arXiv:2412.05776cs.LGq-bio.GN2024-12被引 2

用Transformer融合模型精准预测蛋白序列的基因本体功能,适合长序列和结构差异大的数据。

ProtGO: A Transformer based Fusion Model for accurately predicting Gene Ontology (GO) Terms from full scale Protein Sequences

  • 基于Transformer的融合架构,同时捕捉蛋白序列的短程与长程依赖关系。
  • 在聚类划分数据集上达到当前最优准确率,尤其擅长处理结构差异大的样本。
  • 模型轻量高效,不受序列长度影响,适合多样本长度的实际应用。

新一代测序技术催生了包含数亿条蛋白序列的开放数据库。为使这些序列可用于生物医学研究,需通过实验或文献提取进行精细注释。近年来,研究人员开发了多种基于机器学习与人工智能的自动注释系统。本文提出一种基于Transformer的融合模型,可从全尺度蛋白序列中预测基因本体(GO)术语,在同类系统中表现最佳。该方法在聚类划分数据集上表现尤为出色,训练与测试样本来自不同分布且结构差异大,表明模型能准确识别与各类GO术语相关的结构基序。此外,相比基准方法,本模型更轻量、计算开销更低,且对序列长度不敏感,适用于不同长度序列的多样化应用场景。

原文摘要 · Abstract (English)

Recent developments in next generation sequencing technology have led to the creation of extensive, open-source protein databases consisting of hundreds of millions of sequences. To render these sequences applicable in biomedical applications, they must be meticulously annotated by wet lab testing or extracting them from existing literature. Over the last few years, researchers have developed numerous automatic annotation systems, particularly deep learning models based on machine learning and artificial intelligence, to address this issue. In this work, we propose a transformer-based fusion model capable of predicting Gene Ontology (GO) terms from full-scale protein sequences, achieving state-of-the-art accuracy compared to other contemporary machine learning annotation systems. The approach performs particularly well on clustered split datasets, which comprise training and testing samples originating from distinct distributions that are structurally diverse. This demonstrates that the model is able to understand both short and long term dependencies within the enzyme's structure and can precisely identify the motifs associated with the various GO terms. Furthermore, the technique is lightweight and less computationally expensive compared to the benchmark methods, while at the same time not unaffected by sequence length, rendering it appropriate for diverse applications with varying sequence lengths.

蛋白注释TransformerGO预测序列分析

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