Naren Ramakrishnan

Publications

The Adaptive Code Kitchen: Flexible Tools for Dynamic Application Composition, in Proceedings of the Next Generation Software Systems Workshop, 21st IEEE International Parallel & Distributed Processing Symposium (IPDPS'07), Long Beach, CA, March 2007, to appear (with S. Varadarajan, C.J. Ribbens, and others). [PDF]

Scalable Execution of Legacy Scientific Codes, in Proceedings of the International Conference on Computational Science (ICCS'06), Reading, UK, Vol. 1, pages 46-53, May 2006 (with J. Mukherjee and S. Varadarajan). [PDF]

Novel Runtime Systems Support for Adaptive Compositional Modeling in PSEs, Future Generation Computing Systems (Special Issue on "Complex PSEs for Grid Computing"), Vol. 21, No. 6, pages 878-895, June 2005 (with S. Varadarajan). (c) Elsevier, Netherlands, 2005. [PDF]

Towards Integrated PSEs for Wireless Communications: Experiences with the S^4W and SitePlanner Projects, ACM Mobile Computing and Communications Review, Vol. 8, No. 2, pages 20-34, April 2004. [PDF]

An Experiment Management Component for the WBCSim PSE, Advances in Engineering Software, Vol. 35, No. 2, pages 115-123, Feb 2004. (c) Elsevier, Netherlands, 2004.

From Landscapes to Waterscapes: A PSE for Landuse Change Analysis, Engineering with Computers, Vol. 19, No. 1, pages 9-25, 2003. (c) Springer-Verlag, London, 2003.

BSML: A Binding Schema Markup Language for Data Interchange in PSEs, Scientific Programming, Vol. 11, No. 3, pages 199-224, Aug 2003 (with A. Verstak and others). (c) John Wiley and Sons, USA, 2003. [PS]/[PDF] Figure 5 got misprinted in the published version inspite of identifying the problem at the proof stage (sigh); this version has the right figure.

S^4W: Globally Optimized Design of Wireless Communication Systems, in Proceedings of the Next Generation Software Systems Workshop, 16th International Parallel and Distributed Processing Symposium (IPDPS'02), Fort Lauderdale, FL, Apr 2002 (with L.T. Watson, A. Verstak, J. He, and others). Invited Paper. [PS]/[PDF]. Expanded version appears in IEEE Transactions on Wireless Communications, Vol. 3, No. 6, pages 1906-1911, Nov 2004.

Programming Environments for Multidisciplinary Grid Communities, Concurrency and Computation: Practice and Experience, Vol. 14, Nos. 13-14, pages 1241-1273, Nov-Dec 2002. (with the rest of the PSEs research group). (c) John Wiley and Sons, USA, 2002. [PDF]

MyPYTHIA: A Recommendation Portal for Scientific Software and Services, Concurrency and Computation: Practice and Experience, Vol. 14, Nos. 13-14, pages 1481-1505, Nov-Dec 2002. (with E.N. Houstis, J.R. Rice, A.C. Catlin, N. Dhanjani, and V.S. Verykios). (c) John Wiley and Sons, USA, 2002. [PDF]

GAUSS: An Online Algorithm Selection System for Numerical Quadrature, Advances in Engineering Software, Vol. 33, No. 1, pages 27-36, Jan 2002 (with J.R. Rice and E.N. Houstis). (c) Elsevier, Netherlands, 2002.

Note on Generalization in Experimental Algorithmics, ACM Transactions on Mathematical Software, Vol. 26, No. 4, pages 568-580, Dec 2000. [PDF] (with R.E. Valdés-Pérez).

Mining and Visualizing Recommendation Spaces for Elliptic PDEs with Continuous Attributes, ACM Transactions on Mathematical Software, Vol. 26, No. 2, pages 254-273, June 2000. [PDF] (with C.J. Ribbens).

PYTHIA-II: A Knowledge/Database System for Managing Performance Data and Recommending Scientific Software, ACM Transactions on Mathematical Software, Vol. 26, No. 2, pages 227-253, June 2000 (with the PELLPACK group). [PDF]

Networked Agents for Scientific Computing, Communications of the ACM, Vol. 42, No. 3, pages 48-52 and 54, March 1999. [PDF] (with T.T. Drashansky, E.N. Houstis, and J.R. Rice.)

