GTPLM-GO:通过双分支图形转换器和蛋白质语言模型来增强蛋白质功能预测,融合序列和局部-全球PPI信息
Haotian Zhang1, Yundong Sun1,2, Yansong Wang1
1School of Computer Science and Technology, Harbin Institute of Technology, Weihai 264209, China.
International journal of molecular sciences
|May 14, 2025
概括
我们开发了GTPLM-GO,这是一种使用图形神经网络和蛋白质语言模型进行蛋白质功能预测的新方法. 这种方法有效地整合了本地和全球蛋白质-蛋白质相互作用网络信息,提高了预测准确度.
科学领域:
- 生物信息学是一种生物信息学.
- 计算生物学 计算生物学
- 基因组学就是基因组学.
背景情况:
- 蛋白质与蛋白质相互作用 (PPI) 网络对于理解蛋白质功能至关重要.
- 现有的图形神经网络 (GNN) 方法在过度平滑方面扎,阻碍了准确的蛋白质功能预测.
- 在PPI网络中整合本地和全球信息仍然是一个挑战.
研究的目的:
- 提出GTPLM-GO,一种用于蛋白质功能预测的新方法.
- 通过整合本地和全球信息来解决GNN在PPI网络建模中的局限性.
- 通过结合基于图形和基于语言模型的方法来提高蛋白质功能预测的准确性.
主要方法:
- 开发了GTPLM-GO,一个双分支图形变换器和蛋白质语言模型.
- 采用了图形神经网络和基于线性注意力的变压器编码器,用于协作本地-全球信息建模.
- 集成的PPI网络信息与功能语义编码从蛋白质语言模型.
主要成果:
- 在PPI网络中,GTPLM-GO有效地模拟了地方和全球信息.
- 该方法成功地将网络拓与蛋白质序列衍生的功能语义相结合.
- 实验结果显示,GTPLM-GO在各种PPI网络尺度上优于现有的基于网络和基于序列的方法.
结论:
- 通过克服GNN的局限性,GTPLM-GO提供了一种优越的蛋白质功能预测方法.
- 双分支架构有效地捕捉了PPI网络中的复杂关系.
- 这种方法通过提高蛋白质功能预测的准确性和范围来推进生物信息学领域.
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