SciR: A Controllable Benchmark for Scientific Reasoning in LLMs
Authors: Pierre Beckmann, Marco Valentino, Andre Freitas
Organizations: Idiap Research Institute, Switzerland · EPFL, Switzerland · School of Computer Science, University of Sheffield, UK · Department of Computer Science, University of Manchester, UK · National Biomarker Centre, CRUK Manchester Institute, UK
Abstract
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.
Large language models (LLMs) are increasingly deployed as autonomous agents in scientific tasks. Yet whether these systems can effectively engage in forms of inductive reasoning relevant to scientific discovery remains an open question. In this work, we introduce FALSIFYBENCH, an evaluation framework for hypothesis-driven reasoning inspired by the classic Wason 2-4-6 task, in which agents must discover hidden semantic properties by iteratively proposing examples and receiving feedback. This task captures key elements of scientific reasoning: hypothesis generation, evidence gathering, and belief revision in response to both confirming and disconfirming evidence. Our evaluation of 12 LLMs across model families and scales shows that reasoning models are generally stronger scientific reasoners than instruction-tuned models, although no model comes close to optimal performance. The primary driver of success is the capacity for negative testing: models that actively seek to falsify their hypotheses consistently outperform those that primarily seek confirmation. Moreover, a fine-grained turn-level analysis, neglected in previous work, reveals that failure is tied to identifiable patterns in how models navigate the hypothesis space.
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.
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