- talks - lists.cs.princeton.edu

Eric Xing talk 4:15pm TODAY
by Olga Troyanskaya 10 Oct '07

10 Oct '07

Please come to an exciting colloquium talk by Eric Xing from CMU. Eric is speaking today (Wednesday, October 10) at 4:15 P.M. in the Small Auditorium (Room 105). Title: "Probabilistic Graphical Models and Algorithms for Integrative Bioinformatics" Abstract: Probabilistic graphical model is a formalism that exploits the conjoined talents of graph theory and probability theory to build complex models out of simpler pieces. It offers a powerful language to elegantly define expressive distributions under complex scenarios in high-dimensional space, and provides a systematic computational framework for probabilistic inference. These virtues have particular relevance in bioinformatics, where many core inferential problems e.g., linkage analysis, phylogenetic analysis, network reconstruction are already naturally expressed in probabilistic terms, and must deal with experimental data with complex structure and temporal and/or spatial dynamics. I will discuss our recent work on graphical model inferential methodology in three areas in bioinformatics: (1) Population structure and recombination hotspot inference, using a novel approach based on Dirichlet process priors. I present a hidden Markov version of the Dirichlet process which allows us to infer recombination events among haplotypes in an "open" ancestral space. (2) Comparative genomics prediction of imperfectly conserved transcription factor binding sites, where multi-resolution phylogenetic inference combines with Markovian inference to provide sensitive detection of motifs and their evolutionary turnovers in eleven Drosophila species. (3) Reverse-engineering of temporally rewiring networks from gene expression time courses, where a novel hidden temporal exponential random graph model is employed to model temporal evolution of network topologies during a biological process, and to facilitate the inference of transient (rather than a single universal) regulatory circuitry underlying each time-point of the microarray time series. Bio: Eric Xing is an assistant professor in the Machine Learning Department, the Language Technology Institute, and the Computer Science Department within the School of Computer Science at Carnegie Mellon University. His principal research interests lie in the development of machine learning and statistical methodology; especially for building quantitative models and predictive understandings of the evolutionary mechanism, regulatory circuitry, and developmental processes of biological systems; and for building computational intelligence systems involving automated learning, reasoning, and decision-making in open, evolving possible worlds. Professor Xing received his B.S. in Physics from Tsinghua University, his first Ph.D. in Molecular Biology and Biochemistry from Rutgers University, and then his second Ph.D. in Computer Science from UC Berkeley. He has been a member of the faculty at Carnegie Mellon University since 2004, and his current work involves, 1) graphical models, Bayesian methodologies, inference algorithms, and optimization techniques for analyzing and mining high-dimensional, longitudinal, and relational data; 2) computational and comparative genomic analysis of biological sequences, systems biology investigation of gene regulation, and statistical analysis of genetic variation, demography and disease linkage; and 3) application of statistical learning in text/image mining, vision, and machine translation. -- ______________________________________________________ Olga Troyanskaya, Ph.D. Assistant Professor Department of Computer Science and Lewis-Sigler Institute for Integrative Genomics Princeton University, NJ 08544 (609)258-1749(ph) (609)258-1771(f) ______________________________________________________

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Talk Wednesday - October 10
by Ginny Hogan 08 Oct '07

08 Oct '07

Eric Xing will present his talk "Probabilistic Graphical Models and Algorithms for Integrative Bioinformatics" Wednesday, October 10, at 4:15pm Computer Science Room 105

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Refreshments -
by Ginny Hogan 03 Oct '07

03 Oct '07

Refreshments are now available in the tea room - followed by Peter Wayner's talk Policing Online Games -- Defining A Strong, Mutually Verifiable Reality in Virtual Games at 4:15 Computer Science Room 105.

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Colloquium speaker today -
by Ginny Hogan 03 Oct '07

03 Oct '07

Peter Wayner will present his talk "Policing Online Games - Defining A Strong, "Mutually Verifiable Reality in Virtual Games" today at 4:15pm Computer Science Room 105 - Refreshments will be in the tea room at 3:30 -

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Speaker Wednesday - Oct 3rd -
by Ginny Hogan 01 Oct '07

01 Oct '07

Peter C. Wayner, will present his talk "Policing Online Games - Defining a Strong, Mutually Verifiable Reality in Virtual Games" On Wednesday, Oct 3rd at 4:15pm - COS 105 Refreshments will be in the tea room at 3:30pm -

