Automating Exploratory Proteomics Research via Language Models

Ning Ding; Shang Qu; Linhai Xie; Yifei Li; Zaoqu Liu; Kaiyan Zhang; Yibai Xiong; Yuxin Zuo; Zhangren Chen; Ermo Hua; Xingtai Lv; Youbang Sun; Yang Li; Dong Li; Fuchu He; Bowen Zhou

arXiv · 2411.03743

Automating Exploratory Proteomics Research via Language Models

Ning Ding·Shang Qu·Linhai Xie·Yifei Li·Zaoqu Liu·Kaiyan Zhang·Yibai Xiong·Yuxin Zuo·Zhangren Chen·Ermo Hua·Xingtai Lv·Youbang Sun·Yang Li·Dong Li·Fuchu He·Bowen Zhou

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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.

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Ning Ding, Shang Qu, Linhai Xie, Yifei Li, Zaoqu Liu, Kaiyan Zhang, Yibai Xiong, Yuxin Zuo, Zhangren Chen, Ermo Hua, Xingtai Lv, Youbang Sun, Yang Li, Dong Li, Fuchu He, Bowen Zhou. 2024-11-06. Automating Exploratory Proteomics Research via Language Models. https://arxiv.org/abs/2411.03743

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