|
A. Keshavarzi, N. Kannan and K. J. Kochut, “RegPattern2Vec: Link Prediction in Knowledge Graphs,”
2021 IEEE International IOT, Electronics and Mechatronics Conference (IEMTRONICS),
doi: 10.1109/IEMTRONICS52119.2021.9422604, pp. 1-7, 2021.
A. Priyadarshi and K. J. Kochut, “WawPart: Workload-Aware Partitioning of Knowledge Graphs,”
International Conference on Industrial, Engineering and Other Application of Applied Intelligent Systems,
Springer, IEA/AIE 2021: Advances and Trends in Artificial Intelligence. Artificial Intelligence Practices,
pp. 383-395, 2021.
A. Kushk and K.J. Kochut, “ESDL: Entity Summarization with Deep Learning,”
10th International Joint Conference on Knowledge Graphs (IJCKG), 2021.
R. Taujale, S. Soleymani, A. Priyadarshi, W. Yeung, K.J. Kochut, N. Kannan,
“The GTXplorer portal to access, navigate and mine evolutionary relationships of fold A glycosyltransferases,”
Glycobiology, Vol 30 (12), pp 1117-1118, 2021.
A. Keshavarzi and K. J. Kochut, “KGdiff: Tracking the Evolution of Knowledge Graphs,”
IEEE 21st International Conference on Information Reuse and Integration for Data Science (IRI), IEEE, pp. 279-286, 2020.
S. Pouriyeh, M. Allahyari, Q. Liu, G. Cheng, H. Arabnia, M. Atzori, F. Mohammadi, and K. J. Kochut,
“Ontology summarization: Graph-based methods and beyond,”
International Journal of Semantic Computing, Vol. 13, No. 02, 2019, pp. 259-283.
A. Kwon, S. Scott, R. Taujale, W. Yeung, K.J. Kochut, P.A. Eyers, and N. Kannan,
“Tracing the Origin and Evolution of Pseudokinases Across the Tree of Life,"
Science Signaling, 12(578), 19 pages. doi:10.1126/scisignal.aav3810, 2019.
S. Pouriyeh, M. Allahyari, G. Cheng, H. Arabnia, K. Kochut,
“R-LDA: Profiling RDF datasets using Knowledge-based Topic Modeling,”
13th IEEE International Conference on Semantic Computing, ICSC 2019, 2019, pp. 146-149.
S. Pouriyeh, M. Allahyari, Q. Liu, G. Cheng, H. Arabnia, M. Atzori, K. Kochut,
“Graph-based Methods for Ontology Summarization: A Survey,”
The First IEEE International Conference on Artificial Intelligence and Knowledge Engineering, AIKE 2018, 2018, pp. 85-92.
S. Pouriyeh, M. Allahyari, K. Kochut, G. Cheng, H. Arabnia,
“Combining Word Embedding and Knowledge-Based Topic Modeling for Entity Summarization,”
12th IEEE International Conference on Semantic Computing, ICSC 2018, 2018, pp. 252-255.
L.-C., Huang, K.E. Ross, T.R. Baffi, H. Drabkin, K.J. Kochut, Z. Ruan, P.D. Eustachio,
D. McSkimming, C. Arighi, C. Chen, D.A. Natale, C. Smith, P. Gaudet, A.C. Newton, C. Wu, and N. Kannan,
“Integrative annotation and knowledge discovery of kinase post-translational modifications and
cancer-associated mutations through federated protein ontologies and resources,”
Scientific Reports, Nature Publishing Group, Vol. 8, No. 1, PMID: 29695735, doi: 10.1038/s41598-018-24457-1, 2018.
K. Al Jadda, M. Korayem, C. Ortiz, T. Grainger, J.A. Miller, K.M. Rasheed,
K.J. Kochut, H. Peng, W.S. York, R. Ranzinger, M. Porterfield,
“Mining massive hierarchical data using a scalable probabilistic graphical model,”
Information Sciences, Vol. 425, pp. 62-75, 2018.
