Publications by topic

Group by: year, topic
Jump to: Network Analysis, Kinship, AnimalID+IBEIS, Sparse Linear Algebra on GPUs, Other

Network Analysis:

• C. Tantipathananandh.
  Detecting and Tracking Communities in Social Networks
  PhD Thesis, University of Illinois at Chicago.


• K. Reda, C. Tantipathananandh, A. Johnson, J. Leigh, T. T. Berger-Wolf
  Visualizing the Evolution of Community Structures in Dynamic Social Networks
  Proceedings of the EuroVis 2011--13th annual Visualization Symposium, June 2011, Bergen, Norway.


• A. Maiya and T. Y. Berger-Wolf.
  Benefits of Bias: Towards Better Characterization of Network Sampling
  Proc. of the 17th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD '11), San Diego, CA, August 2011.


• M. C. Crofoot, D. I. Rubenstein, A. S. Maiya, T. Y. Berger-Wolf,
  Aggression, Grooming and Group-level Cooperation in White-faced Capuchins (Cebus capucinus): Insights from Social Networks
  American Journal of Primatology, (in press).


• C. Tantipathananandh, T. Y. Berger-WOlf
  Finding Communities in Dynamic Social Networks
  IEEE International Conference on Data Mining (ICDM), 2011.


• T. Y. Berger-Wolf, C. Tantipathananandh, and D. Kempe
  Community Identification in Dynamic Social Networks
  Link Mining: Models, Algorithms and Applications, Philip S. Yu, Christos Faloutsos, and Jiawei Han (Editors), Springer, 2010.


• Habiba, T. Y. Berger-Wolf, Y. Yu, J. Saia,
  Finding Spread Blockers in Dynamic Networks
  Advances in Social Network Mining and Analysis, Lecture Notes in Computer Science, 5498, 55-76, Springer, 2010.


• M. Lahiri and M. Cebrian.
  The genetic algorithm as a general diffusion model for social networks
  Proc. of the 24th AAAI Conference on Artificial Intelligence (AAAI 2010), Atlanta, Georgia, 2010.


• A. S. Maiya and T. Y. Berger-Wolf
  Expansion and Search in Networks
  Proc. 19th ACM Intl. Conference on Information and Knowledge Management (CIKM '10). Toronto, CA, October 2010.


• A. S. Maiya and T. Y. Berger-Wolf
  Online Sampling of High Centrality Individuals in Social Networks
  Proc. Pacific-Asia Conference on Knowledge Discovery and Data Mining (PAKDD '10). Hyderabad, India, June 2010.


• A. S. Maiya and T. Y. Berger-Wolf
  Sampling Community Structure
  Proc. Intl. Conference on the World Wide Web (WWW '10). Raleigh, NC, USA, April 2010.


• M. Lahiri, T. Y. Berger-Wolf,
  Mining Periodic Behavior in Dynamic Social Networks
  Journal of Knowledge and Information Systems 24(3): 467-498.


• R. Sulo, T. Berger-Wolf, R. Grossman
  Meaningful Selection of Temporal Resolution for Dynamic Networks
  Proc. of the Eighth Workshop on Mining and Learning with Graphs (MGL), 2010.


• T. Y. Berger-Wolf, M. Lahiri, C. Tantipathananandh, and D. Kempe
  Finding Structure in Dynamic Networks
  Proceedings of the Workshop on Information in Networks (WIN-09), September 2009, New York, NY.


• A. S. Maiya and T. Y. Berger-Wolf
  Inferring the Maximum Likelihood Hierarchy in Social Networks
  Proc. Intl. Conference on Social Intelligence and Networking (SIN-09) at IEEE SocialCom-09. Vancouver, CA, August 2009.


• C. Tantipathananandth and T. Y. Berger-Wolf
  Constant-Factor Approximation Algorithm for Identifying Dynamic Communities
  Proc. of the 15th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, Paris, France, June 2009.


• K. Reda, C. Tantipathananandh, T. Y. Berger-Wolf, J. Leigh, A. E. Johnson
  SocioScape - a Tool for Interactive Exploration of Spatio-Temporal Group Dynamics in Social Networks
  Proc. of the IEEE Information Visualization Conference (INFOVIS 09), Atlantic City, New Jersey, 2009.


