Predicting Clinical Anticancer Drug Response of Patients by using Domain Alignment and Prototypical Learning.

ABSTRACT

Anticancer drug response prediction is crucial in developing personalized treatment plans for cancer patients. However, High-quality patient anticancer drug response data are scarce and cell line data and patient data have different distributions, models trained solely on cell line data perform poorly. Some existing methods predict anticancer drug response by transferring knowledge from the cell line domain to the patient domain using transfer learning. However, the robustness of these classifiers is affected by anomalies in the cell line data, and they do not utilize the knowledge in the unlabeled target domain data. To this end, we proposed a model called DAPL to predict patient responses to anticancer drugs. The model extracts domain-invariant features from cell lines and patients by constructing multiple VAEs and extracts drug features using GNNs. These features are then combined for prototypical learning to train a classifier, resulting in better predictions of patient anticancer drug response. We used the cell line datasets CCLE and GDSC as source domains and the patient datasets TCGA and PDTC as target domains and conducted experiments. The results indicate that DAPL shows excellent performance in predicting patient anticancer drug response compared to other state-of-the-art methods.