M. Allahyari, S. Pouriyeh, M. Assefi, S. Safaei, E. Trippe, J.B. Gutierrez, and K.J. Kochut,
“Text Summarization Techniques: A Brief Survey”,
International Journal of Advanced Computer Science and Applications (IJACSA), Vol. 8, No. 10, pp. 397-405, 2017.
M. Allahyari, S. Pouriyeh, K.J. Kochut, H.R. Arabnia,
“A Knowledge-based Topic Modeling Approach for Automatic Topic Labeling”,
Journal of Advanced Computer Science and Applications (IJACSA), Vol. 8, No. 9, pp. 335-349, 2017.
S. Pouriyeh, M. Allahyari, K.J. Kochut, G. Cheng, H.R. Arabnia,
“ES-LDA: Entity Summarization using Knowledge-based Topic Modeling”,
The 8th International Joint Conference on Natural Language Processing (IJCNLP 2017), Taiwan, pp. 316-325, 2017.
R. Ranzinger, K.J. Kochut, J.A. Miller, M. Eavenson, T. Lütteke, W.S. York,
“GLYDE-II: The GLYcan data exchange format,”
Perspectives in Science, Elsevier, Vol. 11, pp. 24-30, DOI: 10.1016/j.pisc.2016.05.013, 2017.
M. Allahyari and K.J. Kochut, “Using
Semantically-extended LDA Topic Model for Semantic Tagging,” International Journal of Semantic Computing, Vol. 10, No. 04, pp. 503-525, 2016.
M. Allahyari and K.J. Kochut, “Semantic Context-aware Recommendation via Topic Models Leveraging Linked Open Data,” In 17th International Conference on Web Information Systems Engineering (WISE 2016), Lecture Notes in Computer Science (LNCS), Vol. 10041, Springer Verlag, Heidelberg, Germany, 2016, pp. 263-277, 2016.
M. Allahyari and K.J. Kochut, “Discovering Coherent
Topics with Entity Topic Models,” In 2016 IEEE/WIC/ACM
International Conference on Web Intelligence (WI), pp. 26-33, 2016.
M. Allahyari and K.J. Kochut, “Semantic Tagging Using Topic Models exploiting Wikipedia Category Network,” Proceedings of the 10th IEEE International Conference on Semantic Computing (ICSC 2016), 2016, pp. 63 - 70.
J. A. Miller, Lakshmish Ramaswamy, Krys J. Kochut and Arash J.Z. Fard, “Directions for Big Data Graph Analytics Research,” International Journal of Big Data (IJBD), Vol. 2, No. 1, 2015, pp. 15-27.
J. A. Miller, Lakshmish Ramaswamy, Arash J.Z. Fard and Krys J. Kochut, “Research Directions in Big Data Graph Analytics,” Proceedings of the 4th IEEE International Congress on Big Data (ICBD'15), New York, New York, 2015, pp. 785-794.
M. Allahyari and K.J. Kochut, “Automatic Topic Labeling using Ontology-based Topic Models, ” 14th IEEE International Conference on Machine Learning and Applications (ICMLA 2015), 2015, pp. 259-264 . This paper won the Best Paper Award.
S. Dastgheib, D.I. McSkimming, N. Kannan, K.J. Kochut, “SPARQLing: A Graphical Interface for SPARQL,” The 14th International Semantic Web Conference (ISWC 2015), Demonstrations Track, 2015.
S. Dastgheib, D.I. McSkimming, N. Kannan, K.J. Kochut, “Creating Biomedical Ontologies Using mOntage,” 11-th International Conference on Data Integration in the Life Sciences, Springer International Publishing, 2015, pp. 118-132.
D.I. McSkimming, S. Dastgheib, E. Talevich, A. Narayanan, S. Katiyar, S.S. Taylor, K.J. Kochut, and N. Kannan, “ProKinO: A Unified Resource for Mining the Cancer Kinome,” Human Mutation, 36(2), ,2015, pp. 175-186.
M. Eavenson, K. Kochut, J.A. Miller, R. Ranzinger, M. Tiemeyer, K. Aoki and W. York, “Qrator: A web-based curation tool for glycan structures,” Glycobiology, 25(1), 2015, pp. 66-73.