• Habiba, T. Y. Berger-Wolf
  Graph Theoretic Measures for Identifying Effective Blockers of Spreading Processes in Dynamic Networks
  Proc. of the MLG-ICML Workshop on Machine Learning on Graphs, Helskinki, Finland, July 2008.


• M. Lahiri, A. S. Maiya, R. Sulo, Habiba and T. Y. Berger-Wolf
  The Impact of Structural Changes on Predictions of Diffusion in Networks
  ICDM Workshop on Analysis of Dynamic Networks, Pisa, Italy. December 2008.


• Habiba, T. Y. Berger-Wolf, Y. Yu, J. Saia
  Finding Spread Blockers in Dynamic Networks
  Proc. of the 2nd Workshop on Social Network Mining and Analysis at KDD'08 (SNA-KDD'08), Las Vegas, CA, August 2008.


• M. Lahiri, T. Y. Berger-Wolf
  Mining Periodic Behavior in Dynamic Social Networks
  Proc. of the 8th IEEE International Conference on Data Mining (ICDM 2008), Pisa, Italy, December 2008.


• Habiba and T. Y. Berger-Wolf.
  Maximizing the Extent of Spread in a Dynamic Network
  DIMACS Technical Report, 2007-20, 2007.


• Habiba, C. Tantipathananandh, and T. Y. Berger-Wolf.
  Betweenness Centrality Measure in Dynamic Networks
  DIMACS Technical Report, 2007-19, 2007.


• M. Lahiri and T. Y. Berger-Wolf
  Structure Prediction in Temporal Networks using Frequent Subgraphs
  IEEE Symposium on Computational Intelligence and Data Mining (CIDM), Honolulu, Hawaii, April, 2007.


• C. Tantipathananandth, T. Y. Berger-Wolf, and D. Kempe
  A Framework For Community Identification in Dynamic Social Networks
  Proc. of the 13th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, San Jose, CA, USA, August 2007.


• C. Tantipathananandh.
  Community Identification in Dynamic Social Networks Using Generalized Coloring
  Master's Thesis, University of Illinois at Chicago.


• T. Y. Berger-Wolf and J. Saia
  A framework for analysis of dynamic social networks
  Proc. of the 12th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, Philadelphia, PA, USA, 523-528, August 2006.


• T. Y. Berger-Wolf and J. Saia.
  Critical Groups in Dynamic Social Networks
  DIMACS Technical Report, 26 July 2005.





Kinship:

• M. V. Ashley, T. Y. Berger-Wolf, W. Chaovalitwongse, and B. DasGupta, A. Khokhar
  On Approximating an Implicit Cover Problem in Biology
  Discrete Mathematics, Algorithms and Applications (in press).


• C.-A. Chou, W. A. Chaovalitwongse, T. Y. Berger-Wolf, B. DasGupta, M. V. Ashley,
  Capacitated Clustering Problem in Computational Biology: Combinatorial and Statistical Approach for Sibling Reconstruction
  Computers and Operations Research (in press).


• M. V. Ashley, T. Y. Berger-Wolf, I. C. Caballero, W. Chaovalitwongse, B. DasGupta, and S. I. Sheikh
  Full Sibling Reconstruction in Wild Populations From Microsatellite Genetic Markers
  Computational Biology: New Research, pp. 231-258, Nova Publishers.


• D. Brown and T. Y. Berger-Wolf,
  Discovering kinship through small subsets
  Proc. of the Workshop on Algorithms in Bioinformatics (WABI-10), September 2010, Leads, England.


• W. Chaovalitwongse, C.-A. Chou, T. Y. Berger-Wolf, B. DasGupta, S. I. Sheikh, M. V. Ashley, I. C. Ca- ballero,
  New Optimization Model and Algorithm for Sibling Reconstruction from Genetic Markers
  INFORMS Journal of Computing, 22(2): 179-193, 2010.


• S. Sheikh, A. Khokhar, and T. Y. Berger-Wolf,
  Efficient and scalable parallel reconstruction of sibling relationships from genetic data in wild populations
  Proc. of the 9th IEEE International Workshop on High Performance Computational Biology (HiCOMB-10), April 2010, Atlanta, GA.


