期刊
IEEE JOURNAL OF BIOMEDICAL AND HEALTH INFORMATICS
卷 23, 期 3, 页码 1290-1303出版社
IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC
DOI: 10.1109/JBHI.2018.2845866
关键词
Protein-protein interactions; prediction; multimodal deep polynomial network; regularization extreme learning machine
类别
资金
- integration project of production teaching and research by Guangdong Province
- Ministry of Education [2012B091100495]
- National Natural Science Foundation of Guangdong Province [2017A030313377, 2016A030313047]
- Shenzhen Key Basic Research Project [JCYJ20170818142347251, JCYJ20170818094109846, JCYJ201-50930105133185, JCYJ20170302153337765, JCYJ2012061311 3419607]
- Innovation and Entrepreneurship Training Program for College Students [803-000027060214, 803-000027060216]
Predicting the protein-protein interactions (PPIs) has played an important role in many applications. Hence, a novel computational method for PPIs prediction is highly desirable. PPIs endow with protein amino acid mutation rate and two physicochemical properties of protein (e.g., hydrophobicity and hydrophilicity). Deep polynomial network (DPN) is well-suited to integrate these modalities since it can represent any function on a finite sample dataset via the supervised deep learning algorithm. We propose a multimodal DPN (MDPN) algorithm to effectively integrate these modalities to enhance prediction performance. MDPN consists of a two-stage DPN, the first stage feeds multiple protein features into DPN encoding to obtain high-level feature representation while the second stage fuses and learns features by cascading three types of high-level features in the DPN encoding. We employ a regularized extreme learning machine to predict PPIs. The proposed method is tested on the public dataset of H. pylori, Human, and Yeast and achieves average accuracies of 97.87%, 99.90%, and 98.11%, respectively. The proposed method also achieves good accuracies on other datasets. Furthermore, we test our method on three kinds of PPI networks and obtain superior prediction results.
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