Grounding LLMs in Scientific Discovery via Embodied Actions

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.

Artificial intelligence has demonstrated remarkable capability in predicting scientific properties, yet scientific discovery remains an inherently physical, long-horizon pursuit governed by experimental cycles. Most current computational approaches are misaligned with this reality, framing discovery as isolated, task-specific predictions rather than continuous interaction with the physical world. Here, we argue for embodied science, a paradigm that reframes scientific discovery as a closed loop tightly coupling agentic reasoning with physical execution. We propose a unified Perception-Language-Action-Discovery (PLAD) framework, wherein embodied agents perceive experimental environments, reason over scientific knowledge, execute physical interventions, and internalize outcomes to drive subsequent exploration. By grounding computational reasoning in robust physical feedback, this approach bridges the gap between digital prediction and empirical validation, offering a roadmap for autonomous discovery systems in the life and chemical sciences.

Large language models (LLMs) have shown strong capabilities in reasoning, planning, and tool use, but many scientific and engineering tasks require more than plausible text and code generation. They require understanding how a system responds to intervention, which in practice depends on controlled experimentation. In this work, we propose a multi-agent framework that enables LLM agents to conduct controlled experiments with scientific simulation models for pharmaceutical process design. Given a user query and a baseline configuration, the system constructs a structured task representation, designs experiments, executes comparative simulation, interprets the resulting outcomes, and synthesizes evidence-based recommendations for process parameter optimization. By coupling language models with high-fidelity simulation models in an interactive agent framework, the proposed system supports reasoning through intervention, comparison, and observation. As a result, it produces more specific and actionable outputs than language-only reasoning. In an industrial application setting, this advantage is reflected in higher output specificity as well as improved user-rated correctness and helpfulness. Ablation studies and visualized case analyses further demonstrate the effectiveness and practical utility of simulation-integrated experimental reasoning.