Abstract
The integration of large language models (LLMs) into scientific workflows is accelerating, yet their ability to reconstruct the reasoning underlying published research remains unexplored. Papers specify explicit procedures while leaving many methodological dependencies-data selection, calibration corrections, priors, and domain assumptions-implicit. This ambiguity complicates the evaluation of LLM-based agents, since a failure to reproduce a result may reflect either limitations of the agent or underspecification in the source. We present a framework that evaluates agents through end-to-end reproduction, separating execution from verification and computational failure from methodological ambiguity. We apply it to fourteen astronomy studies: a case study from The Astrophysical Journal and thirteen papers published in Nature. Eleven of the thirteen contained an ambiguity preventing a uniquely specified reproduction path. In a controlled case study, twelve predefined paths, a 3x2x2 sensitivity analysis over sample definition, sky masking, and parallax zero-point treatment-gave estimates from 2.16 to 3.53 kpc for the same quantity, with only one recovering the published value (about 2.70 kpc). The published value was never used as an optimization target, selection criterion, or stopping condition; the matching path was found only after all twelve had run. Crucially, the decisive information (a +0.02 mas parallax zero-point correction) was already in the paper, but the agents did not recognize its causal relevance until the analysis made the effect visible. Matching a published outcome therefore does not validate reconstruction of the underlying reasoning, and the bottleneck is as often a failure to connect relevant information as to retrieve it. End-to-end reproduction thus serves both as a test of reproducibility and as a framework for evaluating implicit scientific knowledge in AI systems.
Abstract (translated)
URL
https://arxiv.org/abs/2609.35900
