CURRICULUM VITAE

OREGON HEALTH & SCIENCE UNIVERSITY

 

 

 

NAME:

 

Aaron Michael Cohen

 

UPDATED:

 

Sep 08 2008

 

 

 

 

 

 

 

 

 

 

 

PRESENT POSITION AND ADDRESS:

 

Academic Rank:

 

Assistant Professor

 

Department/Division:

 

Medical Informatics and Clinical Epidemiology

 

Professional Address:

 

3181 S.W. Sam Jackson Park Road, Portland, OR, 97239

Mail Code: BICC

 

E-Mail Address:

 

cohenaa@ohsu.edu

 

Undergraduate and Graduate (Include Year, Degree, and Institution):

  1. 1980-1983, Interdisciplinary Engineering, College of Engineering, University of Michigan, Ann Arbor, Michigan
  2. 1989-1991, Computer Engineering, Department of Computer and Electrical Engineering, Northeastern University, Boston, Massachusetts
  3. 2005, M.S. Biomedical Informatics, Oregon Health & Science University, Portland, Oregon

 

Postgraduate (Include Year, Degree, and Institution):

1. 1987, M.D., University of Michigan, School of Medicine

2. 1987-1988, Transition Year Resident, Internal Medicine Department, Carney Hospital, Boston, Massachusetts

3. 2002-2005, National Library of Medicine Medical Informatics Fellow, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, Oregon

 

Certification (Include Board, Number, Date, and Recertification):

 

Licenses (Include State, Date, Status, Number, and Renewal Date):

Medicine, Massachusetts, 1988, Inactive

 

III.  PROFESSIONAL EXPERIENCE

 

Academic (Include Year, Position, and Institution):

  1. 2002-2004, Teaching Assistant and Lecturer, Computer Science, Department of Medical Informatics and Clinical Epidemiology, School of Medicine, Oregon Health & Science University, Portland, Oregon
  2. 2005-present, Assistant Professor, Department of Medical Informatics and Clinical Epidemiology, School of Medicine, Oregon Health & Science University, Portland, Oregon

 

Administrative (Include Year, Position, and Institution):

None

 

Other (Include Year, Position, and Institution):

  1. 1988-1990, Chief Computer Engineer, Nuclear Medicine Department, Beth Israel Hospital, Brookline, Massachusetts
  2. 1990-1991, Senior Software Engineer, Advanced Video Products, Littleton, Massachusetts
  3. 1991-1993, Associate, Advanced Technology Group, Coopers and Lybrand, Boston, Massachusetts
  4. 1993-1995, Member of Technical Staff, Aware Corporation, Cambridge, Massachusetts
  5. 1995-1998, Staff Software Engineer, Business Video Conferencing Products, Intel Corporation, Hillsboro, Oregon
  6. 1998-2002, Senior Staff Software Engineer, Intel Labs, Intel Corporation, Hillsboro, Oregon

 

IV.  SCHOLARSHIP

 

Area(s) of Research/Scholarly Interest:

Application of text mining and machine learning techniques to the scientific literature and curated databases for aiding researchers in effectively using and exploring the ever-expanding biomedical knowledge base.

 

Funded Grants/Publications/Other Creative Work:

 

Funded Grants

Assisting Systematic Review Preparation Using Automated Document Classification
National Library of Medicine (NLM) Grant Number 1R01LM009501-01
Project Period: 07/15/2007 – 07/14/2010
Principal Investigator: Aaron M. Cohen, MD, MS

 

Identifying Candidate Researchers for Collaboration in Clinical and Translational Research

Oregon Clinical and Translational Research Institute (OCTRI) Pilot Grant

Project Period: 06/01/2008 – 05/31/2009
Principal Investigator: Aaron M. Cohen, MD, MS

 

Peer-reviewed Publications

  1. Cohen AM, Parker JA, Donohoe K, Jansons D, Kolodny GM. Three years' experience with an all-digital nuclear medicine department. Semin Nucl Med 1990;20(3):225-33.

  2. Cohen AM, Stavri PZ, Hersh WR. A categorization and analysis of the criticisms of Evidence-Based Medicine. Int J Med Inf 2004;73(1):35-43.

