# GenoTEX: An LLM Agent Benchmark for Automated Gene Expression Data Analysis

arXiv: https://arxiv.org/abs/2406.15341 · HTML: https://mlsanity.com/paper/2406.15341/

## Key facts

- Cited by 5 papers in the map (data through 14 Oct 2026).
- Placed in Medical and scientific domain agents, one of 16 directions in LLM agents and tool use.
- Builds on 38 of its 94 references that are in the map.
- First posted on arXiv 21 Jun 2024.

## Placed in

- LLM agents and tool use / [Medical and scientific domain agents](https://mlsanity.com/agents/medical-and-scientific-domain-agents/)

## Builds on (most cited first, 30 of 38)

- [GPT-4 Technical Report](https://mlsanity.com/paper/2303.08774/) (2023)
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- [Self-Consistency Improves Chain of Thought Reasoning in Language Models](https://mlsanity.com/paper/2203.11171/) (2022)
- [Self-Refine: Iterative Refinement with Self-Feedback](https://mlsanity.com/paper/2303.17651/) (2023)
- [Tree of Thoughts: Deliberate Problem Solving with Large Language Models](https://mlsanity.com/paper/2305.10601/) (2023)
- [A Survey on Large Language Model based Autonomous Agents](https://mlsanity.com/paper/2308.11432/) (2023)
- [ToolLLM: Facilitating Large Language Models to Master 16000+ Real-world APIs](https://mlsanity.com/paper/2307.16789/) (2023)
- [Large Language Models Encode Clinical Knowledge](https://mlsanity.com/paper/2212.13138/) (2022)
- [MetaGPT: Meta Programming for A Multi-Agent Collaborative Framework](https://mlsanity.com/paper/2308.00352/) (2023)
- [Improving Factuality and Reasoning in Language Models through Multiagent Debate](https://mlsanity.com/paper/2305.14325/) (2023)
- [Datasheets for Datasets](https://mlsanity.com/paper/1803.09010/) (2018)
- [Large Language Models Cannot Self-Correct Reasoning Yet](https://mlsanity.com/paper/2310.01798/) (2023)
- [Teaching Large Language Models to Self-Debug](https://mlsanity.com/paper/2304.05128/) (2023)
- [Graph of Thoughts: Solving Elaborate Problems with Large Language Models](https://mlsanity.com/paper/2308.09687/) (2023)
- [Reasoning with Language Model is Planning with World Model](https://mlsanity.com/paper/2305.14992/) (2023)
- [CRITIC: Large Language Models Can Self-Correct with Tool-Interactive Critiquing](https://mlsanity.com/paper/2305.11738/) (2023)
- [Executable Code Actions Elicit Better LLM Agents](https://mlsanity.com/paper/2402.01030/) (2024)
- [LLM+P: Empowering Large Language Models with Optimal Planning Proficiency](https://mlsanity.com/paper/2304.11477/) (2023)
- [Multi-Agent Collaboration: Harnessing the Power of Intelligent LLM Agents](https://mlsanity.com/paper/2306.03314/) (2023)
- [Towards Revealing the Mystery behind Chain of Thought: A Theoretical Perspective](https://mlsanity.com/paper/2305.15408/) (2023)
- [Self-collaboration Code Generation via ChatGPT](https://mlsanity.com/paper/2304.07590/) (2023)
- [Auto-GPT for Online Decision Making: Benchmarks and Additional Opinions](https://mlsanity.com/paper/2306.02224/) (2023)
- [Unleashing the Emergent Cognitive Synergy in Large Language Models: A Task-Solving Agent through Multi-Persona Self-Collaboration](https://mlsanity.com/paper/2307.05300/) (2023)
- [Data Interpreter: An LLM Agent For Data Science](https://mlsanity.com/paper/2402.18679/) (2024)
- [What can Large Language Models do in chemistry? A comprehensive benchmark on eight tasks](https://mlsanity.com/paper/2305.18365/) (2023)
- [Verify-and-Edit: A Knowledge-Enhanced Chain-of-Thought Framework](https://mlsanity.com/paper/2305.03268/) (2023)
- [RecMind: Large Language Model Powered Agent For Recommendation](https://mlsanity.com/paper/2308.14296/) (2023)
- [DS-Agent: Automated Data Science by Empowering Large Language Models with Case-Based Reasoning](https://mlsanity.com/paper/2402.17453/) (2024)
- [Exchange-of-Thought: Enhancing Large Language Model Capabilities through Cross-Model Communication](https://mlsanity.com/paper/2312.01823/) (2023)

## Built on by (most cited first, 5 of 5)

- [GenoMAS: A Multi-Agent Framework for Scientific Discovery via Code-Driven Gene Expression Analysis](https://mlsanity.com/paper/2507.21035/) (2025)
- [BixBench3: Benchmarking AI agents on research-study-scale computational biology tasks](https://mlsanity.com/paper/2608.25286/) (2026)
- [A2P-Vis: an Analyzer-to-Presenter Agentic Pipeline for Visual Insights Generation and Reporting](https://mlsanity.com/paper/2512.22101/) (2025)
- [Discovery of Disease Relationships via Transcriptomic Signature Analysis Powered by Agentic AI](https://mlsanity.com/paper/2508.04742/) (2025)
- [CP-Agent: Context-Aware Multimodal Reasoning for Cellular Morphological Profiling under Chemical Perturbations](https://mlsanity.com/paper/2606.03435/) (2026)

## Abstract (arXiv)

Recent advancements in machine learning have significantly improved the identification of disease-associated genes from gene expression datasets. However, these processes often require extensive expertise and manual effort, limiting their scalability. Large Language Model (LLM)-based agents have shown promise in automating these tasks due to their increasing problem-solving abilities. To support the evaluation and development of such methods, we introduce GenoTEX, a benchmark dataset for the automated analysis of gene expression data. GenoTEX provides analysis code and results for solving a wide range of gene-trait association problems, encompassing dataset selection, preprocessing, and statistical analysis, in a pipeline that follows computational genomics standards. The benchmark includes expert-curated annotations from bioinformaticians to ensure accuracy and reliability. To provide baselines for these tasks, we present GenoAgent, a team of LLM-based agents that adopt a multi-step programming workflow with flexible self-correction, to collaboratively analyze gene expression datasets. Our experiments demonstrate the potential of LLM-based methods in analyzing genomic data, while error analysis highlights the challenges and areas for future improvement. We propose GenoTEX as a promising resource for benchmarking and enhancing automated methods for gene expression data analysis. The benchmark is available at https://github.com/Liu-Hy/GenoTEX.