Cosmin "Adi" Bejan, PhD

Research Assistant Professor
Department of Biomedical Informatics
Center for Precision Medicine
Vanderbilt University Medical Center
2525 West End Avenue
Suite 1500
Nashville, TN 37203
email: adi.{lastname}@vanderbilt.edu

Brief Bio
I am a computer scientist who is passionate about doing research on natural language processing, biomedical informatics, and machine learning. In particular, I am interested in computational semantics, open domain and clinical information extraction, precision phenomics, and unsupervised learning. Before joining the Department of Biomedical Informatics at Vanderbilt University, I was involved in research projects in the Department of Biomedical Informatics and Medical Education at the University of Washington, the Institute for Creative Technologies at the University of Southern California, and the Human Language Technology Research Institute at the University of Texas at Dallas.
Publications

2018
  • Leveraging electronic health records to map the genetic and phenotypic complexity of preterm birth
    Abin Abraham, Cosmin Bejan, John Capra
    American Society of Human Genetics (ASHG) 2018 Annual Meeting, San Diego, CA, October, 2018.
    abstract ]
  • Large-scale text mining of kidney stone composition from electronic health records
    Ryan S. Hsi, Daniel J. Lee, Cosmin A. Bejan
    36th World Congress of Endourology (WCE), Paris, France, September, 2018.
    abstract ]
  • Mining kidney stone composition from millions of clinical notes within the electronic health record
    Ryan S. Hsi, Daniel J. Lee, Cosmin A. Bejan
    American Urological Association Annual Meeting (AUA), San Francisco, CA, May, 2018.
    abstract ]
  • Identification of myelofibrosis from electronic health records with novel algorithms and JAKextractor
    Cosmin A. Bejan*, Andrew Sochacki*, Shilin Zhao, Yaomin Xu, Michael Savona (*contributed equally)
    American Association for Cancer Research Annual Meeting (AACR), Chicago, IL, April, 2018.
    abstract ]
  • Phenome-Wide Associations of Homelessness in Electronic Health Records
    Jared M. Hendrickson, Joshua C. Denny, Cosmin A. Bejan
    AMIA 2018 Informatics Summit, San Francisco, CA, March, 2018.
    abstract ]

2017
  • Mining 100 million notes to find homelessness and adverse childhood experiences: 2 case studies of rare and severe social determinants of health in electronic health records
    Cosmin A. Bejan, John Angiolillo, Douglas Conway, Robertson Nash, Jana K. Shirey-Rice, Loren Lipworth, Robert M. Cronin, Jill Pulley, Sunil Kripalani, Shari Barkin, Kevin B. Johnson, Joshua C. Denny
    Journal of the American Medical Informatics Association (JAMIA), 2017.
    paper ]
  • Large-Scale Text Mining of Social Determinants from Electronic Health Records: Case Studies of Homelessness and Adverse Childhood Experiences
    Cosmin A. Bejan, John Angiolillo, Douglas Conway, Robertson Nash, Jana K. Shirey-Rice, Loren Lipworth, Robert M. Cronin, Jill Pulley, Sunil Kripalani, Shari Barkin, Kevin B. Johnson, Joshua C. Denny
    American Medical Informatics Association Fall Symposium (AMIA), Washington DC, November, 2017.
    abstract ]
  • A Simple and Efficient Method for the Management of Multiple Electronic Health Record-Driven Phenotype Projects
    Cosmin A. Bejan, Joshua C. Denny
    American Medical Informatics Association Fall Symposium (AMIA), Washington DC, November, 2017.
    abstract ]
  • Development of Specific Electronic Phenotypes for Severe Cutaneous Adverse Drug Reactions Facilitates Genetic Discovery
    Sarah Garon, Lincoln Shade, Michael I Derrick, Cosmin A. Bejan, Elizabeth J. Phillips
    Journal of Allergy and Clinical Immunology, 2017.
    abstract ]

2015
  • You Chen, Joydeep Ghosh, Cosmin Adrian Bejan, Carl A. Gunter, Siddharth Gupta, Abel Kho, David Liebovitz, Jimeng Sun, Joshua Denny, Bradley Malin
    Building bridges across electronic health record systems through inferred phenotypic topics
    Journal of Biomedical Informatics (JBI), 2015.
  • Cosmin Adrian Bejan, Robertson Nash, Douglas Conway, Erica A. Bowton, Kevin B. Johnson, Joshua C. Denny
    [Podium Abstract] Mining phenotypic keywords from a large collection of clinical narrativespdf ]
    AMIA Summit on Clinical Research Informatics (AMIA-CRI), San Francisco, CA, USA, March 2015.

