Benchmark of embedding-based methods for accurate and transferable prediction of drug response

过度拟合 计算机科学 药物反应 水准点(测量) 机器学习 弹性网正则化 人工智能 预测建模 数据挖掘 深度学习 交叉验证 精密医学 药品 特征选择 人工神经网络 生物 大地测量学 地理 心理学 精神科 遗传学
作者
Peilin Jia,Ruifeng Hu,Zhongming Zhao
出处
期刊:Briefings in Bioinformatics [Oxford University Press]
卷期号:24 (3) 被引量:1
标识
DOI:10.1093/bib/bbad098
摘要

Prediction of therapy response has been a major challenge in cancer precision medicine due to the extensive tumor heterogeneity. Recently, several deep learning methods have been developed to predict drug response by utilizing various omics data. Most of them train models by using the drug-response screening data generated from cell lines and then use these models to predict response in cancer patient data. In this study, we focus on and evaluate deep learning methods using transcriptome data for the long-standing question of personalized drug-response prediction. We developed an embedding-based approach for drug-response prediction and benchmarked similar methods for their performance. For all methods, we used pretreatment transcriptome data to train models and then conducted a comprehensive evaluation and comparison of the models using cross-panels, cross-datasets and target genes. We further validated the methods using three independent datasets assessing multiple compounds for their predictive capability of drug response, survival outcome and cell line status. As a result, the methods building on gene embeddings had an overall competitive performance with reduced overfitting when we applied evaluation parameters for model fitting as well as the correlation with clinical outcomes in the validation data. We further developed an ensemble model to combine the results from the three most competitive methods for an overall prediction. Finally, we developed DrVAEN (https://bioinfo.uth.edu/drvaen), a user-friendly and easy-accessible web-server that hosts all these methods for drug-response prediction and model comparison for broad use in cancer research, method evaluation and drug development.
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