocol. Our analysis shows that, under this protocol, both non-expert human evaluators and MLLM-as-Judge systems can achieve relatively high agreement with expert judgments, supporting reproducible evaluation at scale. We benchmark 16 frontier proprietary and open-source models and find that, while automatic perceptual-quality scores cluster tightly across systems, performance on Prompt Grounding and Scientific and Causal Correctness varies substantially, with a pronounced proprietary-open-source gap. These findings show that advances in visual realism have not yet translated into reliable modeling of scientific and causal dynamics.
While large language models excel in reasoning, these generalists often lack knowledge for specialized scientific domains. Conversely, domain models~(specialists), while knowledgeable, suffer from specialization side-effects including diminished logic and reduced robustness.To address this dilemma, we introduce Divergence Decoding, a training-free framework for capability fusion. It reconstructs the "draft-and-verify" skeleton of speculative decoding into an adaptive routing mechanism. The core is using Jensen-Shannon divergence to monitor the distributional disagreement between the two models at each token. When the specialist exhibits significant divergence, our method identifies it as a potential reasoning risk and instantaneously routes control to the generalist. This allows the dynamic injection of general reasoning while preserving domain expertise, achieving inference-time policy composition of the generalist and the specialist.We evaluate Divergence Decoding across diverse model families (Qwen and Llama series) on challenging scientific benchmarks (GPQA, ChemBench, and ChemCoTBench). Experimental results demonstrate that Divergence Decoding outperforms both the domain-specialized and general-purpose models, effectively surpassing the performance of most single-model baseline. This suggests that Divergence Decoding provides a general, training-free paradigm for fusing diverse LLM capabilities through adaptive inference-time collaboration.
We implement an agentic AI workflow built around a large language model (LLM) agent for autonomous experiments with nitrogen-vacancy (NV) centers in diamond. NV centers are a widely used platform for quantum sensing, and the ability to control many measurements from a computer makes NV experiments a natural setting for autonomous workflows. We make two main contributions. First, we demonstrate an autonomous NV experiment workflow that combines persistent project records, quantitative calculation and data analysis tools, and deterministic experiment control. In one autonomous experiment, the agent selected a single NV center, calibrated its resonant frequency, measured \(T_2^\ast\) with Ramsey measurements, and added a Carr--Purcell--Meiboom--Gill (CPMG) measurement to check a weak feature that could be related to nearby \(^{13}\mathrm{C}\). Second, we introduce two offline benchmarks that evaluate the agent's reasoning separately from laboratory execution. We evaluated both benchmarks with GPT-5.4, GPT-5.5, and GPT-5.6 Sol. In the Ramsey checkpoint benchmark, greater reasoning effort generally improved recognition of a residual resonance calibration offset. By contrast, in the pulsed optically detected magnetic resonance (pODMR) data evaluation benchmark, pulse sequence information alone produced more false positive resonance judgments at higher reasoning effort. Requiring an expected signal calculation kept false positive rates low across all three models and reasoning settings. The results suggest a clear division of labor for autonomous experiments. The agent forms scientific hypotheses and uses quantitative tools to evaluate data, while deterministic code controls the hardware and enforces safety constraints.
Scientific Reasoning Graph Extraction (SRGE) aims to recover explicit links among observations, evidence, intermediate claims, and paper-level conclusions. LLMs can produce graph-like scientific explanations, but their outputs often mix malformed syntax, drifting edge labels, incorrectly oriented roots, and weak source anchors. We propose PEARL (Peircean Extraction via Abstraction and Repair Layer), a training-free framework that turns noisy LLM graph responses into auditable reasoning graphs and repairs them toward strict semantic validity. PEARL first materializes explicit graph content under a closed Peircean schema, then uses matched evidence-grounded judge feedback to repair rejected edge types, local inference steps, and terminal roots while preserving an audit trail. On five 70-paper model archives from ARCHE, a benchmark for latent reasoning-chain extraction, PEARL raises strict gate passes from 0/350 for the LLM baseline to 300/350, with average REA improving from 0.339 to 0.906. The graphs provide a reliability layer for research-agent and AI scientist workflows that need inspectable reasoning traces rather than unconstrained graph regeneration. Code and audit artifacts are available at https://github.com/BohanSu/auditable-repair-reasoning-graphs/tree/300-350_workshop .
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.
