- talks - lists.cs.princeton.edu

C Monsanto generals
by Melissa M. Lawson 11 May '12

11 May '12

Chris Monsanto will present his research seminar/general exam on Friday May 18 at 2PM in Room 302 (note room!). The members of his committee are: David Walker (advisor), Jennifer Rexford, and Moses Charikar. 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. ------------------------- Software-defined networks (SDNs) are a new kind of network architecture in which a controller machine manages a distributed collection of switches by instructing them to install or uninstall packet-forwarding rules and report traffic statistics. The recently formed Open Networking Consortium, whose members include Google, Facebook, Microsoft, Verizon, and others, hopes to use this architecture to transform the way that enterprise and data center networks are implemented. We define a high-level, declarative language, called NetCore, for expressing packet-forwarding policies on SDNs. NetCore is expressive, compositional, and has a formal semantics. To ensure that a majority of packets are processed efficiently on switches---instead of on the controller---we present new compilation algorithms for NetCore and couple them with a new run-time system that issues rule installation commands and traffic-statistics queries to switches. Together, the compiler and run-time system generate efficient rules whenever possible and outperform the simple, manual techniques commonly used to program SDNs today. In addition, the algorithms we develop are generic, assuming only that the packet-matching capabilities available on switches satisfy some basic algebraic laws. Overall, we deliver a new design for a high-level network programming language; an improved set of compiler algorithms; a new run-time system for SDN architectures; the first formal semantics and proofs of correctness in this domain; and an implementation and evaluation that demonstrates the performance benefits over traditional manual techniques. Reading list: Types and Programming Languages, Benjamin Pierce Compilers: Principles, Techniques, and Tools, Alfred V. Aho, Ravi Sethi and Jeffrey D. Ullman, chapters 7-10. Nettle: Functional Reactive Programming of OpenFlow Networks. A. Voellmy and P. Hudak. Functional Reactive Animation, Conal Elliott and Paul Hudak. Embedding dynamic dataflow in a call-by-value language. Cooper, et al. An Experimental analysis of Self-Adjusting computation. Acar, et al. OpenFlow: Enabling innovation in campus networks. McKeown, et al. Declarative routing: Extensible routing with declarative queries. Loo, et al. NOX: towards an operating system for networks. Gude, et al. Onix: A distributed control platform for large-scale production networks. Koponen, et al. Flowvisor: A network virtualization layer. Sherwood, et al. Openflow-based server load balancing gone wild. Wang, et al.

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I Davey generals
by Melissa M. Lawson 11 May '12

11 May '12

Ian Davey will present his research seminar/general exam on Friday May 18 at 10AM in Room 302 (note room!). The members of his committee are: Ed Felten (advisor), Michael Freedman, and Zeev Dvir. 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 ----- During the recent wave of popular uprisings, dissidents in droves used social media to organize against repressive regimes. The dictators who remain standing, however, tend to be the ones with the network infrastructure capable of inspecting traffic for forbidden material, logging it, and in some cases even censoring it in-flight. Previous work such as [6] has focused on circumventing these types of systems by simply ignoring their methods, but this essentially creates an arms race; preventing the adversary from noticing forbidden material altogether would be more effective. The approach in [1] might avoid deep packet inspection, allowing users to browse web pages unhindered, but this hardly helps when users ultimately wish to post items on a public forum equally accessible to the adversary. We approach this problem by embracing the fact that it ultimately seems at its core a key distribution problem - how can Alice share information with several others confidentially with no means to exchange or distribute key material out-of-band? We take advantage of the fact that in our case there is a large number of principals in the system but only one adversary. First, we borrow ideas from [8], and have Alice broadcast large amounts of pseudorandom data over time, with which she can derive part of a key. This pseudorandom string is small enough for Bob, one of her followers, to store and use later to derive the same key, but if the adversary wishes to successfully watch an entire nation of Alices, it will need to be able to store everything. Second, we have Alice secretly (and randomly) choose the last few bits of the aforementioned key, effectively creating a client puzzle such as that in [3]. Brute-forcing these bits should only take Bob a few seconds, but the adversary will need a prohibitive amount of processing power to keep up with everybody. In this talk, we will present the proofs and performance measurements for our scheme. We will also address some of the practical design considerations by presenting a mobile Twitter client which uses this scheme. [1] E. Wustrow, S. Wolchok, I. Goldberg, and J. Halderman. Telex: Anticensorship in the network infrastructure. USENIX Security 2011. [2] C. Dwork and M. Naor. Pricing via processing or combatting junk mail. CRYPTO 1992. [3] D. Dean and A. Stubblefield. Using client puzzles to protect TLS. USENIX Security 2001. [4] A. Narayanan and V. Shmatikov. Obfuscated databases and group privacy. CCS 2005. [5] R. Canetti, Y. Dodis, S. Halevi, E. Kushilevitz, and A. Sahai. Exposure-resilient functions and all-or-nothing transformations. EUROCRYPT 2000. [6] R. Clayton, S. Murdoch, and R. Watson. Ignoring the great firewall of China. PET 2006. [7] Y. Dodis and D. Wichs. Non-malleable extractors and symmetric key cryptography from weak secrets. STOC 2009. [8] Y. Aumann, Y. Ding, and M. Rabin. Everlasting security in the bounded storage model. IEEE Trans Inf Theory, June 2002. [9] B. Waters, A. Juels, J. Halderman, and E. Felten. New client puzzle outsourcing techniques for DoS resistance. CCS 2004. [10] N. Ferguson, B. Schneier, and T. Kohno. Cryptography engineering: design principles and practical applications. 2010. [11] R. Anderson. Security engineering: a guide to building dependable distributed systems (2nd ed.). 2008.

