Feature Generation, Feature Selection, Classifiers, and Conceptual Drift for Biomedical Document Triage. - Aaron M. Cohen; Ravi Teja Bhupatiraju; William R. Hersh (TREC, 2004)

TREC 2004 Genomics Track Overview. - William R. Hersh; Ravi Teja Bhupatiraju; L. Ross; Aaron M. Cohen; Dale Kraemer; Phoebe Johnson (TREC, 2004)

A categorization and analysis of the criticisms of Evidence-Based Medicine. - Aaron M. Cohen; P. Zoë Stavri; William R. Hersh (Int. J. Medical Informatics, 2004)

A Comparison of Techniques for Classification and Ad Hoc Retrieval of Biomedical Documents. - Aaron M. Cohen; Jianji Yang; William R. Hersh (TREC, 2005)

TREC 2005 Genomics Track Overview. - William R. Hersh; Aaron M. Cohen; Jianji Yang; Ravi Teja Bhupatiraju; Phoebe M. Roberts; Marti A. Hearst (TREC, 2005)

A survey of current work in biomedical text mining. - Aaron M. Cohen; William R. Hersh (Briefings Bioinform., 2005)

Using co-occurrence network structure to extract synonymous gene and protein names from MEDLINE abstracts. - Aaron M. Cohen; William R. Hersh; Christopher Dubay; Kent A. Spackman (BMC Bioinform., 2005)

An Effective General Purpose Approach for Automated Biomedical Document Classification. - Aaron M. Cohen (AMIA, 2006)

Functional Gene Group Summarization by Clustering MEDLINE Abstract Sentences. - Jianji Yang; Aaron M. Cohen; William R. Hersh (AMIA, 2006)

Combining Lexicon Expansion, Information Retrieval, and Cluster-based Ranking for Biomedical Question Answering. - Aaron M. Cohen; Jianji Yang; Seeger Fisher; Brian Roark; William R. Hersh (TREC, 2006)

TREC 2006 Genomics Track Overview. - William R. Hersh; Aaron M. Cohen; Phoebe M. Roberts; Hari Krishna Rekapalli (TREC, 2006)

Research Paper: Reducing Workload in Systematic Review Preparation Using Automated Citation Classification. - Aaron M. Cohen; William R. Hersh; K. Peterson; Po-Yin Yen (J. Am. Medical Informatics Assoc., 2006)

A comparative analysis of retrieval features used in the TREC 2006 Genomics Track passage retrieval task. - Hari Krishna Rekapalli; Aaron M. Cohen; William R. Hersh (AMIA, 2007)

Automatic Summarization of Mouse Gene Information by Clustering and Sentence Extraction from MEDLINE Abstracts. - Jianji Yang; Aaron M. Cohen; William R. Hersh (AMIA, 2007)

The OHSU Biomedical Question Answering System Framework. - Aaron M. Cohen; Jianji Yang; Seeger Fisher; Brian Roark; William R. Hersh (TREC, 2007)

TREC 2007 Genomics Track Overview. - William R. Hersh; Aaron M. Cohen; Lynn Ruslen; Phoebe M. Roberts (TREC, 2007)

Discovering Synergistic Qualities of Published Authors to Enhance Translational Research. - Nathan J. Bahr; Aaron M. Cohen (AMIA, 2008)

Optimizing Feature Representation for Automated Systematic Review Work Prioritization. - Aaron M. Cohen (AMIA, 2008)

SYRIAC: The SYstematic Review Information Automated Collection System A Data Warehouse for Facilitating Automated Biomedical Text Classification. - Jianji Yang; Aaron M. Cohen; Marian McDonagh (AMIA, 2008)

Case Report: Five-way Smoking Status Classification Using Text Hot-Spot Identification and Error-correcting Output Codes. - Aaron M. Cohen (J. Am. Medical Informatics Assoc., 2008)

Evaluation of a gene information summarization system by users during the analysis process of microarray datasets. - Jianji Yang; Aaron M. Cohen; William R. Hersh (BMC Bioinform., 2009)

Tasks, topics and relevance judging for the TREC Genomics Track: five years of experience evaluating biomedical text information retrieval systems. - Phoebe M. Roberts; Aaron M. Cohen; William R. Hersh (Inf. Retr., 2009)

Research Paper: A System for Classifying Disease Comorbidity Status from Medical Discharge Summaries Using Automated Hotspot and Negated Concept Detection. - Kyle H. Ambert; Aaron M. Cohen (J. Am. Medical Informatics Assoc., 2009)

Research Paper: Cross-Topic Learning for Work Prioritization in Systematic Review Creation and Update. - Aaron M. Cohen; Kyle H. Ambert; Marian McDonagh (J. Am. Medical Informatics Assoc., 2009)

Evidence-based medicine, the essential role of systematic reviews, and the need for automated text mining tools. - Aaron M. Cohen; Clive E. Adams; John M. Davis; Clement T. Yu; Philip S. Yu; Weiyi Meng; Lorna Duggan; Marian McDonagh; Neil R. Smalheiser (IHI, 2010)

Identifying Patients for Clinical Studies from Electronic Health Records: TREC Medical Records Track at OHSU. - Steven Bedrick; Kyle H. Ambert; Aaron M. Cohen; William R. Hersh (TREC, 2011)

Letter: Performance of support-vector-machine-based classification on 15 systematic review topics evaluated with the WSS@95 measure. - Aaron M. Cohen (J. Am. Medical Informatics Assoc., 2011)

