使用基于邻居的协同过滤并去除全局效应进行抗癌药物反应预测。
Anti-cancer Drug Response Prediction Using Neighbor-Based Collaborative Filtering with Global Effect Removal.
作者信息
Liu Hui, Zhao Yan, Zhang Lin, Chen Xing
机构信息
School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, China.
School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, China.
出版信息
Mol Ther Nucleic Acids. 2018 Dec 7;13:303-311. doi: 10.1016/j.omtn.2018.09.011. Epub 2018 Sep 22.
Patients of the same cancer may differ in their responses to a specific medical therapy. Identification of predictive molecular features for drug sensitivity holds the key in the era of precision medicine. Human cell lines have harbored most of the same genetic changes found in patients' tumors and thus are widely used in the research of drug response. In this work, we formulated drug-response prediction as a recommender system problem and then adopted a neighbor-based collaborative filtering with global effect removal (NCFGER) method to estimate anti-cancer drug responses of cell lines by integrating cell-line similarity networks and drug similarity networks based on the fact that similar cell lines and similar drugs exhibit similar responses. Specifically, we removed the global effect in the available responses and shrunk the similarity score for each cell line pair as well as each drug pair. We then used the K most similar neighbors (hybrid of cell-line-oriented and drug-oriented) in the available responses to predict the unknown ones. Through 10-fold cross-validation, this approach was shown to reach accurate and reproducible outcomes of drug sensitivity. We also discussed the biological outcomes based on the newly predicted response values.
患有相同癌症的患者对特定医学疗法的反应可能存在差异。在精准医学时代,识别药物敏感性的预测分子特征是关键所在。人类细胞系具有患者肿瘤中发现的大多数相同基因变化,因此被广泛用于药物反应研究。在这项工作中,我们将药物反应预测表述为一个推荐系统问题,然后采用一种基于邻居的去除全局效应的协同过滤(NCFGER)方法,通过整合细胞系相似性网络和药物相似性网络来估计细胞系的抗癌药物反应,这是基于相似的细胞系和相似的药物表现出相似反应这一事实。具体而言,我们去除了可用反应中的全局效应,并缩小了每个细胞系对以及每个药物对的相似性得分。然后,我们在可用反应中使用K个最相似的邻居(细胞系导向和药物导向的混合)来预测未知反应。通过10折交叉验证,该方法被证明能得出准确且可重复的药物敏感性结果。我们还基于新预测的反应值讨论了生物学结果。