  3. Cohen AM, Hersh W. A Survey of Current Work in Biomedical Text Mining. Briefings in Bioinformatics 2005;6(1):57-71.

  4. Cohen AM, Hersh WR, Dubay C, Spackman K. Using co-occurrence network structure to extract synonymous gene and protein names from MEDLINE abstracts. BMC Bioinformatics 2005;6(103).

  5. Cohen AM. Unsupervised gene/protein entity normalization using automatically extracted dictionaries. In: Linking Biological Literature, Ontologies and Databases: Mining Biological Semantics, Proceedings of the BioLINK2005 Workshop; Detroit, MI: Association for Computational Linguistics; 2005. p. 17-24.

  6. Cohen AM, Hersh WR, Peterson K, Yen PY. Reducing Workload in Systematic Review Preparation Using Automated Citation Classification. JAMIA 2006;13(2):206-219.

  7. Cohen AM, Hersh W. The TREC 2004 Genomics Track Categorization Task: Classifying Full Text Biomedical Documents. Journal of Biomedical Discovery and Collaboration 2006;1(4).

  8. Hersh WR, Bhupatiraju RT, Ross L, Roberts P, Cohen AM, Kraemer DF. Enhancing Access to the Bibliome: The TREC 2004 Genomics Track. Journal of Biomedical Discovery and Collaboration 2006;1(3).

  9. Cohen AM. An effective general purpose approach for automated biomedical document classification. AMIA Annu Symp Proc 2006:161-5.

  10. Yang J, Cohen AM, Hersh WR. Functional Gene Group Summarization by Clustering MEDLINE Abstract Sentences. AMIA Annu Symp Proc 2006:1151.

  11. Cohen AM. Automatically Expanded Dictionaries with Exclusion Rules and Support Vector Machine Text Classifiers: Approaches to the BioCreAtIve 2 GN and PPI-IAS Tasks. In: Proceedings of the Second BioCreative Challenge Evaluation Workshop; Madrid, Spain: CNIO Centro Nacional de Investigaciones Oncológicas. p. 169-174, 2007.

  12. Cohen AM. Five-way Smoking Status Classification using Text Hot-spot Identification and Error-Correcting Output Codes. J Am Med Inform Assoc 2008;15(1):32-35.

  13. Yang J, Hersh W, Cohen A. Automatic Summarization of Mouse Gene Information by Clustering and Sentence Extraction from MEDLINE Abstracts. AMIA Annu Symp Proc 2007.

  14. H. Rekapalli, Hersh W, Cohen A. A Comparative Analysis of Retrieval Features Used in the TREC 2006 Genomics Track Passage Retrieval Task. AMIA Annu Symp Proc 2007.

  15. Cohen AM, McWeeney SK. RMEQ: A tool for computing equivalence groups in repeated measures studies. In: Linking Literature, Information and Knowledge for Biology: Proceedings of the BioLINK2008 Workshop; Toronto, ON; 2008.

  16. Roberts P, Cohen AM, Hersh WR. Tasks, Topics and Relevance Judging for the TREC Genomics Track: Five years of experience evaluating biomedical text information retrieval systems. Information Retrieval (in press).

  17. Cohen AM. Optimizing Feature Representation for Automated Systematic Review Work Prioritization. AMIA Annu Symp Proc 2008 (in press).

  18. Yang J, Cohen AM. SYRIAC: The SYstematic Review Information Automated Collection System, A Data Warehouse for Facilitating Automated Biomedical Text Classification. AMIA Annu Symp Proc 2008 (in press).

  19. Bahr, N, Cohen AM. Discovering synergistic qualities of published authors to enhance translational research. AMIA Annu Symp Proc 2008 (in press).

  20. Yang J, Cohen AM, Hersh WR. Evaluation of a gene information summarization system by users during the analysis process of microarray datasets, BMC Bioinformatics, 2008 AMIA Translational Bioinformatics Summit special issue (in press).

  21. Altman RB, Bergman CM, Blake J, Blaschke C, Cohen A, Gannon F, et al. Text mining for biology - the way forward: opinions from leading scientists. Genome Biology 2008;9(Suppl 2):S9.

