Can AI Scientist Agents Learn from Lab-in-the-Loop Feedback? Evidence from Iterative Perturbation Discovery

Do LLM scientific agents rely only on their initial task context, or do they adapt their decisions in response to experimental feedback? We study this question in neural operator adaptation, where a large language model (LLM) selects fine-tuning configurations under a limited trial budget. Across transfers within and between partial differential equation (PDE) families, the LLM achieves lower held-out test nRMSE than random search and Bayesian optimisation in nearly every matched comparison. Endpoint performance alone cannot distinguish what happens, so we verify each attribution with controlled interventions. Before observing any validation score, the LLM's first configuration already ranks near the top of the corresponding random-search pool, indicating a useful initial bias. A complementary cold-start intervention shows that the selected base learning rate shifts with the PDE description. Once feedback becomes available, reassigning validation scores among evaluated configurations changes the next proposal in every case tested, whereas a value-preserving rewrite produces no comparable aggregate effect. These interventions establish that the LLM's decision-level actions respond to the given task and observed outcomes, showing that it combines a task-dependent prior with sensitivity to experimental feedback.

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.

Scientific model discovery requires proposing candidate models of an unknown system and designing experiments that discriminate among them. However, LLM-based approaches typically rely on in-context learning to predict outcomes and select experiments, lacking explicit model evaluation to systematically guide hypothesis search, while Bayesian approaches enable principled model comparison but are confined to a predefined candidate set which results in limited search spaces. To this end, we introduce BMD, which closes the loop between LLM-driven hypothesis generation and Bayesian experimental design. Specifically, an LLM proposes model families, while a numerical engine fits their parameters, weighs them by model evidence, and averages their predictions. Then, BMD chooses the next experimental conditions by maximizing the joint expected information gain over families and their parameters, while feeding the updated beliefs and residual diagnostics back to the LLM to guide its next proposals. Across four scientific discovery benchmarks, BMD achieves lowest final prediction error than in-context learning and LLM-based scientific agents while recovering exact functional forms more often, with ablations supporting numerical feedback and the joint objective.