Large language models (LLMs) excel at answering pre-specified questions, yet their ability to navigate the open-ended, pre-conclusion stage of discovery remains largely unmeasured. We introduce Prospective Hypothesis Discovery (PHD), which asks models to autonomously construct grounded, discriminative, and testable hypothesis spaces from inconclusive evidence, including anomalous observations and fragmented records, to guide subsequent investigation. To evaluate this capability, we introduce HypoArena, comprising HypoData, a benchmark of 988 cases across six scientific and analytical domains, and HypoEval, an evaluation framework for open-ended hypothesis sets. To construct HypoData at scale, we propose Retrospective Context Regression, a Forge--Audit pipeline that reconstructs pre-conclusion contexts from completed expert documents by removing explicit conclusions, target hypotheses, and retrospective causal attributions while preserving the factual substrate. Because PHD admits multiple valid outputs, HypoEval combines bidirectional pairwise judgments with Bradley--Terry--Davidson aggregation for ranking and six-dimensional rubric scoring for diagnosis. Experiments on 15 frontier LLMs reveal clear capability stratification and model-dependent effects of structured analytical skills, with gains for several lower-performing models on HypoArena but regressions for other systems, including a top-performing model. Compared with absolute rubric scoring, arena evaluation resolves finer-grained differences among models, with aggregated rankings showing strong agreement with human experts and an independent judge. Together, these results support treating PHD as a distinct target for evaluating how LLMs formulate investigative directions when final conclusions are withheld. Our code and data are publicly available at github.com/SKYLENAGE-AI/HypoArena and github.com/SKYLENAGE-AI/HypoArena.
We present S1-Omni, a unified multimodal reasoning model for scientific understanding, prediction, and generation. AI for Science (AI4S) has advanced significantly through domain-specific models, tool-augmented LLMs, and scientific language models. However, model capabilities remain highly fragmented, limiting the joint modeling of heterogeneous data, scientific laws, and expert knowledge. S1-Omni addresses this gap by consolidating these capabilities into a single, coherent scientific reasoning model. The architecture of S1-Omni is built upon three core components: unified representation of scientific data, natural-world knowledge alignment, and decoding for domain-specific tasks. First, S1-Omni maps natural-language instructions and scientific objects, including CIF, SMILES, protein sequences, spectra, and scientific images, into a shared representation space. Second, it incorporates scientific laws and expert knowledge into data construction and training, enabling the model to reason from scientific evidence. Third, it performs task-specific decoding to support a broad range of applications, including property prediction, spectrum-to-molecular generation, protein site and structure prediction, and scientific image generation and editing. S1-Omni is trained on S1-Omni-Corpus, which covers 200 scientific tasks and contains millions of reasoning samples, and is evaluated on over 60 scientific benchmarks. It outperforms GPT-5.5 and Gemini-3.1-Pro on most benchmarks and matches or surpasses domain-specific models on several benchmarks. Overall, S1-Omni provides a practical path toward unified scientific modeling.
While Multimodal Large Language Models (MLLMs) excel in general tasks, rigorous scientific reasoning remains challenging due to the limitations of monolithic, linear planning. Such sequential designs often suffer from visual-semantic misalignment, long-context hallucinations, and brittle execution under fixed task granularity. We propose TopoAgent, a self-evolving topological framework that replaces linear trajectories with dynamic, state-isolated graph evolution. TopoAgent first employs a front-end decomposer to fracture complex queries into visually-grounded atoms. These atoms are organized into a Directed Acyclic Graph (DAG) based on their dependencies, enabling strict context isolation to shield the reasoning engine from irrelevant historical noise. Furthermore, we introduce adaptive atomic fission, which dynamically splits bottleneck nodes into finer-grained sub-atoms at runtime when tool capability boundaries are exceeded. Extensive experiments across mathematics, physics, and chemistry benchmarks demonstrate that TopoAgent significantly outperforms state-of-the-art linear agent frameworks, providing a robust, noise-resistant, and self-correcting paradigm for autonomous scientific reasoning.
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.
Ian Diks, Zhen Yang, Arjun Banerjee +2q-bio.GN cs.AI
Single-cell studies require analysts to convert raw measurements into specific biological claims through multi-step workflows and integration of metadata, assay context, and auxiliary evidence. Existing AI-biology benchmarks largely measure broad knowledge, executable workflows, or local analysis steps. We introduce scBench-Long, a benchmark for long-horizon single-cell biology in which agents must recover scientific conclusions from raw or near-raw data without prescribed methods. The benchmark contains 21 evaluations spanning melanoma CD8 T-cell reactivity, CD8 RNA+ATAC regulatory inference, human--monkey chimera development, KRAS-driven lung tumor aging, and lethal COVID-19 lung pathology. Tasks cover paired scRNA/TCR sequencing, RNA and chromatin profiling, cross-species transcriptomics, combinatorial scRNA-seq, single-nucleus RNA-seq, immune repertoires, ortholog maps, ligand--receptor resources, and validation evidence. Candidate claims are reproduced, reviewed, and converted into controlled answer vocabularies with deterministic grading and trajectory rubrics. Across 1,068 completed trajectories, the strongest model--harness pair passes 16/63 runs (25.4\%). scBench-Long evaluates whether agents can move beyond local analysis steps and make complex scientific claims that are supported by single-cell data.
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.
