# SciToolAgent: A Knowledge Graph-Driven Scientific Agent for Multi-Tool Integration

arXiv: https://arxiv.org/abs/2507.20280 · HTML: https://mlsanity.com/paper/2507.20280/

## Key facts

- Cited by 43 papers in the map (data through 14 Oct 2026).
- Placed in Web, search, and research agents, one of 16 directions in LLM agents and tool use.
- Builds on 23 of its 46 references that are in the map.
- First posted on arXiv 27 Jul 2025.

## Placed in

- LLM agents and tool use / [Web, search, and research agents](https://mlsanity.com/agents/web-search-and-research-agents/)

## Builds on (most cited first, 23 of 23)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [ReAct: Synergizing Reasoning and Acting in Language Models](https://mlsanity.com/paper/2210.03629/) (2022)
- [Reflexion: Language Agents with Verbal Reinforcement Learning](https://mlsanity.com/paper/2303.11366/) (2023)
- [Toolformer: Language Models Can Teach Themselves to Use Tools](https://mlsanity.com/paper/2302.04761/) (2023)
- [A Survey of Large Language Models](https://mlsanity.com/paper/2303.18223/) (2023)
- [A Survey on Large Language Model based Autonomous Agents](https://mlsanity.com/paper/2308.11432/) (2023)
- [ChemCrow: Augmenting large-language models with chemistry tools](https://mlsanity.com/paper/2304.05376/) (2023)
- [Recent Advances in Natural Language Processing via Large Pre-Trained Language Models: A Survey](https://mlsanity.com/paper/2111.01243/) (2021)
- [GPT4Tools: Teaching Large Language Model to Use Tools via Self-instruction](https://mlsanity.com/paper/2305.18752/) (2023)
- [ToolkenGPT: Augmenting Frozen Language Models with Massive Tools via Tool Embeddings](https://mlsanity.com/paper/2305.11554/) (2023)
- [Molecular Transformer - A Model for Uncertainty-Calibrated Chemical Reaction Prediction](https://mlsanity.com/paper/1811.02633/) (2018)
- [What can Large Language Models do in chemistry? A comprehensive benchmark on eight tasks](https://mlsanity.com/paper/2305.18365/) (2023)
- [ChatEDA: A Large Language Model Powered Autonomous Agent for EDA](https://mlsanity.com/paper/2308.10204/) (2023)
- [GeneGPT: Augmenting Large Language Models with Domain Tools for Improved Access to Biomedical Information](https://mlsanity.com/paper/2304.09667/) (2023)
- [A Review of Large Language Models and Autonomous Agents in Chemistry](https://mlsanity.com/paper/2407.01603/) (2024)
- [ProtAgents: Protein discovery via large language model multi-agent collaborations combining physics and machine learning](https://mlsanity.com/paper/2402.04268/) (2024)
- [MechAgents: Large language model multi-agent collaborations can solve mechanics problems, generate new data, and integrate knowledge](https://mlsanity.com/paper/2311.08166/) (2023)
- [ToolNet: Connecting Large Language Models with Massive Tools via Tool Graph](https://mlsanity.com/paper/2403.00839/) (2024)
- [BioT5+: Towards Generalized Biological Understanding with IUPAC Integration and Multi-task Tuning](https://mlsanity.com/paper/2402.17810/) (2024)
- [LLMatDesign: Autonomous Materials Discovery with Large Language Models](https://mlsanity.com/paper/2406.13163/) (2024)
- [CACTUS: Chemistry Agent Connecting Tool-Usage to Science](https://mlsanity.com/paper/2405.00972/) (2024)
- [Controlling risks of AI in chemical science with agents](https://mlsanity.com/paper/2312.06632/) (2023)
- [Language models in molecular discovery](https://mlsanity.com/paper/2309.16235/) (2023)

