UniDL4BioPep: a universal deep learning architecture for binary classification in peptide bioactivity

计算机科学 深度学习 人工智能 嵌入 卷积神经网络 二进制数 机器学习 选择(遗传算法) 选型 模板 模式识别(心理学) 数学 算术 程序设计语言
作者
Zhenjiao Du,Xingjian Ding,Yixiang Xu,Yonghui Li
出处
期刊:Briefings in Bioinformatics [Oxford University Press]
卷期号:24 (3) 被引量:10
标识
DOI:10.1093/bib/bbad135
摘要

Identification of potent peptides through model prediction can reduce benchwork in wet experiments. However, the conventional process of model buildings can be complex and time consuming due to challenges such as peptide representation, feature selection, model selection and hyperparameter tuning. Recently, advanced pretrained deep learning-based language models (LMs) have been released for protein sequence embedding and applied to structure and function prediction. Based on these developments, we have developed UniDL4BioPep, a universal deep-learning model architecture for transfer learning in bioactive peptide binary classification modeling. It can directly assist users in training a high-performance deep-learning model with a fixed architecture and achieve cutting-edge performance to meet the demands in efficiently novel bioactive peptide discovery. To the best of our best knowledge, this is the first time that a pretrained biological language model is utilized for peptide embeddings and successfully predicts peptide bioactivities through large-scale evaluations of those peptide embeddings. The model was also validated through uniform manifold approximation and projection analysis. By combining the LM with a convolutional neural network, UniDL4BioPep achieved greater performances than the respective state-of-the-art models for 15 out of 20 different bioactivity dataset prediction tasks. The accuracy, Mathews correlation coefficient and area under the curve were 0.7-7, 1.23-26.7 and 0.3-25.6% higher, respectively. A user-friendly web server of UniDL4BioPep for the tested bioactivities is established and freely accessible at https://nepc2pvmzy.us-east-1.awsapprunner.com. The source codes, datasets and templates of UniDL4BioPep for other bioactivity fitting and prediction tasks are available at https://github.com/dzjxzyd/UniDL4BioPep.
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