From Residuals to Reasons: LLM-Guided Mechanism Inference from Tabular Data

Large language model (LLM)-based systems are increasingly deployed to conduct scientific research autonomously, yet whether their reasoning adheres to the epistemic norms that make scientific inquiry self-correcting is poorly understood. Here, we evaluate LLM-based scientific agents across eight domains, spanning workflow execution to hypothesis-driven inquiry, through more than 25,000 agent runs and two complementary lenses: (i) a systematic performance analysis that decomposes the contributions of the base model and the agent scaffold, and (ii) a behavioral analysis of the epistemological structure of agent reasoning. We observe that the base model is the primary determinant of both performance and behavior, accounting for 41.4% of explained variance versus 1.5% for the scaffold. Across all configurations, evidence is ignored in 68% of traces, refutation-driven belief revision occurs in 26%, and convergent multi-test evidence is rare. The same reasoning pattern appears whether the agent executes a computational workflow or conducts hypothesis-driven inquiry. They persist even when agents receive near-complete successful reasoning trajectories as context, and the resulting unreliability compounds across repeated trials in epistemically demanding domains. Thus, current LLM-based agents execute scientific workflows but do not exhibit the epistemic patterns that characterize scientific reasoning. Outcome-based evaluation cannot detect these failures, and scaffold engineering alone cannot repair them. Until reasoning itself becomes a training target, the scientific knowledge produced by such agents cannot be justified by the process that generated it.

Automated methods for discovering mechanistic simulator models from observational data offer a promising path toward accelerating scientific progress. Such methods often take the form of agentic-style iterative workflows that repeatedly propose and revise candidate models by imitating human discovery processes. However, existing LLM-based approaches typically implement such workflows via hand-crafted heuristic procedures, without an explicit probabilistic formulation. We recast model discovery as probabilistic inference, i.e., as sampling from an unknown distribution over mechanistic models capable of explaining the data. This perspective provides a unified way to reason about model proposal, refinement, and selection within a single inference framework. As a concrete instantiation of this view, we introduce ModelSMC, an algorithm based on Sequential Monte Carlo sampling. ModelSMC represents candidate models as particles which are iteratively proposed and refined by an LLM, and weighted using likelihood-based criteria. Experiments on real-world scientific systems illustrate that this formulation discovers models with interpretable mechanisms and improves posterior predictive checks. More broadly, this perspective provides a probabilistic lens for understanding and developing LLM-based approaches to model discovery.

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.