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B Brown preFPO - reannounce with room
by Melissa M Lawson 28 Sep '07

28 Sep '07

Benedict Brown will present his preFPO on Monday October 1 at 2PM. His talk will be in Friend 305, which is located inside the Engineering Library. The members of his committee are: Szymon Rusinkiewicz, advisor; David Dobkin and Tom Funkhouser, readers; Adam Finkelstein and Ken Steiglitz, nonreaders. Everyone is invited to attend his talk. His abstract follows below. --------------------------------- Title: Registration and Matching of Large Geometric Datasets for Cultural Heritage Applications Over the last decade, there has been growing interest in acquiring high resolution digital representations of cultural heritage. This includes not only high resolution photographs, but also detailed 3-D models of statues, buildings, paintings, archeological objects, etc. These applications raise a number of challenges in data management, and in designing affordable acquisition systems which are practical, efficient, and usable. This thesis looks at how to handle alignment applications in this framework. We show how to align range scans in the presence of calibration error, as is the case in large, high-resolution models such as the Digital Michelangelo models. At the other extreme, we show how to align small fresco pieces from the Thera project completely automatically; in this case each individual model is small, but because there are tens of thousands of fragments, efficiency and automation are paramount. We also show how registration techniques extend to the problem of matching these fragments to each other. Finally, we look at the problem of aligning high-quality 2-D images of these fragments to the 3-D models. _______________________________________________ talks mailing list talks(a)lists.cs.princeton.edu https://lists.cs.princeton.edu/mailman/listinfo/talks

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J Calandrino generals
by Melissa M Lawson 26 Sep '07

26 Sep '07

Joe Calandrino will present his research seminar/general exam on Tuesday October 2 at 2PM in Room 402. The members of his committee are Ed Felten, Andrew Appel, and David Walker. 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. ----------------------------- Title: Machine-Assisted Election Auditing Abstract: Election audit procedures usually rely on precinct-based audits, in which workers manually review all paper ballots from selected polling places, but these audits can be expensive due to the labor required. In this talk, I propose an alternative audit strategy that allows machines to perform most of the work. Precincts are audited using recounting machines, and their output is manually audited using efficient ballot sampling techniques. This strategy can achieve equal or greater confidence than precinct-based auditing at a significantly lower cost while protecting voter privacy better than previous ballot-based auditing methods. I show how to determine which ballots to audit against the auditing machines' records and compare this new approach to precinct-based audits in the context of Virginia's November 2006 election. Far fewer ballots need to be audited by hand using our approach. I also explore extensions to these techniques, such as varying individual ballots' audit probabilities based on the votes they contain, that promise further efficiency gains. Reading List: 1. R. Anderson. Security Engineering. 2001. 2. N. Ferguson, B. Schneier. Practical Cryptography. 2003. 3. R. G. Saltman. The History and Politics of Voting Technology. 2006. 4. 110TH CONGRESS. H.R. 811: Voter Confidence and Increased Accessibility Act of 2007. 5. A. W. Appel. Effective Audit Policy for Voter-Verified Paper Ballots in New Jersey. 2007. 6. A. Cordero, D. Wagner, D. Dill. The Role of Dice in Election Audits. In Proc. 2006 IAVoSS Workshop On Trustworthy Elections (WOTE 2006). 7. D. Jefferson, E. Ginnold, K. Midstokke, K. Alexander, P. Stark, A. Lehmkuhl. Post-Election Audit Standards Working Group Report: Evaluation of Audit Sampling Models and Options for Strengthening California's Manual Count. 2007. 8. K. C. Johnson. Election Certification by Statistical Audit of Voter-Verified Paper Ballots. 2004. 9. C. A. Neff. Election Confidence: A Comparision of Methodologies and their Relative Effectiveness at Achieving It. 2003. 10. L. Norden, A. Burstein, J. L. Hall, M. Chen. Post-Election Audits: Restoring Trust in Elections. 2007. 11. J. A. Aslam, R. A. Popa, R. L. Rivest. On Estimating the Size and Confidence of a Statistical Audit. In Proc. 2007 USENIX/ACCURATE Electronic Voting Technology Workshop (EVT '07). 12. R. L. Rivest. On Auditing Elections when Precincts Have Different Sizes. 2007.