A. Basharat, I.B. Arpinar, S. Dastgheib, U. Kursuncu, and K.J. Kochut, “Semantically Enriched Task and Workflow Automation in Crowdsourcing for Linked Data Management,” International Journal of Semantic Computing (IJSC), Vol. 08, No. 04, 2014, pp. 415-439.
S. Liu, Shasha, and K.J. Kochut, “A Semantic End-to-End Process Constraint Modeling Framework,” Eighth IEEE International Conference on Semantic Computing (ICSC), 2014, pp. 203-210.
M. Allahyari, K.J. Kochut, and M. Janik, “Ontology-Based Text Classification into Dynamically Defined Topics,” Eighth IEEE International Conference on Semantic Computing (ICSC), 2014, pp. 273-278.
A. Basharat, I.B. Arpinar, S.Dastgheib, U. Kursuncu, K.J. Kochut, and E. Dogdu, E., “CrowdLink: Crowdsourcing for Large-Scale Linked Data Management,” Eighth IEEE International Conference on Semantic Computing (ICSC), 2014, pp. 227-234.
S. Dastgheib, A. Mesbah and K.J. Kochut, “mOntage: Creating Self-Populating Domain Ontologies From Linked Open Data,” International Journal of Semantic Computing (IJSC), Vol. 7, No. 4, 2013, pp. 427-453.
S. Dastgheib, A. Mesbah and K.J. Kochut, “mOntage: Building Domain Ontologies from Linked Open Data,” Seventh IEEE International Conference on Semantic Computing, Irvine, California, USA, 2013, pp. 70-77.
S. Liu, M. Correa, and K.J. Kochut, "An Ontology-Aided Process Constraint Modeling Framework for Workflow Systems", Fifth International Conference on Information, Process, and Knowledge Management (eKNOW 2013), Nice, France, 2013, pp. 178-183.
G. Gosal, K.J. Kochut, N. Kannan, "ProKinO: An Ontology for Integrative Analysis of Protein Kinases in Cancer,” PLoS ONE 6(12): e28782. doi: 10.1371/journal. pone.0028782, 2011.
G. Gosal, N. Kannan, and K.J. Kochut, "ProKinO: A Framework for Protein Kinase Ontology," 2011 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2011, F.-X. Wu, M. Zaki, S. Morishita, Y. Pan, and S. Wong (Eds.), Atlanta, Ga., USA, 2011, pp. 550-555.
W.S. York, K.J. Kochut, and J.A. Miller, "Integration of Glycomics Knowledge and Data," in Handbook of Glycomics, R.D. Cummings and J.M. Pierce, Editors, Elsevier: Academic Press, San Diego, CA., 2009, pp. 179-195.
G.A. Silver, K.R. Bellipady, J.A. Miller, W.S. York and K.J. Kochut, “Supporting Interoperability Using the Discrete-event Modeling Ontology (DeMO)”, Proceedings of the 2009 ACM/IEEE Winter Simulation Conference (WSC’09), Austin, Texas, December 2009, pp. 1399-1410.
G. Gosal, K.J. Kochut, N. Kannan, "ProKinO: An Ontology for Integrative Analysis of Protein Kinases in Cancer,” PLoS ONE 6(12): e28782. doi: 10.1371/journal. pone.0028782, 2011.
G. Gosal, N. Kannan, and K.J. Kochut, "ProKinO: A Framework for Protein Kinase Ontology," 2011 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2011, F.-X. Wu, M. Zaki, S. Morishita, Y. Pan, and S. Wong (Eds.), Atlanta, Ga., USA, 2011, pp. 550-555.
M. Janik, K. Kochut, “Wikipedia in Action: Ontological Knowledge in Text Categorization”, Second IEEE International Conference on Semantic Computing, ICSC 2008, Santa Clara, CA, August 2008, pp. 268-275.