2014
  • Cosmin Adrian Bejan, Wei-Qi Wei, Joshua C. Denny
    Assessing the role of a medication-indication resource in the treatment relation extraction from clinical textPMID: 25336593 ]
    Journal of the American Medical Informatics Association (JAMIA), 2014.
  • Cosmin Adrian Bejan, Joshua C. Denny
    Learning to Identify Treatment Relations in Clinical Textpdf ]
    American Medical Informatics Association Fall Symposium (AMIA), Washington DC, November, 2014.
  • Cosmin Adrian Bejan, Wei-Qi Wei, Joshua C. Denny
    Using SemRep and a medication indication resource to extract treatment relations from clinical notespdf ] (Podium Abstract)
    AMIA Summit on Translational Bioinformatics (AMIA-TBI), San Francisco, CA, USA, April 2014.
  • Cosmin Adrian Bejan, Sanda Harabagiu
    Unsupervised Event Coreference Resolutionpdf | data ]
    Computational Linguistics, 2014.

2013
  • Cosmin Adrian Bejan, Lucy Vanderwende, Heather L. Evans, Mark M. Wurfel, Meliha Yetisgen-Yildiz
    On-time clinical phenotype prediction based on narrative reportsPMID: 24551325 ]
    American Medical Informatics Association Fall Symposium (AMIA) , Washington DC, November, 2013.
    Distinguished Paper Award
  • Meliha Yetisgen-Yildiz, Cosmin Adrian Bejan, Mark M. Wurfel
    Identification of Patients with Acute Lung Injury from Free-Text Chest X-ray Reportspdf ]
    ACL workshop on Biomedical Natural Language Processing (BioNLP), Sofia, Bulgaria, August 2013.
  • Meliha Yetisgen-Yildiz, Cosmin Adrian Bejan, Lucy Vanderwende, Fei Xia, Heather L. Evans, Mark M. Wurfel
    Automated Tools for Phenotype Extraction from Medical Records (Abstract) [ PMID: 24303281 ]
    AMIA Summit on Clinical Research Informatics (AMIA-CRI), San Francisco, CA, USA, March 2013.
  • Cosmin Adrian Bejan, Lucy Vanderwende, Fei Xia, Meliha Yetisgen-Yildiz
    Assertion modeling and its role in clinical phenotype identificationcode | PMID: 23000479 ]
    Journal of Biomedical Informatics (JBI), 2013.

2012
  • Cosmin Adrian Bejan, Lucy Vanderwende, Mark M. Wurfel, Meliha Yetisgen-Yildiz
    Assessing Pneumonia Identification from Time-Ordered Narrative ReportsPMID: 23304388 ]
    American Medical Informatics Association Fall Symposium (AMIA) , Chicago, IL, USA, November 2012.
  • Cosmin Adrian Bejan, Lucy Vanderwende, Mark M Wurfel, Meliha Yetisgen-Yildiz
    Assessing Pneumonia Identification from Time-Ordered Narrative Reports (Poster)
    Pacific Northwest Regional NLP Workshop (NW-NLP), Microsoft Research, Redmond, WA, USA, May 2012.
  • Cosmin Adrian Bejan, Fei Xia, Lucy Vanderwende, Mark M Wurfel, Meliha Yetisgen-Yildiz
    Pneumonia identification using statistical feature selectionPMID: 22539080 ]
    Journal of the American Medical Informatics Association (JAMIA), 2012.
  • Heather Evans, Meliha Yetisgen-Yildiz, Cosmin Adrian Bejan, Keir Warner, Robert Black, Ronald Maier, Mark M. Wurfel
    Chest X-ray Report Language is Incongruous with Quantitative Culture Results in Ventilator-Associated Pneumonia (Abstract)
    Annual Meeting of the Surgical Infection Society (SIS), Dallas, TX, USA, April 2012.

2011
  • Andrew S. Gordon, Cosmin Adrian Bejan, Kenji Sagae
    Commonsense Causal Reasoning Using Millions of Personal Storiespdf ]
    AAAI Conference on Artificial Intelligence (AAAI), San Francisco, CA, USA, August 2011.
  • Melissa Roemmele, Cosmin Adrian Bejan, Andrew S. Gordon
    Choice of Plausible Alternatives: An Evaluation of Commonsense Causal Reasoningpdf ]
    AAAI Spring Symposium on Logical Formalizations of Commonsense Reasoning (Commonsense), Stanford University, Palo Alto, CA, USA, March 2011.
  • Kirk Roberts, Cosmin Adrian Bejan, Sanda Harabagiu
    Using Event Semantics for Toponym Disambiguation
    Applied Natural Language Processing: Identification, Investigation and Resolution, Philip M. McCarthy and Chutima Boonthum-Denecke (Eds.), IGI Global, 2011.
  • Bryan Rink, Cosmin Adrian Bejan, Sanda Harabagiu
    The Role of Textual Graph Patterns in Discovering Event Causality
    Applied Natural Language Processing: Identification, Investigation and Resolution, Philip M. McCarthy and Chutima Boonthum-Denecke (Eds.), IGI Global, 2011.

