# From Single to Multi-Agent Reasoning: Advancing GeneGPT for Genomics QA

arXiv: https://arxiv.org/abs/2601.10581 · HTML: https://mlsanity.com/paper/2601.10581/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Placed in Clinical and biomedical applications, one of 17 directions in LLM reasoning.
- Builds on 15 of its 21 references that are in the map.
- First posted on arXiv 15 Jan 2026.

## Placed in

- LLM reasoning / [Clinical and biomedical applications](https://mlsanity.com/lr/clinical-and-biomedical-applications/)
- LLM agents and tool use / [Medical and scientific domain agents](https://mlsanity.com/agents/medical-and-scientific-domain-agents/)

## Builds on (most cited first, 15 of 15)

- [Language Models are Few-Shot Learners](https://mlsanity.com/paper/2005.14165/) (2020)
- [ReAct: Synergizing Reasoning and Acting in Language Models](https://mlsanity.com/paper/2210.03629/) (2022)
- [Evaluating Large Language Models Trained on Code](https://mlsanity.com/paper/2107.03374/) (2021)
- [GLUE: A Multi-Task Benchmark and Analysis Platform for Natural Language Understanding](https://mlsanity.com/paper/1804.07461/) (2018)
- [Lost in the Middle: How Language Models Use Long Contexts](https://mlsanity.com/paper/2307.03172/) (2023)
- [SuperGLUE: A Stickier Benchmark for General-Purpose Language Understanding Systems](https://mlsanity.com/paper/1905.00537/) (2019)
- [Why Do Multi-Agent LLM Systems Fail?](https://mlsanity.com/paper/2503.13657/) (2025)
- [BioGPT: Generative Pre-trained Transformer for Biomedical Text Generation and Mining](https://mlsanity.com/paper/2210.10341/) (2022)
- [LLMs Get Lost In Multi-Turn Conversation](https://mlsanity.com/paper/2505.06120/) (2025)
- [The Landscape of Emerging AI Agent Architectures for Reasoning, Planning, and Tool Calling: A Survey](https://mlsanity.com/paper/2404.11584/) (2024)
- [GeneGPT: Augmenting Large Language Models with Domain Tools for Improved Access to Biomedical Information](https://mlsanity.com/paper/2304.09667/) (2023)
- [Found in the Middle: Calibrating Positional Attention Bias Improves Long Context Utilization](https://mlsanity.com/paper/2406.16008/) (2024)
- [LLM With Tools: A Survey](https://mlsanity.com/paper/2409.18807/) (2024)
- [Developing ChatGPT for Biology and Medicine: A Complete Review of Biomedical Question Answering](https://mlsanity.com/paper/2401.07510/) (2024)
- [Beyond GeneGPT: A Multi-Agent Architecture with Open-Source LLMs for Enhanced Genomic Question Answering](https://mlsanity.com/paper/2511.15061/) (2025)

## Abstract (arXiv)

Comprehending genomic information is essential for biomedical research, yet extracting data from complex distributed databases remains challenging. Large language models (LLMs) offer potential for genomic Question Answering (QA) but face limitations due to restricted access to domain-specific databases. GeneGPT is the current state-of-the-art system that enhances LLMs by utilizing specialized API calls, though it is constrained by rigid API dependencies and limited adaptability. We replicate GeneGPT and propose GenomAgent, a multi-agent framework that efficiently coordinates specialized agents for complex genomics queries. Evaluated on nine tasks from the GeneTuring benchmark, GenomAgent outperforms GeneGPT by 12% on average, and its flexible architecture extends beyond genomics to various scientific domains needing expert knowledge extraction.