Automating Exploratory Proteomics Research via Language Models

TL;DR

PROTEUS is an automated system leveraging large language models to analyze proteomics data, generate research hypotheses, and streamline scientific discovery without human intervention, significantly accelerating proteomics research workflows.

Contribution

This paper introduces PROTEUS, a novel AI system that automates proteomics data analysis and hypothesis generation using hierarchical planning and iterative refinement with LLMs.

Findings

PROTEUS generated 191 hypotheses across diverse datasets.

The system's results aligned well with existing literature.

PROTEUS demonstrated reliable and coherent analysis outputs.

Abstract

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.