# GeneGPT: Augmenting Large Language Models with Domain Tools for Improved Access to Biomedical Information

arXiv: https://arxiv.org/abs/2304.09667 · HTML: https://mlsanity.com/paper/2304.09667/

## Key facts

- Cited by 117 papers in the map (data through 14 Oct 2026).
- Builds on 20 of its 41 references that are in the map.
- First posted on arXiv 19 Apr 2023.

## Builds on (most cited first, 20 of 20)

- [Language Models are Few-Shot Learners](https://mlsanity.com/paper/2005.14165/) (2020)
- [GPT-4 Technical Report](https://mlsanity.com/paper/2303.08774/) (2023)
- [Chain-of-Thought Prompting Elicits Reasoning in Large Language Models](https://mlsanity.com/paper/2201.11903/) (2022)
- [Retrieval-Augmented Generation for Knowledge-Intensive NLP Tasks](https://mlsanity.com/paper/2005.11401/) (2020)
- [Evaluating Large Language Models Trained on Code](https://mlsanity.com/paper/2107.03374/) (2021)
- [Scaling Laws for Neural Language Models](https://mlsanity.com/paper/2001.08361/) (2020)
- [PaLM: Scaling Language Modeling with Pathways](https://mlsanity.com/paper/2204.02311/) (2022)
- [Toolformer: Language Models Can Teach Themselves to Use Tools](https://mlsanity.com/paper/2302.04761/) (2023)
- [Emergent Abilities of Large Language Models](https://mlsanity.com/paper/2206.07682/) (2022)
- [REALM: Retrieval-Augmented Language Model Pre-Training](https://mlsanity.com/paper/2002.08909/) (2020)
- [Survey of Hallucination in Natural Language Generation](https://mlsanity.com/paper/2202.03629/) (2022)
- [Large Language Models Encode Clinical Knowledge](https://mlsanity.com/paper/2212.13138/) (2022)
- [Improving language models by retrieving from trillions of tokens](https://mlsanity.com/paper/2112.04426/) (2021)
- [PAL: Program-aided Language Models](https://mlsanity.com/paper/2211.10435/) (2022)
- [Capabilities of GPT-4 on Medical Challenge Problems](https://mlsanity.com/paper/2303.13375/) (2023)
- [BioGPT: Generative Pre-trained Transformer for Biomedical Text Generation and Mining](https://mlsanity.com/paper/2210.10341/) (2022)
- [Augmented Language Models: a Survey](https://mlsanity.com/paper/2302.07842/) (2023)
- [TALM: Tool Augmented Language Models](https://mlsanity.com/paper/2205.12255/) (2022)
- [Can large language models reason about medical questions?](https://mlsanity.com/paper/2207.08143/) (2022)
- [Biomedical Question Answering: A Survey of Approaches and Challenges](https://mlsanity.com/paper/2102.05281/) (2021)

