January 2015 - talks - lists.cs.princeton.edu

Colloquium speaker: Ben Raphael, Monday January 12, 4:30pm
by Nicole E. Wagenblast 11 Jan '15

11 Jan '15

Colloquium Speaker Ben Raphael, Brown University Monday, January 12, 4:30pm Computer Science 105 Understanding the molecular alterations that cause cancer is one of the greatest challenges in biology and medicine. Recent advances in DNA sequencing technology now enable large-scale measurement of mutations in cancer genomes and provide an unprecedented opportunity to address this challenge. However, translating this information into deeper insight about the mutational process that drives cancer demands novel computational approaches. In this talk, I will describe algorithms that we have developed to address key problems in cancer genomics. First, I will discuss algorithms that deconvolve DNA sequencing data from a single tumor and determine subpopulations of cancer cells harboring different mutations. These algorithms exploit integrality constraints on copy number aberrations and phylogenetic tree constraints that relate subpopulations. Next, I will describe algorithms to identify combinations of mutations that perturb cellular signaling and regulatory networks. One algorithm employs a heat diffusion process to identify subnetworks of a genome-scale interaction network that are recurrently mutated across samples. A second algorithm finds combinations of mutations that optimize a measure of mutual exclusivity across samples. I will illustrate applications of these approaches to multiple cancer types in The Cancer Genome Atlas (TCGA), including a recent Pan-Cancer study of >3000 samples from 12 cancer types. Ben Raphael is an Associate Professor in the Department of Computer Science and Director of the Center for Computational Molecular Biology (CCMB) at Brown University. His research focuses on the design of algorithms for genome sequencing and interpretation. Recent interests include structural variation in human and cancer genomes, and network/pathway analysis of genetic variants. He received an S.B. in Mathematics from MIT, a Ph.D. in Mathematics from the University of California, San Diego (UCSD), and completed postdoctoral training in Bioinformatics and Computer Science at UCSD. He is the recipient of an NSF CAREER award, a Career Award from the Burroughs Wellcome Fund, and a Sloan Research Fellowship.

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11am-noon Thu Jan 15 talk on "Data Centers, Energy, and Online Optimization"
by Jennifer Rexford 09 Jan '15

09 Jan '15

Speaker: Adam Wierman, CalTech Title: Data Centers, Energy, and Online Optimization Date/time: 11am-noon Thursday January 15 Location: CS 105 (small auditorium) Abstract: This talk will tell two stories, one about designing sustainable data centers and one about the underlying algorithmic challenges, which fall into the context of online convex optimization. Story 1: The typical message surrounding data centers and energy is an extremely negative one: Data centers are energy hogs. This message is pervasive in both the popular press and academia, and it certainly rings true. However, the view of data centers as energy hogs is too simplistic. One goal of this talk is to highlight that, yes, data centers use a lot of energy, but data centers can also be a huge benefit in terms of integrating renewable energy into the grid and thus play a crucial role in improving the sustainability of our energy landscape. In particular, I will highlight a powerful alternative view: data centers as demand response opportunities. Story 2: Typically in online convex optimization it is enough to exhibit an algorithm with low (sub-linear) regret, which implies that the algorithm can match the performance of the best static solution in retrospect. However, what if one additionally wants to maintain performance that is nearly as good as the dynamic optimal, i.e., a good competitive ratio? In this talk, I'll highlight that it is impossible for an online algorithm to simultaneously achieve these goals. Luckily though, in practical settings (like data centers), noisy predictions about the future are often available, and I will show that, under a general model of prediction noise, even very limited predictions about the future are enough to overcome the impossibility result. Bio: Adam Wierman is a Professor in the Department of Computing and Mathematical Sciences at the California Institute of Technology, where he is a founding member of the Rigorous Systems Research Group (RSRG) and maintains a popular blog called Rigor + Relevance. His research interests center around resource allocation and scheduling decisions in computer systems and services. He received the 2011 ACM SIGMETRICS Rising Star award, the 2014 IEEE Communications Society William R. Bennett Prize, and has been coauthor on papers that received of best paper awards at ACM SIGMETRICS, IEEE INFOCOM, IFIP Performance (twice), IEEE Green Computing Conference, IEEE Power & Energy Society General Meeting, and ACM GREENMETRICS.

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Colloquium speaker: Ben Raphael, Monday January 12, 4:30pm
by Nicole E. Wagenblast 06 Jan '15

06 Jan '15

Colloquium Speaker Ben Raphael, Brown University Monday, January 12, 4:30pm Computer Science 105 Understanding the molecular alterations that cause cancer is one of the greatest challenges in biology and medicine. Recent advances in DNA sequencing technology now enable large-scale measurement of mutations in cancer genomes and provide an unprecedented opportunity to address this challenge. However, translating this information into deeper insight about the mutational process that drives cancer demands novel computational approaches. In this talk, I will describe algorithms that we have developed to address key problems in cancer genomics. First, I will discuss algorithms that deconvolve DNA sequencing data from a single tumor and determine subpopulations of cancer cells harboring different mutations. These algorithms exploit integrality constraints on copy number aberrations and phylogenetic tree constraints that relate subpopulations. Next, I will describe algorithms to identify combinations of mutations that perturb cellular signaling and regulatory networks. One algorithm employs a heat diffusion process to identify subnetworks of a genome-scale interaction network that are recurrently mutated across samples. A second algorithm finds combinations of mutations that optimize a measure of mutual exclusivity across samples. I will illustrate applications of these approaches to multiple cancer types in The Cancer Genome Atlas (TCGA), including a recent Pan-Cancer study of >3000 samples from 12 cancer types. Ben Raphael is an Associate Professor in the Department of Computer Science and Director of the Center for Computational Molecular Biology (CCMB) at Brown University. His research focuses on the design of algorithms for genome sequencing and interpretation. Recent interests include structural variation in human and cancer genomes, and network/pathway analysis of genetic variants. He received an S.B. in Mathematics from MIT, a Ph.D. in Mathematics from the University of California, San Diego (UCSD), and completed postdoctoral training in Bioinformatics and Computer Science at UCSD. He is the recipient of an NSF CAREER award, a Career Award from the Burroughs Wellcome Fund, and a Sloan Research Fellowship.

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