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T Pereira generals
by Melissa M. Lawson 10 May '12

10 May '12

Thiago Pereira will present his research seminar/general exam on Thursday May 17 at 2PM in Room 401 (note room!). The members of his committee are: Szymon Rusinkiewicz (advisor), Adam Finkelstein, and Rebecca Fiebrink. 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. ------------------------------------- Recent spatially varying reflectance (svBRDF) printing systems can reproduce an input document as a combi- nation of matte, glossy and metallic inks. Due to the limited number of inks, this reproduction process incurs some distortion. In this work, we present an svBRDF gamut mapping algorithm that minimizes distortions in the angular and spatial domains. To preserve a material’s perceived variation with lighting and view, we introduce an improved BRDF similarity metric that builds on both experimental results on reflectance perception and on the statistics of natural lighting environments. Our experiments show better preservation of object color and high- lights, as validated quantitatively as well as through a perceptual study. As for the spatial domain, we show how to adapt traditional color gamut mapping methods to svBRDFs. Our solution takes into account the contrast between regions, achieving better preservation of textures and edges. Reading List: DROR, R., LEUNG, T., ADELSON, E., AND WILLSKY, A. 2001. Statistics of real-world illumination. In Computer Vision and Pattern Recognition, 2001. CVPR 2001. Proceedings of the 2001 IEEE Computer Society Conference on, vol. 2, II–164 – II–171 vol.2. FATTAL, R., LISCHINSKI, D., AND WERMAN, M. 2002. Gradient domain high dynamic range compression. In Proceedings of the 29th annual conference on Computer graphics and interactive techniques, ACM, New York, NY, USA, SIGGRAPH ’02, 249–256. FLEMING, R., DROR, R. O., AND ADELSON, E. H. 2001. How do humans determine reflectance properties under unknown illumination. In In Proceedings of CVPR Workshop on Identifying Objects Across Variations in Lighting: Psychophysics and Computation,347–368. HEARN, D., AND BAKER, M. P. Computer graphics with opengl. KIMMEL, R., SHAKED, D., ELAD, M., AND SOBEL, I. 2005. Space-dependent color gamut mapping: a variational approach. Image Processing, IEEE Transactions on 14, 6 (june), 796 –803. LAU, C., HEIDRICH, W., AND MANTIUK, R. 2011. Clusterbased color space optimizations. In Proceedings of International Conference on Computer Vision (ICCV) 2011. MATUSIK, W., PFISTER, H., BR, M., AND MCMILLAN, L. 2003. A data-driven reflectance model. ACM Transactions on Graphics 22, 759–769. MATUSIK, W., AJDIN, B., GU, J., LAWRENCE, J., LENSCH, H. P. A., PELLACINI, F., AND RUSINKIEWICZ, S. 2009. Printing spatially-varying reflectance. In ACM SIGGRAPH Asia 2009 papers, ACM, New York, NY, USA, SIGGRAPH Asia ’09, 128:1–128:9. NGAN, A., DURAND, F., AND MATUSIK, W. 2006. Image-driven navigation of analytical brdf models. In Eurographics Symposium on Rendering. NICODEMUS, F. E., RICHMOND, J. C., HSIA, J. J., GINSBERG, I. W., AND LIMPERIS, T. 1992. Radiometry. 94–145. PELLACINI, F., FERWERDA, J. A., AND GREENBERG, D. P. 2000. Toward a psychophysically-based light reflection model for image synthesis. In Proceedings of the 27th annual conference on Computer graphics and interactive techniques, ACM Press/ Addison-Wesley Publishing Co., New York, NY, USA, SIGGRAPH ’00, 55–64. ZOLLIKER, P., AND SIMON, K. 2007. Retaining local image information in gamut mapping algorithms. Image Processing, IEEE Transactions on 16, 3 (march), 664 –672

