April 2014 - talks - lists.cs.princeton.edu

B Hristov general exam
by Melissa M. Lawson 29 Apr '14

29 Apr '14

Borislav Hristov will present his research seminar/general exam on Tuesday May 6 at 10AM in Room 402. The members of his committee are: Mona Singh (advisor), Olga Troyanskaya, and Tom Funkhouser. Everyone is invited to attend his talk, and those faculty wishing to remain for the oral exam following are welcome to do so. His abstract and reading list follow below. ----- Original Message ----- Abstract: The improvement and the decreased cost of next generation DNA sequencing have enabled genome wide measurements in large numbers of individuals. This allows researchers to compare the genome variations in both healthy and sick individuals in order to help uncover the genetic underpinnings of human disease. However, complex diseases are caused by a combination of genetic perturbations- often the same phenotypic outcome (a disease case) can result from a different set of possible mutations, possibly in different loci. Cancer is a disease which exhibits such a great genetic heterogeneity. This makes studying it and identifying causal variants extremely difficult. We combine knowledge of biological interactions with genome sequencing data from The Cancer Genome Atlas to perform an integrated analysis of several types of cancer. Our hypothesis is that even though different patients could have entirely disjoint sets of somatic variants, these variants disturb similar cell processes and hence are closely connected in the biological network. We phrase the problem precisely in mathematical terms and devise an efficient greedy heuristic to solve it. We use a robust framework of cross validation tests to demonstrate the soundness of our approach. We are able to recover well known cancer genes as well as to highlight possible new ones. We show that our method yields both efficient and biologically relevant results. Reading List: Yona, Golan. Introduction to Computational Proteomics . CRC Press, 2011. Chapters: 1-7, 10, 13.2 Dand, Nick, et al. "BioGranat-IG: a network analysis tool to suggest mechanisms of genetic heterogeneity from exome-sequencing data." Bioinformatics 29.6 (2013): 733-741. Vandin, Fabio, Eli Upfal, and Benjamin J. Raphael. "Algorithms for detecting significantly mutated pathways in cancer." Journal of Computational Biology 18.3 (2011): 507-522. Ulitsky, Igor, et al. "DEGAS: de novo discovery of dysregulated pathways in human diseases." PLoS One 5.10 (2010): e13367. Navlakha, Saket, and Carl Kingsford. "The power of protein interaction networks for associating genes with diseases." Bioinformatics 26.8 (2010): 1057-1063. Wang, Peggy I., and Edward M. Marcotte. "It's the machine that matters: Predicting gene function and phenotype from protein networks." Journal of proteomics 73.11 (2010): 2277-2289. Gosline, Sara JC, et al. "SAMNet: a network-based approach to integrate multi-dimensional high throughput datasets." Integrative Biology 4.11 (2012): 1415-1427. Lee, Insuk, et al. "Prioritizing candidate disease genes by network-based boosting of genome-wide association data." Genome research 21.7 (2011): 1109-1121. Hofree, Matan, et al. "Network-based stratification of tumor mutations." Nature methods (2013). Jiang, Peng, and Mona Singh. "SPICi: a fast clustering algorithm for large biological networks." Bioinformatics 26.8 (2010): 1105-1111.

1 0

Colloquium speaker Junfeng Yang, Monday April 28, 4:30pm
by Nicole E. Wagenblast 28 Apr '14

28 Apr '14

Determinism Is Not Enough: Making Parallel Programs Reliable with Stable Multithreading Junfeng Yang, Columbia University Monday, April 28, 4:30pm Computer Science 105 Our accelerating computational demand and the rise of multicore hardware have made parallel programs, especially shared-memory multithreaded programs, increasingly pervasive and critical. Yet, these programs remain extremely difﬁcult to write, test, analyze, debug, and verify. Conventional wisdom has attributed these difﬁculties to nondeterminism (i.e., repeated executions of the same program on the same input may show different behaviors), and researchers have recently dedicated much effort to bringing determinism into multithreading. In this talk, I argue that determinism is not as useful as commonly perceived: it is neither sufﬁcient nor necessary for reliability. We present our view on why multithreaded programs are difﬁcult to get right, describe a promising approach we call stable multithreading to dramatically improve reliability, and summarize our last four years’ research on building and applying stable multithreading systems. Junfeng Yang 's research ( www.cs.columbia.edu/~junfeng ) centers on making reliable and secure systems. He earned his PhD at Stanford, where he created eXplode, a general, lightweight system for effectively finding storage system errors. This work has led to an OSDI '04 best paper, numerous bug fixes to real systems such as the Linux kernel, and a featured article in Linux Weekly news. He worked at Microsoft Research, Silicon Valley from 2007-2008, extending eXplode to check production distributed systems. MoDist, the resultant system, is being transferred to Microsoft product groups. He's now co-directing the Software Systems Lab ( ssl.cs.columbia.edu ) at Columbia University, where his recent work on making reliable parallel programs---the Tern/Peregrine/Parrot stable multithreading systems---was featured in CACM, ACM Tech News, The Register, and many other sites. He won Sloan and AFOSR YIP both in 2012; and NSF CAREER in 2011.