Frontier scientific reasoning remains a major challenge for large language models (LLMs), where even the strongest commercial systems fall short of expert-level performance. A closer look at model behavior reveals substantial complementarity that single-model evaluation hides: different frontier models excel on different question types, and no single model captures the full picture. We present SciOrch, a framework that trains a lightweight 8B model to orchestrate frontier LLMs for scientific reasoning. The orchestrator decomposes each question, delegates sub-problems to selected commercial models through API calls, and synthesizes a final answer. Training such an orchestrator is fundamentally harder than conventional agentic RL: each action triggers an API call that is expensive in both dollar cost and latency, making standard online rollouts infeasible. We address this with MCTS-based approach, producing diverse orchestration trajectories, extracting per-node single-turn samples, and optimizing the orchestrator with GRPO-style training. On a 240-question test set spanning SGI-Reasoning and Scientists' First Exam, SciOrch reaches 56.66% average accuracy, outperforming the strongest single commercial model by 3.74% and the strongest multi-agent baseline by 3.33%. It also attains the best accuracy on both SGI and SFE with less than half the API cost of typical multi-agent methods.
Current LLM-based research agents have advanced through agent orchestration, yet largely overlook scientific knowledge orchestration. Existing works often reduce papers to abstracts, surface mentions, and flat \texttt{cites} edges, omitting key entities, claims, evidence, mechanisms, and method lineages essential for scientific reasoning. To this end, we introduce \textbf{Agents-K1}, an end-to-end knowledge orchestration pipeline that converts raw documents into agent-native scientific knowledge graphs. Agents-K1 integrates three components under a unifying theoretical foundation: a multimodal parser whose five-module schema captures entities, multimodal evidence, citations, and typed inter-entity relations across the full paper rather than abstracts alone; a 4B information-extraction backbone trained with GRPO under a rule-based reward; and a graphanything CLI, a tri-source agent interface that unifies web search, multimodal graph retrieval, and cross-document traversal. On top of this, we process 2.46 million scientific papers across six subjects to produce \textbf{Scholar-KG}, of which we release a one-million-paper subset, and the full Scholar-KG is accessible via the SCP link below. The same pipeline can be extended to general-domain corpora and to schema-conformant data synthesis. Extensive experiments demonstrate that Agents-K1 achieves superior performance in scientific information extraction, knowledge graph construction, and multi-hop scientific reasoning.
Pierre Beckmann, Marco Valentino, Andre Freitascs.AI
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.
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.
Scientific reasoning rarely stops at what is directly observable; it often requires uncovering hidden structure from data. From estimating reaction constants in chemistry to inferring demand elasticities in economics, this latent structure recovery is what distinguishes scientific reasoning from curve fitting. Large language models (LLMs) can often recall and apply relevant scientific formulas, but we show that this ability is surprisingly easy to suppress. We show that adding in-context examples makes models rely less on pretrained domain knowledge, even when those examples are generated by the very same formula. Rather than reinforcing knowledge-driven derivation, examples shift computation toward empirical pattern fitting. We document this knowledge displacement on 60 latent structure recovery tasks across five scientific domains, 6,000 trials, and four models. This displacement is consistent across domains, but its accuracy consequences depend on how the displaced strategy compares to the one that replaces it: the same shift can lower accuracy, leave it unchanged, or appear to improve it. In all cases, however, the model shifts away from knowledge-driven reasoning. For practitioners deploying LLMs on scientific tasks, the message is cautionary: in-context examples may displace, rather than reinforce, the knowledge they are intended to support.
Vision-language models (VLMs) are increasingly proposed as general-purpose tools for scientific data interpretation, yet their reliability on real astronomical observations across diverse modalities remains untested. We present AstroVLBench, a comprehensive benchmark comprising over 4,100 expert-verified instances across five tasks spanning optical imaging, radio interferometry, multi-wavelength photometry, time-domain light curves, and optical spectroscopy. Evaluating six frontier models, we find that performance is strongly modality-dependent: while one model (Gemini 3 Pro) emerges as the most consistently capable across tasks, task-specific strengths vary, and all models substantially underperform domain-specialized methods. Mechanistic ablations reveal that performance depends not only on directing attention to salient visual features but also on grounding those features in physical knowledge. Phenomenological prompts describing what to look for improve accuracy by sharpening model focus, but physical prompts explaining why those features matter perform better overall and yield more balanced classifications with reduced class-specific bias. Consistent with this picture, presenting the underlying one-dimensional measurements directly as numerical tables instead of rendered plots yields up to 13 percentage points improvement. Reasoning quality analysis further demonstrates that, without explicit physical grounding, models may reach correct predictions from phenomenologically plausible cues while providing physically imprecise justifications, establishing that accuracy alone is insufficient for trustworthy scientific deployment. These findings provide the first systematic, multi-modal baselines for VLMs in observational astronomy and identify the specific representation, grounding, and reasoning bottlenecks where current models fail.