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University of Nevada, Las Vegas
Cox-PASNet, Deep neural network, Survival analysis, Glioblastoma multiforme, Ovarian cancer
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Full-Text Articles in Engineering
Interpretable Deep Neural Network For Cancer Survival Analysis By Integrating Genomic And Clinical Data, Jie Hao, Youngsoon Kim, Tejaswini Mallavarapu, Jung Hun Oh, Mingon Kang
Interpretable Deep Neural Network For Cancer Survival Analysis By Integrating Genomic And Clinical Data, Jie Hao, Youngsoon Kim, Tejaswini Mallavarapu, Jung Hun Oh, Mingon Kang
Computer Science Faculty Research
Background: Understanding the complex biological mechanisms of cancer patient survival using genomic and clinical data is vital, not only to develop new treatments for patients, but also to improve survival prediction. However, highly nonlinear and high-dimension, low-sample size (HDLSS) data cause computational challenges to applying conventional survival analysis. Results: We propose a novel biologically interpretable pathway-based sparse deep neural network, named Cox-PASNet, which integrates high-dimensional gene expression data and clinical data on a simple neural network architecture for survival analysis. Cox-PASNet is biologically interpretable where nodes in the neural network correspond to biological genes and pathways, while capturing the nonlinear …