Scalable Amortized GPLVMs for Single Cell Transcriptomics Data

• URL: http://arxiv.org/abs/2405.03879v1
• Date: Mon, 6 May 2024 21:54:38 GMT
• Title: Scalable Amortized GPLVMs for Single Cell Transcriptomics Data
• Authors: Sarah Zhao, Aditya Ravuri, Vidhi Lalchand, Neil D. Lawrence,
• Abstract summary: Dimensionality reduction is crucial for analyzing large-scale single-cell RNA-seq data. We introduce an improved model, the amortized variational model (BGPLVM) BGPLVM is tailored for single-cell RNA-seq with specialized encoder, kernel, and likelihood designs.
• Score: 9.010523724015398
• License: http://creativecommons.org/licenses/by-sa/4.0/
• Abstract: Dimensionality reduction is crucial for analyzing large-scale single-cell RNA-seq data. Gaussian Process Latent Variable Models (GPLVMs) offer an interpretable dimensionality reduction method, but current scalable models lack effectiveness in clustering cell types. We introduce an improved model, the amortized stochastic variational Bayesian GPLVM (BGPLVM), tailored for single-cell RNA-seq with specialized encoder, kernel, and likelihood designs. This model matches the performance of the leading single-cell variational inference (scVI) approach on synthetic and real-world COVID datasets and effectively incorporates cell-cycle and batch information to reveal more interpretable latent structures as we demonstrate on an innate immunity dataset.

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