Homepage of Aaron Michael Cohen, M.D. M.S.

Current contact information:

	Aaron M. Cohen Assistant Professor School of Medicine, Department of Medical Informatics and Clinical Epidemiology (DMICE) Oregon Health & Science University 3181 S.W. Sam Jackson Park Road Mail Code: BICC Portland, Oregon, USA 97239-3098 email: cohenaa(at-sign-goes-here)ohsu.edu
Future Informatics Professor?

Professional Information

Publications:

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

2. 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). [pdf]

3.  Cohen AM, Hersh WR, Bhupatiraju RT. Feature generation, feature selection, classifiers, and conceptual drift for biomedical document triage. In: Proceedings of the Text Retrieval Conference (TREC) 2004; Gaithersburg, MD. [pdf]

4. 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. [pdf]

5. 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. [pdf]

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. [pdf]

7. Cohen AM. An Effective General Purpose Approach for Automated Biomedical Document Classification. In: Proceedings of the American Medical Informatics Association (AMIA) 2006 Annual Symposium; 2006. [pdf]

8. Cohen AM.Five-way Smoking Status Classification using Text Hot-spot Identification and Error-Correcting Output Codes. J Am Med Inform Assoc, 2007. [pdf] [pdf of full paper and data supplement]

9. Cohen AM. Optimizing feature representation for automated systematic review work prioritization. AMIA Annu Symp Proc 2008:121-5. [pdf]

10. Cohen AM, Ambert K, McDonagh MS. Cross-topic Learning for Work Prioritization in Systematic Review Creation and Update. J Am Med Inform Assoc 2009. [pdf]

Curriculum Vitae:

• View my Curriculum Vitae here.

Data Sets:

• Gold standard files for work described in my masters thesis and in the paper Using co-occurrence network structure to extract synonymous gene and protein names from MEDLINE abstracts. You can also view the whole directory at once.
• Systematic drug class review data extracted from Endnote files created by the OHSU Evidence-based Practice Center.

Software:

• RMEQ: A tool for Computing Equivalence Groups in Repeated Measures Studies

Personal Information

I like programming the iPhone, building and playing ukuleles, folding origami, listening to podcasts, reading (to myself and my kids), playing board games, and watching Doctor Who (when I have the time).

Web Resources

Here are a few of my favorite biomedical text mining resources on the Web:

• BLIMP (Biomedical Literature and Text Mining Publications), a forum for collection, compilation, and exchange of publications on biomedical text mining.
• Alex Morgan's page on BioNLP resources, although it has been a while since it has been updated.
• TREC Genomics Track home page.
• BioPython project home page. Not geared specifically to text mining BioPython contains lots of tools for working with resources useful in biomedical text mining.
• Python.org, the home of the Python language. You do know about Python, right? After spending years getting paid to program in Assembly, C, C++, and Java, I now do almost all of my text mining research using Python. It's my favorite language.