Doubly non-central beta matrix factorization for DNA methylation data
Aaron Schein, Anjali Nagulpally, Hanna Wallach, Patrick Flaherty
Abstract
We present a new non-negative matrix factorization model for $(0,1)$ bounded-support data based on the doubly non-central beta (DNCB) distribution, a generalization of the beta distribution. The expressiveness of the DNCB distribution is particularly useful for modeling DNA methylation datasets, which are typically highly dispersed and multi-modal; however, the model structure is sufficiently general that it can be adapted to many other domains where latent representations of $(0,1)$ bounded-support data are of interest. Although the DNCB distribution lacks a closed-form conjugate prior, several augmentations let us derive an efficient posterior inference algorithm composed entirely of analytic updates. Our model improves out-of-sample predictive performance on both real and synthetic DNA methylation datasets over state-of-the-art methods in bioinformatics. In addition, our model yields meaningful latent representations that accord with existing biological knowledge.
BibTeX
@InProceedings{pmlr-v161-schein21a,
title = {Doubly non-central beta matrix factorization for {DNA} methylation data},
author = {Schein, Aaron and Nagulpally, Anjali and Wallach, Hanna and Flaherty, Patrick},
booktitle = {Proceedings of the Thirty-Seventh Conference on Uncertainty in Artificial Intelligence},
pages = {1895--1904},
year = {2021},
editor = {de Campos, Cassio and Maathuis, Marloes H.},
volume = {161},
series = {Proceedings of Machine Learning Research},
month = {27--30 Jul},
publisher = {PMLR},
pdf = {https://proceedings.mlr.press/v161/schein21a/schein21a.pdf},
url = {https://proceedings.mlr.press/v161/schein21a.html},
abstract = {We present a new non-negative matrix factorization model for $(0,1)$ bounded-support data based on the doubly non-central beta (DNCB) distribution, a generalization of the beta distribution. The expressiveness of the DNCB distribution is particularly useful for modeling DNA methylation datasets, which are typically highly dispersed and multi-modal; however, the model structure is sufficiently general that it can be adapted to many other domains where latent representations of $(0,1)$ bounded-support data are of interest. Although the DNCB distribution lacks a closed-form conjugate prior, several augmentations let us derive an efficient posterior inference algorithm composed entirely of analytic updates. Our model improves out-of-sample predictive performance on both real and synthetic DNA methylation datasets over state-of-the-art methods in bioinformatics. In addition, our model yields meaningful latent representations that accord with existing biological knowledge.}
}