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Amarnath Gupta (858) 793-7239 gupta@sdsc.edu |
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CURRENT POSITION |
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Director, Advanced Query Processing Laboratory, Science R&D Division Research Scientist |
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Education |
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Ph.D. (Engineering) in Computer Science |
1994 |
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Research Area: Database Management |
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M.S. in Biomedical Engineering |
1987 |
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Research Area: Automatic Gait Analysis |
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Indian
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B.Tech. Honors in Mechanical Engineering |
1984 |
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Undergraduate Research: Robot Vision |
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Current RESEARCH INTERESTS |
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· Information and Knowledge Modeling for Biomedical Sciences |
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· Information Integration for Scientific Domains |
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· Graph Data management for Biological Networks |
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· Management and Utilization of Ontological Information |
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· Multimedia Data Management |
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RESEARCH Experience |
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Research Scientist |
2007-current |
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Associate Research Scientist |
2001-2007 |
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· Design of a Type-Extensible, Ontology-Enabled Mediator · Design, Implementation and Deployment of Information Integration System for multiple Neuroscience Databases · Design and Development of Graph Data Warehouse for Gene Regulatory and Metabolic Networks · Development of Ontology Management Tools over Integrated Ontology Sources for Neurosciences · Development of specialized query languages and engines for Complex Data Types used in multiple scientific disciplines |
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Assistant Research Scientist |
1998-2001 |
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· Techniques for preservation of software-dependent digital objects · Techniques for information integration of spatial data from distributed data sources · Developed query-translation techniques from Datalog-like query languages to specialized data sources like Oracle Spatial, and ArcXML |
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Virage, Inc., |
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Research Scientist |
1995 - 1998 |
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· Development of image and video query engine · Development of techniques for searching and combining multiple media data · Development of multimedia searching applications in the areas of histopathology, radiology and trademarks · 8 patents |
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Indian Statistical Institute, |
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Computer Engineer |
1988-1994 |
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· Developed a Classificatory Data Model for Retrieval and Post-Analysis of Archaeological Artifacts with an Image Database · Developed an Expert Image Database Engine for Machine Fault Diagnosis from Ferrogram Images · Developed an Industrial Object Model Database Engine for Computer Vision · Developed a Semantic Network Based Data and Indexing Method for primary and secondary memory · Developed a Method for Information Retrieval using automated Handwritten Document Analysis |
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TEACHING Experience |
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Lectures in Process Modeling for Advanced Topics in CSE Faculty Research Seminar, Computer Science Neuroinformatics Seminar Multimedia Systems |
2004 2003, 2004 2003 2001 |
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Indian Statistical Institute |
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Graduate Courses in Database Systems, Software Engineering, Compiler Construction, Image Processing |
1988 - 1994 |
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GRANTS |