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Y Liu generals
by Melissa M. Lawson 10 May '12

10 May '12

Yiming Liu will present his research seminar/general exam on Thursday May 17 at 10AM in Room 402. The members of his committee are: Szymon Rusinkiewicz (advisor), Adam Finkelstein, and Kai Li. 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. ----------------------- Single-shot Multispectral Imaging Multispectral imaging is a method to obtain the spectrum of each pixel in a 2D image. Instead of roughly aggregating light arriving at each pixel into one channel (e.g. gray-scale images) or three channels (RGB images), multispectral imaging divides the spectrum of each pixel into much narrower wavelength bands, obtaining a 3D cube of data indexed by spatial position and wavelength. Some prior works have shown promising acquisition quality, but they either require tedious manual work and very long acquisition time, or need active illumination or even additional cameras. Our work is a single-shot multispectral imaging method, which tries to capture a multispectral cube with one camera and within a single camera shot. A diffraction grating is put between camera lens and the scene to diffract lights from the scene into one clear zero-order image, and several dispersed first-order images. Each image is a projection of the 3D spectral cube on a plane. Based on these images and projections, and based on a prior assumption that camera noise is with a Poisson distribution, an maximum likelihood estimation algorithm is applied to infer the 3D spectral cube. Several synthetic and real experiments are designed to analyze the sensitivity of the acquisition quality with respect to calibration error and camera noise. ---------------------------- Reading list: Textbook: Szeliski, R. (2010). Computer vision: Algorithms and applications. Springer-Verlag New York Inc. Papers: 1. Cao, X., Du, H., Tong, X., Dai, Q.,& Lin, S. (2011). A Prism-Mask System for Multispectral Video Acquisition. IEEE transactions on pattern analysis and machine intelligence, 1-14. 2. Cao, X., Tong, X.,& Dai, Q. (2011). High resolution multispectral video capture with a hybrid camera system. CVPR. 3. Descour, M.,& Dereniak, E. (1995). Computed-tomography imaging spectrometer: experimental calibration and reconstruction results. Applied optics, 34(22), 4817-26. 4. Habel, R., Kudenov, M.,& Wimmer, M. (2012). Practical Spectral Photography. Eurographics (Vol. 31). 5. Hagen, N.,& Dereniak, E. L. (2008). Analysis of computed tomographic imaging spectrometers. I. Spatial and spectral resolution. Applied optics, 47(28), F85-95. 6. Mohan, A., Raskar, R.,& Tumblin, J. (2008). Agile Spectrum Imaging: Programmable Wavelength Modulation for Cameras and Projectors. Eurographics. 7. Schechner, Y. (2002). Generalized mosaicing: Wide field of view multispectral imaging. Pattern Analysis and Machine, 24(10), 1334-1348. 8. Brodzik, A. K.,& Mooney, J. M. (1999). Convex projections algorithm for restoration of limited-angle chromotomographic images. Journal of the Optical Society of America A, 16(2), 246.

