Department of Computer Science

Machine Learning Research Group

University of Texas at Austin Artificial Intelligence Lab

Publications: Bioinformatics

Bioinformatics concerns the development of computer databases and algorithms for learning, managing and processing biological information. Currently we are focusing on extracting structured information such as protein names and relationships from biological documents using natural language learning for information extraction.

By mining over 750,000 Medline abstracts for human protein interactions and integrating the results with existing databases, we have developed a fairly comprehensive database of 31,609 known human protein interactions. The resulting database is accessible though a web interface at Human Gene ID-SERVE


Show abstracts
  1. Sparse Meets Dense: A Hybrid Approach to Enhance Scientific Document Retrieval
    [Details] [PDF] [Slides (PPT)]
    Priyanka Mandikal, Raymond Mooney
    In The 4th Workshop on Scientific Document Understanding, AAAI, February 2024.
  2. Discriminative Structure and Parameter Learning for Markov Logic Networks
    [Details] [PDF] [Slides (PPT)]
    Tuyen N. Huynh and Raymond J. Mooney
    In Proceedings of the 25th International Conference on Machine Learning (ICML), Helsinki, Finland, July 2008.
  3. Integrating Co-occurrence Statistics with Information Extraction for Robust Retrieval of Protein Interactions from Medline
    [Details] [PDF]
    Razvan Bunescu, Raymond Mooney, Arun Ramani and Edward Marcotte
    In Proceedings of the HLT-NAACL Workshop on Linking Natural Language Processing and Biology (BioNLP'06), 49-56, New York, NY, June 2006.
  4. Consolidating the Set of Known Human Protein-Protein Interactions in Preparation for Large-Scale Mapping of the Human Interactome
    [Details] [PDF]
    A.K. Ramani, R.C. Bunescu, Raymond J. Mooney and E.M. Marcotte
    Genome Biology, 6(5):r40, 2005.
  5. Using Biomedical Literature Mining to Consolidate the Set of Known Human Protein-Protein Interactions
    [Details] [PDF]
    A. Ramani, E. Marcotte, R. Bunescu and Raymond J. Mooney
    In Proceedings of the ISMB/ACL-05 Workshop of the BioLINK SIG: Linking Literature, Information and Knowledge for Biology, Detroit, MI, June 2005.
  6. Comparative Experiments on Learning Information Extractors for Proteins and their Interactions
    [Details] [PDF]
    Razvan Bunescu, Ruifang Ge, Rohit J. Kate, Edward M. Marcotte, Raymond J. Mooney, Arun Kumar Ramani, and Yuk Wah Wong
    Artificial Intelligence in Medicine (special issue on Summarization and Information Extraction from Medical Documents)(2):139-155, 2005.
  7. Collective Information Extraction with Relational Markov Networks
    [Details] [PDF]
    Razvan Bunescu and Raymond J. Mooney
    In Proceedings of the 42nd Annual Meeting of the Association for Computational Linguistics (ACL-04), 439-446, Barcelona, Spain, July 2004.
  8. Relational Markov Networks for Collective Information Extraction
    [Details] [PDF]
    Razvan Bunescu and Raymond J. Mooney
    In Proceedings of the ICML-04 Workshop on Statistical Relational Learning and its Connections to Other Fields, Banff, Alberta, July 2004.
  9. Learning to Extract Proteins and their Interactions from Medline Abstracts
    [Details] [PDF]
    Razvan Bunescu, Ruifang Ge, Rohit J. Kate, Raymond J. Mooney, Yuk Wah Wong, Edward M. Marcotte, and Arun Kumar Ramani
    In Proceedings of the ICML-03 Workshop on Machine Learning in Bioinformatics, 46-53, Washington, DC, August 2003.
  10. Extracting Gene and Protein Names from Biomedical Abstracts
    [Details] [PDF]
    Razvan Bunescu, Ruifang Ge, Raymond J. Mooney, Edward Marcotte, and Arun Kumar Ramani
    March 2002. Unpublished Technical Note.