1 2

M Jayakumar MSE thesis talk
by Melissa M. Lawson 25 Apr '14

25 Apr '14

Madhu Jayakumar will present her MSE thesis talk on Wednesday April 30 at 2PM in Room 402. The members of her committee are Vivek Pai (advisor) and Kai Li. Everyone is invited to attend her talk. Her abstract follows below. -------------------------- Network traffic to mobile devices has exponentially increased over the past five years and is expected to continue growing. As these devices become more computationally powerful, mobile users have started to consume more and more traffic including high-definition video and audio. As wireless networks are more bandwidth-constrained, it is useful to understand and develop techniques to reduce mobile data traffic. We observed traffic from some of the most frequently visited mobile websites, and quantify the different types of traffic in terms of content type, cacheability and compression characteristics. Our analysis revealed redundancies across requests on repeat visits and we evaluate the effectiveness of using chunking and Rabin fingerprinting to deduplicate this traffic. Finally, we offer two system implementations and associated protocols that can be used for a content-based caching system which optimizes mobile web traffic by decreasing bandwidth.

1 0

X Chen FPO
by Melissa M. Lawson 25 Apr '14

25 Apr '14

Xiaobai Chen will present his FPO on Monday May 5 at 4:15 in Room 302 (note room!). The members of his committee are: Tom Funkhouser, advisor; Szymon Rusinkiewicz and Dan Goldman (Adobe), readers; Adam Finkelstein and David Dobkin, nonreaders. A copy of his thesis, "Shape Analysis with Crowdsourced Data" is available in Room 310. Everyone is invited to attend his talk.

1 0

A Soviani FPO
by Melissa M. Lawson 25 Apr '14

25 Apr '14

Adrian Soviani will present his FPO on Friday May 2 at 1PM in Room 402. The members of his committee are: JP Singh, advisor; Kai Li and David August, readers; Brian Kernighan and Andrea LaPaugh, nonreaders. A copy of his thesis, "A Hybrid SPMD - Coarse Grain Dataflow Parallel Programming Model" is available in Room 310. Everyone is invited to attend his talk.

1 0

S Ravi MSE thesis talk
by Melissa M. Lawson 25 Apr '14

25 Apr '14

Sachin Ravi will present his MSE thesis talk on Thursday May 1 at 2:30 PM in Room 301 (note room!). The members of his committee are: Kai Li (advisor) and Moses Charikar. Everyone is invited to attend his talk. His abstract follows below. Nearest Neighbor search is a fundamental problem in computer vision, machine learning, data mining, and other fields. In today's Internet age, as the size of images and other non-text data grows exponentially, it is crucial to scale solutions to larger datasets. Current research involves the approximate nearest neighbor problem where we are willing to sacrice some percentage of accuracy so that the approximate algorithm is one or two orders of magnitude faster than a naive linear scan of the data. Most recently, advances in performance for the K-Nearest Neighbor (K-NN) search problem have been made using a graph-based data structure. To this end, we consider adapting a graph-based index for approximate Epsilon-Nearest Neighbor (Epsilon- NN) search. Through analysis of various data sets, we show that this problem is very relevant to the requirements of current applications. We then introduce a new data structure Epsilon-NN graph for online nearest neighbor search and an algorithm for constructing this index on existing data. Through experimental evaluation on extracted data sets, we show the high performance of this data structure compared to existing methods.