• S. I. Sheikh, T. Y. Berger-Wolf, A. Khokhar, I. C. Caballero, M. V. Ashley, W. Chaovalitwongse, C.-A. Chou, B. DasGupta,
  Combinatorial Reconstruction of Half-sibling Groups from Microsatellite Data
  Journal of Bioinformatics and Computational Biology: Selected Papers from CSB2009, 8(2), Apr 2010, 337-56.


• M. V. Ashley, T. Y. Berger-Wolf, W. Chaovalitwongse, and B. DasGupta, A. Khokhar
  On Approximating An Implicit Cover Problem in Biology
  5th International Conference on Algorithmic Aspects in Information and Management (AAIM 2009), June 2009, San Francisco.


• M. V. Ashley, T. Y. Berger-Wolf, P. Berman, W. Chaovalitwongse, B. DasGupta, M.-Y. Kao,
  On Approximating Four Covering and Packing Problems
  Journal of Computer and System Sciences, 75 (5), 287-302, 2009.


• M. V. Ashley, I. C. Caballero, W. Chaovalitwongse, B. DasGupta, P. Govindan, S. I. Sheikh, T. Y. Berger-Wolf,
  KINALYZER, A Computer Program for Reconstructing Sibling Groups
  Molecular Ecology Resources, 9 (4), July 2009, 1127-1131.


• S. I. Sheikh, T. Y. Berger-Wolf, A. Khokhar, I. C. Caballero, M. V. Ashley, W. Chaovalitwongse, B. DasGupta
  Combinatorial Reconstruction of Half-Sibling Groups
  8th International Conference on Computational Systems Bioinformatics (CSB), August 2009, Stanford, CA.


• S. I. Sheikh, T. Y. Berger-Wolf, A. A. Khokhar and B. DasGupta
  Consensus Methods for Reconstruction of Sibling Relationships from Genetic Data
  Proc. of the AAAI Multidisciplinary Workshop on Advances in Preference Handling (MPREF), Chicago, IL, July 2008.


• S. I. Sheikh, T. Y. Berger-Wolf, M. V. Ashley, I. C. Caballero, W. Chaovalitwongse and B. DasGupta
  Error Tolerant Sibship Reconstruction for Wild Populations
  Proc. of the 7th Annual International Conference on Computational Systems Biology (CSB), Paulo Alto, CA, USA, August 2008.


• T. Y. Berger-Wolf, S. I. Sheikh, B. DasGupta, M.V. Ashley, I.C. Caballero, W. Chaovalitwongse, S. L. Putrevu
  Reconstructing Sibling Relationships in Wild Populations
  Proc. of the 15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), Vienna, Austria [same as Bioinformatics publication in journals], July 2007.


• T. Y. Berger-Wolf, S. I. Sheikh, B. DasGupta, M. V. Ashley, I. C. Caballero, W. Chaovalitwongse, S. L. Putrevu
  Reconstructing Sibling Relationships in Wild Populations
  Bioinformatics, 23(13), 49-56, July 2007.


• W. Chaovalitwongse, T. Y. Berger-Wolf, B. DasGupta, and M. V. Ashley
  Set covering approach for reconstruction of sibling relationships
  Optimization Methods and Software (Special Issue on Systems Analysis, Optimization and Data Mining in Biomedicine), 22(1), 11-24, Feb 2007.


• S. I. Sheikh, T. Y. Berger-Wolf, W. Chaovalitwongse, B. DasGupta, and M. Ashley
  Reconstructing Sibling Relationships from Microsatellite Data
  European Conf. on Computational Biology (ECCB), Eilat, Israel, Jan 2007.


• W. Chaovalitwongse, T. Y. Berger-Wolf, B. DasGupta, and M. V. Ashley.
  Set covering approach for reconstruction of sibling relationships
  Optimization Methods and Software (Special Issue on Systems Analysis, Optimization and Data Mining in Biomedicine), 22(1), Feb 2007, 11-24.


• T. Y. Berger-Wolf, B. DasGupta, W. Chaovalitwongse and M. V. Ashley
  Combinatorial Reconstruction of Sibling Relationships
  Proc. of the 6th International Symposium on Computational Biology and Genome Informatics (CBGI 05), Utah, pp. 1252-1255, July 2005.





