MPC Member Publications

This database contains a listing of population studies publications written by MPC Members. Anyone can add a publication by an MPC student, faculty, or staff member to this database; new citations will be reviewed and approved by MPC administrators.

Full Citation

Title: Zero-inflated Poisson factor model with application to microbiome read counts

Citation Type: Journal Article

Publication Year: 2021

ISSN: 15410420

DOI: 10.1111/biom.13272

PMID: 32277466

Abstract: Dimension reduction of high-dimensional microbiome data facilitates subsequent analysis such as regression and clustering. Most existing reduction methods cannot fully accommodate the special features of the data such as count-valued and excessive zero reads. We propose a zero-inflated Poisson factor analysis model in this paper. The model assumes that microbiome read counts follow zero-inflated Poisson distributions with library size as offset and Poisson rates negatively related to the inflated zero occurrences. The latent parameters of the model form a low-rank matrix consisting of interpretable loadings and low-dimensional scores that can be used for further analyses. We develop an efficient and robust expectation-maximization algorithm for parameter estimation. We demonstrate the efficacy of the proposed method using comprehensive simulation studies. The application to the Oral Infections, Glucose Intolerance, and Insulin Resistance Study provides valuable insights into the relation between subgingival microbiome and periodontal disease.

Url: https://pubmed.ncbi.nlm.nih.gov/32277466/

User Submitted?: No

Authors: Xu, Tianchen; Demmer, Ryan T.; Li, Gen

Periodical (Full): Biometrics

Issue: 1

Volume: 77

Pages: 91-101

Countries:

IPUMS NHGIS NAPP IHIS ATUS Terrapop