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P Sun generals
by Melissa M. Lawson 09 May '12

09 May '12

Peng Sun will present his research seminar/general exam on Wednesday May 16 at 2PM in Room 402. The members of his committee are: Jennifer Rexford (advisor), Michael Freedman, 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. ------------------------------------------------- Abstract: Datacenters run many traffic management tasks to manage the flow of applications' traffic. They are very important in achieving better application performance, and lower server/network workload. However, many traffic management tasks in the datacenters are divided based on physical boundaries between the servers and the network infrastructure. Network-based traffic management doesn’t have access to fine-grained per-connection information due to scalability concerns, and it can’t obtain the information in the application and transport layer. At the same time, the end hosts are able to collect per-connection and higher-layer statistics in a more efficient way, but they don't know the routing configurations and link statuses in the network. The division leads to uncoordinated responses to the same events, poor visibility into the root cause of performance problems, and missed opportunities to jointly optimize application performance and resource usage. So we propose to bring the end hosts into traffic management in datacenters. The end hosts can help datacenters achieve a more application-oriented traffic management solution with more fine-grained data in a more efficient and scalable way. In addition, traffic management tasks vary in what measurement data they need, how they use the data for computation, and what control actions they generate. Designing each one from scratch is hard. A generic platform is needed to offer reusable and expressive interface to make traffic management easier. We find that all datacenter traffic management tasks share a common pattern of a three-stage pipeline: measurement, analysis, and control. We propose a programming framework that abstracts each stage and offers a sufficiently expressive interface. The framework is based on streaming MapReduce-like functional programming, and it offers great freedom in defining diverse traffic management functionalities, while enabling partitioning the programs into distributed and scalable execution. Extending to include end hosts and making traffic management programmable, we present our joint HOst-NEtwork traffic management system for datacenters - HONE. HONE offers these things: 1) a host agent that makes fine-grained data from end hosts available for traffic management, 2) an expressive programming framework for defining management functionality, and 3) automatic partitioning of the program across the controller and the end hosts for efficient and scalable execution. We evaluate the performance of our prototype, and demonstrate HONE's power with typical traffic management tasks in datacenters: distributed rate limiting, network diagnosis, and flow scheduling. Reading list: L. Peterson, and B. Davie, "Computer Networks: A Systems Approach" , Morgan Kaufmann, 5e, 2011 D. Clark, "The Design Philosophy of the DARPA Internet Protocols" , ACM SIGCOMM, August 1988 J.Saltzer, D.Reed and D.Clark, "End-to-End Arguments in System Design" , ACM Transactions on Computer Systems, Nov 1984 S.Kandula, S. Sengupta, A. Greenberg, P. Patel, R. Chaiken, "The Nature of Data Center Traffic: Measurement & Analysis" , ACM SIGCOMM conference on Internet Measurement Conference (IMC), November 2009 J. Dean, S. Ghemawat. "MapReduce: Simplified Data Processing on Large Clusters" , USENIX OSDI, 2004 Y. Ylleyu, M. Isard, D. Fetterly, M. Budiu, U. Erlingsson, P. Gunda, J. Currey, "DryadLINQ: A System for General -Purpose Distributed Data-Parallel Computing Using a High-Level Language" , USENIX OSDI, 2008 N. Foster, R. Harrison, M. Freedman, C. Monsanto, J. Rexford, A. Story, D. Walker, "Frenetic: A Network Programming Language" , ACM SIGPLAN International Conference on Functional Programming (ICFP), September 2011 R. Newton, L. Girod, M. Craig, S. Madden, G. Morrisett, "WaveScript: A Case-Study in Applying a Distributed Stream-Processing Language" , MIT CSAIL Technical Report MIT-CSAIL-TR-2008-005, 2008 M. Yu, A. Greenberg, D. Maltz, J. Rexford, L. Yuan, S. Kandula, C. Kim, "Profiling network performance for multi-tier data center applications" , USENIX NSDI, March 2011 S. Kandula, S Agarwal, R. Mahajan, P. Verkaik, J. Padhye, P. Bahl, "Detailed Diagnosis in Enterprise Networks" , ACM SIGCOMM, August 2009 B. Raghavan, K. Vishwanath, S. Ramabhadran, K. Yocum, A. Snoeren, "Cloud Control with Distributed Rate Limiting" , ACM SIGCOMM, August 2007 M. Al-Fares,S. Radhakrishnan, B. Raghavan, N. Huang, A. Vahdat, "Hedera: Dynamic Flow Scheduling for Data Center Networks" , USENIX NSDI, April 2010

