- talks - lists.cs.princeton.edu

Y Pritykin preFPO
by Melissa M. Lawson 27 Nov '13

27 Nov '13

Yuri Pritykin will present his preFPO on Friday December 6 at 1:30 PM in Room 402. The members of his committee are: Mona Singh, advisor; Olga Troyanskaya and Bernard Chazelle, readers; Tom Funkhouser and Stanislav Shvartsman (CBE/Genomics), nonreaders. Everyone is invited to attend his talk. His abstract follows below. Title: Intermodular and intramodular proteins in protein interaction networks The availability of large-scale protein-protein interaction networks for numerous organisms provides an opportunity to comprehensively analyze the roles proteins play in the functional organization of the cell. First, we re-examine an influential but controversial characterization of the dynamic modularity of the S. cerevisiae interactome that incorporated gene expression data into network analysis. We analyse the protein-protein interaction networks of five organisms, S. cerevisiae, H. sapiens, D. melanogaster, A. thaliana, and E. coli, and confirm significant and consistent functional and structural differences between hub proteins that are co-expressed with their interacting partners and those that are not, and support the view that the former tend to be intramodular whereas the latter tend to be intermodular. However, we also demonstrate that in each of these organisms, simple topological measures are significantly correlated with the average co-expression of a hub with its partners, and therefore also reflect protein intra- and inter- modularity. Further, cross-interactomic analysis demonstrates that these simple topological characteristics of hub proteins tend to be conserved across organisms. Overall, we give evidence that purely topological features of static interaction networks reflect aspects of the dynamics and modularity of interactomes as well as previous measures incorporating expression data, and are a powerful means for understanding the dynamic roles of hubs in interactomes. Second, we study the role of multifunctional genes (and proteins they encode) in protein interaction networks. Many genes in a genome have more than one function. However, genome-wide analysis of multifunctional genes and an explanation of the mechanisms underlying multifunctionality are still lacking. We leverage functional annotations of genes to extract a group of genes each of which has at least two completely different functions, and distinguish these, the most multifunctional genes, from the remaining genes that are currently known to have a single function. We find biologically significant differences between multifunctional and all other genes on a large scale. We show that multifunctional genes are intermodular and play a central role in the interactome, bridging different functional modules.

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Systems talk on stable multithreading, Junfeng Yang, Monday Nov 25, 3:00pm
by Mike Freedman 25 Nov '13

25 Nov '13

Speaker: Junfeng Yang, Columbia Title: Determinism Is Not Enough: Making Parallel Programs Reliable with Stable Multithreading Date/time: 3-4pm on Monday November 25 Location: CS 402 Abstract: 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. Bio: Junfeng Yang's research (http://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.

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3pm Tue Nov 26 talk on Internet censorship and control in CS 105 (small auditorium)
by Jennifer Rexford 21 Nov '13

