The Deep Generative Decoder: MAP estimation of representations improves modelling of single-cell RNA data

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Learning low-dimensional representations of single-cell transcriptomics has become instrumental to its downstream analysis. The state of the art is currently represented by neural network models, such as variational autoencoders, which use a variational approximation of the likelihood for inference. Results: We here present the Deep Generative Decoder (DGD), a simple generative model that computes model parameters and representations directly via maximum a posteriori estimation. The DGD handles complex parameterized latent distributions naturally unlike variational autoencoders, which typically use a fixed Gaussian distribution, because of the complexity of adding other types. We first show its general functionality on a commonly used benchmark set, Fashion-MNIST. Secondly, we apply the model to multiple single-cell datasets. Here, the DGD learns low-dimensional, meaningful, and well-structured latent representations with sub-clustering beyond the provided labels. The advantages of this approach are its simplicity and its capability to provide representations of much smaller dimensionality than a comparable variational autoencoder.

Original languageEnglish
Article numberbtad497
JournalBioinformatics
Volume39
Issue number9
Number of pages14
ISSN1367-4803
DOIs
Publication statusPublished - 2023

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© 2023 The Author(s). Published by Oxford University Press.

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