Sparse PCA with Applications in Genomics

Speaker: Eran Halperin
Affiliation: University of California, Los Angeles - CS

Abstract:  I will introduce a very simple new algorithm for sparse PCA. I will show its applications in epigenomics, where whole-genome methylation data is measured across a large number of individuals. In this application, the low rank signal arises from the fact that the measurements are taken across a mixture of cell types, while the cell counts are unknown. I will show how in this type of the data our new algorithm improves upon other algorithms for dimensionality reduction, including standard methods such as PCA, factor analysis, and sparse PCA using L1 regularization, and more specialized methods that are tailored to methylation data. I will further introduce recent extensions of the algorithm with specific applications in mind, particularly the inference of cell composition from methylation data using a Bayesian approach, and the inference of ancestry from methylation data. Finally, I will describe some asymptotic behavior of the algorithm and compare those to the standard truncated singular value decomposition, and to the sparse PCA algorithm of Johnstone and Lu.

Biography: Eran Halperin is a professor in the department of Computer Science and the department of Anesthesiology in the University of California, Los Angeles (UCLA). His research focuses on the intersection between genetics, machine learning, and statistics. He received his doctorate in theoretical computer science from Tel-Aviv University in 2001, after which he held postdoctoral and research positions in UC Berkeley and Princeton from 2001 to 2004. He was a faculty member in the International Computer Science Institute (ICSI) in Berkeley from 2005, and Tel-Aviv University from 2008 until 2016. He joined UCLA as a faculty in the summer of 2016. He published over 100 peer reviewed publications in theoretical computer science, computational biology, and in genetics. He has received various awards for his research, including the Krill Prize and the Technion-Juludan Research Fund prize.

For more information contact Professor Sam Emaminejad ()

Date(s) - Jun 05, 2017
1:00 pm - 2:00 pm

EE-IV Shannon Room #54-134
420 Westwood Plaza - 5th Flr., Los Angeles CA 90095