Chitta Baral

Professor

Short Bio.

Ph.D in Computer Science (1991), University of Maryland.

Research lab and other affiliations at ASU

Projects

• CBioC:: Annotate while you read: a short blurb on CBioC in June 23rd, 2006 issue of Science Magazine.

Office Hours

** Brickyard 572 **

• Fall 2010 W 12:00-1:00 PM; Th 4:30 - 5:30 PM

Selected Recent Teaching

• [Spring 2003: CSE 591 D : Computational Molecular Biology ]; [Fall 2003: CSE 591 : Application of AI to Molecular Biology ]; [Spring 2004: CSE 355 : Introduction to theoretical Computer Science ]; [Fall 2004: CSE 591 : Autonomous agents: theory and practice ]; [Spring 2005: CSE 571 : Artificial Intelligence ]; [Fall 2005 : I was on Sabbatical]; [Spring 2006: [CSE 494/598/CBS 598: Application of AI to molecular biology ]; [Fall 2006: CSE/BMI/CBS 591 Computational Pharmacogenomics ]; [Spring 2007: 35714 CSE 571 Artificial Intelligence]; [Fall 2007: 85005 CSE 591-1002 Autonomous Agents]

• Spring 2008

  CSE 355-1001 LEC 24974 : Introduction to theoretical Computer Science
  1:40 -- 2:55 PM, TTh BYAC 150
  

• Fall 2008

  CSE 576: Introduction to Natural Language Processing (co-taught with Dr. Greg Aist)
  12:15 -- 1:30 PM, MW BYAC 240
  

• Spring 2009

  CSE 591: Multi-agent Systems (In this class we will discuss issues about agents in a multi-agent setting. Of particular concern will be reasoning about agents' knowledge about other agents and planning in a multi-agent setting. This will be a PhD level class and we will go over many papers.)

• Fall 2009

  CSE 101 - Introduction to Computer Science & Engineering: M 12:55 PM - 1:45 PM BYAC 270 (Lab Th: 2 - 4:50 PM)

  CSE 591 - Analysis of Biomolecular networks and their components: T Th 4:30 Pm - 5:45 PM. (Dr. Joerg Hakenberg is the main instructor of this class.) BYAC 190.

• Spring 2010

  CSE 576 - Topics in Natural Language Processing: M W 3:30 - 4:45 PM BYAC 240

• Fall 2010

  CSE 471/598 Intro. To Artificial Intelligence: T Th 3:15 - 4:30 PM BYAC 190

  ASU 101 The ASU Experience: W 10:45 AM - 11:35 AM BYENG 510

Past teaching

Research

• Research Statement
• Selected recent research results and papers (1992-2005)
• Selected Publications (and drafts) between 2006-now
  • Chitta Baral, Gregory Gelfond, Enrico Pontelli, Tran Cao Son: Logic programming for finding models in the logics of knowledge and its applications: A case study. Theory and Practice of Logic Programming. 10(4-6): 675-690 (2010)

  • J. Hakenberg, Robert Leaman, Nguyen Ha Vo, Siddhartha Jonnalagadda, Ryan Sullivan, Christopher Miller, Luis Tari, Chitta Baral, Graciela Gonzalez: Efficient Extraction of Protein-Protein Interactions from Full-Text Articles. IEEE/ACM Trans. Comput. Biology Bioinform. 7(3): 481-494 (2010)

  • L. Tari, S. Anwar, S. Liang, J. Cai and C. Baral. Discovering drug interactions: a text mining and reasoning approach based on properties of drug metabolism. To appear in Bioinformatics issue for ECCB. (accepted for ECCB 2010.)

  • L. Tari, P. Tu, J. Hakenberg, Y. Chen, T. Son, G. Gonzalez and C. Baral. Parse Tree Database for information Extraction. To appear in IEEE Transactions on Knowledge & Data Engineering.

  • Vo Ha Nguyen, J. Hakenberg, Luis Tari, Chitta Baral, Illes Solt, Domonkos Tikk, Quang Long Nguyen, Ulf Leser: Molecular event extraction from Link Grammar parse trees in the BioNLP'09 Shared Task. To appear in Computational Intelligence (COIN), 2010.

  • Luis Tari, Saadat Anwar, Shanshan Liang, Jorg Hakenberg, Chitta Baral. Synthesis of Pharmacokinetic Pathways through Knowledge Acquisition and Automated Reasoning. Pacific Symposium on Biocomputing 15:465-476(2010)

  • Juraj Dzifcak, Matthias Scheutz, Chitta Baral and Paul Schermerhorn (2009) What to do and how to do it: Translating natural language directives into temporal and dynamic logic representation for goal management and action execution. Proceedings of the 2009 IEEE international conference on robotics and automation (ICRA '09)

  • Chitta Baral, Michael Gelfond and Nelson Rushton. Probabilistic Reasoning with Answer Sets. In Theory and Practice of Logic Programming. 2009

  • Luis Tari, Joerg Hakenberg, Graciela Gonzalez, Chitta Baral. Querying parse tree database of medline text to synthesize user-specific biomolecular networks. In PSB'09.