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Title of Proposal: Web Based Information Technologies Proposal to the Federal Web Consortium Granting Agency: National Science Foundation Time Period of Grant/Contract: 4/1/98-7/31/99 Amount of Award: $175,000 Title of Proposal: Digital Government: Web Based Information Technologies: Advancing Federal Information Infrastructures Granting Agency: National Science Foundation Time Period of Grant/Contract: 08/01/99 – 07/31/02 Amount of Award: $199,970 Title of Proposal: Methodologies for Preservation and Access of Software-dependent Electronic Records Granting Agency: National Historical Publications and Records Commission, National Archives and Records Administration Time Period of Grant/Contract: 1/1/00 – 12/31/02 Amount of Award: $300,000 Title of Proposal: I2T: An Information Integration Testbed for Digital Government Granting Agency: National Science Foundation Time Period of Grant/Contract: 07/01/2000 – 06/30/2003 Amount of Award: $750,000 Title of Proposal: Structured Analysis of the Retina Granting Agency: National Institutes of Health Time Period of Grant/Contract: 07/01/2000 – 06/30/2003 Amount of Award: $54,784 (SDSC Direct) Title of Proposal: Evaluating Information Integration Architectures for a National Statistical Data Infrastructure Granting Agency: National Science Foundation Time Period of Grant/Contract: 10/01/1999 – 06/30/2000 Amount of Award: $45,000 Title of Proposal: Causes of Robustness and Vulnerability in Real-world Networks: Lessons in Biology Granting Agency: National Science Foundation Time Period of Grant/Contract: 09/15/2001 – 09/14/2003 Amount of Award: $32,501 annual (SDSC Direct) Title of Proposal: NBCR Supplement: Biomedical Informatics Research Network- Coordinating Center Granting Agency: NCRR, National Institutes of Health Time Period of Grant/Contract: 04/30/2001 – 03/31/2004 Amount of Award: $1,761,373 (SDSC Direct) – 25% is for Data Integration Title of Proposal: ITR: A Twin Framework to Analyze, Model and Design Robust, Complex Networks Using Biological and Computatational Principles Granting Agency: National Science Foundation Time Period of Grant/Contract: 10/01/2002 – 09/30/2006 Amount of Award: $216,723 annual (SDSC Direct) Title of Proposal: NPACI Neuroscience Thrust: Federation of Brain Data Granting Agency: National Science Foundation Time Period of Grant/Contract: 10/01/2002 – 09/30/2004 Amount of Award: $100,000 annual (SDSC Direct) Title of Proposal: Development of a 3D Cell-Centered Neuronal Database Granting Agency: NIDA, National Institutes of Health Time Period of Grant/Contract: 4/1/2003 – 3/31/2008 Amount of Award: $3,397,213 – 33% is for Data Model Development Title of Proposal: Biomedical Informatics Research Network - Coordinating Center Granting Agency: NCRR, National Institutes of Health Time Period of Grant/Contract: 5/1/2004-4/30/2009 Amount of Award: ~ $5M – 20% for Data Integration Title of Proposal: National Biomedical Computational Center Granting Agency: NCRR, National Institutes of Health Time Period of Grant/Contract: 10/01/2004 – 09/30/2009 Amount of Award: $100,000 annual Title of Proposal: Toward a distributed information system for marine biology and limnology Granting Agency: Gordon and Betty Moore Foundation Time Period of Grant/Contract: 10/15/2004 – 10/14/2006 Amount of Award: $1,762,420.00 |
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Publications |
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· See next page |
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Memberships |
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· Association of Computing Machinery · NIH Biomedical Informatics Research Network Ontology Task Force · Society for Neuroscience, Neuroinformatics Committee |
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PUBLICATIONS
2005
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M. Baitaluk, X., Qian,
· B. Liu, A. Gupta and R. Jain "A Live Multimedia Stream Querying System", 2nd Int. Conf. Computer Vision Meets Databases (CVDB), June. 2005 (to appear).
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L. Chen, A. Gupta, M. E. Kurul,
"Efficient Algorithms for Pattern Matching on Directed Acyclic Graphs”,
IEEE Int. Conf. on Data Engineering (ICDE),
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S. Yamini and A. Gupta, "Spatiotemporal
annotation graph (STAG): A data model for composite digital objects",
Demonstration Track, IEEE Int. Conf. on Data Engineering (ICDE),
· Y. Wang, S. Santini and A. Gupta, "Efficiently querying spatial histograms", Storage and Retrieval Methods and Applications for Multimedia, SPIE, Vol. 5682, pp. 183-194, Jan. 2005.
2004
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S. Santini, A. Gupta "Modeling functional
data sources as relations ", 23rd Int. Conf. on Conceptual Modeling (ER),
· I. Zaslavsky, H. He, J. Tran, M.E. Martone, A. Gupta, "Integrating Brain Data Spatially: Spatial Data Infrastructure and Atlas Environment for Online Federation and Analysis of Brain Images ", Biological Data Management Workshop (BIDM 2004) in conjunction with 15th International Workshop on Database and Expert Systems Applications (DEXA'04), pp. 389-393, Zaragosa, Spain, Aug/Sept. 2004.
· A. Gupta, "Life Science Research and Data Management", SIGMOD Record, 33(2), June 2004, pp. 12-14.
· M.E. Martone, A. Gupta and M.H. Ellisman, "e-Neuroscience: challenges and triumphs in integrating distributed data from molecules to brains", Nature Neuroscience, 7(5), May 2004, pp. 467-472.
· M. Chagoyen, M.E. Kurul, P.A. De-Alarcón, J.M. Carazo and A. Gupta, "Designing and executing scientific workflows with a programmable integrator", Bioinformatics, 20(13), pp. 2092-2100, September, 2004
· A. Gupta, B. Liu, P. Kim, R. Jain, "Using Stream Semantics for Continuous Queries in Media Stream Processors ", IEEE Int. Conf. on Data Engineering (ICDE), (Demonstration), pp. 854, March. 2004
2003
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A. Gupta, B. Ludäscher, J.S.
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M.E. Martone, S. Zhang, A. Gupta, X. Qian, H.
He, D.L. Price, M. Wong,
· A. Gupta and B. Ludäscher, "The Many Faces of Process Interaction Graphs: A Data Management Perspective", OMICS - A Journal of Integrative Biology, Vol. 7, No. 1, pp. 105-108, Spring 2003.
· T. Wang, S. Santini, A. Gupta, "An Interpolated Volume Model for Databases", 22nd Int. Conf. on Conceptual Modeling (ER), pp. 335-348, Oct. 2003.
· T. Wang, S. Santini, A. Gupta, "An Interpolated Volume Data Model ", ACM Conf. on Very Large Databases (VLDB), (Demonstration), pp. 1121-1124, Sept. 2003.
· M. Chagoyen, M.E. Kurul, P.A. De-Alarcon, S. Santini, B. Ludäscher, J.M. Carazo, A. Gupta, "A Semantic Mediation Approach for Problems in Computational Molecular Biology", IEEE Computer Society Bioinformatics Conference (CSB2003), pp. 386-387, Aug. 2003.
· B. Ludäscher, A. Gupta, I. Altintas, "Compiling Abstract Scientific Workflows into Web Service Workflows", Int. Conf. on Statistical and Scientific Data Management (SSDBM), pp. 251-254, July 2003.
· S. Zhang, X. Qian, A. Gupta, M.E. Martone, "A Practical Approach for Microscopy Imaging Data Management (MIDM) in Neuroscience", Int. Conf. on Statistical and Scientific Data Management (SSDBM), pp. 237-240, July 2003.
· I. Altintas, S. Bhagwanani, D. Buttler, S. Chandra, M. Coleman, T. Critchlow, A. Gupta, W. Han, L. Liu, B. Ludäscher, R. Moore, C. Pu, A. Shoshani, M. Vouk, "A Modeling and Execution Environment for Distributed Scientific Workflows", Int. Conf. on Statistical and Scientific Data Management (SSDBM), pp. 247,250, July 2003.
· A. Gupta, B. Ludäscher, M.E. Martone, A. Rajasekar, E. Ross, X. Qian, S. Santini, H. He, I. Zaslavsky, "BIRN-M: A Semantic Mediator for Solving Real-World Neuroscience Problems ", ACM Conf. on Management of Data (SIGMOD) (Demonstration), page 678, June 2003.
· B. Ludäscher, A. Gupta, M.E. Martone , A Model Based Mediator System for Scientific Data Management. In Z. Lacroix and T. Critchlow(eds.), Bioinformatics: Managing Scientific Data, pp. 335-370, Morgan Kaufmann Publishers, 2003.
· A. Gupta, Y. Yang, A. Bagchi, A. Ray, Declarative Specification of Gene Regulatory Networks and Query Evaluation in PathSys, Proc. of Workshop on Bioinformatics, in conjunction with Intl. Conf. on Data Engineering (ICDE), March 2003.
2002
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· S. Santini, A. Gupta, Conceptual Integration of Multiple Partial Geometric Models, 21st International Conference on Conceptual Modeling, (ER), Tampere, Finland, pp. 365-379, October 2002.
· A. Gupta, B. Ludäscher, M. E. Martone, Registering Scientific Information Sources for Semantic Mediation, 21st International Conference on Conceptual Modeling, (ER), Tampere, Finland, pp. 182-198, October 2002.
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· P.A. De Alarcon, A. Pascual-Montano, A Gupta, J.M. Carazo, "Modeling Shape and Topology of 3D Images of Biological Specimens", Proc. Int. Conf. On Image Proc. And Pattern Recog. (ICPR), Vol. 1, pp. 79-82, August 2002.
· A. Gupta, B. Ludäscher, M.E. Martone, X. Qian, J. Tran and I. Zaslavsky "A System for Managing Alternate Models in Model-based Mediation", British National Conference on Databases (BNCOD), pp. 54-57, July 2002.
· A. Gupta, B. Ludäscher, R.W. Moore "Ontology Services for Curriculum Development in NSDL", ACM/IEEE-CS Joint Conference on Digital Libraries (JCDL), July 2002.
· M. E. Martone, A. Gupta, M. Wong, X. Qian, G. Sosinsky, S. Lamont, B. Ludäscher, and M. H. Ellisman, “A Cell-Centered Database for Electron Tomographic Data”, Journal of Structural Biology 138(1-2), 145-155, 2002.
· B. Ludäscher, I. Altintas and A. Gupta, "Time to Leave the Trees: From Syntactic to Conceptual Querying of XML", Proc. of Workshop on XML Data Management (XMLDM), in conjunction with Intl. Conf. on Extending Database Technology (EDBT), March 2002.
