TY - JOUR
T1 - Protein-Protein Interactions Prediction via Multimodal Deep Polynomial Network and Regularized Extreme Learning Machine
AU - Lei, Haijun
AU - Wen, Yuting
AU - You, Zhuhong
AU - Elazab, Ahmed
AU - Tan, Ee Leng
AU - Zhao, Yujia
AU - Lei, Baiying
N1 - Publisher Copyright:
© 2013 IEEE.
PY - 2019/5
Y1 - 2019/5
N2 - 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.
AB - 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.
KW - multimodal deep polynomial network
KW - prediction
KW - Protein-protein interactions
KW - regularization extreme learning machine
UR - http://www.scopus.com/inward/record.url?scp=85048573564&partnerID=8YFLogxK
U2 - 10.1109/JBHI.2018.2845866
DO - 10.1109/JBHI.2018.2845866
M3 - 文章
C2 - 29994278
AN - SCOPUS:85048573564
SN - 2168-2194
VL - 23
SP - 1290
EP - 1303
JO - IEEE Journal of Biomedical and Health Informatics
JF - IEEE Journal of Biomedical and Health Informatics
IS - 3
M1 - 8382154
ER -