M. Janik, K. Kochut, “Training-less Ontology-based Text Categorization”, Workshop on Exploiting Semantic Annotations in Information Retrieval (ESAIR 2008) at the 30th European Conference on Information Retrieval (ECIR’08), Glasgow, Scotland, March 2008, pp. 3-14.
M. Eavenson, M. Janik, S. Nimmagadda, J. A. Miller, K. J. Kochut, and W. S. York, “GlycoBrowser: A Tool for Contextual Visualization of Biological Data and Pathways Using Ontologies”, 4th International Symposium on Bioinformatics Research and Applications, Atlanta, GA, 2008, pp. 305-316.
S. Nimmagadda, A. Basu, M. Eavenson, J. Han, M. Janik, R. Narra, K. Nimmagadda, A. Sharma, K. J. Kochut, J. A. Miller and W. S. York, “GlycoVault: A Bioinformatics Infrastructure for Glycan Pathway Visualization, Analysis and Modeling”, 5th International Conference on Information Technology: New Generations (ITNG), Las Vegas, NV, 2008, pp. 692-697.
L. Deligiannidis, K. Kochut and A. Sheth, “RDF Data Exploration and Visualization”, ACM Workshop on CyberInfrastructure: Information Management in eScience (CIMS), Lisboa, Portugal, 2007, pp. 39-46
Krys Kochut, Maciej Janik, "SPARQLeR: Extended Sparql for Semantic Association Discovery", Fourth European Semantic Web Conference, ESWC 2007, Innsbruck, Austria, June 2007, pp. 145-159.
C. Ramakrishnan, K. Kochut, A. Sheth, “A Framework for Schema-Driven Relationship Discovery from
Unstructured Text,” Fifth International Semantic Web Conference, Athens, Georgia, 2006; published in Lecture Notes in Computer Science (LNCS), Vol. 4273, Springer Verlag, Heidelberg, Germany, 2006, pp. 583-596.
M. Janik and K. Kochut, “BRAHMS: A WorkBench RDF Store And High Performance Memory System for Semantic Association Discovery,” Fourth International Semantic Web Conference, Galway, Ireland, 6-10 November 2005; published in Lecture Notes in Computer Science (LNCS), Vol. 3729, Springer Verlag, Heidelberg, Germany, 2005, pp. 431-445.
X. Yi and K. Kochut, “JCPNet Tool and Automated Analysis of Distributed Systems,” 43rd ACM Southeast Conference, March, 2005, Atlanta, GA.
A. Sheth, B. Aleman-Meza, B. Arpinar, C. Bertram, Y. Warke, C. Ramakrishnan, C. Halaschek, K. Anyanwu, D. Avant, F. S. Arpinar, K. Kochut, “Semantic Association Identification and Knowledge Discovery for National Security Applications,” Special Issue of Journal of Database Management on Database Technology for Enhancing National Security, Eds: L. Zhou and W. Kim, 16 (1), 2005, pp. 33-53.
W.S. York, A. Sheth, K. Kochut, J. Miller, C. Thomas, K. Gomadam, X. Yi, and M. Nagarajan, “Semantic Integration of Glycomics Data and Information,” 1st Workshop on Human Disease Glycomics/Proteome Initiative: Functional Glycomics in Disease, Osaka, Japan, 2004, pp. 23-24.
A. Sheth, W. York, C. Thomas, M. Nagarajan, J. Miller, K. Kochut, S. Saho, X. Yi, “Semantic Web technology in support of Bioinformatics for Glycan Expression,” W3C Workshop on Semantic Web for Life Sciences, Cambridge, Massachusetts, USA., 2004, pp. 27-28.
X. Yi and Krys J. Kochut, “A CP-nets-based Design and Verification Framework for Web Services Composition”, Proceedings of 2004 IEEE International Conference on Web Services, San Diego, California, USA, pp. 756-760, 2004.
X. Yi and Krys J. Kochut, “Towards Efficient Integration of Complex Web Services Using a Unified Model for Protocol and Process”, Proceedings of 5th International Conference on Internet Computing (IC 2004), Las Vegas, Nevada, USA. 2004, pp. 467-474.
