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Professional Information
Publications:
My research interests center around the development,
application, and evaluation of text mining, machine
learning, and classification techniques and tools for
biomedical researchers. Here are some significant papers I
have published in these areas:
- Cohen AM, Hersh W. A Survey of Current Work
in Biomedical Text Mining. Briefings in
Bioinformatics 2005;6(1):57-71. [pdf]
- 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]
- 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]
- 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]
- 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]
- 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]
- 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]
- Cohen AM. Optimizing feature representation
for automated systematic review work prioritization.
AMIA Annu Symp Proc 2008:121-5. [pdf]
- 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]
- 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. [pdf]
- 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. [pdf]
- Edinger T, Cohen AM. A
Large-Scale Analysis of the Reasons Given for Excluding
Articles that are Retrieved by Literature Search During
Systematic Review. AMIA Annu
Symp Proc. 2013. [pdf]
- Jiang Y, Lin C, Meng W,
Yu C, Cohen AM,
Smalheiser NR. Rule-based deduplication of article records
from bibliographic databases. Database: the journal of
biological databases and curation.
2014;2014. [pdf]
- Cohen AM, Smalheiser NR, McDonagh MS, Yu C, Adams CE,
Davis JM, et al. Automated confidence ranked
classification of randomized controlled trial articles:
an aid to evidence-based medicine. J Am Med Inform
Assoc. 2015 Feb 5. [pdf]
- Lugli G, Cohen AM,
Bennett DA, Shah RC, Fields CJ, Hernandez AG, et al.
Plasma Exosomal miRNAs in Persons with and
without Alzheimer Disease: Altered Expression and
Prospects for Biomarkers. PLoS
ONE. 2015 Oct 1;10(10):e0139233.
[pdf]
- Wallace BC, Noel-Storr A, Marshall IJ, Cohen AM,
Smalheiser NR, Thomas J. Identifying reports of
randomized controlled trials (RCTs) via a hybrid machine
learning and crowdsourcing approach. J Am Med Inform
Assoc. 2017 May 25.
- Edinger T, Demner-Fushman D, Cohen AM, Bedrick
S, Hersh W. Evaluation of Clinical Text Segmentation to
Facilitate Cohort Retrieval. AMIA Annu Symp Proc.
2017;2017:660-9.
- Smalheiser NR, Cohen AM. Design of a generic,
open platform for machine learning-assisted indexing and
clustering of articles in PubMed, a biomedical
bibliographic database. Data and Information Management.
2018;2(1):27-36.
- Cohen AM, Dunivin ZO, Smalheiser NR. A
probabilistic automated tagger to identify human-related
publications. Database (Oxford). 2018 01;2018:1-8.
- Smalheiser NR, Cohen AM, Bonifield G.
Unsupervised Low-Dimensional Vector Representations for
Words, Phrases and Text that are Transparent, Scalable,
and produce Similarity Metrics that are not Redundant
with Neural Embeddings. J Biomed Inform. 2019 Jan
14;103096.
- Weiskopf NG, Cohen AM, Hamman J, Jarmon T,
Dorr D. Towards augmenting structured EHR data: a
comparison of manual chart review and patient
self-report. AMIA Annu Symp Proc;
2019.
- Leung ET, Raboin MJ, McKelvey J, Graham A, Lewis A,
Prongay K, Cohen AM, Vinson A. Modelling disease
risk for amyloid A (AA) amyloidosis in non-human
primates using machine learning. Amyloid. 2019 Jun
18;0(0):1-9.
- Chamberlin SR, Bedrick SD, Cohen AM, Wang Y,
Wen A, Liu S, Liu H, Hersh WR, A query taxonomy
describes performance of patient-level retrieval from
electronic health record data, Health Search and Data
Mining (HSDM) Workshop, Web Search and Data Mining
(WSDM) Conference, medRxiv 19012294, 2020.
-
Chamberlin
SR, Bedrick SD, Cohen AM, Wang Y, Wen A, Liu
S, et al. Evaluation of patient-level retrieval from
electronic health record data for a cohort discovery
task. Jamia Open [Internet]. Available from: https://academic.oup.com/jamiaopen/article/doi/10.1093/jamiaopen/ooaa026/5876567
- Cohen AM, Chamberlin S, Deloughery T, Nguyen M,
Bedrick S, Meninger S, et al. Detecting rare diseases in
electronic health records using machine learning and
knowledge engineering: Case study of acute hepatic
porphyria. PLOS ONE. 2020 Jul 2;15(7):e0235574.
- Schneider J, Hoang L, Kansara Y, Cohen AM,
Smalheiser NR. Evaluation of publication type tagging as
a strategy to screen randomized controlled trial
articles in preparing systematic reviews. JAMIA Open.
2021 Mar 12 (in press).
Curriculum Vitae:
Data Sets:
Software:
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