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Bioinformatics

Mining Novellas from PubMed Abstracts using a Storytelling Algorithm, Technical Report TR-07-08, Department of Computer Science, Virginia Tech (with J. Gresock, R. Helm, and others). [PDF]

Using Relative Importance Methods to model High-throughput Gene Perturbation Screens, in Proceedings of the 7th Annual International Conference on Computational Systems Bioinformatics (CSB'08), Stanford, CA, Aug 2008, to appear (with Y. Jin, L.S. Heath, and R.F. Helm). [PDF]

Memory Switches in Chemical Reaction Space, PLoS Computational Biology, Vol. 4, No. 7, e1000122, 9 pages, July 2008 (with U.S. Bhalla). [PDF]

Protein Design by Sampling an Undirected Graphical Model of Residue Constraints, in Poster Proceedings of the 12th Annual International Conference on Research in Computational Molecular Biology (RECOMB'08), NUS, Singapore, Mar-Apr 2008. [PDF] (with J. Thomas and C. Bailey-Kellogg). Full version available as Dartmouth Computer Science Technical Report TR007-587, March 2007. [PDF]

Graphical Models of Residue Coupling in Protein Families, IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol. 5, No. 2, pages 183-197, April-June 2008 (with J. Thomas and C. Bailey-Kellogg). [PDF]

Compositional Mining of Multirelational Biological Datasets, ACM Transactions on Knowledge Discovery from Data, Vol. 2, No. 1, Article 2, 35 pages, March 2008 (with Y. Jin and T.M. Murali). [PDF]

Simultaneously Segmenting Multiple Gene Expression Courses by Analyzing Cluster Dynamics, in Proceedings of the Sixth Asia-Pacific Bioinformatics Conference (APBC 2008), pages 297-306, Kyoto, Japan, Jan 2008 (with S. Tadepalli, L.T. Watson, and others). [PDF]

CMGSDB: Integrating Heterogeneous C. elegans Data Sources using Compositional Data Mining, Nucleic Acids Research, Vol. 36, D69-D76, Jan 2008 (Database Issue; with A. Pati, Y. Jin, L.S. Heath, and others). [PDF]

Validation and Estimation of Parameters for a General Probabilistic Model of the PCR Process, Journal of Computational Biology, Vol. 14, No. 1, pages 97-112, Jan 2007 (with L.T. Watson, N. Saha, and others). [PDF]

PLANAR: RNA Sequence Alignment using Non-Affine Gap Penalty and Secondary Structure, in Proceedings of the International Symposium on Computational Biology and Bioinformatics, Bhubaneshwar, India, 5 pages, Dec 2006 (with O.S. Gill and B. Mishra). [Paper PDF]/[Slides PDF]

Remembrance of Experiments Past: A Redescription Approach for Knowledge Discovery in Complex Systems, in Proceedings of the International Conference on Complex Systems, Boston, MA, 8 pages, June 2006 (with S. Kleinberg, M. Antoniotti, S. Tadepalli, and B. Mishra). [PDF]

Transcriptional Response of Sachharomyces cerevisiae to Desiccation and Rehydration, Applied and Environmental Microbiology, Vol. 71, No. 12, pages 8752-8763, Dec 2005, (with J.A. Singh, D. Kumar, M. Potts, R.F. Helm, and others). [PDF]

Graphical Models of Residue Coupling in Protein Families, in Proceedings of the 5th ACM SIGKDD Workshop on Data Mining in Bioinformatics (BioKDD'05), Chicago, IL, Aug 2005 (with C. Bailey-Kellogg and J. Thomas). [PDF]

Reconstructing Formal Temporal Models of Cellular Events using the GO Process Ontology, in Proceedings of the Eighth Annual Bio-Ontologies Meeting (ISMB'05 Satellite Workshop), Detroit, MI, June 2005, to appear (with B. Mishra and M. Antoniotti). [PDF]

GOALIE, A Common Lisp Application to Discover Kripke Models: Redescribing Biological Processes from Time Course Data, in Proceedings of the International Lisp Conference, Stanford, CA, July 2005, to appear (with B. Mishra and M. Antoniotti). [PDF]

The JigCell Model Builder and Run Manager, Bioinformatics, Vol. 20, No. 18, pages 3680-3681, 2004 (with the JigCell group). [PubMed] Expanded version appears in IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol. 3, No. 2, pages 155-164, Apr-June 2006.

