Article
Standard machine learning approaches outperform deep representation learning on phenotype prediction from transcriptomics data.
BMC bioinformatics - 20 Mar 2020
Smith Aaron M, Walsh Jonathan R, Long John, Davis Craig B, Henstock Peter, Hodge Martin R, Maciejewski Mateusz, Mu Xinmeng Jasmine, Ra Stephen, Zhao Shanrong, Ziemek Daniel, Fisher Charles K
Abstract excerpt
BACKGROUND: The ability to confidently predict health outcomes from gene expression would catalyze a revolution in molecular diagnostics. Yet, the goal of developing actionable, robust, and reproducible predictive signatures of phenotypes such as clinical outcome has not been attained in almost any disease area. Here, we report a comprehensive analysis spanning prediction tasks from ulcerative colitis, atopic...
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