  • Chitta Baral, Jicheng Zhao. Non-monotonic Temporal Logics that Facilitate Elaboration Tolerant Revision of Goals. AAAI 2008, pages 406-411.

  • Chitta Baral, Juraj Dzifcak, Tran Cao Son. Using Answer Set Programming and Lambda Calculus to Characterize Natural Language Sentences with Normatives and Exceptions.AAAI 2008, pages 818-823.

  • C. Baral, T. Eiter, M. Bjaereland and M. Nakamura. Maintenance goals of agents in a dynamic environment: formulation and policy construction. AI Journal. 172 (12-13), pages 1429-1469. 2008.

  • N. Tran, C. Baral. (2007) Hypothesizing and reasoning about signaling networks. Journal of Applied Logic (In press).

  • N. Tran, C. Baral. (2007) Reasoning about non-immediate triggers in biochemical networks. Annals of Mathematics and Artificial Intelligence (In press).

  • M. Balduccini, C. Baral and Y. Lierler. Knowledge representation and Question Answering. In Handbook of Knowledge Representation, editors Vladimir Lifschitz, Frank van Harmelen and Bruce Porter, 2008.

  • Chitta Baral, Juraj Dzifcak, Luis Tari: Towards Overcoming the Knowledge Acquisition Bottleneck in Answer Set Prolog Applications: Embracing Natural Language Inputs. ICLP 2007: 1-21 (invited paper) (presentation)

  • Phan Huy Tu, Tran Cao Son, and Chitta Baral. Reasoning and Planning with Sensing Actions, Incomplete Information, and Static Causal Laws using Answer Set Programming. Theory and Practice of Logic Programming. Volume 7, Issue 4, July 2007.

  • Chitta Baral, Jicheng Zhao. Non-monotonic Temporal Logics for Goal Specification. In Proc. of IJCAI 2007. (abstract) pages 236-242.

  • Chitta Baral, Matt Hunsaker. Using the Probabilistic Logic Programming Language P-log for Causal and Counterfactual Reasoning and Non-Naive Conditioning. In Proc. of IJCAI 2007. (abstract) pages 243-249.

  • Graciela Gonzalez, Juan C. Uribe, Luis Tari, Colleen Brophy, Chitta Baral. Mining Gene-Disease Relationships from Biomedical Literature: Weighting Protein-protein Interactions and Connectivity. Pacific Symposium on Biocomputing 12:28-39(2007)

  • Tuan Le, Chitta Baral, Son Tran. A State-Based Regression Formulation for Domains with Sensing Actions and Incomplete Information. In Logical Methods in Computer Science (Electronic journal) Volume 2, Issue 4, 2006. (no page numbers)

  • Tran Cao Son, Chitta Baral, Sheila McIlraith, and Nam Tran. Planning with domain-dependent knowledge of different kinds -- an answer set programming approach. ACM Transactions on Computational Logic. Volume 7, Number 4 (October 2006), pages 1-70.

  • Chitta Baral, Juraj Dzifcak, Nam Tran and Jicheng Zhao. Reasoning about Actions in Biophysical Systems. AAAI 2006 Workshop on Cognitive Robotics.

  • Enrico Pontelli, Chitta Baral and Tran Son. A Framework for Composition and Interoperation of Rules in the Semantic Web. In Proceedings of Rules and Rule Markup languages for the Semantic Web. (RuleML 2006). pages 39-50. (extended version with additional co-author Omar Elkhatib)

• Publications in 2005-06

  • Goal specification, non-determinism and quantifying over policies. Chitta Baral and Jicheng Zhao. To appear in AAAI'06.

  • Macros, Macro calls and use of ensembles in modular answer set programming. Chitta Baral, Juraj Dzifcak and Hiro Takahashi. To appear in ICLP'06.

  • Genomic information retrieval through seletive extraction and tagging by the ASU-BioAI Group. Lian Yu, Syed Toufeeq Ahmed, Graciela Gonzalez, Brandon Logsdon, Mutsumi Nakamura, Shawn Nikkila, Kalpesh Shah, Luis Tari, Ryan Wendt, Amanda Zeigler and Chitta Baral. Proceedings of the 2005 TREC Genomics track.

