期刊
IEEE JOURNAL OF BIOMEDICAL AND HEALTH INFORMATICS
卷 26, 期 3, 页码 1384-1393出版社
IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC
DOI: 10.1109/JBHI.2021.3102186
关键词
Drugs; Gene expression; Cancer; Prediction algorithms; Bioinformatics; Sensitivity; Heterogeneous networks; Drug response prediction; multi-omics fusion; graph convolutional neural network
类别
资金
- National Natural Science Foundation of China [61972185]
- Natural Science Foundation of Yunnan Province of China [2019FA024]
- Yunnan Key Research and Development Program [2018IA054]
- Yunnan Ten Thousand Talents Plan Young
This study proposes an algorithm, MOFGCN, to predict drug response in cell lines using Multi-Omics Fusion and Graph Convolution Network. The algorithm first calculates cell line similarity and constructs a heterogeneous network. It then learns the latent features for cancer cell lines and drugs using graph convolution operations on the network. The algorithm applies linear correlation coefficient to predict drug sensitivity. Experimental results show that MOFGCN outperforms state-of-the-art algorithms in predicting missing drug responses.
Different cancer patients may respond differently to cancer treatment due to the heterogeneity of cancer. It is an urgent task to develop an efficient computational method to identify drug responses in different cell lines, which guides us to design personalized therapy for an individual patient. Hence, we propose an end-to-end algorithm, namely MOFGCN, to predict drug response in cell lines based on Multi-Omics Fusion and Graph Convolution Network. MOFGCN first fuses multiple omics data to calculate the cell line similarity and then constructs a heterogeneous network by combining the cell line similarity, drug similarity, and the known cell line-drug associations. Secondly, it learns the latent features for cancer cell lines and drugs by performing graph convolution operations on the heterogeneous network. Finally, MOFGCN applies the linear correlation coefficient to reconstruct the cancer cell line-drug correlation matrix to predict drug sensitivity. To our knowledge, this is the first attempt to combine graph convolutional neural network and linear correlation coefficient for this significant task. We performed extensive evaluation experiments on the Genomics of Drug Sensitivity in Cancer (GDSC) and Cancer Cell Line Encyclopedia (CCLE) databases to validate MOFGCN's performance. The experimental results show that MOFGCN is superior to the state-of-the-art algorithms in predicting missing drug responses. It also leads to higher performance in predicting drug responses for new cell lines, new drugs, and targeted drugs.
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