A General Probabilistic Model of the PCR Process, in Proceedings of the 26th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, Sep 2004 (with N. Saha, L.T. Watson, A. Onufriev, and others). [PDF] Longer version appears in Applied Mathematics and Computation, Vol. 182, No. 1, pages 232-243, Nov 2006.

Improving the Development Process for Eukaryotic Cell Cycle Models with a Modeling Support Environment, in Proceedings of the 2003 Winter Simulation Conference, pages 782-790, Dec 2003 (with the JigCell group). Also in Simulation, Vol. 79, No. 12, pages 674-688, Dec 2003. [PDF]

Photosynthetic Acclimation is Reflected in Specific Patterns of Gene Expression in Drought-Stressed Loblolly Pine (Pinus Taeda, L.), Plant Physiology, Vol. 133, No. 4, pages 1702-1716, Dec 2003 (with the Expresso group). [PubMed]

JigCell: Modeling Regulatory Networks at Virginia Tech, Omics Journal of Integrative Biology, Vol. 7, No. 3, pages 285-300, Fall 2003 (with the Jigcell group). [PDF]/[PubMed]

Clustering Mass Spectrometry Data using Order Statistics, Proteomics, Vol. 3, No. 9, pages 1687-1691, Sep 2003 (with D.J. Slotta, L.S. Heath, and others). [PDF]/[PubMed]

Expresso and Chips: Creating a Next Generation Microarray Experiment Management System, in Proceedings of the Next Generation Software Systems Workshop, 17th International Parallel and Distributed Processing Symposium (IPDPS'02), Nice, France, Apr 2003 (with the Expresso group). [PDF] Invited Paper.

The Emerging Landscape of Bioinformatics Software Systems (Guest Editors' Introduction to the Special Issue on Bioinformatics Software), IEEE Computer, Vol. 35, No. 7, pages 41-45, July 2002 (with L.S. Heath). [PDF]

Studying the Functional Genomics of Stress Responses in Loblolly Pine with the Expresso Microarray Experiment Management System, Comparative and Functional Genomics, Vol. 3, No. 3, pages 226-243, June 2002 (with L.S. Heath, R. Grene, and others).

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Data Mining

Reconstructing Chemical Reaction Networks: Data Mining meets System Identification, in Proceedings of the 14th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD'08), Las Vegas, NV, Aug 2008, to appear (with Y.J. Cho and Y. Cao). [PDF]

Deriving Kripke Structures from Time Series Segmentation Results, in Workshop on Discrete Event Systems (WODES'08), Goteborg, Sweden, May 2008. [PDF]

C4.5, in Top 10 Algorithms in Data Mining (X. Wu and V. Kumar, eds.), Chapman and Hall/CRC Press, 2008, to appear.

Capturing Truthiness: Mining Truth Tables in Binary datasets, Technical Report TR-07-10, Department of Computer Science, Virginia Tech (with C.C. Owens and T.M. Murali). [PDF]

Proceedings of the Seventh IEEE International Conference on Data Mining (ICDM'07), edited with O. Zaiane, Y. Shi, C. Clifton, X. Wu, IEEE Press, 2007.

Gaussian Process Models in Spatial Data Mining, in Encyclopedia of Geographic Information Science (S. Shekhar and H. Xiong, editors), pages 325-329, 2008 (with C. Bailey-Kellogg).

Network Reconstruction from Dynamic Data, ACM SIGKDD Explorations, Vol. 8, No. 2, pages 90-91, Dec 2006. Report from the Fourth SIGKDD Workshop on Temporal Data Mining. [PDF]

Reconstructing Partial Orders from Linear Extensions, in Proceedings of the Fourth SIGKDD Workshop on Temporal Data Mining: Network Reconstruction from Dynamic Data, Aug 2006 (with P.L. Fernandez, L.S. Heath, and J.P. Vergara). [PDF]

Spatial Data Mining to Support Pandemic Preparedness, ACM SIGKDD Explorations, Vol. 8, No. 1, pages 80-82, June 2006 (with C. Bailey-Kellogg and M.V. Marathe). [PDF] Report from the SIAM Data Mining 2006 Workshop on Mining Spatial Data.

