Title: Unleashing Scientific Reasoning for Bio-experimental Protocol Generation via Structured Component-based Reward Mechanism
Primary area: applications to physical sciences (physics, chemistry, biology, etc.)
Keywords: AI for biology, Protocol Generation, Scientific Reasoning, Large Language Model, Reinforcement Learning

Abstract: The foundation of reproducible science lies in protocols that are precise, logically ordered, and executable. The autonomous generation of these protocols through natural language queries could greatly improve the efficiency of the reproduction process. However, current leading large language models (LLMs) often generate incomplete or inconsistent protocols, limiting their utility. To address this limitation, we first introduce SciRecipe, a large-scale dataset of over 12K structured protocols spanning 27 biological subfields and encompassing both comprehension and problem-solving tasks. To further improve protocol generation, we propose the "Sketch-and-Fill" paradigm, which separates analysis, structuring, and expression to ensure each step is explicit and verifiable. Complementing this, the structured component-based reward mechanism evaluates step granularity, action order, and semantic fidelity, aligning model optimization with experimental reliability. Building on these components, we develop Thoth, trained through a staged Knowledge-to-Action process that progresses from knowledge acquisition to operational reasoning and ultimately to robust, executable protocol generation. Across multiple benchmarks, Thoth consistently surpasses both proprietary and open-source LLMs, achieving significant improvements in step alignment, logical sequencing, and semantic accuracy. Our approach paves the way for reliable scientific assistants that bridge knowledge with experimental execution.

TL;DR: We introduce SciRecipe, a large-scale protocol dataset, and the SCORE mechanism with the “Sketch-and-Fill” paradigm, enabling Thoth to generate precise, executable scientific protocols that surpass existing LLMs.