X. Yi and K. Kochut, “Process Composition of Web Services with Complex Conversation Protocols: a Colored Petri Nets Based Approach,” Proceedings of the Design, Analysis, and Simulation of Distributed Systems 2004, Washington, D.C., 2004, pp. 141-148.
J. Cardoso, A. Sheth, J. Miller, J. Arnold, and K. Kochut, “Quality of Service for Workflows and Web Service Processes,” Journal of Web Semantics, Vol. 1, No. 3, 2004, pp. 281-308.
J. Arnold, H.B. Schuttler, D.A. Logan, D. Battogtokh, J. Griffith, B. Arpinar, S.M Bhandarkar, S. Datta, K.J. Kochut, E.Kraemer, J.A. Miller, A. Sheth, G. Strobel, T. Taha, B. Aleman-Meza, J. Doss, L. Harris, and A. Hyong, “Metabolomics,” in Handbook of Industrial Mycology, Mercel-Dekker, New York, N.Y., pp. 597-633, 2004.
Z. Luo, A. Sheth, K. Kochut, and B. Arpinar, “Exception Handling for Conflict Resolution in Cross-Organizational Workflows,” International Journal on Distributed and Parallel Databases, Vol. 13 , No. 3, 2003, pp. 271-306.
K. Anyanwu, A. Sheth, J. Cardoso, J. Miller, and K. Kochut, “Healthcare Enterprise Process Development and Integration,” Journal of Research and Practice in Information Technology, 35 (2), May 2003, pp. 83-98.
Z. Xu, B. Lance, C. Vargas, I. B. Arpinar, E. Kraemer, K. J. Kochut, J. A. Miller, J. R. Wagner, M. J. Weise, J. K. Wunderlich, J. Stringer, G. Smilian, M. T. Cushion and J. Arnold, "Mapping by Sequencing the Pneumocystis Genome Using the Ordering DNA Sequences V3 Tool," Genetics (GENE), Genetics Society of America, Vol. 163, 2003, pp. 1299-1313.
K. Kochut, J. Arnold, A. Sheth, J. Miller, E. Kraemer, B. Arpinar and Jorge Cardoso, “IntelliGEN: A Distributed Workflow System for Discovering Protein-Protein Interactions,” International Journal on Distributed and Parallel Databases, Vol. 13, No. 1, 2003, pp. 43-72.
D. Hall, J. Miller, J. Arnold, K. Kochut, A. Sheth, and M. Weise, “Using Workflow to Build an Information Management System for a Geographically Distributed Genome Sequence Initiative,” Genomics of Plants and Fungi, R.A. Prade and H.J. Bohner, Editors, Marcel Dekker, Inc., New York, N.Y., 2003, pp. 359-371.
B. Hammond, A. Sheth, K. Kochut, “Semantic Enhancement Engine: A Modular Document Enhancement Platform for Semantic Applications over Heterogeneous Content,” in Real World Semantic Web Applications, V. Kashyap and L. Shklar, Eds., IOS Press, 2002, pp. 29-49.
A.P. Sheth, J. Cardoso, J.A. Miller, K.J. Kochut and M. Kang, "QoS for Service-Oriented Middleware," Proceedings
of the 2002 Conference on Systemics, Cybernetics and Informatics (SCI'02), Orlando, Florida, 2002, pp. 528-534.
A. Sheth, C. Bertram, D. Avant, B. Hammond, K. Kochut, Y. Warke,
"Semantic Content Management for Enterprises and the Web'',
IEEE Internet Computing, July/August 2002, pp. 80-87.
Amit Sheth, John Miller, Krys Kochut and Budak Arpinar, "Research
in Multi-Organizational Processes and Semantic Information Bokering
at the LSDIS Lab,"SIGMOD Record, 30 (4) December 2001, pp.
123-128.
J. Cardoso, Z. Luo, J. Miller, A. Sheth and K. Kochut, ``Survivability
Architecture for Workflow Management Systems,'' Proceedings of
the 39th Annual ACM Southeast Conference (ACMSE'01), Athens,
Georgia, 2001, pp. 207-214.