21 Nov '13

Speaker: Nick Feamster, Georgia Tech Title: Defending Against Internet Censorship and Control, from Firewalls to Filter Bubbles Date/time: 3-4pm on Tuesday November 26 Location: CS 105 (small auditorium) Abstract: The Internet's promise of open communication and transparency is threatened by both censorship (blocking communication outright) and manipulation (otherwise affecting the performance that a user experiences or the information that a user sees). Censorship is a pervasive threat, with more than 60 countries around the world censoring Internet communications in some form. Unfortunately, many conventional censorship circumvention tools are detectable and can be blocked; in some cases, the use of such software may even be incriminating. Thus, users may need not only to defeat censorship mechanisms but also to hide the fact that they are doing so in the first place. In the first part of the talk, I will describe two systems that achieve this goal, Infranet and Collage. In addition to circumventing censorship firewalls, both Infranet and Collage provide users with the deniability that they are using the censorship circumvention system in the first place. In both systems, we achieve deniability by designing them so that the observable network traffic that they generate is statistically indistinguishable from the user's "normal" traffic patterns if the tools were not in use. Infranet achieves deniability by hiding a user's requests for Web content in other Web traffic that resembles a user's typical browsing pattern. Collage achieves deniability by hiding content in user-generated content sites and encoding a user's request for the content in a sequence of operations that a given user is likely to perform. In recent years, however, circumvention alone is insufficient: sophisticated organizations can also control users by manipulating network traffic. Manipulation can take many forms, from degrading performance to such an extent that a user does not want to use the service, to using Internet communication to generate propaganda (e.g., via social media), to attacking personalization algorithms to affect the results that a user sees in response to a search query. In the second part of the talk, I will describe several manipulation attacks that we have studied and inference techniques that we have developed to detect them. I will conclude with our ongoing efforts to tackle open challenges in this area, such as the deceptively challenging problem of confirming the existence of various forms of censorship in the first place. Bio: Nick Feamster is an associate professor in the College of Computing at Georgia Tech. He received his Ph.D. in Computer science from MIT in 2005, and his S.B. and M.Eng. degrees in Electrical Engineering and Computer Science from MIT in 2000 and 2001, respectively. His research focuses on many aspects of computer networking and networked systems, with a focus on network operations, network security, and censorship-resistant communication systems. In December 2008, he received the Presidential Early Career Award for Scientists and Engineers (PECASE) for his contributions to cybersecurity, notably spam filtering. His honors include the Technology Review 35 "Top Young Innovators Under 35" award, the ACM SIGCOMM Rising Star Award, a Sloan Research Fellowship, the NSF CAREER award, the IBM Faculty Fellowship, the IRTF Applied Networking Research Prize, and award papers at the SIGCOMM Internet Measurement Conference (measuring Web performance bottlenecks), SIGCOMM (network-level behavior of spammers), the NSDI conference (fault detection in router configuration), Usenix Security (circumventing web censorship using Infranet), and Usenix Security (web cookie analysis).

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Colloquium Speaker Arjun Guha Thurs Nov 21, 4:30pm
by Nicole E. Wagenblast 20 Nov '13

20 Nov '13

Reclaiming Security for Web Programmers Arjun Guha , University of Massachusetts, Amherst Thursday, November 21, 4:30pm Computer Science, 105 The Web enables new classes of programs that pose new security risks. For example, because Web programs freely mix data and code from untrusted sources, major websites have been compromised by third-party components, such as malicious ads. In addition, users cannot fully control which programs run; Web programs are visited, not installed. Therefore, Web security is entirely in the hands of programmers, not users. I address the problem of securing existing Web programs, which are universally written in JavaScript. Unfortunately, JavaScript has several warts that make it difficult to reason about even simple snippets of code. Several companies have developed "Web sandboxes" to make JavaScript programming safe. However, these Web sandboxes have no security guarantees. In this talk, I show how programing languages research can be used to verify properties of Web applications. I present a type-based verification method for JavaScript that we use to find bugs in and produce the first verification of an existing, third-party Web sandbox. Programming language techniques can give us mathematical proofs of security, but attackers attack implementations, not theorems. I discuss our approach to doing principled, real-world Web security research, which combines semantics with systems. I also review additional projects that use our tools and techniques. Arjun Guha is an assistant professor of Computer Science at UMass Amherst. He enjoys tackling practical problems, while adhering to the mathematical foundations of programming languages. For example, his dissertation on JavaScript semantics and type-checking, from Brown University, is used by several other researchers as a foundation for their own work. As a postdoc at Cornell University, he developed a model of software-defined networking (SDN) in the Coq Proof Assistant, which is the foundation for a verified runtime and other SDN tools. For his research, he has developed and contributed to several software systems, such as LambdaJS, Frenetic, and Flapjax that are in active use.