2010
  • Cosmin Adrian Bejan, Sanda Harabagiu
    Unsupervised Event Coreference Resolution with Rich Linguistic Featurespdf | data ]
    Annual Meeting of the Association for Computational Linguistics (ACL), Uppsala, Sweden, July 2010.
  • Kirk Roberts, Srikanth Gullapalli, Cosmin Adrian Bejan, Sanda Harabagiu
    A Linguistic Resource for Semantic Parsing of Motion Eventspdf ]
    International Conference on Language Resources and Evaluation (LREC), Valletta, Malta, May 2010.
  • Bryan Rink, Cosmin Adrian Bejan, Sanda Harabagiu
    Learning Textual Graph Patterns to Detect Causal Event Relationspdf ]
    Florida Artificial Intelligence Research Society International Conference (FLAIRS), Daytona Beach, FL, USA, May 2010.
    Best Paper in Track Award
  • Kirk Roberts, Cosmin Adrian Bejan, Sanda Harabagiu
    Toponym Disambiguation Using Eventspdf ]
    Florida Artificial Intelligence Research Society International Conference (FLAIRS), Daytona Beach, FL, USA, May 2010.
  • Sanda Harabagiu, Cosmin Adrian Bejan
    A Knowledge Extraction Framework for Biomedical Pathwayspdf | PMID: 21347132 ]
    AMIA Summit on Translational Bioinformatics (AMIA-STB), San Francisco, CA, USA, March 2010.

2009
  • Cosmin Adrian Bejan
    Learning Event Structures from Textpdf ]
    PhD Dissertation, The University of Texas at Dallas, December 2009.
  • Cosmin Adrian Bejan, Matthew Titsworth, Andy Hickl, Sanda Harabagiu
    Nonparametric Bayesian Models for Unsupervised Event Coreference Resolutionpdf | data ]
    Advances in Neural Information Processing Systems 23 (NIPS), Vancouver, Canada, December 2009.

2008
  • Cosmin Adrian Bejan, Sanda Harabagiu
    Using Clustering Methods for Discovering Event Structures (Abstract) [ pdf ]
    AAAI Conference on Artificial Intelligence (AAAI), Chicago, IL, USA, July 2008.
  • Cosmin Adrian Bejan, Sanda Harabagiu
    A Linguistic Resource for Discovering Event Structures and Resolving Event Coreferencepdf ]
    International Conference on Language Resources and Evaluation (LREC), Marrakech, Morocco, 2008.
  • Cosmin Adrian Bejan
    Unsupervised Discovery of Event Scenarios from Textspdf ]
    Florida Artificial Intelligence Research Society International Conference (FLAIRS), Coconut Grove, FL, USA, May 2008.
    Best Paper in Track Award
    Best Student Paper Award

2007
  • Cosmin Adrian Bejan, Chris Hathaway
    UTD-SRL: A Pipeline Architecture for Extracting Frame Semantic Structurespdf ]
    ACL workshop on on Semantic Evaluations (SemEval ), Prague, Czech Republic, June 2007.
  • Cosmin Adrian Bejan
    Deriving Chronological Information from Texts through a Graph-based Algorithm (Poster) [ pdf ]
    Florida Artificial Intelligence Research Society International Conference (FLAIRS), Key West, FL, USA, May 2007.

2006
  • Sanda Harabagiu, Cosmin Adrian Bejan
    An Answer Bank for Temporal Inferencepdf ]
    International Conference on Language Resources and Evaluation (LREC), Genoa, Italy, 2006.

2005
  • Sanda Harabagiu, Cosmin Adrian Bejan, Paul Morarescu
    Shallow Semantics for Relation Extractionpdf ]
    International Joint Conference on Artificial Intelligence (IJCAI), Edinburgh, Scotland, 2005.
  • Sanda Harabagiu, Cosmin Adrian Bejan
    Question Answering Based on Temporal Inferencepdf ]
    AAAI Workshop on Inference for Textual Question Answering, Pittsburgh, PA, USA, 2005.

2004
  • Cosmin Adrian Bejan, Alessandro Moschitti, Paul Morarescu, Gabriel Nicolae, Sanda Harabagiu
    Semantic Parsing Based on FrameNetpdf ]
    ACL workshop on the Evaluation of Systems for the Semantic Analysis of Text (SENSEVAL3), Barcelona, Spain, 2004.
    Best System of the Automatic Labeling of Semantic Roles Challenge
  • Alessandro Moschitti, Cosmin Adrian Bejan
    A Semantic Kernel for Predicate Argument Classificationpdf ]
    Conference on Computational Natural Language Learning (CoNLL), Boston, MA, USA, 2004.
  • Sanda Harabagiu, Steven Maiorano, Alessandro Moschitti, Cosmin Adrian Bejan
    Intentions, Implicatures and Processing of Complex Questionspdf ]
    HLT-NAACL Workshop on Pragmatics of Question Answering, Boston, MA, USA, 2004.