  Cancer is a primary cause of human death, but discovering drugs and tailoring
cancer therapies are expensive and time-consuming. We seek to facilitate the
discovery of new drugs and treatment strategies for cancer using variational
autoencoders (VAEs) and multi-layer perceptrons (MLPs) to predict anti-cancer
drug responses. Our model takes as input gene expression data of cancer cell
lines and anti-cancer drug molecular data and encodes these data with our {\sc
{GeneVae}} model, which is an ordinary VAE model, and a rectified junction tree
variational autoencoder ({\sc JTVae}) model, respectively. A multi-layer
perceptron processes these encoded features to produce a final prediction. Our
tests show our system attains a high average coefficient of determination
($R^{2} = 0.83$) in predicting drug responses for breast cancer cell lines and
an average $R^{2} = 0.845$ for pan-cancer cell lines. Additionally, we show
that our model can generates effective drug compounds not previously used for
specific cancer cell lines.