  22. Morgan AA, Lu Z, Wang X, Cohen AM, Fluck J, Ruch P, et al. Overview of BioCreative II gene normalization. Genome Biology 2008;9(Suppl 2):S3.
     

Non-peer-reviewed Publications

 

  1. Cohen AM, Resnikoff HL. Image Compression for Radiology and Telemedicine. SPIE Applications of Digital Image Processing XVII 1994;2298:304.
  2. Aaron Michael Cohen, “How do I Process Images with Java?” Dr. Dobb’s Journal, #287, July 1998: pp. 109-113.
  3. Cohen AM, Hersh WR. Guest Editorial: Criticisms of Evidence-Based Medicine. Evidence-based Cardiovascular Medicine 2004;8(3):197-198.
  4. Hersh WR, Bhupatiraju RT, Ross L, Cohen AM, Kraemer DF. TREC 2004 Genomics Track Overview. In: The Thirteenth Text Retrieval Conference - TREC 2004; Gaithersburg, MD; http://trec.nist.gov/pubs/trec13/papers/GEO.OVERVIEW.pdf.
  5. Cohen AM, Hersh WR, Bhupatiraju RT. Feature generation, feature selection, classifiers, and conceptual drift for biomedical document triage. In: Proceedings of the Thirteenth Annual Text REtrieval Conference, TREC 2004, Gaithersburg, MD, NIST SP 500-261, http://trec.nist.gov/pubs/trec13/papers/ohsu-hersh.geo.pdf.
  6. Cohen AM, Yang J, Hersh WR. A Comparison of Techniques for Classification and Ad Hoc Retrieval of Biomedical Documents. In: Proceedings of the Fourteenth Annual Text REtrieval Conference, TREC 2005, Gaithersburg, MD; http://trec.nist.gov/pubs/trec14/papers/ohsu-geo.pdf.
  7. Hersh W, Cohen A, Yang J, Bhupatiraju RT,  Roberts P, Hearst M. TREC 2005 Genomics Track Overview. In: Proceedings of the Fourteenth Annual Text REtrieval Conference, TREC 2005, Gaithersburg, MD; http://trec.nist.gov/pubs/trec14/papers/GEO.OVERVIEW.pdf.
  8. Cohen AM, Yang J, Fisher S, Roark B, Hersh WR. Combining Lexicon Expansion, Information Retrieval, and Cluster-based Ranking for Biomedical Question Answering. In: Proceedings of the Fifteenth Annual Text REtrieval Conference - TREC 2006; 2006; Gaithersburg, MD; 2006.
  9. Hersh W, Cohen A, Roberts P, Rekapalli H. TREC 2006 Genomics Track Overview. In: Proceedings of the Fifteenth Annual Text REtrieval Conference - TREC 2006; 2006; Gaithersburg, MD; 2006.
  10. Cohen AM, Yang J, Fisher S, Roark B, Hersh WR. The OHSU Biomedical Question Answering System Framework. In: Proceedings of the Sixteenth Annual Text Retrieval Conference (TREC) 2007, Gaithersburg, MD.
  11. Hersh W, Cohen A, Roberts P. TREC 2007 Genomics Track Overview. In: Proceedings of the Sixteenth Annual Text Retrieval Conference (TREC) 2007, Gaithersburg, MD.

 

Books

Aaron Cohen and Mike Woodring, Win32 Multithreaded Programming, O’Reilly & Associates, Inc, Sebastopol, CA, 1998.

 

Chapters

 

Electronic Publications

  1. Jeff Ayars, Dick Bulterman, Aaron Cohen, et al., Synchronized Multimedia Integration Language (SMIL 2.0), World Wide Web Consortium (W3C) Recommendation, August 7, 2001, available at “http://www.w3c.org/TR/smil20/”.
  2. Patrick Schmitz, Aaron Cohen, SMIL Animation, World Wide Web Consortium (W3C) Recommendation, September 4, 2001, available at “http://www.w3c.org/TR/smil-animation/”.

