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Updated: Sep 10, 2025
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Evidence-based Knowledge Synthesis and Hypothesis Validation: Navigating Biomedical Knowledge Bases via Explainable AI and Agentic Systems
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SciToolAgent: a knowledge-graph-driven scientific agent for multitool integration
Keyan Ding1,2, Jing Yu2,3, Junjie Huang2
1College of Computer Science and Technology, Zhejiang University, Hangzhou, China.
Nature Computational Science
|August 20, 2025
Summary
SciToolAgent automates hundreds of scientific tools in biology, chemistry, and materials science using a knowledge graph. This large language model-powered agent makes complex research tools accessible to all scientists.
Area of Science:
- Computational biology
- Computational chemistry
- Materials science
Background:
- Scientific research increasingly depends on specialized computational tools, demanding significant domain expertise.
- Large language models (LLMs) show potential for tool automation but struggle with orchestrating multiple tools for complex workflows.
Purpose of the Study:
- To introduce SciToolAgent, an LLM-powered agent designed to automate hundreds of scientific tools across diverse disciplines.
- To enable intelligent tool selection and execution for complex scientific workflows.
Main Methods:
- SciToolAgent utilizes a scientific tool knowledge graph for graph-based retrieval-augmented generation.
- A comprehensive safety-checking module is integrated for responsible and ethical tool usage.
Main Results:
- SciToolAgent successfully automates hundreds of scientific tools in biology, chemistry, and materials science.
- Evaluations on a curated benchmark show SciToolAgent outperforms existing approaches.
- Case studies demonstrate automation of complex workflows in protein engineering, chemical reactivity prediction, chemical synthesis, and MOF screening.
Conclusions:
- SciToolAgent effectively automates complex scientific workflows, enhancing accessibility to advanced research tools.
- The agent bridges the gap for both experts and non-experts in utilizing sophisticated computational resources.
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