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FDS Colloquium: Lior Pachter (Caltech), “Some open and solved problems in dimensionality reduction (for single-cell genomics data)”

Wednesday, April 3, 2024    
11:30AM to 1:00PM
Yale Institute for Foundations of Data Science & Webcast
219 Prospect Street
New Haven, CT 06511
 _223_https://campuspress.yale.edu/fds/files/2024/02/GUEST-Lior_Pachter-747627c118de8881-256x300.jpg

Speaker: Lior S. Pachter
Bren Professor of Computational Biology and Computing Mathematical Sciences
Division of Biology and Biological Engineering
California Institute of Technology

Wednesday, April 3, 2024
Lunch: 11:30 am (Kitchen)
Talk: 12:00 pm (Seminar Room #1327)
at the Yale institute for Foundations of Data Science, Kline Tower, 13th Floor
Webcast (Starts at 12:00 pm): https://yale.zoom.us/s/3369431653

Title: “Some open and solved problems in dimensionality reduction (for single-cell genomics data)”

Abstract: Dimensionality reduction is commonly applied as a first step prior to analysis of data in a variety of disciplines. In machine learning, dimensionality reduction often is the analysis via embedding of data in a “latent space”. In the field of single-cell genomics, dimensionality reduction is particularly popular, specifically dimensionality reduction to two dimensions. After discussing the motivation for dimensionality reduction in single-cell genomics, I will present several results, along with open problems, related to how and when one should perform dimensionality reduction, with a focus on insights gleaned from the genomics field.

The is joint work with Tara Chari.

Bio: Lior Pachter was born in Ramat Gan, Israel, and grew up in Pretoria, South Africa where he attended Pretoria Boys High School. After receiving a B.S. in Mathematics from Caltech in 1994, He left for MIT where he was awarded a PhD in applied mathematics in 1999. He then moved to the University of California at Berkeley where he was a postdoctoral researcher (1999-2001), assistant professor (2001-2005), associate professor (2005-2009), and until 2018 the Raymond and Beverly Sackler professor of computational biology and professor of mathematics and molecular and cellular biology with a joint appointment in computer science. Since January 2017 he has been the Bren professor of computational biology at Caltech.

His research interests span the mathematical and biological sciences, and he has authored over 100 research articles in the areas of algorithms, combinatorics, comparative genomics, algebraic statistics, molecular biology and evolution. He has taught a wide range of courses in mathematics, computational biology and genomics. He is a Fellow of the International Society of Computational Biology and has been awarded a National Science Foundation CAREER award, a Sloan Research Fellowship, the Miller Professorship, and a Federal Laboratory Consortium award for the successful technology transfer of widely used sequence alignment software developed in his group.

He is married to Ingileif B. Hallgrímsdóttir and has three daughters.

Website: https://pachterlab.github.io/index.html


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