Dimensionality Reduction as Probabilistic InferenceDownload PDF

Published: 20 Jun 2023, Last Modified: 18 Jul 2023AABI 2023Readers: Everyone
Keywords: dimensionality reduction, latent variable models, gaussian processes, bayesian, variational inference, probabilistic interpretation, graph, single-cell, pca, sne, t-sne, umap, isomap, lle, laplacian eigenmaps, diffusion maps, mds, probabilistic programming, stan, mvu, meu, drtree
TL;DR: We show that a large class of dimensionality reduction algorithms are inference algorithms of models in a unified variational framework.
Abstract: Dimensionality reduction (DR) algorithms compress high-dimensional data into a lower dimensional representation while preserving important features of the data. DR is a critical step in many analysis pipelines as it enables visualisation, noise reduction and efficient downstream processing of the data. In this work, we introduce the ProbDR variational framework, which interprets a wide range of classical DR algorithms as probabilistic inference algorithms in this framework. ProbDR encompasses PCA, CMDS, LLE, LE, MVU, diffusion maps, kPCA, Isomap, (t-)SNE, and UMAP. In our framework, a low-dimensional latent variable is used to construct a covariance, precision, or a graph Laplacian matrix, which can be used as part of a generative model for the data. Inference is done by optimizing an evidence lower bound. We demonstrate the internal consistency of our framework and show that it enables the use of probabilistic programming languages (PPLs) for DR. Additionally, we illustrate that the framework facilitates reasoning about unseen data and argue that our generative models approximate Gaussian processes (GPs) on manifolds. By providing a unified view of DR, our framework facilitates communication, reasoning about uncertainties, model composition, and extensions, particularly when domain knowledge is present.
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