Single-Cell Techniques and Deep Learning in Predicting Drug Response.

Rapidly developing single-cell sequencing analyses produce more comprehensive profiles of the genomic, transcriptomic, and epigenomic heterogeneity of tumor subpopulations than do traditional bulk sequencing analyses. Moreover, single-cell techniques allow the response of a tumor to drug exposure to be more thoroughly investigated. Deep learning (DL) models have successfully extracted features from complex bulk sequence data to predict drug responses. We review recent innovations in single-cell technologies and DL-based approaches related to drug sensitivity predictions. We believe that, by using insights from bulk sequence data, deep transfer learning (DTL) can facilitate the use of single-cell data for training superior DL-based drug prediction models. A comprehensive understanding of heterogeneous tumor subpopulations will benefit drug sensitivity prediction and combination drug treatment design. Deep learning models are powerful and extensively used in drug sensitivity prediction and in inferring drug–target interactions. Single-cell sequencing techniques offer precise and accurate profiling of tumor subpopulations and reveal subtle differences in their response to drug treatments. Applying deep transfer learning to predict drug sensitivity allows us to not only take advantage of prior knowledge obtained from massive bulk sequencing data but also utilize the heterogeneous landscapes generated by single-cell sequencing techniques. The integration of single-cell multi-omic data for drug sensitivity prediction using transfer learning methods poses a special challenge. [ABSTRACT FROM AUTHOR]