Keith Noto

knotocs.ucsd.edu ⋅ (608) 695-3215

Education

• Postdoc, University of California—San Diego, 2007-2009.
• PhD, University of Wisconsin—Madison, Computer Sciences, 2007.
  Thesis Title: Learning Expressive Computational Models of Gene Regulatory Sequences and Responses
• MS, University of Wisconsin—Madison, Computer Sciences, 2002.
• BA, University of Wisconsin—Madison, Computer Sciences and Philosophy, 1998.

Selected Peer-Reviewed Publications

• K. Noto, M. H. Saier, Jr. and C. Elkan.
  Learning to Find Relevant Biological Articles Without Negative Training Examples.
  Twenty-First Australasian Joint Conference on Artificial Intelligence (AI 2008) (acceptance rate 29%),
  In Lecture Notes in Bioinformatics 5360:202-213. Springer-Verlag.
• C. Elkan and K. Noto.
  Learning Classifiers from Only Positive and Unlabeled Data.
  Proceedings of the 14th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD 2008), 213-220 (acceptance rate 18.6%).
• K. Noto and M. Craven.
  Learning Hidden Markov Models for Regression using Path Aggregation.
  Proceedings of the 24th Uncertainty in Artificial Intelligence Conference (UAI 2008), 444-451 (acceptance rate 13%).
• K. Noto and M. Craven.
  Learning Probabilistic Models of cis-Regulatory Modules that Represent Logical and Spatial Aspects.
  Proceedings of the 2006 European Conference on Computational Biology (acceptance rate 18%),
  In Bioinformatics 23(2):e156-162.
• K. Noto and M. Craven.
  A Specialized Learner for Inferring Structured cis-Regulatory Modules.
  BMC Bioinformatics 7:528, 2006.
• K. Noto and M. Craven.
  Learning Regulatory Network Models that Represent Regulator States and Roles.
  RECOMB 2004 Workshop on Regulatory Genomics.
  In Lecture Notes in Bioinformatics 3318, pages 52-64. Springer-Verlag, 2004.
• M. H. Saier, Jr., M. R. Yen, K. Noto, D. G. Tamang, and C. Elkan.
  The Transporter Classification Database: Recent Advances.
  Nucleic Acids Research 37:(Database issue), D274-D278, 2009.
• A. K. Sehgal, S. Das, K. Noto, M. H. Saier, Jr. and C. Elkan.
  Identifying Relevant Data for a Biological Database: Handcrafted Rules Versus Machine Learning.
  In IEEE/ACM Transactions on Computational Biology and Bioinformatics (to appear, 2009)

Presentations and Posters

• Paper presentation, 2008 Conference on Uncertainty in Artificial Intelligence (UAI) in Helsinki, Finland.
• Invited speaker, National Library of Medicine (NLM) Informatics Training Conference 2006, hosted by Vanderbilt University.
• Paper presentation, 2006 European Conference on Computational Biology (ECCB) in Eilat, Israel.
• K. Noto and M. Craven, Poster: A Specialized Learner for Inferring Structured cis-Regulatory Modules. 2005 International Conference on Intelligent Systems for Molecular Biology (ISMB) in Detroit, MI.
• Paper presentation, RECOMB 2004 Workshop on Regulatory Genomics, hosted by the University of California—San Diego.

Research Experience

• Research Interests
  • Machine learning algorithm development and application.
  • Probabilistic methods/probabilistic graphical models (Bayesian networks, hidden Markov models).
  • Applying machine learning to biological domains (bioinformatics).
  • Development of software beyond research level to create real-world tools.
• Research Projects
  • Inferring gene regulatory networks from differential gene expression (microarray) and cellular conditions (RECOMB workshop 2004).
  • Discovering modules of transcription factor binding sites, including spatial and logical relationships between sites, primarily from sequence and expression data (ECCB 2006, BMC Bioinformatics 2006).
  • Adapting a sequence classification algorithm for regression tasks using hidden Markov models (UAI 2008) and support vector machines (2009;in preparation).
  • Biomedical text classification for a specialized database (KDD 2008, AJCAI 2008, NAR 2009).

