Aaron M. Cohen

Office: BICC 2nd
Phone: 503.494.4502
Fax: 503.494.4551
E-mail: cohenaa@ohsu.edu
URL:  http://skynet.ohsu.edu/~cohenaa


Aaron is an associate professor in OHSU's Department of Medical Informatics and Clinical Epidemiology (DMICE). His research interests focus on the development and application of text mining and machine learning techniques to multi-modal data sources, including the scientific literature and clinical text, to improve scientific discovery and secondary use of clinical and scientific data. 

Current research projects include: use of text classification and extraction techniques for reducing the workload of biomedical database curators and authors of systematic reviews; application of machine learning methods to multi-modal data to improve risk assessment for improved patient and population care; and adaption of advanced algorithms from text processing to protein inference, a fundamental problem in proteomics research. 

Aaron is also the Director of Commercial Partnerships and Collaboration for the DMICE Informatics Discovery Lab (IDL) at OHSU: a collaborative environment in which learners, teachers, and researchers partner with healthcare delivery organizations, industry, and philanthropy to solve real-world problems. The IDL’s mission is to address the major information-related challenges in health care and biomedicine through strong collaboration with industry and health system partners. 

Aaron received an MD from the University of Michigan, and holds a master's degree in biomedical informatics (MBI) from OHSU.

Selected Publications

  • Cohen AM, Ambert K, McDonagh M. Studying the potential impact of automated document classification on scheduling a systematic review update. BMC Medical Informatics and Decision Making. 2012 Apr 19;12(1):33.
  • Ambert KH, Cohen AM. k-Information Gain Scaled Nearest Neighbors: A Novel Approach to Classifying Protein-Protein Interaction-Related Documents. IEEE IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2011.
  • Dorr D, Cohen AM, Pierre-Jacques Williams M, Hurdle J. From simply inaccurate to complex and inaccurate: complexity in standards-based quality measures. AMIA Annu Symp Proc; 2011.
  • Wright H, Cohen A, Sönmez K, Yochum G, McWeeney S. Occupancy Classification of Position Weight Matrix-Inferred Transcription Factor Binding Sites. PLoS ONE. 2011 Nov 4;6(11):e26160.
  • Cohen AM, Ambert K, McDonagh M. A Prospective Evaluation of an Automated Classification System to Support Evidence-based Medicine and Systematic Review. AMIA Annu Symp Proc; 2010.
  • Campbell E, Sittig D, Chapman W, Hazlehurst B, Cohen AM. Understanding Inter-rater Disagreement: A Mixed Methods Approach. AMIA Annu Symp Proc; 2010. (Distinguished Paper Award Nominee)
  • Cohen AM, Adams CE, Davis JM, Yu C, Yu P, Meng W, et al. Evidence-Based Medicine,  the Essential Role of Systematic Reviews, and the Need for Automated Text Mining Tools.  In: IHI'10.  Arlington, Virginia, USA, 2010.
  • Yu H, Agrarwal S, Johnston M, Cohen A. Are figure legends sufficient? Evaluating the contribution of associated text to biomedical figure comprehension. Journal of Biomedical Discovery and Collaboration 2009;4(1).
  • Ambert KH, Cohen AM. A System for Classifying Disease Co-morbidity Status from Medical Discharge Summaries Using Automated Hotspot and Negated Concept Detection. J Am Med Inform Assoc 2009.
  • Cohen AM, Ambert K, McDonagh MS. Cross-topic Learning for Work Prioritization in Systematic Review Creation and Update. J Am Med Inform Assoc 2009.
  • Cohen AM. Optimizing feature representation for automated systematic review work prioritization. AMIA Annu Symp Proc 2008:121-5. (Distinguished Paper Awardee)
  • Yang J, Cohen A, McDonagh MS. SYRIAC: The SYstematic Review Information Automated Collection System A Data Warehouse for Facilitating Automated Biomedical Text Classification. AMIA Annu Symp Proc 2008:825-9.
  • Bahr, N, Cohen AM. Discovering synergistic qualities of published authors to enhance translational research. AMIA Annu Symp Proc 2008:31-5.
  • 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.
  • 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, OnlineFirst: DOI 10.2007/s10791-008-9072-x.
    Cohen AM, Hersh WR, Peterson K, Yen PY. Reducing Workload in Systematic Review Preparation Using Automated Citation Classification. JAMIA 2006;13(2):206-219.
  • 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).
  • 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).
  • Cohen AM. An effective general purpose approach for automated biomedical document classification. AMIA Annu Symp Proc 2006:161-5.
  • Yang J, Cohen AM, Hersh WR. Functional Gene Group Summarization by Clustering MEDLINE Abstract Sentences. AMIA Annu Symp Proc 2006:1151.
  • Cohen AM, Hersh W. A Survey of Current Work in Biomedical Text Mining. Briefings in Bioinformatics 2005;6(1):57-71.
  • 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).
  • 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.