 

Reviews

 

Abstracts

 

Other

 

Invited Lectures, Conference Presentations or Professorships:

 

International and National

  1. Cohen, AM. Knowledge Extraction from MEDLINE with Symbolic Network Logical Analysis. Presented at the National Library of Medicine Medical Informatics Fellow Annual Meeting, June 9, 2004, Indianapolis, Indiana.
  2. Cohen, AM, Bhupatiraju RT, Hersh WR. Feature Generation, Feature Selection, Classifiers, and Conceptual Drift for Biomedical Document Triage (poster). Presented at the Text Retrieval Conference (TREC) 2004, November 17-19, 2004, Gaithersburg, Maryland.
  3. Cohen, AM. Unsupervised gene/protein entity normalization using automatically extracted dictionaries. Presented at BioLINK 2005 SIG ACL-05/ISMB-05, June 24, 2005, Detroit, Michigan.
  4. Cohen, AM. Introduction to Biomedical Text Mining. Presented at the American Medical Informatics Association Annual Symposium, Washington D.C., October 26, 2005.
  5. Cohen AM, Yang J, Hersh WR. A Comparison of Techniques for Classification and Ad Hoc Retrieval of Biomedical Documents (poster). Presented at Text Retrieval Conference (TREC) 2005, November 15-16. 2005, Gaithersburg, Maryland.
  6. Cohen AM, Hersh WR. Enhancing Access to the Genomics Literature: The TREC 2005 Genomics Track (poster). Presented at the American Medical Informatics Association (AMIA) Spring Congress, May 16-18, 2006, Phoenix, AZ.
  7. Cohen AM. Literature Based Discovery (invited presentation and panelist), American Medical Informatics Association Spring Congress, Phoenix, AZ, May 16-18, 2006.
  8. Cohen AM, Carson SM, Hersh WR, Brown N, Peterson K, Helfand M. Elements and features of results databases recommended by experienced systematic reviewers (poster). Presented at XIV Cochrane Colloquium, Dublin, Ireland, 2006.
  9. Carson SM, Cohen AM, Hersh WR, Brown N, Helfand M. Systematic evaluation of web-based, publicly accessible clinical trial results databases (oral presentation). Presented at XIV Cochrane Colloquium, Dublin, Ireland, 2006.
  10. Cohen AM, Yang J, Fisher S, Roark B, Hersh WR. Combining Lexicon Expansion, Information Retrieval, and Cluster-based Ranking for Biomedical Question Answering (poster). Presented at Text Retrieval Conference (TREC) 2006, November 15-17, 2006, Gaithersburg, Maryland.
  11. Cohen AM. An Effective General Purpose Approach for Biomedical Document Classification. Presented at the American Medical Informatics Association (AMIA) Annual Symposium, Washington D.C., November 13, 2006.
  12. Craven CK, Smith CA, Cohen AM, Gorman J, Fiszman, M, Lehmann CU, Pevsner J. Careers in Medical Informatics (panel). Presented at the American Medical Informatics Association (AMIA) Annual Symposium, Washington D.C., November 14, 2006.
  13. Yang J, Cohen AM, Hersh WR. Functional Gene Group Summarization by Clustering Medline Abstract Sentences (poster). Presented at Presented at the American Medical Informatics Association (AMIA) Annual Symposium, Washington D.C., November 14, 2006.
  14. Cohen, AM. Enhancing access to the bibliome for genomics with evaluation tasks derived from user information needs: The TREC Genomics Track (invited presentation). Presented at the Second BioCreative Challenge Evaluation Workshop, Madrid, Spain, April 23-25, 2007.
  15. Cohen, AM. The BioCreAtIve 2 GN and PPI-IAS Tasks: Approaches and Analysis (invited presentation). Presented at the Second BioCreative Challenge Evaluation Workshop, Madrid, Spain, April 23-25, 2007.
  16. Cohen, AM. RMEQ: A tool for computing equivalence groups in repeated measures studies. BioLINK 2008 SIG Workshop, ISMB 2008, Toronto, ON, July 18, 2008.

