To make decisions based on a model fit with auto-encoding variational Bayes (AEVB), practitioners often let the variational distribution serve as a surrogate for the posterior distribution.
Building upon domain adaptation work, we propose gimVI, a deep generative model for the integration of spatial transcriptomic data and scRNA-seq data that can be used to impute missing genes.
Class labels are often imperfectly observed, due to mistakes and to genuine ambiguity among classes.
We show how to apply this method to a range of problems, including the problems of learning invariant representations and the learning of interpretable representations.
We propose a probabilistic model for interpreting gene expression levels that are observed through single-cell RNA sequencing.
We also extend our framework to account for batch effects and other confounding factors, and propose a Bayesian hypothesis test for differential expression that outperforms DESeq2.