Fisher-R1: Training LLM Agents for Reliable Hypothesis Testing
Authors: Jiacheng Miao, Jin Mu, Guanhua Chen, James Zou
Organizations: Department of Biomedical Data Science, Stanford University · Department of Genetics, Stanford University · Department of Biostatistics and Medical Informatics, University of Wisconsin–Madison · Department of Statistics, University of Wisconsin–Madison · Department of Electrical Engineering, Stanford University · Department of Computer Science, Stanford University
Abstract
Reliable hypothesis testing is the foundation of many empirical scientific claims. Large language model (LLM) agents are increasingly used to automate this process, as they can inspect datasets, generate code, and produce analyses end-to-end. However, we show that they frequently make subtle inferential errors that lead to incorrect conclusions despite correctly executed analyses. Existing benchmarks fail to capture this failure mode, as they rarely assess whether a reported p-value is statistically valid given the assumptions underlying the data. We address this gap by building P-Bench, a benchmark comprising 425 open-ended, realistic hypothesis-testing tasks spanning economics, biology, and medicine. Each task requires an agent to select a statistical method, compute a p-value, and draw a conclusion given only a scientific hypothesis and a dataset. We further introduce Fisher-R1, an open-weight LLM agent trained for rigorous hypothesis testing using synthetic tasks and reinforcement learning. On P-Bench, Fisher-R1-14B substantially improves over its backbone and outperforms strong proprietary and open-source baselines, including GPT-5.4 and DeepSeekV4-Pro, achieving a 21% average relative improvement in single-trial success over DeepSeek-V4-Pro, with gains up to 26% on the most challenging tasks. Our results demonstrate that current LLM agents lack reliable statistical reasoning for hypothesis testing and that reinforcement learning on tasks with verified statistical reward substantially improves reliability.
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.
Despite rapid advances in large language models (LLMs), statistical reasoning remains underrepresented in existing LLM benchmarks, which often do not reflect the layered, proof-driven nature of real statistical practice. To address this gap, we introduce \textbf{StatEval}, the first large-scale benchmark for statistical reasoning across curricular and research-level settings. StatEval includes over 100,000 curated problems, with 20,000+ foundational questions spanning undergraduate and graduate curricula and 80,000+ research-level proof tasks extracted from leading statistical journals. To construct StatEval, we develop \textbf{TRACE} (Topology and Reasoning-Aware Context Extractor), a multi-agent pipeline with human-in-the-loop validation that converts unstructured academic texts into self-contained theorem-level reasoning tasks. We also propose an Adaptive Process-Based Scoring Pipeline for complex statistical proofs, enabling fine-grained evaluation beyond final-answer matching. Experiments show that while LLMs perform reasonably on foundational tasks, they struggle with rigorous research-level reasoning. Beyond evaluation, StatEval serves as a resource for improving reasoning, as retrieval-augmented generation and domain-specific alignment consistently enhance performance. Together, these results establish StatEval as both a benchmark and an infrastructure for advancing statistical reasoning in LLMs.
Statistical analysis is a broad, complex field requiring both domain knowledge and tool proficiency. While prior work has evaluated large language models (LLMs) in this domain, existing benchmarks remain limited in scope and format. To bridge this gap, we introduce StatABench (Statistical AnalysisBenchmark), a benchmark designed to systematically assess LLMs' statistical analysis capabilities. StatABench comprises two complementary components: Stat-Closed, containing 404 questions across 18 statistical topics in multiple formats (multiple-choice, fill-in-the-blank, decision-making, and practical application), and Stat-Open, featuring 30 complex open-ended modeling tasks adapted from professional competitions. We evaluate diverse LLMs using the LangChain MCP framework and multiple data science agents, and assess Stat-Open solutions via a validated LLM-as-Judge protocol. Experiments show that even GPT-5.1 achieves only 68.6% on Stat-Closed, while the best open-source model reaches 60.6%. On Stat-Open, the top agent framework scores 61.86 on average. These results reveal the gap between current LLMs and reliable statistical analysis, highlighting persistent challenges in tool-grounded reasoning, methodological decision-making, and end-to-end statistical modeling.