  • Joint learning of logic relationships for studying protein function using phylogenetic profiles and the Rosetta Stone method. Xin Zhang, Seungchan Kim, Tie Wang and Chitta Baral. To appear in IEEE Transactions on Signal Processing.

  • Knowledge-Based Framework for Hypothesis Formation in Biochemical Networks: application to the p53 network. Nam Tran, Chitta Baral, Vinay Nagaraj and Lokesh Joshi. Proc. of the European Conference on Computational Biology (ECCB'2005), Bioinforamtics, 21: ii213-ii219. (A preliminary version in the DILS'05 workshop.)

  • Using AnsProlog with Link Grammar and WordNet for QA with deep reasoning. Luis Tari and Chitta Baral. Proc. of AAAI'05 workshop on Inference for Textual Question Answering.

  • Textual Inference by combining multiple logic programming paradigms. Chita Baral, Gregory Gelfond, Michael Gelfond and Richard Scherl. Proc. of AAAI'05 workshop on Inference for Textual Question Answering.

  • Issues in reasoning about cellular interactions: necessity of event ordering knowledge. Nam Tran, Chitta Baral and Carron Shankland. Proc. of AAAI'05, 676-681.

  • Reasoning about intended actions. Chitta Baral and Michael Gelfond. Proc. of AAAI'05, 689-694.

  • Using SAT and Logic Programming to Design Polynomial-Time Algorithms for Planning in Non-deterministic Domains. Chitta Baral, Thomas Eiter and Jicheng Zhao. Proc. of AAAI'05, 575-583.

  • Reasoning about the ERK signal transduction pathway using BioSigNet-RR. Carron Shankland, Nam Tran, Chitta Baral, and Walter Kolch. In Computational Methods in Systems Biology (CMSB'05) 2005. 3-5 April 2005, Edinburgh, Scotland.

  • An algorithm to learn causal connection between genes from steady state data: simulation and its application to melanoma dataset. Xin Zhang, Chitta Baral, Seungchan Kim. Proc. of 10th Conference on Artificial Intelligence in Medicine (AIME 05) 23 - 27 July 2005 Aberdeen, Scotland. pages 524-534.

  • Knowledge-Based Integrative Framework for Hypothesis Formation in Biochemical Networks. Nam Tran, Chitta Baral, Vinay Nagaraj and Lokesh Joshi. Proc. of the 2nd International Workshop on Data Integration in the Life Sciences (DILS'05), San Diego, July 20-22, 2005. 121-136.

  • BioLog: A Browser Based Collaboration and Resource Navigation Assistant for BioMedical Researchers. Prabhdeep Singh, Ravi Bhimavarapu, Hasan Davulcu, Chitta Baral, Seungchan Kim, Huan Liu, Mike Bittner and I.V. Ramakrishnan. Proc. of the 2nd International Workshop on Data Integration in the Life S ciences (DILS'05), San Diego, July 20-22, 2005. 19-30.

  • Collaborative Curation of Data from Bio-medical Texts and Abstracts and its integration. Chitta Baral, Hasan Davulcu, Mutsumi Nakamura, Prabhdeep Singh, Lian Yu and Luis Tari. Proc. of he 2nd International Workshop on Data Integration in the Life Sciences (DILS'05), San Diego, July 20–22, 2005. 309-312.

  • IntEx: A Syntactic Role Driven Protein-Protein Interaction Extractor for Bio-Medical Text. Syed Toufeeq Ahmed, Deepthi Chidambaram, Hasan Davulcu and Chitta Baral. Proc. of BioLINK SIG: Linking Literature, Information and Knowledge for Biology, a Joint Meeting of The ISMB BioLINK Special Interest Group on Text Data Mining and The ACL Workshop on Linking Biological Literature, Ontologies and Databases: Mining Biological Semantics (Biolink'2005), Detroit, Michigan, June 24, 2005.

  • Logic Programming and Reasoning about actions. C. Baral and M. Gelfond. In Handbook of Temporal reasoning in AI. Michael Fisher, Dov Gabbay, Lluis Vila editor. Elsevier Publications, 2005. pages 389-428.

  • Knowledge updates: Semantics and complexity issues. C. Baral and Y. Zhang. Artificial Intelligence, 164(1-2): 209-243 (2005)

  • Understanding the global properties of functionally related gene networks using the gene ontology. L. Tari, C. Baral and Partha Dasgupta. In Proceedings of Pacific Symposium on Biocomputing 2005. (PSB'05), pages 209-220.

