Protein Interaction Network Reconstruction Through Ensemble Deep Learning With Attention Mechanism

• Main Authors: Feifei Li, Fei Zhu, Xinghong Ling, Quan Liu
• Format: Article
• Language: English
• Published: Frontiers Media S.A. 2020-05-01
• Series: Frontiers in Bioengineering and Biotechnology
• Subjects: protein-protein interaction network; protein-protein interaction; ensemble learning; deep learning; attention mechanism; multi-layer convolutional neural network
• Online Access: https://www.frontiersin.org/article/10.3389/fbioe.2020.00390/full

Protein interactions play an essential role in studying living systems and life phenomena. A considerable amount of literature has been published on analyzing and predicting protein interactions, such as support vector machine method, homology-based method and similarity-based method, each has its pros and cons. Most existing methods for predicting protein interactions require prior domain knowledge, making it difficult to effectively extract protein features. Single method is dissatisfactory in predicting protein interactions, declaring the need for a comprehensive method that combines the advantages of various methods. On this basis, a deep ensemble learning method called EnAmDNN (Ensemble Deep Neural Networks with Attention Mechanism) is proposed to predict protein interactions which is an appropriate candidate for comprehensive learning, combining multiple models, and considering the advantages of various methods. Particularly, it encode protein sequences by the local descriptor, auto covariance, conjoint triad, pseudo amino acid composition and combine the vector representation of each protein in the protein interaction network. Then it takes advantage of the multi-layer convolutional neural networks to automatically extract protein features and construct an attention mechanism to analyze deep-seated relationships between proteins. We set up four different structures of deep learning models. In the ensemble learning model, second layer data sets are generated with five-fold cross validation from basic learners, then predict the protein interaction network by combining 16 models. Results on five independent PPI data sets demonstrate that EnAmDNN achieves superior prediction performance than other comparing methods.