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J Nelson generals
by Melissa M. Lawson 09 May '12

09 May '12

Jude Nelson will present his research seminar/general exam on Wednesday May 16 at 10AM in Room 402. The members of his committee are: Larry Peterson (advisor), Michael Freedman, and Vivek Pai. 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. ------------------------- Syndicate Abstract On the Internet today, an increasingly common strategy for efficiently disseminating a large dataset to a scalable number of readers (but not writers) is to employ a content distribution network (CDN). Readers query the CDN for the data, and the CDN reads the data from its origin servers and replicates the data in its network caches, thereby allowing the caches to service future read requests. However, there are two limitations in this approach that hinder origin servers and clients from achieving read/write semantics on the dataset. First, a CDN's caches are neither coherent nor consistent--if the data on an origin server changes, there will be a window of time where the CDN may still cache and serve stale or even corrupt data. Second, each CDN implements its own content naming scheme and caching policy, requiring origin servers and possibly clients to be designed for a specific CDN instance. We address these limitations with Syndicate, a wide-area read-write distributed filesystem that transparently leverages arbitrary CDNs to drive data distribution between its clients. A mounted Syndicate filesystem exposes a client's files to the CDN and translates other clients' remote read operations into CDN-specific data queries. Regardless of the CDN's caching policies, Syndicate ensures that readers only read the latest known versions of each file, and ensures that each file has close-to-open consistency in the face of multiple writers. Syndicate provides clients the means to coordinate file discovery and I/O through a fault-tolerant metadata service, as well as the means to back up their files to arbitrary remote storage through a global replication service. By leveraging CDNs to handle a scalable number of readers and allowing clients to fully control file and metadata propagation, Syndicate fully decouples the problem of file persistence from read performance--Syndicate clients need only concern themselves with enhancing the persistence of their data, beyond presenting it to applications. In this work, we will present Syndicate's architecture, protocols, and design. We will then present a series of micro and macro benchmarks of our Syndicate prototype, which is currently deployed on PlanetLab and VICCI and leverages a private deployment of the CoBlitz CDN. Reading list TEXTBOOK Peterson, Larry L., and Davie, Bruce S. "Computer Networks, a Systems Approach. 4th Ed." CLASSICAL PAPERS Cerf, V., and Kahn, R. "A Protocol for Packet Network Intercommunication." Lamport, L. "Time, clocks, and the ordering of events in a distributed system." Schneider, F. "Implementing Fault-Tolerant Services Using the State Machine Approach: A Tutorial" MODERN PAPERS Park, K. and Pai, V. "Scale and Performance in the CoBlitz Large-File Distribution Service." L. Wang, V. Pai, and Peterson, L. "The Effectiveness of Request Redirection on CDN Robustness." Annapureddy, S., Freedman, M., and Mazieres, D. "Shark : Scaling File Servers via Cooperative Caching." Burrows, M. "The Chubby lock service for loosely-coupled distributed systems." Peterson, L., Bavier, A., Fiuczynski, M., Muir, S. "Experineces Building PlanetLab." Belaramani, N., Dahlin, M., Gao, L., et. al. "PRACTI Replication." Stribling, J., Sovran, Y., Zhang, I., et. al. "Flexible , Wide-Area Storage for Distributed Systems with WheelFS." Freedman, M., Freudenthal, E., Mazieres, D. "Democratizing content publication with Coral." Vahdat, A., Eastham, P., Yoshikawa, C., et. al. "WebOS: Operating System Services for Wide Area Applications."