Z. Luo, A. Sheth, K. Kochut, and J. Miller, ``Exception Handling
in Workflow Systems,'' International Journal of Artificial Intelligence,
Neural Networks, and Complex Problem-Solving Technologies, Vol.
13, No. 2, Kluwer Academic Publishers, 2000, pp. 125-147.
J. Miller, A. Sheth, K. Kochut, and Z. Luo, ``Recovery Issues
in Web-Based Workflow,'' Proceedings of the 12th International
Conference on Computer Applications in Industry and Engineering
(CAINE-99)'', Atlanta, Georgia, 1999, pp. 101-105.
K. Kochut, A. Sheth, and J. Miller, ``Optimizing Workflow,'' Component
Strategies, Vol. 1, No. 9, 1999, pp. 45-57.
M. Kang, J. Froscher, A. Sheth, K. Kochut, J. Miller, ``A Multilevel
Secure Workflow Management System,'' CAISE*99, 11th Conference
on Advanced Information Systems Engineering, Heidelberg, Germany,
published as Lecture Notes in Computer Science (LNCS), Vol. 1626,
Springer Verlag, Heidelberg, Germany, 1999, pp. 271-285.
J. Miller, A. Sheth, and K. Kochut, ``Perspectives in Modeling:
Simulation, Database and Workflow,'' Conceptual Modeling: Current
Issues and Future Directions: Selected Papers from the Workshop
on Conceptional Modeling, Lecture Notes in Computer Science,
Vol. 1565, P.P. Chen, J. Akoka, H. Kangassalo, B. Thalheim, Editors,
Springer Verlag, Berlin-Heidelberg, 1999, pp. 154-167.
Z. Luo, A. Sheth, J. Miller, and K. Kochut, ``Defeasible Workflow,
its Computation and Exception Handling,'' Online Proceedings of
the 1998 Computer-Supported Cooperative Work Workshop (CSCW-98):
Towards Adaptive Workflow Systems, Seattle, Washington (November
1998).
J. Miller, D. Palaniswami, A. Sheth, K. Kochut, and H. Singh,
``WebWork: METEOR2's Web-based Workflow Management System,'' Journal
of Intelligent Information Systems, Vol. 10 (2), 1998, pp. 186-215.
A. Sheth and K. Kochut, ``Workflow Application to Research Agenda:
Scalable and Dynamic Work Coordination and Collaboration Systems,'' Workflow Management Systems and Interoperability, Springer-Verlag,
Series F: Computer and Systems Sciences, Vol. 164, 1998, pp. 35-60
(also published as in proceedings Advances in Workflow Management
Systems and Interoperability, NATO-ASI, Istanbul, Turkey, August
1997).
A. Sheth and K. Kochut, ``Workflow Application to Research Agenda:
Scalable and Dynamic Work Coordination and Collaboration Systems,'' Advances in Workflow Management Systems and Interoperability,
NATO-ASI, Istanbul, Turkey, August 1997, pp. 34-59.
J. Miller, A. Sheth, K. Kochut, and D. Palaniswami, ``The Future
of Web-Based Workflows,'' Proceedings of the International Workshop
on Research Directions in Process Technology, Nancy, France,
July 1997.
A. Sheth, D. Worah, K. Kochut, J. Miller, K. Zheng, D. Palaniswami,
and S. Das, ``The METEOR Workflow Management System and Its Use
in Prototyping Significant Healthcare Applications,'' Towards
An Electronic Patient Record (TEPR '97), Conference proceedings,
April-May 1997, Nashville, TN.
R.A. Prade, J. Griffith, K.J. Kochut J. Arnold, W.E. Timberlake,
``In Vitro Reconstruction of the Aspergillus Nidulans Genome,'' Proceedings of the National Academy of Sciences, Vol. 94,
1997, pp. 14564-14569.
J. A. Miller, W. D. Potter, K. J. Kochut, and D. Ramesh, ``Object-Oriented
Simulation Languages and Environments: A Four-Level Architecture,'' Object Oriented Simulation, Zobrist, Editor, 1997, pp. 53-58.
|