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Nagpal from Harvard CS to speak on Friday at 3:30 pm in Friend 113 on Taming the Swarm
by Scott Karlin 20 Nov '13

20 Nov '13

Friday, November 22nd 3:30 PM Friend Center 113 Taming the Swarm Prof. Radhika Nagpal Harvard University Cambridge, MA Biological systems, from cells to social insects, get tremendous mileage from the cooperation of vast numbers of cheap, and limited individuals. Cells with identical DNA cooperate to self-assemble large and complex organisms, and even regenerate after damage. Large colonies of tiny ants cooperate to forage over vast unknown areas, move large objects, and achieve as a group what no single ant could ever achieve. What would it take to create (build and program) our own artificial collectives of the scale and complexity that nature achieves? In this talk, I will discuss one of our recent and ongoing endeavors – the Kilobot project - which aims to create a 1024 ("kilo") robot swarm testbed for studying collective intelligence. Creating an autonomous robot collective at this scale poses many challenges, e.g. how do we bulk manufacture robust but low-cost robots, how do we move from micromanaging single robots to managing and programming a thousand autonomous entities? At the same time such a swarm allows us to study at scale many collective algorithms, inspired by engineering (coordinate systems), social insects (collective transport), and cells (self-assembly). I will talk about both the design of the Kilobot swarm and several algorithms we have studied using this system. A common theme in all of our work is understanding the global-to-local relationship: how complex and robust collective behavior can be systematically achieved from large numbers of simple agents. Radhika Nagpal is the Kavli Professor of Computer Science at Harvard University and a core faculty member of the Wyss Institute for Biologically Inspired Engineering. She received her PhD degree in Computer Science from MIT, and spent a year as a research fellow at the Systems Biology Department in Harvard Medical School. At Harvard she leads the self-organizing systems research group and her research interests span computer science, robotics, and biology. She has received several awards, including the 2012 Radcliffe Fellowship, the 2010 Borg Early Career Award, an NSF Career Award, and the Microsoft New Faculty Fellowship Award. Social Period following the seminar. For inquiries, please contact the Dept. of Mechanical & Aerospace Engineering at 609-258-0315 ALL VISITORS ARE WELCOME!

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4:30pm talk today on routing algebras in room 302
by Jennifer Rexford 19 Nov '13

19 Nov '13

Speaker: Joao Sobrinho, Instituto de Telecomunicações Title: Algebra: A Tool for a Unifying View of Routing Protocol Behavior Date/time: 4:30-5:30pm, Tuesday November 19 Location: room 302 in the CS building Abstract: The Internet routing system is composed of millions of routers running one or more of several routing protocols---BGP, OPSF, IS-IS, RIP, EIGRP, DSR, AODV, OLSR, RPL---with the goal of guiding data-packets from sources to destinations. Beyond the specificity of every routing protocol, a number of questions are pertinent across wide classes of them, namely: • Does the routing protocol always terminate in a stable state devoid of forwarding loops and forwarding deflections? • Are the paths followed by data-packets optimal in some sense? • How much of the inherent resiliency of the network does the routing protocol exploit? • Does the routing protocol scale with the number of destinations? Routing selects paths for the transport of data-packets indirectly, through attributes they possess. Routing protocols operate by continually interleaving two processes: that of computing attributes of paths from characteristics of its constituent links; and that of choosing best attributes. The algebraic approach studies how the entwining of these two processes determines the global behavior of a routing protocol, providing answers to the questions above. In this talk, I will illustrate the unifying power of the algebraic approach by delving into the non-optimality of paths determined by EIGRP (Enhanced Interior Gateway Routing Protocol) and termination and resiliency issues raised by BGP (Border Gateway Protocol). In addition, I will survey recent applications of the algebraic approach, notably to the interconnection of routing instances and to route aggregation in the Internet. Bio: João Luís Sobrinho received his Licenciatura and Ph.D. degrees in Electrical and Computer Engineering from the Technical University of Lisbon, Portugal, in 1990 and 1995, respectively. During 1995 and 1996, he was a Member of the Technical Staff at Bell Labs, Nieuwegein, The Netherlands; he further consulted for Bell Labs, Murray Hill, NJ, from 1997 to 1999. He is currently Associate Professor at the Faculty of Engineering of the Technical University of Lisbon and a Researcher at the Telecommunications Institute. Prof. Sobrinho is a member of the IEEE and of the ACM. http://www.lx.it.pt/~jls/