Sparse Linear Algebra on GPUs:

• M. Maggioni
  Sparse Convex Optimization on GPUs
  PhD Thesis, University of Illinois at Chicago.


• M. Maggioni and T. Y. Berger-Wolf
  CoAdELL: Adaptivity and Compression for Improving Sparse Matrix-Vector Multiplication on GPUs
  International Workshop on Accelerators and Hybrid Exascale Systems, 2014, Phoenix, May 20, to appear


• M. Maggioni and T. Y. Berger-Wolf
  Adaptivity and Compression: a Recipe for Sparse Matrix-Vector Multiplication on GPUs
  NVIDIA GPU Technology Conference, 2014, San Jose, March 24-27


• M. Maggioni and T. Y. Berger-Wolf
  AdELL: An Adaptive Warp-Balancing ELL Format for Efficient Sparse Matrix- Vector Multiplication on GPUs
  International Conference on Parallel Processing, 2013, Lyon, France, October 1-4, pp. 11-20


• M. Maggioni and T. Y. Berger-Wolf
  An Architecture-Aware Technique for Optimizing Sparse Matrix-Vector Multiplication on GPUs
  International Conference on Computational Science, 2013, Barcelona, Spain, June 5-7, pp. 329-338


• M. Maggioni, T. Y. Berger-Wolf and J. Liang
  GPU-based Steady-State Solution of the Chemical Master Equation
  International Workshop on High Performance Computational Biology, 2013, Boston, May 20, pp. 579-588


• M. Maggioni, T. Y. Berger-Wolf and J. Liang
  Unveiling Cellular Mechanisms using GPU-based Sparse Linear Algebra
  NVIDIA GPU Technology Conference, 2013, San Jose, March 18-21





Other:

• M. Schumer, R. Birger, C. Tantipathananandh, J. Aurisano, M. Maggioni, and P. Mwangi.
  Infestation by a Common Parasite is correlated with Ant Symbiont Identity in a Plant-Ant Mutualism
  Biotropica.


• M. Lahiri, C. Tantipathananandh, R. Warungu, D. I. Rubenstein and T. Y. Berger-Wolf
  Biometric Animal Databases from Field Photographs: Identification of Individual Zebra in the Wild
  Proc. of the ACM International Conference on Multimedia Retrieval (ICMR), 2011.


• T. Y. Berger-Wolf, C. Moore and J. Saia
  A computational approach to animal breeding
  Journal of Theoretical Biology, 244(3), 433-439, Feb 2007.


• M. Laifenfeld, A. Trachtenberg, and T. Y. Berger-Wolf
  Identifying Codes and the Set Cover Problem
  Proc. of the 44th Annual Allerton Conference on Communication, Control, and Computing, Allerton, IL, September 2006.


• T. Y. Berger-Wolf, W. E. Hart, and J. Saia
  Discrete Sensor Placement Problems in Distribution Networks
  Journal of Mathematical and Computer Modelling, 42 (13), 1385-1396, Dec 2005.


• T. Y. Berger-Wolf, T. Williams, B. M. E. Moret, and T. Warnow,
  An Experimental Evaluation of Phylogenetic Consensus Methods
  Technical Report TR-CS-2003-19, University of New Mexico.


• T. Y. Berger-Wolf
  Online Consensus and Agreement of Phylogenetic Trees
  Algorithms in Bioinformatics, 4th International Workshop (WABI), Bergen, Norway, September 17-21, 2004, Proceedings. Lecture Notes in Computer Science, 3240, Springer, 350-361.


• T. Y. Berger-Wolf, T. Williams, B. M. E. Moret ,U. Roshan, and T. Warnow,
  The Relationship Between Maximum Parsimony Scores and Phylogenetic Tree Topologies
  UNM Technical Report TR-CS-2004-04.


• T. Y. Berger-Wolf and E. M. Reingold.
  Index assignment for multichannel communication under failure
  IEEE Transactions on Information Theory, 48(10), Oct 2002, 2656-2668.


• T. Y. Berger-Wolf and E. M. Reingold,
  Optimal multichannel communication under failure
  Proc. of the Tenth Annual ACM-SIAM Symposium on Discrete Algorithms, Baltimore, Maryland, 1999.