arXiv:2410.09968cs.LGq-bio.CB2024-10被引 1

用LSTM模型预测细菌赖氨酸乙酰化位点,准确率超现有方法。

Deep-Ace: LSTM-based Prokaryotic Lysine Acetylation Site Predictor

  • 采用LSTM捕捉蛋白质序列长期依赖关系,提升特征表达能力。
  • 在8种细菌中准确率最高达83%,平均超过75%。
  • 方法可拓展至真核生物,助力疾病诊断研究。

赖氨酸乙酰化(K-Ace)是原核与真核生物中重要的翻译后修饰,对细胞生物学和疾病病理至关重要,因此准确识别其位点意义重大。以往基于机器学习的方法多依赖人工设计特征,忽略序列中的长程依赖关系,导致性能下降。本文提出Deep-Ace,一种基于长短期记忆网络(LSTM)的深度学习框架,能有效建模序列中长距离依赖,提取更具判别性的特征表示。该方法在8种不同细菌(包括B. subtilis、C. glutamicum、E. coli、G. kaustophilus、S. eriocheiris、B. velezensis、S. typhimurium和M. tuberculosis)上进行预测,准确率分别为0.80、0.79、0.71、0.75、0.80、0.83、0.756和0.82,优于当前主流模型。经微调后,该方法亦可应用于真核系统,为人类多种疾病的预诊与诊断提供工具支持。

原文摘要 · Abstract (English)

Acetylation of lysine residues (K-Ace) is a post-translation modification occurring in both prokaryotes and eukaryotes. It plays a crucial role in disease pathology and cell biology hence it is important to identify these K-Ace sites. In the past, many machine learning-based models using hand-crafted features and encodings have been used to find and analyze the characteristics of K-Ace sites however these methods ignore long term relationships within sequences and therefore observe performance degradation. In the current work we propose Deep-Ace, a deep learning-based framework using Long-Short-Term-Memory (LSTM) network which has the ability to understand and encode long-term relationships within a sequence. Such relations are vital for learning discriminative and effective sequence representations. In the work reported here, the use of LSTM to extract deep features as well as for prediction of K-Ace sites using fully connected layers for eight different species of prokaryotic models (including B. subtilis, C. glutamicum, E. coli, G. kaustophilus, S. eriocheiris, B. velezensis, S. typhimurium, and M. tuberculosis) has been explored. Our proposed method has outperformed existing state of the art models achieving accuracy as 0.80, 0.79, 0.71, 0.75, 0.80, 0.83, 0.756, and 0.82 respectively for eight bacterial species mentioned above. The method with minor modifications can be used for eukaryotic systems and can serve as a tool for the prognosis and diagnosis of various diseases in humans.

蛋白质预测LSTM乙酰化生物信息

Thank you to arXiv for use of its open access interoperability. PaperDance 不是 arXiv 官方产品;中文卡片由大模型生成,请以原文为准。