· S. Santini and A. Gupta, “Principles of Schema Design in Multimedia Databases”, IEEE Trans. on Multimedia Systems 4(2), pp. 248-259, June 2002.
· P. A. de-Alarcon, A. Pascual-Montano, A. Gupta and J.M. Carazo," Modeling Shape and Topology of Low-resolution Density Maps of Biological Macromolecules", Biophysical Journal, 83(2), 619-632, August 2002.
· X.Qian, B. Ludäscher, M.E. Martone and A. Gupta, "Navigating Virtual Information Sources with Know-ME", Proc. of Conference on Extending Database Technology (EDBT 2002), pp.739-41, Prague, March 2002.
· S. Santini and A. Gupta, “An Extensible Feature Management Engine for Image Retrieval”, Proc. SPIE Storage and Retrieval for Media Databases, vol. 4676, pp. 86-97, January 2002.
2001
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S. Santini and A. Gupta, “A Data Model for
Querying Wavelet Features in Image Databases”, Intl. Workshop on Multimedia
Information Systems,
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S. Santini and A. Gupta, “A Wavelet Data Model
for Image Databases”, IEEE Intl. Conf. on Multimedia and Expo,
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B. Ludäscher, A. Gupta, M. E. Martone,
“Model-Based Mediation with Domain Maps”, 17th Intl. Conference on Data Engineering
(ICDE),
· S. Santini, A. Gupta and R. Jain, “Emergent Semantics through Interaction in Image Databases”, IEEE Trans. Knowledge and Data Engineering, vol. 13. No. 3, pp. 337-351, May/June 2001.
2000
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A.W.M. Smeulders, M. Worring,
· M.H. Goldbaum, A. Gupta, V. Kouznetsova, I. Zaslavsky, D.J. Nazafi, “General Medical Image (online) Description Grammar”, poster, American Association of Ophthalmologists, November, 2000.
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I. Zaslavsky, B. Ludäscher, A. Gupta, and R. Marciano, “Accuracy Mediation in a Spatial Wrapper Mediator
System”, 1st Geographic Information Science Conference,
· G. Burns, K. Stephan, B. Ludäscher, A. Gupta, “Towards a Federated Neuroscientific Knowledge Management System Using Brain Atlases”, Computational Neuroscience Meeting (CNS), poster paper, Brugge, Belgium, 2000.
· Moore, R.; Baru, C.; Rajasekar, A.; Ludäscher, B.; Marciano, R.; Wan, M.; Schroeder, W.; Gupta, A. Collection-based persistent digital archives. 2. D-Lib Magazine, vol.6, (no.4), Corporation for National Research Initiatives, April 2000.
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B. Ludäscher, A. Gupta and M. Martone, “A
Mediator System for Model-based Information Integration”, Int. Conf. VLDB,
2000.
· I. Zaslavsky, R. Marciano, A. Gupta, C. Baru, “XML-based Spatial Data Mediation Infrastructure for Global Interoperability ”, 4th Global Spatial Data Infrastructure Conference , Cape Town, South Africa, 13-15 March 2000.
· Moore, R.; Baru, C.; Rajasekar, A.; Ludäscher, B.; Marciano, R.; Wan, M.; Schroeder, W.; Gupta, A. Collection-based persistent digital archives. 1. D-Lib Magazine, vol.6, (no.3), Corporation for National Research Initiatives, March 2000.
· M. Trivedi, S. Bhonsle and A. Gupta, "Database Architecture for Autonomous Transportation Agents for On-scene Networked Incident Management (ATON)", Int. Conf. Pattern Recognition, 2000 (poster paper).
· A. Gupta, B. Ludäscher and M. Martone, “Knowledge-based Integration of Neuroscience Data Sources”, 12th Int. Conf. Scientific and Statistical Database Management Systems, Berlin, 39-52, 2000.
· I. Zaslavsky, A. Gupta and R. Marciano, “Combined Query and Transformation Planning in Spatial Mediators”, Spatial Data Handling, 2000.
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A. Gupta and S. Santini, “Toward a Feature
Algebra for Visual Databases: a Case Study with Histogram Algebra”, VDB-5, Int.
Conf. On Visual Databases,
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S. Bhonsle, A. Gupta,
1999
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B. Ludäscher and A. Gupta, “Modeling Interactive
Web Sources for Information Mediation”, Proc. WWWCM’99, Conceptual Modeling for
the World Wide Web,
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Gupta, R. Marciano, I.