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Young-suk Lee generals
by Melissa M. Lawson 08 May '12

08 May '12

Young-suk Lee will present his research seminar/general exam on Tuesday May 15 at 2PM in Room 401 (note room!). The members of his committee are: Olga Troyanskaya (advisor), Mona Singh, and David Blei. 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. --------------------------- A microarray experiment measures the abundance of thousands of transcript in a given biological sample in order to quantify its unique transcriptome. Many research groups and institutions have used microarrays, and have been publishing them and their associated sample description on the GEO (Gene Expression Omnibus) database website. The most valuable biological sample can arguably be human tissue samples, and so most human microarray studies have been so far limited to few experiments for certain tissue-types. GEO has made these human microarray data publicly available, but the free-text sample description hinders a large-scale tissue-specific microarray analysis. We present a hierarchical multi-label tissue prediction algorithm that returns a rank of predicted tissue-types for a given microarray data. This algorithm may be used to annotate the many human microarrays in GEO in which their tissue information is hidden or even absent. We propose that all tissue prediction algorithms must return a rank because most, if not all, biological samples consist of multiple tissue types that have a hierarchical order. So even a single accurate prediction may not completely describe the biological sample. We compare the performance of prediction algorithms with and without hierarchical information, and our algorithm that uses Bayesian correction to combine multiple tissue classifiers. In the biological community, this algorithm may be used as a comprehensive background or sanity-check on new human microarray datasets that measures potential contamination and tissue composition of the biological sample. Reading list Introduction to Machine Learning (Adaptive Computation and Machine Learning) by Ethem Alpaydin Ch 1 Introduction Ch 2 Supervised Learning Ch 3 Bayesian Decision Theory Ch 4 Parametric Methods Ch 5 Multivariate Methods Ch 8 Nonparametric Methods Ch 10 Linear Discrimination Ch 14 Assessing and Comparing Classification Algorithms Ch 15 Combining Multiple Learners Papers: Matthew N. McCall, Karan Uppal, Harris A. Jaffee, Michael J. Zilliox, and Rafael A. Irizarry The Gene Expression Barcode: leveraging public data repositories to begin cataloging the human and murine transcriptomes Nucl. Acids Res. (2011) 39(suppl 1): D1011-D1015 doi:10.1093/nar/gkq1259 Zafer Barutcuoglu, Robert E. Schapire, and Olga G. Troyanskaya Hierarchical multi-label prediction of gene function Bioinformatics (2006) 22(7): 830-836 first published online January 12, 2006 doi:10.1093/bioinformatics/btk048 Seon-Young Kim and David J Volsky PAGE: Parametric Analysis of Gene Set Enrichment BMC Bioinformatics (2005) 6:144 doi:10.1186/1471-2105-6-144 Kilpinen S, Autio R, Ojala K, Iljin K, Bucher E, Sara H, Pisto T, Saarela M, Skotheim RI, Björkman M, Mpindi JP, Haapa-Paananen S, Vainio P, Edgren H, Wolf M, Astola J, Nees M, Hautaniemi S, Kallioniemi O. Systematic bioinformatic analysis of expression levels of 17,330 human genes across 9,783 samples from 175 types of healthy and pathological tissues. Genome Biol. 2008;9(9):R139. Disease signatures are robust across tissues and experiments. Dudley JT, Tibshirani R, Deshpande T, Butte AJ. Mol Syst Biol. 2009;5:307. Marion Gremse, Antje Chang, Ida Schomburg, Andreas Grote, Maurice Scheer, Christian Ebeling, and Dietmar Schomburg The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources Nucl. Acids Res. (2011) 39(suppl 1): D507-D513 first published online October 28, 2010 doi:10.1093/nar/gkq968 Tanya Barrett, Dennis B. Troup, Stephen E. Wilhite, Pierre Ledoux, Carlos Evangelista, Irene F. Kim, Maxim Tomashevsky, Kimberly A. Marshall, Katherine H. Phillippy, Patti M. Sherman, Rolf N. Muertter, Michelle Holko, Oluwabukunmi Ayanbule, Andrey Yefanov, and Alexandra Soboleva NCBI GEO: archive for functional genomics data sets—10 years on Nucl. Acids Res. (2011) 39(suppl 1): D1005-D1010 first published online November 21, 2010 doi:10.1093/nar/gkq1184 Shai S Shen-Orr, Robert Tibshirani, Purvesh Khatri, Dale L Bodian, Frank Staedtler, Nicholas M Perry, Trevor Hastie, Minnie M Sarwal, Mark M Davis and Atul J Butte Cell type–specific gene expression differences in complex tissues Nature Methods 7, 287 - 289 (2010) Published online: 7 March 2010 | doi:10.1038/nmeth.1439 Troyanskaya OG. Putting microarrays in a context: integrated analysis of diverse biological data. Brief Bioinform. 2005 Mar;6(1):34-43.

