  Predicting the response of cancer cells to drugs is an important problem in
pharmacogenomics. Recent efforts in generation of large scale datasets
profiling gene expression and drug sensitivity in cell lines have provided a
unique opportunity to study this problem. However, one major challenge is the
small number of samples (cell lines) compared to the number of features (genes)
even in these large datasets. We propose a collaborative filtering (CF) like
algorithm for modeling gene-drug relationship to identify patients most likely
to benefit from a treatment. Due to the correlation of gene expressions in
different cell lines, the gene expression matrix is approximately low-rank,
which suggests that drug responses could be estimated from a reduced dimension
latent space of the gene expression. Towards this end, we propose a joint
low-rank matrix factorization and latent linear regression approach.
Experiments with data from the Genomics of Drug Sensitivity in Cancer database
are included to show that the proposed method can predict drug-gene
associations better than the state-of-the-art methods.