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FW: (no subject)
by Ginny Hogan 25 Sep '07

25 Sep '07

-----Original Message----- From: Michele Brown [mailto:mjbrown@CS.Princeton.EDU] Sent: Tuesday, September 25, 2007 10:34 AM To: gch(a)CS.Princeton.EDU Subject: (no subject) *Internet visionaries 're-imagine the Internet'* Robert Kahn, considered one of the fathers of the Internet, will join Larry Peterson, chair of the computer science department, in a public talk on the future of the Internet at 4:30 p.m. Thursday, Sept. 27, in the Friend Center auditorium. http://engineering.princeton.edu/news/kahn_internet

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G Ottoni preFPO
by Melissa M Lawson 24 Sep '07

24 Sep '07

Guilherme Ottoni will present his preFPO on Monday October 1 at 11AM in Room 301. The members of his committee are: David August, advisor; Sharad Malik (EE) and Vivek Sarkar (Rice), readers; Margaret Martonosi and David Walker, nonreaders. Everyone is invited to attend his talk. His abstract follows below. -------------------- Global Instruction Scheduling for Multi-Threaded Architectures Recently, the microprocessor industry has moved toward chip multiprocessor (CMP) designs as a means of utilizing the increasing transistor counts in the face of physical and micro-architectural limitations. Despite this move, CMPs do not directly improve the performance of single-threaded codes, a characteristic of most applications. In effect, the move to CMPs has shifted even more the task of improving performance from the hardware to the software. Since developing parallel applications has long been recognized as significantly harder than developing sequential ones, it is very desirable to have automatic tools to extract parallelism from sequential applications. Unfortunately, automatic parallelization has only been successful in the restricted domain of scientific and data-parallel applications, which usually have regular array-based memory accesses and little control flow. In order to support parallelization of general-purpose applications, computer architects have proposed CMPs with light-weight, fine-grained (scalar) communication mechanisms. Despite such support, most existing compiler multi-threading techniques have generally demonstrated little effectiveness in extracting parallelism from non-scientific applications. The main reason for this is that such techniques are mostly restricted to extracting parallelism within local, straight-line regions of code. As observed in several limit studies, local regions of code have limited parallelism, and control dependence analysis and multiple control units are necessary to extract most of the parallelism opportunities. In this talk, I will describe a general compiler framework to perform Global Multi-Threaded (GMT) instruction scheduling, based on a Program Dependence Graph (PDG) representation, graph partitioning algorithms, and a novel Multi-Threaded Code Generation (MTCG) algorithm. Based on this framework, two techniques to perform GMT instructions scheduling are proposed. The first one, Decoupled Software Pipelining (DSWP), extracts pipeline parallelism from arbitrary loop nests. The second technique, GREMIO, is applicable to arbitrary (intra-procedural) code regions, and can also exploit other forms of parallelism. Finally, I will present several communication optimizations to improve the MTCG algorithm, and thus all GMT instruction scheduling techniques based on it. All these techniques are implemented in the VELOCITY compiler and evaluated on an accurate CMP simulator built on top of validated Itanium 2 core models. The results demonstrate the effectiveness of the proposed compiler techniques, with speedups on a number of real applications written in C.

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B Brown preFPO
by Melissa M Lawson 24 Sep '07

24 Sep '07

Benedict Brown will present his preFPO on Monday October 1 at 2PM. Room will be announced later. The members of his committee are; Szymon Rusinkiewicz, advisor; David Dobkin and Tom Funkhouser, readers; Adam Finkelstein and Ken Steiglitz, nonreaders. Everyone is invited to attend his talk. His abstract follows below. --------------------------------- Title: Registration and Matching of Large Geometric Datasets for Cultural Heritage Applications Over the last decade, there has been growing interest in acquiring high resolution digital representations of cultural heritage. This includes not only high resolution photographs, but also detailed 3-D models of statues, buildings, paintings, archeological objects, etc. These applications raise a number of challenges in data management, and in designing affordable acquisition systems which are practical, efficient, and usable. This thesis looks at how to handle alignment applications in this framework. We show how to align range scans in the presence of calibration error, as is the case in large, high-resolution models such as the Digital Michelangelo models. At the other extreme, we show how to align small fresco pieces from the Thera project completely automatically; in this case each individual model is small, but because there are tens of thousands of fragments, efficiency and automation are paramount. We also show how registration techniques extend to the problem of matching these fragments to each other. Finally, we look at the problem of aligning high-quality 2-D images of these fragments to the 3-D models.

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