Zaslavsky and C. Baru, “Integrating GIS and Imagery through XML-Based
Information Mediation”, Proc. NSF International Workshop on Integrated Spatial
Databases: Digital Images and GIS,
· C. Baru, A. Gupta, B. Ludäscher, R. Marciano, Y. Papakonstantinou, P. Velikhov, V. Chu, “XML-Based Information Mediation for Digital Libraries”, Proc. Digital Libraries ’99, 1999.
· P. A. de Alarcón, A. Gupta, J. M. Carazo, “A Framework for Querying a Database for Structural Information on 3D Images of Macromolecules: A Web-Based Query-by-Content Prototype on the BioImage Macromolecular Server”, Journal of Structural Biology, Vol. 125, No. 2/3, Apr 1999, pp. 112-122 (PDF).
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S. Bhonsle, A. Gupta,
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C. Baru, A. Gupta, B. Ludäscher, R. Marciano, Y. Papakonstantinou, P. Velikhov,
V. Chu, “XML-Based Information Mediation with MIX”.
Proc. of the ACM SIGMOD'99, June 1-3, 1999,
· A. Gupta and C. Baru, “An Extensible Information Model for Shared Scientific Data Collections”, Future Generation Computer Systems, vol. 16, No. 9, 1999, pp. 9-20.
· S. Santini, A. Gupta, and R. Jain, "User Interfaces for Emergent Semantics in Image Databases,'' In Proceedings of the 8th IFIP Working Conference on Database Semantics (DS-8) Rotorua (New Zealand), January 1999 pp. 123-143.
· S. Santini, A. Gupta, and R. Jain, "Querying Multiple Perspective Video", Proceedings of SPIE Vol. 3656 Storage and Retrieval for Image and Video Databases VII, San Jose, January 1999, pp. 264-273.
1998
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A. Gupta, S. Bhonsle,
S. Santini and R. Jain, "An Event Management
Architecture for Activity Recognition in a Multistream
Video Database". In Proceedings of the 1998 Image Understanding Workshop,
Older Publications
· Gupta, A.; Jain, R. “Visual information retrieval”, Communications of the ACM, May 1997, vol.40, (No.5): 70-9.
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Gupta, A. Hampapur H.,
Gorkani, M., Jain, R., “On Summarization of Video”,
International Conference on Image Processing, IEEE,
· Gupta A., Santini, S. Jain, R. “In Search of Information in Visual Media”, Communications of the ACM, December 1997, vol. 40 (No. 12): 35:42.
· Hampapur, A.; Gupta, A.; Horowitz, B.; Chiao-Fe Shu; and others. “Virage Video Engine” In Proc. Storage and Retrieval for Image and Video Databases V, San Jose, CA, USA, 13-14 Feb. 1997, vol.3022:188-98.
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Gupta, B. Chanda, “A
· Katkere, A.; Schlenzig, J.; Gupta, A.; Jain, R., “Interactive video on WWW: beyond VCR-like interfaces”, Computer Networks and ISDN Systems, May 1996, vol.28, (no.7-11):1559-72.
· Bach, J.R.; Fuller, C.; Gupta, A.; Hampapur, A.; and others. “The Virage Image Search Engine: an open framework for image management”, In Proc. Storage and Retrieval for Still Image and Video Databases IV, San Jose, CA, USA, 1-2 Feb. 1996, vol.2670:76-87.
· Jain, R. and Gupta, A., "Computer Vision and Visual Information Retrieval", Book Chapter, In. Advances in Image Understanding: A Festschrift for Prof. Azriel Rosenfeld, IEEE Computer Society Press. 1996, 301-315.
· Kelly, P.H.; Gupta, A.; Jain, R., “Visual computing meets data modeling: defining objects in multi-camera video databases”, In Proc. Storage and Retrieval for Still Image and Video Databases IV, San Jose, CA, USA, 1-2 Feb. 1996, vol.2670:120-31.
· A . Gupta, S. Moezzi, A. Taylor, S. Chatterjee, R. Jain, M. Goldbaum, S. Burgess, “Content-based retrieval of ophtalmological images” In Proc. International Conference on Image Processing, Lusanne,1996, vol.3: 701-704, 1996.
· A. Gupta "Visual Information Retrieval: a Virage Perspective", Technical Report, Virage, Inc., 1996.
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A. Gupta and A. Bagchi, “Learning object models
in visual semantic networks”, In Proc. International Conference on Tools with
Artificial Intelligence, TAI '92, Arlington, VA, USA, 10-13 Nov. 1992.
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Gupta, A.;
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Gupta, A.;
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Gupta, A.;