Drug-induced gene expression profiles are rich information sources that can help to measure the effect of a drug on the transcriptional state of cells. However, the available experimental data only covers a limited set of conditions such as treatment time, dosages, and cell lines. This poses a challenge for neural network models to learn embeddings that can be generalized to new experimental conditions. In this project, we focus on the cell line as the confounder variable and train an Adversarial Neural Network to extract transcriptional effects that are conserved across multiple cell lines, and can thus be more confidently generalized to the biological setting of interest. Additionally, we investigate several methods to test whether our approach can simultaneously learn biologically valid embeddings and deconfound the effect of cell lines on the data distribution