  • Domain-Dependent Knowledge in Answer Set Planning. Tran Cao Son, Chitta Baral, Nam Tran, and Sheila McIlraith. To appear in ACM transactions on computational logic. (final version submitted for print in September 2004)

• Graduate Text Book cum Research Monograph:
  Knowledge representation, reasoning and declarative problem solving , Cambridge University Press, 2003. Slides based on the book. (pdf) (ps)
• A (somewhat dated) list of my reports, publications -- by research areas
• Lecture notes and tutorial slides.
• My Google Scholar listing; DBLP listing ; Computer Science Bibliography Listing ; and citeseer citations.
• Research Genealogy starting from thesis advisor .
• More Information

A Sample of Current and Recent Sponsored Projects

• A systematic approach to reasoning about actions and change. NSF CAREER award. 1995-2001
• Reasoning and planning with sensing actions and their applications. NSF. 4/1/00 -- 3/31/05.
• Agent development and control verification using dual characterizations. NASA 01-04.
• Answering complex questions and performing deep reasoning in advance question answering systems , AQUAINT program , ARDA 04-06.
• Integrating knowledge based reasoning, common sense reasoning and natural language semantics in a QA system, DTO/IARPA. 10/1/06-12/31/07.

• Generalized Text Extraction form Life Science and Biomedicine Abstracts: empowering the CBioC Mass Collaborative Curation and Reasoning Systems. Science Foundation of Arizona, 03/01/07 - 08/28/08.

• Knowledge representation, reasoning, and problem solving in a cellular domain, NSF 8/1/04-7/31/09
• Human-Robot Interaction in Littoral and Urban Military Domains: Human-Unmanned Systems Interactions. MURI award from ONR with Indiana University as the lead, 7/1/2007-6/30/2012.

Student Co-authors with thesis/project

• Tran Cao Son (Ph.D 2000), Professor, New Mexico State University. Selected Publications
• Raul Trejo , (Ph.D 2001), Assistant Professor, ITESM, Mexico, Selected Publications
• Graciela Gonzalez , (Ph.D 2000), Assistant Research Professor, Arizona State University. Selected Publications.
• Le-Chi Tuan , (Ph.D Dec 2004), Selected Publications
• Nam Tran , (Ph.D defended Oct 27 2006) Selected Publications , Post-doctoral researcher, UCLA
• Xin Zhang (Ph.D defended July 10 2008), Cisco
• Jicheng Zhao (continuing Ph.D)
• Luis Ng Tari (Ph.D defended Summer 2009), F. Hoffmann-La Roche Ltd
• Juraj Dzifcak (continuing Ph.D)
• Bob Leaman (Continuing Ph.D)
• Saadat Anwar (Continuing Ph.D)
• Gregory Gelfond (Started Ph.D)
• Jiayu Zhou (Started Ph.D)
• Shanshan Liang (Started Ph.D)
• Alfredo Gabaldon , (MS 1996, Ph.D at U of Toronto 2004, Currently researcher at NICTA Sydney) Selected Publications
• David Morales (MS 1998), Selected Publications
• Arron Hardesty (MS 2000), Selected Publications
• Amarendra Nandigam (MS 1998), Selected Publications

Curriculum Vitae (postscript), (pdf)

Honors, Awards, and Professional Service

• Associate Editor, 2007-2010 Journal of AI Research.
• Area Editor (Non-monotonic reasoning and answer sets), ACM Transactions on Computational Logic
• Editorial Advisor, Theory and Practice of Logic Programming, a Cambridge University Press Journal.
• Invited Speaker, KR 2010. (slides)
• Invited Speaker, AAAI'05. (slides)
• Best paper award, CooPIS 2000.
• Best paper award, ATAL (Agents, theories and languages) 99.
• Research Initiation Award, National Science Foundation, 1992-1995
• CAREER Award, National Science Foundation, 1995-2001
• 3rd place finish in the AAAI 96 robot contest for office navigation.
• 1st place finish in the AAAI 97 robot contest for home vacuuming.

Editorials and Op-eds in Indian Express: with references

• January 20th 2007: Looking for the lost keys under the street lamp: Why central universities in bac kward/tribal district clusters make sense?
• December 21st 2006: Will the HRD ministry and planning commission take steps to correct the existing regional imbalance in higher education opportunities?
• Nov 17th 2006: The Gold that keeps Orissa poor.
• July 11th and July 1st 2006: Inequity and favouritism in India's Human Resource Developement(HRD) budget allocations
  • http://www.indianexpress.com/story/7592.html
  • http://www.indianexpress.com/story/8266.html

Other Interests

Member, Director's Advisory Board, Indian Institute of Technology, Bhubaneswar.

Member, Higher Education Task Force, Orissa, India.

Blog/Compilation on Education in Orissa and India.

Blog/Compilation on infrastructure development of Orissa.

Tweets on Orissa.

Travel pictures: [Yellowstone, May27-29 2005]