Barriers to Retrieving Patient Information from Electronic Health Record Data: Failure Analysis from the TREC Medical Records Track. - Tracy Edinger; Aaron M. Cohen; Steven Bedrick; Kyle H. Ambert; William R. Hersh (AMIA, 2012)

Identifying Patients for Clinical Studies from Electronic Health Records: TREC 2012 Medical Records Track at OHSU. - Steven Bedrick; Tracy Edinger; Aaron M. Cohen; William R. Hersh (TREC, 2012)

Studying the potential impact of automated document classification on scheduling a systematic review update. - Aaron M. Cohen; Kyle H. Ambert; Marian McDonagh (BMC Medical Informatics Decis. Mak., 2012)

k-Information Gain Scaled Nearest Neighbors: A Novel Approach to Classifying Protein-Protein Interaction-Related Documents. - Kyle H. Ambert; Aaron M. Cohen (IEEE ACM Trans. Comput. Biol. Bioinform., 2012)

Finna: A Paragraph Prioritization System for Biocuration in the Neurosciences. - Kyle H. Ambert; Aaron M. Cohen; Gully A. P. C. Burns; Eilis Boudreau; M. Kemal Sönmez (AAAI Fall Symposia, 2013)

A Large-Scale Analysis of the Reasons Given for Excluding Articles that are Retrieved by Literature Search During Systematic Review. - Tracy Edinger; Aaron M. Cohen (AMIA, 2013)

Virk: an active learning-based system for bootstrapping knowledge base development in the neurosciences. - Kyle H. Ambert; Aaron M. Cohen; Gully A. P. C. Burns; Eilis Boudreau; M. Kemal Sönmez (Frontiers Neuroinformatics, 2013)

Rule-based deduplication of article records from bibliographic databases. - Yu Jiang; Can Lin; Weiyi Meng; Clement T. Yu; Aaron M. Cohen; Neil R. Smalheiser (Database J. Biol. Databases Curation, 2014)

Design and implementation of Metta, a metasearch engine for biomedical literature retrieval intended for systematic reviewers. - Neil R. Smalheiser; Can Lin; Lifeng Jia; Yu Jiang; Aaron M. Cohen; Clement T. Yu; John M. Davis; Clive E. Adams; Marian S. McDonagh; Weiyi Meng (Health Inf. Sci. Syst., 2014)

Automated confidence ranked classification of randomized controlled trial articles: an aid to evidence-based medicine. - Aaron M. Cohen; Neil R. Smalheiser; Marian S. McDonagh; Clement T. Yu; Clive E. Adams; John M. Davis; Philip S. Yu (J. Am. Medical Informatics Assoc., 2015)

A Mixed Methods Task Analysis of the Implementation and Validation of EHR-Based Clinical Quality Measures. - Nicole Gray Weiskopf; Faiza Khan; David A. Dorr; Deborah V. Woodcock; Joaquin E. Cigarroa; Aaron M. Cohen (AMIA, 2016)

Evaluation of Clinical Text Segmentation to Facilitate Cohort Retrieval. - Tracy Edinger; Dina Demner-Fushman; Aaron M. Cohen; Steven Bedrick; William R. Hersh (AMIA, 2017)

Identifying reports of randomized controlled trials (RCTs) via a hybrid machine learning and crowdsourcing approach. - Byron C. Wallace; Anna Noel-Storr; Iain James Marshall; Aaron M. Cohen; Neil R. Smalheiser; James Thomas 001 (J. Am. Medical Informatics Assoc., 2017)

Call for Papers! Special Issue on Models of Discovery: Mining the Scientific Literature. - Neil R. Smalheiser; Aaron M. Cohen (J. Data Inf. Sci., 2017)

OHSU CLEF 2018 Task 2 Diagnostic Test Accuracy Ranking using Publication Type Cluster Similarity Measures. - Aaron M. Cohen; Neil R. Smalheiser (CLEF (Working Notes), 2018)

A probabilistic automated tagger to identify human-related publications. - Aaron M. Cohen; Zackary O. Dunivin; Neil R. Smalheiser (Database J. Biol. Databases Curation, 2018)

Design of a generic, open platform for machine learning-assisted indexing and clustering of articles in PubMed, a biomedical bibliographic database. - Neil R. Smalheiser; Aaron M. Cohen (Data Inf. Manag., 2018)

Towards augmenting structured EHR data: a comparison of manual chart review and patient self-report. - Nicole Gray Weiskopf; Aaron M. Cohen; Joely Hannan; Thad Jarmon; David A. Dorr (AMIA, 2019)

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. - Neil R. Smalheiser; Aaron M. Cohen; Gary Bonifield (J. Biomed. Informatics, 2019)

A Query Taxonomy Describes Performance of Patient-Level Retrieval from Electronic Health Record Data. - Steve Chamberlin; Steven Bedrick; Aaron M. Cohen; Yanshan Wang; Andrew Wen; Sijia Liu 002; Hongfang Liu; William R. Hersh (HSDM@WSDM, 2020)

Identifying main finding sentences in clinical case reports. - Mengqi Luo; Aaron M. Cohen; Sidharth Addepalli; Neil R. Smalheiser (Database J. Biol. Databases Curation, 2020)

Automatically pre-screening patients for the rare disease aromatic l-amino acid decarboxylase deficiency using knowledge engineering, natural language processing, and machine learning on a large EHR population. - Aaron M. Cohen; Jolie Kaner; Ryan Miller; Jeffrey W. Kopesky; William R. Hersh (J. Am. Medical Informatics Assoc., 2024)