DrugPilot: LLM-based Parameterized Reasoning Agent for Drug Discovery

Abstract Large language models (LLMs) integrated with autonomous agents hold significant potential for advancing scientific discovery through automated reasoning and task execution. However, applying LLM agents to drug discovery is still constrained by challenges such as large-scale multimodal data processing, limited task automation, and poor support for domain-specific tools. To overcome these limitations, we introduce DrugPilot, a LLM-based agent system with a parameterized reasoning architecture designed for end-to-end scientific workflows in drug discovery. DrugPilot enables multi-stage research processes by integrating structured tool use with a novel parameterized memory pool. The memory pool converts heterogeneous data from both public sources and user-defined inputs into standardized representations. This design supports efficient multi-turn conversation, reduces information loss during data exchange, and enhances complex scientific decision-making. To support training and benchmarking, we construct a drug instruction dataset covering eight core drug discovery tasks. Under the Berkeley function-calling benchmark, DrugPilot significantly outperforms state-of-the-art agents such as ReAct and LoT, achieving task completion rates of 98.0%, 93.5%, and 64.0% for simple, multi-tool, and multi-turn categories, respectively. These results highlight DrugPilot's strong potential as a generalizable agent framework for automated, interactive, and data-driven reasoning across computational science applications.