Modelling Cellular Perturbations with the Sparse Additive Mechanism Shift Variational Autoencoder

Generative models of observations under interventions have been a vibrant topic of interest across machine learning and the sciences in recent years. For example, in drug discovery, there is a need to model the effects of diverse interventions on cells in order to characterize unknown biological mechanisms of action. We propose the Sparse Additive Mechanism Shift Variational Autoencoder, SAMS-VAE, to combine compositionality, disentanglement, and interpretability for perturbation models. SAMS-VAE models the latent state of a perturbed sample as the sum of a local latent variable capturing sample-specific variation and sparse global variables of latent intervention effects. Crucially, SAMS-VAE sparsifies these global latent variables for individual perturbations to identify disentangled, perturbation-specific latent subspaces that are flexibly composable.