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T Wang generals
by Melissa M. Lawson 08 May '12

08 May '12

Tian Wang will present his research seminar/general exam on Tuesday May 15 at 10:30AM in Room 402. The members of his committee are: David Blei (advisor), Rob Schapire, and Rebecca Fiebrink. 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: Supervised Hierarchical Dirichlet Process Abstract: Hierarchical Dirichlet Process have been proved effective as a Bayesian non-parametric model for text document topic modeling. HDP places a non-parametric prior on distribution of topics, thus allowing the number of topics to be learnt through data. It works as a Bayesian non-parametric extension to Latent Dirichlet Allocation. In my research, I introduce Supervised Hierarchical Dirichlet Process, a Bayesian non-parametric extension to Supervised Latent Dirichlet Allocation. In topic modeling setting, Supervised Hierarchical Dirichlet Process relates a continuous response variable, typically a rating to a document, to the topic assignments of all words in a document. For learning I use Markov Chain Monte Carlo method to sample the intractable posterior. More specifically, I derived and implemented a collapsed Gibbs sampler for Supervised Hierarchal Dirichlet Process. I also derived posterior sampling equations for Supervised Latent Dirichlet Allocation, which is not published before or in any software package. Like Supervised Latent Dirichlet Allocation, the main application of this model is to predict document ratings given the documents. I use movie reviews and movie review ratings as my data set. Supervised Hierarchical Dirichlet Process is compared with a conventional Hierarchical Dirichlet Process followed by a separate regression with the response variable in terms of prediction error on new documents. Reading List: [1] C. Bishop. Pattern Recognition and Machine Learning (Information Science and Statistics), chapter 8,11. Springer-Verlag New York, Inc., Secaucus, NJ, USA, 2006. [2] D. Blei and P. Frazier. Distance dependent chinese restaurant processes. Journal of Machine Learning Research, 12:2461–2488, 2011. [3] D. Blei and M. Jordan. Variational methods for the dirichlet process. Journal of Bayesian Analysis, 1[1]:121–144, 2006. [4] D. Blei, A. Ng, and M. Jordan. Latent dirichlet allocation. Journal of Machine Learning Research, 2003.  1 [5] D. Blei and J. McAuliffe. Supervised topic models. In J.C. Platt, D. Koller, Y. Singer, and S. Roweis, editors, Advances in Neural Information Processing Systems 20, pages 121–128. MIT Press, Cambridge, MA, 2008. [6] S. Gershman and D. Blei. A tutorial on bayesian nonparametric models. June 2011. [7] R. Neal. Markov chain sampling methods for dirichlet process mixture models. JOURNAL OF COMPUTATIONAL AND GRAPHICAL STATISTICS, 9(2):249–265, 2000. [8] Y. Teh, M. Jordan, M. Beal, and D. Blei. Hierarchical dirichlet processes. Journal of the American Statistical Association, 101[476]:1566–1581, 2006. [9] Y. W. Teh. Dirichlet processes. In Encyclopedia of Machine Learning. Springer, 2010. [10] C. Wang, J. Paisley, and D. Blei. Online variational inference for the hierarchical dirichlet process. Artificial Intelligence and Statistics, 2011.

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S Berkiten general exam
by Melissa M. Lawson 07 May '12