BLOSOM: A Framework for Mining Boolean Expressions, in Proceedings of the Twelfth ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD'2006), Philadelphia, PA, pages 827-832, Aug 2006 (with M.J. Zaki and L. Zhao). [PDF]

Algorithms for Storytelling, in Proceedings of the Twelfth ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD'2006), Philadelphia, PA, pages 604-610, Aug 2006 (with D. Kumar, M. Potts, and R. Helm). [PDF] Expanded version appears in IEEE Transactions on Knowledge and Data Engineering, Vol. 20, No. 6, pages 736-751, June 2008. Featured article in the June 2008 issue.

Reasoning about Sets using Redescription Mining, in Proceedings of the Eleventh ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD'2005), Chicago, IL, pages 364-373, Aug 2005 (with M.J. Zaki). [Paper PDF]/[Slides PDF]

Redescription Mining: Structure Theory and Algorithms, in Proceedings of the Twentieth National Conference on Artificial Intelligence (AAAI'05), Pittsburgh, PA, pages 837-844, July 2005 (with L. Parida). [Paper PDF]/[Poster PDF]. Preliminary version appears as IBM Research Technical Report RC23565, Feb 2005.

Non-Orthogonal Decomposition of Binary Matrices for Bounded-Error Data Compression and Analysis, ACM Transactions on Mathematical Software, Vol. 32, No. 1, pages 33-69, March 2006 (with A.Y. Grama and M. Koyuturk). [PDF]

Algorithms for Feature Selection in Rank Order Spaces, Technical Report TR-05-08, Department of Computer Science, Virginia Tech, Apr 2005 (with D.J. Slotta, J.P. Vergara, and L.S. Heath). [PDF]

Compression, Clustering, and Pattern Discovery in Very High Dimensional Discrete-Attributed Datasets, IEEE Transactions on Knowledge and Data Engineering, Vol. 17, No. 4, pages 447-461, Apr 2005 (with A.Y. Grama and M. Koyuturk). [PDF]

Gaussian Processes for Active Data Mining of Spatial Aggregates, in Proceedings of the SIAM International Conference on Data Mining, Newport Beach, CA, 2005. [PDF]. Selected among `Best of SIAM Data Mining 2005' for presentation at Interface'05. Preliminary version appears in Proceedings of the 18th International Workshop on Qualitative Reasoning, Evanston, IL, pages 67-74, 2004 (with C. Bailey-Kellogg, S. Tadepalli, and V.N. Pandey).

Turning CARTwheels: An Alternating Algorithm for Mining Redescriptions, in Proceedings of the Tenth ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD'2004), Seattle, WA, pages 266-275, Aug 2004 (with D. Kumar, B. Mishra, M. Potts, and R. Helm). [PS]/[PDF]

Spatial Aggregation for Qualitative Assessment of Scientific Computations, in Proceedings of the Nineteenth National Conference on Artificial Intelligence (AAAI'04), pages 585-591, July 2004 (with C. Bailey-Kellogg). PS/[PDF]. Preliminary version appears in Proceedings of the 17th International Workshop on Qualitative Reasoning, Brasilia, Brazil, pages 23-30, Aug 2003.

Gaussian Process Models of Spatial Aggregation Algorithms, in Proceedings of the Eighteenth International Joint Conference on Artificial Intelligence (IJCAI'03), Acapulco, Mexico, pages 1045-1051, Aug 2003 (with C. Bailey-Kellogg). [PDF]

Using Hierarchical Data Mining to Characterize Performance of Wireless System Configurations, Technical Report cs.CE/0208040, Computing Research Repository (CoRR), Aug 2002 (with A. Verstak, W.H. Tranter, L.T. Watson, and others). [PS]/[PDF]