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4:30pm Tue Nov 19 talk on routing algebras
by Jennifer Rexford 16 Nov '13

16 Nov '13

Speaker: Joao Sobrinho, Instituto de Telecomunicações Title: Algebra: A Tool for a Unifying View of Routing Protocol Behavior Date/time: 4:30-5:30pm, Tuesday November 19 Location: room 302 in the CS building Abstract: The Internet routing system is composed of millions of routers running one or more of several routing protocols---BGP, OPSF, IS-IS, RIP, EIGRP, DSR, AODV, OLSR, RPL---with the goal of guiding data-packets from sources to destinations. Beyond the specificity of every routing protocol, a number of questions are pertinent across wide classes of them, namely: • Does the routing protocol always terminate in a stable state devoid of forwarding loops and forwarding deflections? • Are the paths followed by data-packets optimal in some sense? • How much of the inherent resiliency of the network does the routing protocol exploit? • Does the routing protocol scale with the number of destinations? Routing selects paths for the transport of data-packets indirectly, through attributes they possess. Routing protocols operate by continually interleaving two processes: that of computing attributes of paths from characteristics of its constituent links; and that of choosing best attributes. The algebraic approach studies how the entwining of these two processes determines the global behavior of a routing protocol, providing answers to the questions above. In this talk, I will illustrate the unifying power of the algebraic approach by delving into the non-optimality of paths determined by EIGRP (Enhanced Interior Gateway Routing Protocol) and termination and resiliency issues raised by BGP (Border Gateway Protocol). In addition, I will survey recent applications of the algebraic approach, notably to the interconnection of routing instances and to route aggregation in the Internet. Bio: João Luís Sobrinho received his Licenciatura and Ph.D. degrees in Electrical and Computer Engineering from the Technical University of Lisbon, Portugal, in 1990 and 1995, respectively. During 1995 and 1996, he was a Member of the Technical Staff at Bell Labs, Nieuwegein, The Netherlands; he further consulted for Bell Labs, Murray Hill, NJ, from 1997 to 1999. He is currently Associate Professor at the Faculty of Engineering of the Technical University of Lisbon and a Researcher at the Telecommunications Institute. Prof. Sobrinho is a member of the IEEE and of the ACM. http://www.lx.it.pt/~jls/

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Colloquium speaker Michael Isard Monday Nov 4, 4:30pm
by Nicole E. Wagenblast 11 Nov '13

11 Nov '13

Practical Elegance: Designing programming models for large-scale systems Michael Isard , Microsoft Research Monday, November 11, 4:30pm Computer Science 105 The growing need for systems that operate on large datasets is well known, but most programming models for such systems are either too low level to appeal to non-expert programmers, or are specialized to tightly restricted problem domains. I will describe the evolution of a programming model, and its associated systems, that I have worked on at Microsoft Research. The model encourages programmers to describe an algorithm as a series of data-parallel steps, embedded within a familiar language and programming environment (C#/.NET). In order to write code this way programmers must think indirectly about data-dependencies, but can leave out the messy details of concurrency. We believe this elegantly balances our desire to insulate programmers from implementation details with the need for the system to automatically infer safe parallel and distributed execution strategies. We have been able to design systems that take programs written in this model and execute them efficiently on large datasets and clusters of hundreds of computers. As the model has evolved we have made it more expressive, so that it now encompasses both incremental and iterative computation, while keeping the ability to execute these richer programs efficiently, at scale. Our ultimate goal is to integrate data-parallelism seamlessly into all aspects of a general-purpose programming language. Michael Isard started out as a computer vision researcher, but for the last few years has mostly been building distributed execution engines and thinking about how to program them. He received his D.Phil in computer vision from the Oxford University Engineering Science Department in 1998, and worked at the Compaq Systems Research Center in Palo Alto for three years before joining Microsoft Research in Silicon Valley in 2002.