07 May '12

Sema Berkiten will present her research seminar/general exam on Monday May 14 at 10AM in Room 402. The members of her committee are: Szymon Rusinkiewicz (advisor), Adam Finkelstein, and Kai Li. Everyone is invited to attend her talk and those faculty wishing to remain for the oral exam following are welcome to do so. Her abstract and reading list follow below. ----- Original Message ----- Abstract: Image alignment is one of the very first steps for most computer vision algorithms. Image fusion, image mosaicing, image panorama, object recognition and detection, photometric stereo enhanced rendering are some of the examples in which image alignment is a crucial step for a promising result. In this work, we focused on a specific problem which is alignment of high-resolution images taken from the same viewpoint under different light directions. Although images are taken from the same viewpoint, there might be some misalignment due to perturbations to the camera and the effect of optical image stabilization. For this specific alignment problem, we made a broad literature survey and try different tools and algorithms to compare different approaches and find out the best approach to solve this problem. Based on our experiments, we saw that the best approaches are the feature-based ones. We found SIFT and SURF reliable for most cases. For feature-based approaches, one of the main problems is elimination of outliers, and we solved this problem with using RANSAC framework. Also datasets that we focus on have many images, between 30-60, of the same object, and in order to take advantage of having many images, we constructed a graph on images so that the most similar images are connected. Minimum spanning tree is one way of constructing such a data structure. As a future work we are planning to explore how to distribute the accumulated alignment error because of the tree structure. Reading List: 1. Chunming Tang; Yan Dong; Xiaohong Su; , "Automatic Registration Based on Improved SIFT for Medical Microscopic Sequence Images," Intelligent Information Technology Application, 2008. IITA '08. Second International Symposium on , vol.1, no., pp.580-583, 20-22 Dec. 2008 2. Matthew Brown and David G. Lowe. 2007. Automatic Panoramic Image Stitching using Invariant Features. Int. J. Comput. Vision 74, 1 (August 2007), 59-73. DOI=10.1007/s11263-006-0002-3 http://dx.doi.org/10.1007/s11263-006-0002-3 3. David G. Lowe. 2004. Distinctive Image Features from Scale-Invariant Keypoints. Int. J. Comput. Vision 60, 2 (November 2004), 91-110. DOI=10.1023/B:VISI.0000029664.99615.94 http://dx.doi.org/10.1023/B:VISI.0000029664.99615.94 4. Bruce D. Lucas and Takeo Kanade. 1981. An iterative image registration technique with an application to stereo vision. In Proceedings of the 7th international joint conference on Artificial intelligence - Volume 2 (IJCAI'81), Vol. 2. Morgan Kaufmann Publishers Inc., San Francisco, CA, USA, 674-679. 5. Greg Ward. Fast, robust image registration for compositing high dynamic range photographcs from hand-held exposures. Journal of Graphics Tools, 8(2):17–30, 2003. 6. Bingjian Wang; Dongliang Wu; Wenzheng Xu; Quan Lu; Fan Li; Shangqian Liu; Guowang Gao; Rui Lai; , "A new image registration method for infrared images and visible images," Image and Signal Processing (CISP), 2010 3rd International Congress on , vol.4, no., pp.1745-1749, 16-18 Oct. 2010 7. Barbara Zitová, Jan Flusser, Image registration methods: a survey, Image and Vision Computing, Volume 21, Issue 11, October 2003, Pages 977-1000, ISSN 0262-8856, 10.1016/S0262-8856(03)00137-9. 8. Herbert Bay, Andreas Ess, Tinne Tuytelaars, and Luc Van Gool. 2008. Speeded-Up Robust Features (SURF). Comput. Vis. Image Underst. 110, 3 (June 2008), 346-359. DOI=10.1016/j.cviu.2007.09.014 http://dx.doi.org/10.1016/j.cviu.2007.09.014 9. Feng Zhao; Qingming Huang; Wen Gao; , "Image Matching by Normalized Cross-Correlation," Acoustics, Speech and Signal Processing, 2006. ICASSP 2006 Proceedings. 2006 IEEE International Conference on , vol.2, no., pp.II, 14-19 May 2006 10. Shun'ichi Kaneko, Yutaka Satoh, Satoru Igarashi, Using selective correlation coefficient for robust image registration, Pattern Recognition, Volume 36, Issue 5, May 2003, Pages 1165-1173, ISSN 0031-3203, 10.1016/S0031-3203(02)00081-X. 11. Martin A. Fischler and Robert C. Bolles. 1981. Random sample consensus: a paradigm for model fitting with applications to image analysis and automated cartography. Commun. ACM 24, 6 (June 1981), 381-395. DOI=10.1145/358669.358692 http://doi.acm.org/10.1145/358669.358692 12. Winder, S. & Brown, M. Picking the best DAISY. IEEE Conference on Computer Vision and Pattern Recognition (2009) 0, 178-185 (2009).

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J Cesareo and D Drutskoy MSE talks rescheduled
by Melissa M. Lawson 07 May '12

07 May '12

Due to a conflict this morning, the two MSE talks have been rescheduled for today at 2:45 (Cesareo) and 3:15 (Drutskoy) in Room 302.

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