# Automating Exploratory Proteomics Research via Language Models

arXiv: https://arxiv.org/abs/2411.03743 · HTML: https://mlsanity.com/paper/2411.03743/

## Key facts

- Cited by 12 papers in the map (data through 14 Oct 2026).
- Builds on 24 of its 84 references that are in the map.
- First posted on arXiv 6 Nov 2024.

## Builds on (most cited first, 24 of 24)

- [GPT-4 Technical Report](https://mlsanity.com/paper/2303.08774/) (2023)
- [The Llama 3 Herd of Models](https://mlsanity.com/paper/2407.21783/) (2024)
- [Measuring Massive Multitask Language Understanding](https://mlsanity.com/paper/2009.03300/) (2020)
- [On the Opportunities and Risks of Foundation Models](https://mlsanity.com/paper/2108.07258/) (2021)
- [Qwen Technical Report](https://mlsanity.com/paper/2309.16609/) (2023)
- [GPQA: A Graduate-Level Google-Proof Q&A Benchmark](https://mlsanity.com/paper/2311.12022/) (2023)
- [Qwen2 Technical Report](https://mlsanity.com/paper/2407.10671/) (2024)
- [Mixtral of Experts](https://mlsanity.com/paper/2401.04088/) (2024)
- [Large Language Models Encode Clinical Knowledge](https://mlsanity.com/paper/2212.13138/) (2022)
- [What Disease does this Patient Have? A Large-scale Open Domain Question Answering Dataset from Medical Exams](https://mlsanity.com/paper/2009.13081/) (2020)
- [PubMedQA: A Dataset for Biomedical Research Question Answering](https://mlsanity.com/paper/1909.06146/) (2019)
- [DeepSeek-V2: A Strong, Economical, and Efficient Mixture-of-Experts Language Model](https://mlsanity.com/paper/2405.04434/) (2024)
- [Length-Controlled AlpacaEval: A Simple Way to Debias Automatic Evaluators](https://mlsanity.com/paper/2404.04475/) (2024)
- [ChemCrow: Augmenting large-language models with chemistry tools](https://mlsanity.com/paper/2304.05376/) (2023)
- [MedMCQA : A Large-scale Multi-Subject Multi-Choice Dataset for Medical domain Question Answering](https://mlsanity.com/paper/2203.14371/) (2022)
- [Towards Expert-Level Medical Question Answering with Large Language Models](https://mlsanity.com/paper/2305.09617/) (2023)
- [Benchmarking Retrieval-Augmented Generation for Medicine](https://mlsanity.com/paper/2402.13178/) (2024)
- [Pre-Trained Models: Past, Present and Future](https://mlsanity.com/paper/2106.07139/) (2021)
- [Tool Learning with Foundation Models](https://mlsanity.com/paper/2304.08354/) (2023)
- [Capabilities of Gemini Models in Medicine](https://mlsanity.com/paper/2404.18416/) (2024)
- [GeneGPT: Augmenting Large Language Models with Domain Tools for Improved Access to Biomedical Information](https://mlsanity.com/paper/2304.09667/) (2023)
- [UltraMedical: Building Specialized Generalists in Biomedicine](https://mlsanity.com/paper/2406.03949/) (2024)
- [Med42 -- Evaluating Fine-Tuning Strategies for Medical LLMs: Full-Parameter vs. Parameter-Efficient Approaches](https://mlsanity.com/paper/2404.14779/) (2024)
- [CellAgent: An LLM-driven Multi-Agent Framework for Automated Single-cell Data Analysis](https://mlsanity.com/paper/2407.09811/) (2024)

## Built on by (most cited first, 12 of 12)

- [Agent Laboratory: Using LLM Agents as Research Assistants](https://mlsanity.com/paper/2501.04227/) (2025)
- [From AI for Science to Agentic Science: A Survey on Autonomous Scientific Discovery](https://mlsanity.com/paper/2508.14111/) (2025)
- [AgentRxiv: Towards Collaborative Autonomous Research](https://mlsanity.com/paper/2503.18102/) (2025)
- [AI4Research: A Survey of Artificial Intelligence for Scientific Research](https://mlsanity.com/paper/2507.01903/) (2025)
- [LLM Agents Making Agent Tools](https://mlsanity.com/paper/2502.11705/) (2025)
- [K-Dense Analyst: Towards Fully Automated Scientific Analysis](https://mlsanity.com/paper/2508.07043/) (2025)
- [Large Language Models for Zero-shot Inference of Causal Structures in Biology](https://mlsanity.com/paper/2503.04347/) (2025)
- [EpidemIQs: Prompt-to-Paper LLM Agents for Epidemic Modeling and Analysis](https://mlsanity.com/paper/2510.00024/) (2025)
- [Large Language Models for Bioinformatics](https://mlsanity.com/paper/2501.06271/) (2025)
- [TCA-SIR: Learning Target-Conditioned Abstractions for Scientific Inspiration Retrieval](https://mlsanity.com/paper/2607.28498/) (2026)
- [Biomedical reasoning in action: Multi-agent System for Auditable Biomedical Evidence Synthesis](https://mlsanity.com/paper/2510.05335/) (2025)
- [Evaluating Agentic Bioinformatics through Function, Evidence, and Validation](https://mlsanity.com/paper/2607.27556/) (2026)

## Abstract (arXiv)

With the development of artificial intelligence, its contribution to science is evolving from simulating a complex problem to automating entire research processes and producing novel discoveries. Achieving this advancement requires both specialized general models grounded in real-world scientific data and iterative, exploratory frameworks that mirror human scientific methodologies. In this paper, we present PROTEUS, a fully automated system for scientific discovery from raw proteomics data. PROTEUS uses large language models (LLMs) to perform hierarchical planning, execute specialized bioinformatics tools, and iteratively refine analysis workflows to generate high-quality scientific hypotheses. The system takes proteomics datasets as input and produces a comprehensive set of research objectives, analysis results, and novel biological hypotheses without human intervention. We evaluated PROTEUS on 12 proteomics datasets collected from various biological samples (e.g. immune cells, tumors) and different sample types (single-cell and bulk), generating 191 scientific hypotheses. These were assessed using both automatic LLM-based scoring on 5 metrics and detailed reviews from human experts. Results demonstrate that PROTEUS consistently produces reliable, logically coherent results that align well with existing literature while also proposing novel, evaluable hypotheses. The system's flexible architecture facilitates seamless integration of diverse analysis tools and adaptation to different proteomics data types. By automating complex proteomics analysis workflows and hypothesis generation, PROTEUS has the potential to considerably accelerate the pace of scientific discovery in proteomics research, enabling researchers to efficiently explore large-scale datasets and uncover biological insights.