Before the Action: Benchmarking LLMs on Prospective Hypothesis Discovery
Authors: Tianyun Zhong, Wangyi Jiang, Wei Wang, Xuanang Chen, Yaojie Lu, Shiwei Ye, Yuzhen Shi, Boyu Yang, +10 more
Organizations: University of Chinese Academy of Sciences · Institute of Software, Chinese Academy of Sciences · 3Alibaba Group
Abstract
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.
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.
Large language models (LLMs) increasingly help people solve problems, from debugging code to repairing machinery. This process requires generating plausible hypotheses from partial descriptions, then updating them as more information arrives. Yet how LLMs perform this form of inference, and how close it is to optimal, remains unclear. We study this question in the number game, a controlled setting in which a learner infers the hypothesis supported by a few positive integers, such as {16,8,2,64}: a rule like powers of 2 or an interval like numbers near 20. We measure the posterior over hypotheses using three complementary probes: posterior prediction, hypothesis evaluation, and hypothesis generation. We then compare LLM behavior with an optimal Bayesian model and human behavior, and test whether the same posterior is expressed across probes. LLMs are often well described by a two-parameter Bayesian fit, but with systematic offsets: by default they show a strong-sampling assumption that creates an implicit Occam's razor, favoring narrower hypotheses, while thinking mode shifts them toward greater prior reliance. We also find a robust evaluation--generation gap: LLMs select more correct hypotheses during hypothesis evaluation but generate simpler, more rule-like hypotheses. Finally, this Bayesian-with-bias pattern does not extrapolate. Models can behave as if they hold rule-like hypotheses over observed examples, yet generalize poorly to parts of the hypothesis domain not covered by those examples. Our results highlight a limitation of LLMs as general problem solvers, especially for scientific inference, where hypotheses must go beyond the data.
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.