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Colloquium Speaker Barbbara Englehardt Wed Nov 6, 4:30pm
by Nicole E. Wagenblast 06 Nov '13

06 Nov '13

Bayesian models of structured sparsity for discovery of regulatory genetic variants Barbara Engelhardt , Duke University Wednesday, November 6th 4:30pm Computer Science 105 In genomic sciences, the amount of data has grown faster than statistical methodologies necessary to analyze those data. Furthermore, the complex underlying structure of these data means that simple, unstructured statistical models do not perform well. We consider the problem of identifying allelic heterogeneity, or multiple, functionally independent, co-localized genetic regulators of gene transcription. Sparse regression techniques have been critical to the discovery of allelic heterogeneity because of their computational tractability in large data settings. These traditional models are hindered by the substantial correlation between genetic variants induced by linkage disequilibrium. I describe a new model for Bayesian structured sparse regression. This model uses positive definite covariance matrices to incorporate the arbitrarily complex structure of the predictors directly into a Gaussian field to yield structure-aware sparse regression coefficients. This broadly applicable model of Bayesian structured sparsity enables more efficient parameter estimating techniques than models assuming independence would allow. On simulated data, we find that our approach substantially outperforms the state-of-the-art models and methods. We applied this model to a large study of expression quantitative trait loci, and found that our approach yields highly interpretable, robust solutions for allelic heterogeneity, particularly when the interactions between genetic variants are well approximated by an additive model.

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Distinguished Colloquium Speaker Susan Dumais Tues Nov 5 4:30pm Friend 006
by Nicole E. Wagenblast 05 Nov '13

05 Nov '13

Temporal Dynamics and Information Retrieval Susan Dumais , Microsoft Research Tuesday, November 5 4:30pm Friend Center 006 Many digital resources, like the Web, are dynamic and ever-changing collections of information. However, most tools developed for interacting with Web content, such as browsers and search engines, focus on a single static snapshot of the information. In this talk, I will present analyses characterizing how Web content changes over time, how people re-visit Web pages over time, and how re-visitation patterns are influenced by changes in user intent and content. These results have implications for many aspects of information management including crawling policy, ranking and information extraction algorithms, result presentation, and system evaluation. I will describe a prototype that supports people in understanding how the information they interact with changes over time, and new information retrieval models that incorporate the temporal dynamics to improve ranking. Finally, I will conclude with speculations about "slow search" and an overview of challenges that need to be addressed to fully incorporate temporal dynamics into information systems. Susan Dumais is a Distinguished Scientist and manager of the Context, Learning and User Experience for Search (CLUES) Group at Microsoft Research. Prior to joining Microsoft Research, she was at Bell Labs and Bellcore for many years, where she worked on Latent Semantic Analysis, interfaces for combining search and navigation, and organizational impacts of new technology. Her current research focuses on user modeling and personalization, context and search, temporal dynamics of information, and novel evaluation methods. She has worked closely with several Microsoft groups (Bing, Windows Desktop Search, SharePoint, and Office Online Help) on search-related innovations. Susan has published widely in the fields of information science, human-computer interaction and cognitive science, and holds several patents on novel retrieval algorithms and interfaces. Susan is an adjunct professor in the Information School at the University of Washington. She is Past-Chair of ACM's Special Interest Group in Information Retrieval (SIGIR), and serves on several editorial boards, technical program committees, and government panels. She was elected to the CHI Academy in 2005, an ACM Fellow in 2006, received the SIGIR Gerard Salton Award for Lifetime Achievement in 2009, and was elected to the National Academy of Engineering (NAE) in 2011. More information is available at her homepage, http://http://research.microsoft.com/en-us/um/people/sdumais/

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