 

Regional and Local

  1. Cohen AM. Using co-occurrence network structure to extract synonymous gene and protein names from MEDLINE abstracts, Oregon Health & Science University, Masters degree thesis defense, July 1, 2004, Portland, Oregon.
  2. Cohen AM. Introduction to Biomedical Informatics, Oregon Biosciences Association Bioinformatics Special Interest Group, May 3, 2005, Portland, Oregon.
  3. Cohen AM. Reducing workload in systematic review preparation using automated citation classification, Systematic Reviews Discussion Group, Oregon Health & Science University, February 28, 2006, Portland, Oregon.
  4. Cohen AM, Hersh WR, Research challenges and collaboration opportunities in information retrieval and text mining, Cancer Research Group, Oregon Cancer Institute, Oregon Health & Science University, December 12, 2007, Portland, Oregon.
  5. Cohen AM. Why Python?, BioDev Research Group, Oregon Cancer Institute, Oregon Health & Science University, March 27, 2008, Portland, Oregon.
  6. Cohen AM. Introduction to biomedical text mining, Guest Lecture, CSE 554/654, Oregon Graduate Institute, May 5, 2008, Portland, Oregon.

 

Patents

  1. Cohen, Aaron M., Method and Apparatus for Software Licensing Electronically Distributed Programs, U.S. Patent Number 6,233,567, awarded May 15, 2001.
  2. Cohen, Aaron M., Gorman, Christopher L., Apparatus and method for progressively rendered procedural textures, U.S. Patent Number 6,459,434, awarded October 1, 2002.
  3. Woodring, Michael C., Cohen, Aaron M., Menon, Rama, Information streaming in a multi-process system using shared memory, U.S. Patent Number 6,519,686, awarded February 11, 2003.
  4. Cohen, Aaron M., Gorman, Christopher L., Hybrid procedural/pixel based textures, U.S. Patent Number 6,765,582, awarded July 20, 2004.
  5. Cohen, Aaron M., Gupta, Ajay G., Video conferencing method and apparatus with improved initialization through command pruning, U.S. Patent Number 6,774,927 , awarded August 10, 2004.
  6. Cohen, Aaron M., Gorman, Christopher L., Hybrid procedural/pixel based textures, U.S. Patent Number 7,123,268, awarded October 17, 2006.

 

Other

May 2005, Outstanding Masters Thesis Award, Oregon Health & Science University, Portland, Oregon

 

V.  SERVICE

 

Membership in Professional Societies:

  1. 2003-2005, Student Member, American Medical Informatics Association
  2. 2005-present, Full Member, American Medical Informatics Association

 

Granting Agency Review Work:

 

Editorial and Ad Hoc Review Activities:

  1. August 2005, Manuscript Submission Reviewer, SIGIR 2005 Conference, Salvador, Brazil
  2. 2005-present, Editorial Board, BMC Journal of Biomedical Discovery and Collaboration
  3. July 2005, Program Committee Member, ACL/ISMB BioLINK 2005 Meeting, Detroit, Michigan
  4. October 2005, Manuscript Submission Reviewer, Medical Decision Making
  5. October 2005, Manuscript Submission Reviewer, Toxicology
  6. January 2006, Manuscript Submission Reviewer, Pacific Symposium on Biocomputing (PSB), Wailea, Hawaii
  7. February 2006, Manuscript Submission Reviewer, Medical Decision Making
  8. February 2006, Manuscript Submission Reviewer, SIGIR 2006 Conference, Seattle, Washington
  9. February 2006, Field Editor, BMC Journal of Biomedical Discovery and Collaboration
  10. March 2006, Program Committee Member, HLT-NAACL BioNLP 2006 Workshop, Brooklyn, New York
  11. March 2006, Manuscript Submission Reviewer, International Journal of Medical Informatics
  12. April 2006, Manuscript Submission Reviewer, American Medical Informatics Association (AMIA) Fall Symposium 2006, Washington, D.C.
  13. July 2006, Manuscript Submission Reviewer, Pacific Symposium on Biocomputing (PSB) 2007, Wailea, Hawaii
  14. July 2006, Manuscript Submission Reviewer, BMC Bioinformatics
  15. July 2006, Manuscript Submission Reviewer, TMBio 2006 Conference, Arlington VA
  16. February, 2007, Manuscript Submission Reviewer, International Journal of Medical Informatics
  17. February 2007, Manuscript Submission Reviewer, SIGIR 2007 Conference, Amsterdam, Netherlands
  18. March 2007, Manuscript Submission Reviewer, Bioinformatics.
  19. April 2007, Program Committee Member, BioNLP workshop, ACL 2007 Conference, Prague, Czech Republic
  20. April 2006, Manuscript Submission Reviewer, American Medical Informatics Association (AMIA) Fall Symposium 2007, Chicago, Illinois.
  21. May 2007, Program Committee Member, BioLink workshop, ISMB 2007 Conference, Vienna, Austria.
  22. October 2007, Field Editor, BMC Journal of Biomedical Discovery and Collaboration.
  23. October 2007, Manuscript Submission Reviewer, Bioinformatics.
  24. November 2007, Manuscript Submission Reviewer, Information Processing and Management.
  25. March, 2008, Manuscript Submission Reviewer, International Journal of Medical Informatics
  26. March 2008, Manuscript Submission Reviewer, BMC Bioinformatics
  27. April 2008, Manuscript Submission Reviewer, American Medical Informatics Association (AMIA) Fall Symposium 2008, Washington, D.C.
  28. April 2008, Program Committee Member, Brazilian Symposium on Bioinformatics 2008,  Santo Andre, Brazil.
  29. April 2008, Program Committee Member, BioNLP workshop, ACL 2008 Conference, Columbus, Ohio.
  30. May 2008, Program Committee Member, BioLink workshop, ISMB 2008 Conference, Toronto, Ontario, Canada.
  31. May 2008, Manuscript Submission Reviewer, Information Retrieval

 

Committees:

International/National

  1. 1999-2002, Chairman, World Wide Web Consortium (W3C), Synchronized Multimedia Working Group
  2. 2002, Intel Lead Representative, Java Community Process (JCP)

 

Regional

 

Institutional

  1. 2006, Bioinformatics Subcommittee, OHSU Clinical and Translational Science Award Grant Proposal Committee
  2. 2006, OHSU Outstanding Masters Thesis Review Committee

 

Departmental

  1. September 2005, PhD Qualifying Exam Review Committee, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University
  2. 2005-present, Professional Conduct Committee, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University
  3. 2006-present, Department Web Site Committee, Chairman, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University
  4. 2007-present, Internship Committee, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University

 

Community Service:

  1. September 2005, Susan G. Komen, Race for the Cure, Portland, Oregon

  2. Where the Jobs Are...Biosciences, Social Sciences, Mathematics, Panel discussion and Q & A, Reed College, February 13, 2007.

Clinical Responsibilities (since last promotion):

 

VI.  TEACHING (OHSU Educator’s Portfolio):

 

Overview of your Role as an Educator:

 

Scholarship of Teaching:

 

Curriculum Development

Assisted in design of Bioinformatics Masters and PhD curriculum

Advanced Topics: Biomedical Text Mining, BMI 607, Spring 2006 

Software Engineering, BMI 546/646, Spring 2007

 

Educational Publications

 

Educational Conference Presentations

 

Education Grants and Contracts:

 

Educational Activity (see Appendix A and B):

  1. Fall 2002, BMI 540, On-campus lecturer, Advanced Computer Programming, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University
  2. Fall 2003, BMI 540, On-campus lecturer, Advanced Computer Programming, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University
  3. Fall 2004, BMI 540, On-campus lecturer, Advanced Computer Programming, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University

  4. Spring 2006, BMI 607, Assistant Professor, Advanced Topics: Biomedical Text Mining, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University

  5. Spring 2007, BMI 546/646, Assistant Professor, Software Engineering, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University

  6. Spring 2008, BMI 546/646, Assistant Professor, Software Engineering, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University

     

Effectiveness of Educational Activity:

 

Service and Membership of Educational Committees:

August 2005-present, Bioinformatics Curriculum Track Creation Committee, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University

August 2005-present, Curriculum Committee, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University

 

Honors and Awards for Education:

 

Collaborative Skills:

 

Professional Development in Education: