About:

Abraham Heifets holds a PhD from the Department of Computer Science at the University of Toronto, where he was a member of the Ontario Cancer Institute, University Health Network of research hospitals, MaRS, Terrence Donnelly Centre for Cellular and Biomolecular Research, and the IBM Life Sciences Discovery Centre. He was supervised by Prof. Igor Jurisica. He received his Bachelors and Masters degrees from Cornell University.

Abraham co-founded Atomwise. Previously, he applied classical artificial intelligence techniques to organic synthesis planning. Prior to attending the University of Toronto, he explored high-performance processing of XML at the IBM T.J. Watson Research Center. Previously, he worked on a world champion robotic soccer team, a publish-subscribe system for location-based services, and single-agent search algorithms.

Projects:

• Computer-Assisted Organic Synthesis - Tools to simplify drug discovery, design and production.

• SCRIPDB - Patent-oriented molecule search. Full paper in Nucleic Acids Research.

• LigAlign - Automated Ligand-Based Active Site Alignment. Poster presented at ISMB2008. Full paper in Journal of Molecular Graphics and Modelling.

Publications:

• Heifets, A., AUTOMATED SYNTHETIC FEASIBILITY ASSESSMENT: A DATA-DRIVEN DERIVATION OF COMPUTATIONAL TOOLS FOR MEDICINAL CHEMISTRY . PhD thesis.
• Heifets, A., Jurisica, I., Construction of New Medicines via Game Proof Search. Proceedings of the 26th AAAI Conference on Artificial Intelligence (Toronto, Canada, July 22-26, 2012). AAAI '12. AAAI Press.
• Heifets, A., Jurisica, I., SCRIPDB: a portal for easy access to syntheses, chemicals and reactions in patents. Nucl. Acids Res. (2012) 40 (D1): D428-D433. doi: 10.1093/nar/gkr919
• Heifets, A., Lilien, R., LigAlign: Flexible ligand-based active site alignment and analysis. Journal of Molecular Graphics and Modelling. Volume 29, Issue 1, 24 August 2010, Pages 93-101.
• Matsa, M., Perkins, E., Heifets, A., Kostoulas M. G., Silva, D., Mendelsohn, N., Leger, M. A High-Performance Interpretive Approach to Schema-Directed Parsing. Proceedings of the 16th International Conference on World Wide Web (Banff, Canada, May 8 - 12, 2007). WWW '07. ACM Press, New York, NY, 1093-1102. Presented at WWW2007. [PDF]
• Kostoulas, M. G., Matsa, M., Mendelsohn, N., Perkins, E., Heifets, A., and Mercaldi, M. XML Screamer: an integrated approach to high performance XML parsing, validation and deserialization. Proceedings of the 15th International Conference on World Wide Web (Edinburgh, Scotland, May 23 - 26, 2006). WWW '06. ACM Press, New York, NY, 93-102. Nominated for Best Paper Award. [PDF]
• Perkins, E., Matsa, M., Kostoulas, M. G., Heifets, A., and Mendelsohn, N. 2006. Generation of efficient parsers through direct compilation of XML Schema grammars. IBM Systems Journal 45(2):225-245. 2006. [PDF]
• Perkins, E., Kostoulas, M. G., Heifets, A., Matsa, M., Mendelsohn, N. Performance Analysis of XML APIs. Proceedings of the XML 2005 Conference and Exposition (November 14-18, 2005). XML2005. [PDF]

Patents:

• Heifets, A., Matsa, M., Method for dynamically streaming an XSLT transformation. US Patent 7,603,655. Granted October 13, 2009.
• Babu, A., Heifets, A., Krauszer, A., Paterson, R., White Eagle, B., System and method for aggregating information to determine users' locations. US Patent 7,139,252. Granted November 21, 2006.
• Babu, A., Heifets, A., Krauszer, A., Paterson, R., White Eagle, B., System and method for handling location information. US Patent Application 20020143930. Filed October 3, 2002.
• Quan, D., Perkins, E., Murthy, C., Heifets, A., Kesselman, J., Matsa, M., Methods and apparatus for views of input specialized references. US Patent Application 20080034010. Filed August 7, 2006.
• Heifets, A., Kostoulas, M., Matsa, M., Perkins, E., High-level Virtual Machine for Fast XML Parsing and Validation. US Patent Application 20080104592. Filed June 5, 2007.
• Heifets, A., Kostoulas, M., Matsa, M., Perkins, E., Schema Specific Parser Generation. US Patent Application 20080104105. Filed June 5, 2007.
• Heifets, A., Kostoulas, M., Matsa, M., Perkins, E., Orthogonal Integration of De-serialization into an Interpretive Validating XML Parser. US Patent Application 20080104095. Filed June 5, 2007.

Contact:

• Email:

  abeweb@cs.toronto.edu

• Office:

  [Map1] [Map2]
  Ontario Cancer Institute
  Division of Signaling Biology
  IBM Life Sciences Discovery Centre
  Toronto Medical Discovery Tower, 9-303
  101 College Street Toronto, Ontario M5G 1L7
  416.581.7443
  

• Mailing:

  Abraham Heifets c/o Soleil Miron
  Toronto Medical Discovery Tower, 9-801
  101 College Street Toronto, Ontario M5G 1L7