Generative Distribution Embeddings
This addresses the need for scalable distribution modeling in fields like computational biology, offering a novel framework with broad applications, though it builds incrementally on autoencoder concepts.
The paper tackles the problem of modeling entire distributions rather than single data points by introducing generative distribution embeddings (GDEs), which lift autoencoders to distribution spaces and enable learning representations that approximate Wasserstein distances and optimal transport trajectories, demonstrating strong performance on synthetic datasets and applications in computational biology with datasets ranging from 150K to 253M sequences.
Many real-world problems require reasoning across multiple scales, demanding models which operate not on single data points, but on entire distributions. We introduce generative distribution embeddings (GDE), a framework that lifts autoencoders to the space of distributions. In GDEs, an encoder acts on sets of samples, and the decoder is replaced by a generator which aims to match the input distribution. This framework enables learning representations of distributions by coupling conditional generative models with encoder networks which satisfy a criterion we call distributional invariance. We show that GDEs learn predictive sufficient statistics embedded in the Wasserstein space, such that latent GDE distances approximately recover the $W_2$ distance, and latent interpolation approximately recovers optimal transport trajectories for Gaussian and Gaussian mixture distributions. We systematically benchmark GDEs against existing approaches on synthetic datasets, demonstrating consistently stronger performance. We then apply GDEs to six key problems in computational biology: learning representations of cell populations from lineage-tracing data (150K cells), predicting perturbation effects on single-cell transcriptomes (1M cells), predicting perturbation effects on cellular phenotypes (20M single-cell images), modeling tissue-specific DNA methylation patterns (253M sequences), designing synthetic yeast promoters (34M sequences), and spatiotemporal modeling of viral protein sequences (1M sequences).