Anticancer drug synergy prediction in understudied tissues using transfer learning. (11th October 2020)

• Record Type: Journal Article
• Authors: Kim, Yejin; Zheng, Shuyu; Tang, Jing; Jim Zheng, Wenjin; Li, Zhao; Jiang, Xiaoqian
• Is Part Of: Journal of the American Medical Informatics Association. Volume 28:Number 1(2021)
• Page Start: 42
• Page End: 51
• Publication Date: 2020-10-11
• Subjects: ranking -- data paucity -- data scarcity -- multitask learning -- external validation -- drug sensitivity; Medical informatics -- Periodicals; Information Services -- Periodicals; Medical Informatics -- Periodicals; Médecine -- Informatique -- Périodiques; Informatica; Geneeskunde; Informatique médicale; Computer network resources; Electronic journals; 610.285
• DOI: 10.1093/jamia/ocaa212
• Languages: English
• ISSNs: 1067-5027

Abstract

Abstract: Objective: Drug combination screening has advantages in identifying cancer treatment options with higher efficacy without degradation in terms of safety. A key challenge is that the accumulated number of observations in in-vitro drug responses varies greatly among different cancer types, where some tissues are more understudied than the others. Thus, we aim to develop a drug synergy prediction model for understudied tissues as a way of overcoming data scarcity problems. Materials and Methods: We collected a comprehensive set of genetic, molecular, phenotypic features for cancer cell lines. We developed a drug synergy prediction model based on multitask deep neural networks to integrate multimodal input and multiple output. We also utilized transfer learning from data-rich tissues to data-poor tissues. Results: We showed improved accuracy in predicting synergy in both data-rich tissues and understudied tissues. In data-rich tissue, the prediction model accuracy was 0.9577 AUROC for binarized classification task and 174.3 mean squared error for regression task. We observed that an adequate transfer learning strategy significantly increases accuracy in the understudied tissues. Conclusions: Our synergy prediction model can be used to rank synergistic drug combinations in understudied tissues and thus help to prioritize future in-vitro experiments. Code is available at https://github.com/yejinjkim/synergy-transfer .