通过大型语言模型生成的信号网络的基准测试
Jeevan Tewari1,2, Benjamin W Dahl1,2, Jeffrey J Saucerman2
1co-equal contributors.
bioRxiv : the preprint server for biology
|August 6, 2025
概括
大型语言模型 (LLM) 可以生成信号网络模型,但当前的准确性有限. 这项研究对计算生物学的LLM进行了基准测试,为未来的模型开发提供了一条道路.
科学领域:
- 计算生物学是一种计算生物学.
- 系统生物学 系统生物学
- 生物信息学是一种生物信息学.
背景情况:
- 分子信号网络的计算模型对于理解细胞决策至关重要.
- 从科学文献中手动整理这些模型是耗时且经常不完整的.
研究的目的:
- 评估通用大型语言模型 (LLM) 在生成蜂信号网络准确的计算模型方面的能力.
- 在这个领域建立LLM绩效的基准.
主要方法:
- 测试通用LLM以生成特定生物过程的信号网络模型 (心肌细胞缩,肌纤维细胞激活,机械信号).
- 将LLM生成的网络组件与手动策划的,文学衍生网络进行比较.
- 评估LLM生成网络在预测细胞对干扰反应的准确性.
主要成果:
- 一般用途的LLM在文献策划的信号网络中产生了24-58%的反应.
- 预测网络对干扰的反应的准确性在5%-26%之间.
结论:
- 目前的通用LLM在生成全面和精确的信号网络模型方面显示出有限的准确性.
- 这项研究为推进基于LLM的计算系统生物学方法提供了基础管道和绩效基准.
更多相关视频
10:44Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline
Published on: December 7, 2021
2.3K
03:37Author Spotlight: Impact of Intergenic Interactions on Disease-Identifying Dark Biomarkers
Published on: March 1, 2024
900
相关概念视频
Interactions Between Signaling Pathways
6.4K
Signaling cascades usually lack linearity. Multiple pathways interact and regulate one another, allowing cells to integrate and respond to diverse environmental stimuli.
Convergence and divergence, and cross-talk between signaling pathways
Two distinct signaling pathways can converge on a single functional unit, which may either be a single protein or a complex of proteins. The response is either functionally distinct or synergistic between the two pathways but different from the response...
Convergence and divergence, and cross-talk between signaling pathways
Two distinct signaling pathways can converge on a single functional unit, which may either be a single protein or a complex of proteins. The response is either functionally distinct or synergistic between the two pathways but different from the response...
6.4K
Assembly of Signaling Complexes
5.9K
Multiprotein signaling complexes are formed in a dynamic process involving protein-protein interactions at the cytoplasmic domain of transmembrane receptors or enzymatic and non-enzymatic proteins associated with the receptor. These complexes ensure the activation and propagation of intracellular signals that regulate cell functions.
Interaction domains in cell signaling
Interaction domains recognize exposed features of their binding partners containing post-translationally modified sequences,...
Interaction domains in cell signaling
Interaction domains recognize exposed features of their binding partners containing post-translationally modified sequences,...
5.9K
Signal Flow Graphs
318
Signal-flow graphs offer a streamlined and intuitive approach to representing control systems, providing an alternative to traditional block diagrams. These graphs use branches to symbolize systems and nodes to represent signals, effectively illustrating the relationships and interactions within the system.
In a signal-flow graph, branches denote the system's transfer functions, while nodes represent the signals. The direction of signal flow is indicated by arrows, with the corresponding...
In a signal-flow graph, branches denote the system's transfer functions, while nodes represent the signals. The direction of signal flow is indicated by arrows, with the corresponding...
318