Algebraic Techniques for Analysis of Large Discrete-Valued Datasets, in Proceedings of the 6th European Conference on Principles and Practice of Knowledge Discovery in Databases (PKDD'02), Helsinki, Finland, pages 311-324, Aug 2002 (with M. Koyuturk and A.Y. Grama). [PS]

Sampling Strategies for Mining in Data-Scarce Domains, IEEE/AIP Computing in Science and Engineering (CiSE), Vol. 4, No. 4 (Special issue on Data Mining), pages 31-43, July/Aug 2002 (with C. Bailey-Kellogg). [PDF]

Compression of Particle Data from Hierarchical Approximate Methods, ACM Transactions on Mathematical Software, Vol. 27, No. 3, pages 317-339, September 2001 (with A.Y. Grama, D.-Y. Yang, and V. Sarin). [PDF]

Ambiguity-Directed Sampling for Qualitative Analysis of Sparse Data from Spatially Distributed Physical Systems, in Proceedings of the Seventeenth International Joint Conference on Artificial Intelligence (IJCAI-01) (B. Nebel, Ed.), Seattle, WA, pages 43-50, August 2001 (with C. Bailey-Kellogg). [PS]/[PDF]. A nice overview of the SAL system used in this paper is available here.

Data Mining Applications in Bioinformatics, in Data Mining for Scientific and Engineering Applications, Chapter 8, Kluwer Academic Publishers, pages 125-140, 2001. (online copy not available due to copyright restrictions)

Mining Scientific Data, Advances in Computers (M. Zelkowitz, Ed.), Vol. 55, pages 119-169, Academic Press, September 2001. Invited Paper. [PDF] (with A.Y. Grama)

Data Mining: From Serendipity to Science (Guest Editors' Introduction to the Special Issue on Data Mining), IEEE Computer, Vol. 32, No. 8, pages 34-37, August 1999. [PDF] (with A.Y. Grama).

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Recommender Systems, Web Search/Interaction, Personalization

Compositional Specification and Realization of Mixed-Initiative Web Dialogs, International Journal of Web Engineering and Technology, Vol. 4, No. 3, pages 336-366, July 2008 (with M. A. Perez and A. Shenoy). [PDF]

Search: The New Incarnations (Area Editor's Introduction to the Special Issue on Search), IEEE Computer, Vol. 40, No. 8, pages 31-32, Aug 2007. [PDF]

Mining Web Functional Dependencies for Flexible Information Access, Journal of the Americal Society for Information Science and Technology (Special Issue on Mining Web Resources for Enhancing Information Retrieval), Vol. 58, No. 12, pages 1805-1819, 2007 (with S. Perugini). [PDF]

Interacting with Web Hierarchies, IEEE IT Professional, Vol. 8, No. 4, pages 19-28, July/Aug 2006 (with S. Perugini). [PDF]

Scouts, Promoters, and Connectors: The Roles of Ratings in Nearest-Neighbor Collaborative Filtering, in Proceedings of the ACM Conference on Electronic Commerce (EC'06), Ann Arbor, MI, pages 250-259, June 2006 (with M.B. Kumar and B.J. Keller). [PDF]. Expanded version appears in ACM Transactions on the Web, Vol. 1, No. 2, Article 8, 30 pages, August 2007. One of only three papers from EC'06 recommended for fast track publication in ACM TWeb.

Frontiers of Search (Area Editor's Introduction to the Special Issue on Search), IEEE Computer, Vol. 38, No. 10, pages 26-27, Oct 2005. [PDF]

A Generative Programming Approach to Interactive Information Retrieval: Insights and Experiences, in Proceedings of the Fourth International Conference on Generative Programming and Component Engineering (GPCE'05), Tallinn, Estonia, pages 205-220, Sep-Oct 2005 (with S. Perugini). [PDF]

The Traits of the Personable, in LNCS/LNAI State-of-the-Art Survey on Intelligent Techniques in Web Personalization, Vol. 3169 (LNAI Series), Springer-Verlag (B. Mobasher and S.S. Anand, Eds.), pages 53-68, 2005. Invited Book Chapter [PDF]

Personalization by Program Slicing, Journal of Object Technology (Proceedings from the GPCE'04 Young Researcher's Workshop), Vol. 4, No. 3, pages 5-11, Apr 2005. Online Link.