1 0

R Mendes de Oliveira generals
by Melissa M. Lawson 24 Apr '14

24 Apr '14

Rafael Mendes de Oliveira will present his research seminar/general exam on Wednesday April 30 at 10:15AM in Room 402. The members of his committee are: Zeev Dvir, advisor, Mark Braverman, and Sanjeev Arora. Everyone is invited to attend his talk, and those faculty wishing to remain for the oral exam following are welcome to do so. His abstract and reading list follow below. ----- Original Message ----- Abstract: We show that if f(x_1,...,x_n) is a polynomial with s monomials and g(x_1,...,x_n) divides f then g has at most \max(s^{O(\log s \log\log s)},d^{O(\log d)}) monomials, where d is a bound on the individual degrees of f. This answers a question of von zur Gathen and Kaltofen (JCSS 1985) who asked whether a quasi-polynomial bound holds in this case. This work is joint work with my advisor, Prof. Dvir. Reading list: Book: Arora Barak, Computational Complexity - A Modern Approach Papers: Nisan, Noam. "Lower bounds for non-commutative computation." Proceedings of the twenty-third annual ACM symposium on Theory of computing . ACM, 1991. Nisan, Noam, and Avi Wigderson. "Hardness vs randomness." Journal of Computer and System Sciences 49.2 (1994): 149-167. Klivans, Adam R., and Daniel Spielman. "Randomness efficient identity testing of multivariate polynomials." Proceedings of the thirty-third annual ACM symposium on Theory of computing . ACM, 2001. Kayal, Neeraj. "Affine projections of polynomials." Proceedings of the 44th symposium on Theory of Computing . ACM, 2012. Dvir, Zeev, Shubhangi Saraf, and Avi Wigderson. "Improved rank bounds for design matrices and a new proof of Kelly's theorem." arXiv preprint arXiv:1211.0330 (2012). Malod, Guillaume, and Natacha Portier. "Characterizing Valiant's algebraic complexity classes." Journal of complexity 24.1 (2008): 16-38. Hrubeš, Pavel, Avi Wigderson, and Amir Yehudayoff. "Non-commutative circuits and the sum-of-squares problem." Journal of the American Mathematical Society 24.3 (2011): 871-898. Kaltofen, Erich. "Factorization of polynomials given by straight-line programs." Randomness and Computation 5 (1989): 375-412. Nisan, Noam, and Avi Wigderson. "Lower bounds on arithmetic circuits via partial derivatives." Computational Complexity 6.3 (1996): 217-234. Valiant, Leslie G. Graph-theoretic arguments in low-level complexity . Springer Berlin Heidelberg, 1977.

1 0

R Dannenfelser MSE talk - time change
by Melissa M. Lawson 24 Apr '14

24 Apr '14

Ruth's talk has been changed to a 2:45 start time from 3PM. --Melissa

1 0

Fwd: MSE talk abstract
by Melissa M. Lawson 24 Apr '14

24 Apr '14

Christian Eubank will present his MSE thesis talk on Tuesday April 29 at 11AM in Room 301. The members of his committee are: Arvind Narayanan, advisor and Ed Felten, reader. Everyone is invited to attend his talk. His abstract follows below. ----- Original Message ----- Web privacy measurement experiments have heavily influenced privacy debates by shedding light into practices such as third party online tracking and price discrimination. However, these research experiments have typically been one-off projects, with different groups encountering similar methodological and engineering challenges without forming an institutional knowledge base. As an illustrative example of this trend of repeating effort through self-contained experiments, we present the results of one study comparing mobile and desktop tracking and discuss how challenges from this study and other works in the literature shaped the formation of general design principles intended to improve the efficiency of such experiments. We present a robust and modular web measurement platform that enables scalable and repeatable experiments while avoiding many common pitfalls observed by the research community. We describe case studies performed on this framework, including the detection of unique cookie identifiers, the detection of third-party synchronization of these IDs and an examination into the personalization of the content on news sites based on user history. Finally, we present an online web privacy measurement census that visualizes cookie ID information flows over time using data periodically collected and updated by our infrastructure.

1 0

7:30pm Mon Apr 28 on buying energy for the princeton campus Friend Center, 109 - Thomas A. Nyquist
by Jennifer Rexford 22 Apr '14

22 Apr '14

> From: "Barbara J. Fruhling" <bfruhlin(a)Princeton.EDU> > Date: April 22, 2014 at 12:43:36 PM EDT > To: ee-seminar(a)Princeton.EDU > Subject: EE Seminar - April 28, 2014, 7:30 pm, Friend Center, 109 - Thomas A. Nyquist > Reply-To: "Barbara J. Fruhling" <bfruhlin(a)Princeton.EDU> > > > > > > Speaker: Thomas A. Nyquist > Princeton University Executive Director, Engineering and Campus Energy, Engineering and Construction > Title: Buying energy for the Princeton campus > Lecture series on Contemporary Challenges in Electric Power > Date: Monday, April 28, 2014 > Time: 7:30 p.m. > Room: Friend Center, 109 > Host: Prof. Sigurd Wagner > > Outline: > > 1. How we used to purchase power and our plant operations when we operated using the old PSEG tariff. > > 2. The new PJM electric market and how we changed our operations to adapt to the new economic structure. > > 3. Why we changed the design of our new chilled water plant in response to the new PJM rates. > > 4. Explain new Federal Energy Regulatory Commission orders; our response to them; and the economic benefits. > > 5. Finally, the CO2 benefits of cogeneration, and potential operational changes to reduce CO2 emissions. >

1 0