A Bayesian Approach to Restricted Latent Class Models for Scientifically-Structured Clustering of Multivariate Binary Outcomes

TL;DR

This paper introduces a Bayesian framework for clustering multivariate binary data with scientific restrictions, incorporating prior knowledge and ensuring parameter identifiability, demonstrated through an application to auto-antibody data.

Contribution

It develops a novel Bayesian method that combines evidence of varying quality, respects scientific context restrictions, and estimates the number of clusters and latent structures simultaneously.

Findings

Effective clustering of biomedical binary data demonstrated

Method identifies meaningful latent classes with sparse patterns

Algorithm incorporates external prior knowledge

Abstract

In this paper, we propose a general framework for combining evidence of varying quality to estimate underlying binary latent variables in the presence of restrictions imposed to respect the scientific context. The resulting algorithms cluster the multivariate binary data in a manner partly guided by prior knowledge. The primary model assumptions are that 1) subjects belong to classes defined by unobserved binary states, such as the true presence or absence of pathogens in epidemiology, or of antibodies in medicine, or the "ability" to correctly answer test questions in psychology, 2) a binary design matrix $\Gamma$ specifies relevant features in each class, and 3) measurements are independent given the latent class but can have different error rates. Conditions ensuring parameter identifiability from the likelihood function are discussed and inform the design of a novel posterior inference algorithm that simultaneously estimates the number of clusters, design matrix $\Gamma$, and model parameters. In finite samples and dimensions, we propose prior assumptions so that the posterior distribution of the number of clusters and the patterns of latent states tend to concentrate on smaller values and sparser patterns, respectively. The model readily extends to studies where some subjects' latent classes are known or important prior knowledge about differential measurement accuracy is available from external sources. The methods are illustrated with an analysis of protein data to detect clusters representing auto-antibody classes among scleroderma patients.