The Good, Bad, and the Indifferent: Explorations in Recommender System Health, in Proceedings of Beyond Personalization: The Next Stage of Recommender Systems Research, IUI'05, San Diego, CA, pages 43-47, Jan 2005 (with B.J. Keller and others). [PDF]

Enhancing Usability in CITIDEL: Multimodal, Multilingual, and Interactive Visualization Interfaces, in Proceedings of the ACM/IEEE-CS Joint Conference on Digital Libraries (JCDL'04), Tucson, AZ, pages 315-324, June 2004. [PDF]

Staging Transformations for Multimodal Web Interaction Management, in Proceedings of the Thirteenth International World Wide Web Conference (WWW' 2004), New York, NY, pages 212-223, May 2004 (with the pied PIPErs). [PDF]/ OOT Web Site

The Staging Transformation Approach to Mixing Initiative, in G. Tecuci, ed., Working Notes of the IJCAI'03 Workshop on Mixed-Initiative Intelligent Systems, Acapulco, Mexico, pages 23-29, Aug 2003 (with the PIPE and dialog modeling gang). [PDF]

Personalizing Interactions with Information Systems, Advances in Computers (M. Zelkowitz, Ed.), Vol. 57, pages 323-382, Academic Press, Sep 2003. [PDF]

Personalizing Web Sites with Mixed-Initiative Interaction, IEEE IT Professional, Vol. 5, No. 2, pages 9-15, Mar/Apr 2003 (with S. Perugini). [PDF]

Studying Recommendation Algorithms by Graph Analysis, Journal of Intelligent Information Systems, Vol. 20, No. 2, pages 131-160, March 2003 (with B.J. Mirza and B.J. Keller). [PDF]

Mixed-Initiative Interaction = Mixed Computation, in Proceedings of the ACM SIGPLAN Workshop on Partial Evaluation and Semantics-Based Program Manipulation (PEPM'02) (P. Thiemann, Ed.), pages 119-130, January 2002 (with R. Capra and M.A. Pérez-Quiñones). [PS]/[PDF]. Also appears in ACM SIGPLAN Notices, Vol. 37, No. 3, March 2002. Audio recordings for some of the dialogs in this paper are also available: Fig. 1, Fig. 2, and Fig. 4.

Privacy Risks in Recommender Systems, IEEE Internet Computing, Vol. 5, No. 6, pages 54-62, Nov-Dec 2001 (Special Issue on "Personalization and Privacy"; with B.J. Keller, B.J. Mirza, A.Y. Grama, and G. Karypis). [PDF]

WebContext: Remote Access to Shared Context, in Proceedings of the Workshop on Perceptive User Interfaces (PUI'2001), Dec 2001 (with R. Capra and M.A. Pérez-Quiñones). [PDF]

Modeling and Building Personalized Digital Libraries with PIPE and 5SL, in Proceedings of the Joint DELOS-NSF Workshop on Personalization and Recommender Systems in Digital Libraries (A.F. Smeaton and J. Callan, Eds.), pages 67-72, Dublin, Ireland, June 2001 (with M.A. Goncalves, A.A. Zafer, and E.A. Fox). [PDF]

PIPE: Web Personalization By Partial Evaluation, IEEE Internet Computing, Vol. 4, No. 6, pages 21-31, Nov-Dec 2000. [PDF] (some slips in the printed version touched up courtesy of Acrobat Exchange). Recognized with the 2001 New Century Technology Council Innovation award.

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Misc.

A Digital Library for Recovery, Research, and Learning from April 16, 2007 at Virginia Tech, Traumatology, Vol. 14, No. 1, pages 64-84, March 2008. [PDF] (with the DL416 group).

Reinforcing Reachable Routes, Computer Networks, Vol. 43, No. 3, pages 389-416, Oct 2003 (with S. Varadarajan and M. Thirunavukkarasu). PS/[PDF]

Dynamic Data Structures for a Direct Search Algorithm, Computational Optimization and Applications, Vol. 23, No. 1, pages 5-25, Oct 2002 (with J. He, L.T. Watson, A. Verstak, and others). [PDF]

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