Teaching Experience

• Taught Introduction to Artificial Intelligence  at the University of Wisconsin—Madison, 2002. 
  • Taught about 30 undergraduate students taking this "core" undergraduate course.
  • Prepared and gave lectures.
  • Prepared written and programming homework assignments.
  • Wrote and administered exams.
• Teaching assistant at the University of Wisconsin—Madison.
  • Machine Learning (Fall 2001, Prof. Jude Shavlik).
  • Introduction to Algorithms (Spring 2002, Prof. Deborah Joseph).
  • Advanced Artificial Intelligence (Fall 2002, Prof. David Page).
  • Introduction to Artificial Intelligence (Fall 2002, Prof. Jude Shavlik).
• Co-Mentor of an undergraduate student for the Computational Biology and Biostatistics (CBB) summer research program at the University of Wisconsin—Madison, June-August, 2006.
  • Designed a two-month computational biology project for the student.
  • Advised on all aspects of the project: Code design, computational experiments, analysis of results and a final report.
  • Attended a seminar course for mentors.
• Guest lecturer for
  • Introduction to Algorithms (University of Wisconsin—Madison).
  • Advanced Artificial Intelligence (University of Wisconsin—Madison).
  • Advanced Bioinformatics (University of Wisconsin—Madison).
  • Introduction to Artificial Intelligence (University of California—San Diego).

Professional Service

• I have reviewed papers for Machine Learning, the Journal of Machine Learning Research, the IBM Journal of Research and Development, and Data Mining and Knowledge Discovery
• I was on the 2008 program committee for the 2008 AAAI Conference on Artificial Intelligence.
• I served on an NSF grant review panel in the area of robust intelligence in 2009.

Awards

• Computation and Informatics in Biology and Medicine (CIBM) fellowship, April 2003-2006 (http://www.cibm.wisc.edu).
• CIBM fellowship (second award), April 2006-2007
• Travel fellowship award for ECCB 2006 from Biosapiens, funded by the EU.
• Travel fellowship award for the RECOMB 2004 workshop.
• Distinctive scholastic achievement (top 20% of graduating class), B.A. from the University of Wisconsin—Madison, 1998.

Software

• Rupa (Regression Using Path Aggregation), a package for learning a regression model (based on hidden Markov models) from the real-valued response associated with each of a set of training sequences (written in C and Python)
  (http://www.cs.ucsd.edu/~knoto/rupa).
• Scrm (Structured cis-Regulatory Modules, versions 1 and 2), packages for learning the arrangements of multiple DNA-binding sites from sequence data (written in C++)
  (http://pages.cs.wisc.edu/~noto/crm).

Previous Employment

• September 1998 - January 2002: Software engineer,  Legislative Technology Services Bureau (Wisconsin state government).
  • Developed software used by the Wisconsin state representatives, senators and staff, including several features of the Assembly and Senate voting systems.
  • Developed software that communicates with Wisconsin's "InSession" sites.
    • http://www.legis.state.wi.us/insession/assembly
    • http://www.legis.state.wi.us/insession/senate

References

• Prof. Mark Craven (Ph.D. advisor)
  University of Wisconsin—Madison, Dept. of Biostatistics and Medical Informatics
  1300 University Avenue #6730 MSC, Madison WI 53706
  E-mail: cravenbiostat.wisc.edu
  Phone: (608) 265-6181
• Prof. Charles Elkan (Postdoc Mentor)
  University of California at San Diego, Dept. of Computer Science and Engineering
  9500 Gilman Drive (EBU3B, MC0404), La Jolla, CA 92093
  E-mail: elkancs.ucsd.edu
  Phone: (858) 534-8897
• Prof. Milton H. Saier, Jr.
  University of California at San Diego, Dept. of Biology
  9500 Gilman Drive, La Jolla, CA 92093
  E-mail: saierbiomail.ucsd.edu
  Phone: (858) 534-4084
• Prof. Jude Shavlik
  University of Wisconsin—Madison, Dept. of Computer Sciences
  1210 West Dayton Street, Madison WI 53706
  E-mail: shavlikcs.wisc.edu
  Phone: (608) 263-7625
• Prof. David Page
  University of Wisconsin—Madison, Dept. of Biostatistics and Medical Informatics
  1300 University Avenue #6743 MSC, Madison WI 53706
  E-mail: pagebiostat.wisc.edu
  Phone: (608) 265-6186
• Jeffrey Ylvisaker
  Director, Legislative Technology Services Bureau (Wisconsin)
  17 W. Main St. Suite 200, Madison WI 53703
  E-mail: jeff.ylvisakerlegis.state.wi.us
  Phone: (608) 267-9528