## Built on by (most cited first, 30 of 43)

- [A Survey of Scientific Large Language Models: From Data Foundations to Agent Frontiers](https://mlsanity.com/paper/2508.21148/) (2025)
- [CASCADE: Cumulative Agentic Skill Creation through Autonomous Development and Evolution](https://mlsanity.com/paper/2512.23880/) (2025)
- [Foam-Agent 2.0: An End-to-End Composable Multi-Agent Framework for Automating CFD Simulation in OpenFOAM](https://mlsanity.com/paper/2509.18178/) (2025)
- [Graph-Augmented Large Language Model Agents: Current Progress and Future Prospects](https://mlsanity.com/paper/2507.21407/) (2025)
- [HealthFlow: A Self-Evolving AI Agent with Meta Planning for Autonomous Healthcare Research](https://mlsanity.com/paper/2508.02621/) (2025)
- [Autonomous Agents for Scientific Discovery: Orchestrating Scientists, Language, Code, and Physics](https://mlsanity.com/paper/2510.09901/) (2025)
- [Code2MCP: Transforming Code Repositories into MCP Services](https://mlsanity.com/paper/2509.05941/) (2025)
- [AutoScientists: Self-Organizing Agent Teams for Long-Running Scientific Experimentation](https://mlsanity.com/paper/2605.28655/) (2026)
- [El Agente Quntur: A research collaborator agent for quantum chemistry](https://mlsanity.com/paper/2602.04850/) (2026)
- [Dynamic Tool Dependency Retrieval for Lightweight Function Calling](https://mlsanity.com/paper/2512.17052/) (2025)
- [K-Dense Analyst: Towards Fully Automated Scientific Analysis](https://mlsanity.com/paper/2508.07043/) (2025)
- [Experience-Evolving Multi-Turn Tool-Use Agent with Hybrid Episodic-Procedural Memory](https://mlsanity.com/paper/2512.07287/) (2025)
- [Agentic reinforcement learning empowers next-generation chemical language models for molecular design and synthesis](https://mlsanity.com/paper/2601.17687/) (2026)
- [SimMOF: AI agent for Automated MOF Simulations](https://mlsanity.com/paper/2603.29152/) (2026)
- [Experience-Driven Multi-Agent Systems Are Training-free Context-aware Earth Observers](https://mlsanity.com/paper/2602.02559/) (2026)
- [MDGYM: Benchmarking AI Agents on Molecular Simulations](https://mlsanity.com/paper/2605.08941/) (2026)
- [ReX-MLE: The Autonomous Agent Benchmark for Medical Imaging Challenges](https://mlsanity.com/paper/2512.17838/) (2025)
- [Learning Agent Routing From Early Experience](https://mlsanity.com/paper/2605.07180/) (2026)
- [AGAPI-Agents: An Open-Access Agentic AI Platform for Accelerated Materials Design on AtomGPT.org](https://mlsanity.com/paper/2512.11935/) (2025)
- [Rank-and-Reason: Multi-Agent Collaboration Accelerates Zero-Shot Protein Mutation Prediction](https://mlsanity.com/paper/2602.00197/) (2026)
- [CeProAgents: A Hierarchical Agents System for Automated Chemical Process Development](https://mlsanity.com/paper/2603.01654/) (2026)
- [ToolRosella: Translating Code Repositories into Standardized Tools for Scientific Agents](https://mlsanity.com/paper/2603.09290/) (2026)
- [CFD-copilot: leveraging domain-adapted large language model and model context protocol to enhance simulation automation](https://mlsanity.com/paper/2512.07917/) (2025)
- [Embodied Science: Closing the Discovery Loop with Agentic Embodied AI](https://mlsanity.com/paper/2603.19782/) (2026)
- [Plausible but Wrong: A case study on Agentic Failures in Astrophysical Workflows](https://mlsanity.com/paper/2604.25345/) (2026)
- [Bidirectional Semantic Complementary Tool Retrieval for Remote Sensing Agents](https://mlsanity.com/paper/2606.07538/) (2026)
- [Pepti-Agent: An AI Agent for Peptide Design and Optimization](https://mlsanity.com/paper/2606.15422/) (2026)
- [Prospects for Using Artificial Intelligence to Understand Intrinsic Kinetics of Heterogeneous Catalytic Reactions](https://mlsanity.com/paper/2510.18911/) (2025)
- [Autonomous computational catalysis through an agentic research system](https://mlsanity.com/paper/2601.13508/) (2026)
- [InfEngine: A Self-Verifying and Self-Optimizing Intelligent Engine for Infrared Radiation Computing](https://mlsanity.com/paper/2602.18985/) (2026)

## Abstract (arXiv)

Scientific research increasingly relies on specialized computational tools, yet effectively utilizing these tools demands substantial domain expertise. While Large Language Models (LLMs) show promise in tool automation, they struggle to seamlessly integrate and orchestrate multiple tools for complex scientific workflows. Here, we present SciToolAgent, an LLM-powered agent that automates hundreds of scientific tools across biology, chemistry, and materials science. At its core, SciToolAgent leverages a scientific tool knowledge graph that enables intelligent tool selection and execution through graph-based retrieval-augmented generation. The agent also incorporates a comprehensive safety-checking module to ensure responsible and ethical tool usage. Extensive evaluations on a curated benchmark demonstrate that SciToolAgent significantly outperforms existing approaches. Case studies in protein engineering, chemical reactivity prediction, chemical synthesis, and metal-organic framework screening further demonstrate SciToolAgent's capability to automate complex scientific workflows, making advanced research tools accessible to both experts and non-experts.