## Built on by (most cited first, 30 of 117)

- [ToolLLM: Facilitating Large Language Models to Master 16000+ Real-world APIs](https://mlsanity.com/paper/2307.16789/) (2023)
- [Retrieval-Augmented Generation for AI-Generated Content: A Survey](https://mlsanity.com/paper/2402.19473/) (2024)
- [MedAgents: Large Language Models as Collaborators for Zero-shot Medical Reasoning](https://mlsanity.com/paper/2311.10537/) (2023)
- [ToolQA: A Dataset for LLM Question Answering with External Tools](https://mlsanity.com/paper/2306.13304/) (2023)
- [ToolkenGPT: Augmenting Frozen Language Models with Massive Tools via Tool Embeddings](https://mlsanity.com/paper/2305.11554/) (2023)
- [Tool Learning with Large Language Models: A Survey](https://mlsanity.com/paper/2405.17935/) (2024)
- [Survey on Factuality in Large Language Models: Knowledge, Retrieval and Domain-Specificity](https://mlsanity.com/paper/2310.07521/) (2023)
- [Evaluating Large Language Models: A Comprehensive Survey](https://mlsanity.com/paper/2310.19736/) (2023)
- [MDAgents: An Adaptive Collaboration of LLMs for Medical Decision-Making](https://mlsanity.com/paper/2404.15155/) (2024)
- [LAB-Bench: Measuring Capabilities of Language Models for Biology Research](https://mlsanity.com/paper/2407.10362/) (2024)
- [Continual Learning for Large Language Models: A Survey](https://mlsanity.com/paper/2402.01364/) (2024)
- [Domain Specialization as the Key to Make Large Language Models Disruptive: A Comprehensive Survey](https://mlsanity.com/paper/2305.18703/) (2023)
- [StableToolBench: Towards Stable Large-Scale Benchmarking on Tool Learning of Large Language Models](https://mlsanity.com/paper/2403.07714/) (2024)
- [Opportunities and Challenges for ChatGPT and Large Language Models in Biomedicine and Health](https://mlsanity.com/paper/2306.10070/) (2023)
- [ToolChain*: Efficient Action Space Navigation in Large Language Models with A* Search](https://mlsanity.com/paper/2310.13227/) (2023)
- [Towards Scientific Intelligence: A Survey of LLM-based Scientific Agents](https://mlsanity.com/paper/2503.24047/) (2025)
- [Self-Distillation Bridges Distribution Gap in Language Model Fine-Tuning](https://mlsanity.com/paper/2402.13669/) (2024)
- [I-Design: Personalized LLM Interior Designer](https://mlsanity.com/paper/2404.02838/) (2024)
- [Cognitive Mirage: A Review of Hallucinations in Large Language Models](https://mlsanity.com/paper/2309.06794/) (2023)
- [ToolSword: Unveiling Safety Issues of Large Language Models in Tool Learning Across Three Stages](https://mlsanity.com/paper/2402.10753/) (2024)
- [If LLM Is the Wizard, Then Code Is the Wand: A Survey on How Code Empowers Large Language Models to Serve as Intelligent Agents](https://mlsanity.com/paper/2401.00812/) (2024)
- [EHRAgent: Code Empowers Large Language Models for Few-shot Complex Tabular Reasoning on Electronic Health Records](https://mlsanity.com/paper/2401.07128/) (2024)
- [Tell Me More! Towards Implicit User Intention Understanding of Language Model Driven Agents](https://mlsanity.com/paper/2402.09205/) (2024)
- [SciAgent: Tool-augmented Language Models for Scientific Reasoning](https://mlsanity.com/paper/2402.11451/) (2024)
- [MedCalc-Bench: Evaluating Large Language Models for Medical Calculations](https://mlsanity.com/paper/2406.12036/) (2024)
- [Matching Patients to Clinical Trials with Large Language Models](https://mlsanity.com/paper/2307.15051/) (2023)
- [Confucius: Iterative Tool Learning from Introspection Feedback by Easy-to-Difficult Curriculum](https://mlsanity.com/paper/2308.14034/) (2023)
- [Seal-Tools: Self-Instruct Tool Learning Dataset for Agent Tuning and Detailed Benchmark](https://mlsanity.com/paper/2405.08355/) (2024)
- [Tool Learning in the Wild: Empowering Language Models as Automatic Tool Agents](https://mlsanity.com/paper/2405.16533/) (2024)
- [Learning to Use Tools via Cooperative and Interactive Agents](https://mlsanity.com/paper/2403.03031/) (2024)

## Abstract (arXiv)

While large language models (LLMs) have been successfully applied to various tasks, they still face challenges with hallucinations. Augmenting LLMs with domain-specific tools such as database utilities can facilitate easier and more precise access to specialized knowledge. In this paper, we present GeneGPT, a novel method for teaching LLMs to use the Web APIs of the National Center for Biotechnology Information (NCBI) for answering genomics questions. Specifically, we prompt Codex to solve the GeneTuring tests with NCBI Web APIs by in-context learning and an augmented decoding algorithm that can detect and execute API calls. Experimental results show that GeneGPT achieves state-of-the-art performance on eight tasks in the GeneTuring benchmark with an average score of 0.83, largely surpassing retrieval-augmented LLMs such as the new Bing (0.44), biomedical LLMs such as BioMedLM (0.08) and BioGPT (0.04), as well as GPT-3 (0.16) and ChatGPT (0.12). Our further analyses suggest that: (1) API demonstrations have good cross-task generalizability and are more useful than documentations for in-context learning; (2) GeneGPT can generalize to longer chains of API calls and answer multi-hop questions in GeneHop, a novel dataset introduced in this work; (3) Different types of errors are enriched in different tasks, providing valuable insights for future improvements.