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  • Jimeno-Yepes A, Wilkowski B, Mork J, van Lenten E, Demner-Fushman D, Aronson AR. A bottom-up approach to MEDLINE indexing recommendations. AMIA Annu Symp Proc. 2011;2011:1583-92. Epub 2011 Oct 22.
    Abstract | PMID:  22195224 | PMCID:  PMC3243198
  • He Y, Kayaalp M. A Comparison of 13 Tokenizers on MEDLINE December 2006 Technical Report.
    Abstract | tr2006003.pdf
  • Kilicoglu H, Rosemblat G, Cairelli M, Rindflesch TC. A Compositional Interpretation of Biomedical Event Factuality. Proc of the Second Workshop on Extra-Propositional Aspects of Meaning in Computational Semantics (ExProM 2015).
    Abstract | pub9223.pdf
  • Sharp M, Bodenreider O, Wacholder N. A Framework for Characterizing Drug Information Sources AMIA Annu Symp Proc. 2008 Nov 6:662-6
    Abstract | PMID:  18999182 | PMCID:  PMC2656044
  • Fiszman M, Shin D, Sneiderman CA, Jin H, Rindflesch TC. A Knowledge Intensive Approach to Mapping Clinical Narrative to LOINC. AMIA Annu Symp Proc. 2010 Nov 13;2010:227-31.
    Abstract | pub2010029.pdf | PMID:  21346974 | PMCID:  PMC3041410
  • Workman TE, Rosemblat G, Fiszman M, Rindflesch TC. A literature-based assessment of concept pairs as a measure of semantic relatedness. AMIA Annu Symp Proc. 2013 Nov 16;2013:1512-21. eCollection 2013.
    Abstract | PMID:  24551423 | PMCID:  PMC3900161
  • Lu C, Humphrey SM, Browne AC. A method for verifying a vector-based text classification system AMIA Annu Symp Proc. 2008 Nov 6:1030.
    Abstract | pub2008078.pdf | PMID:  18998786
  • Bashyam V, Divita G, Bennett DB, Browne AC, Taira RK. A normalized lexical lookup approach to identifying UMLS concepts in free text. Stud Health Technol Inform. 2007;129(Pt 1):545-9.
    Abstract | PMID:  17911776
  • Rosemblat G, Graham L. A Pragmatic Approach to Summary Extraction in Clinical Trials Proc HLT-NAACL 06, pages 124-125, New York City, June 2006
    Abstract | pub2006012.pdf
  • Osborne R, Aronson A, Cohen K. A repository of semantic types in the MIMIC II database clinical notes. BioNLP 2014. pp. 93-97.
    Abstract
  • Leroy G, Rindflesch TC, Libbus B, Kilicoglu H, Chen H. A Syntactic Parser with Semantic Filtering for Biomedical Text. Proceedings of Pacific Symposium on Biocomputing.
    Abstract
  • Lynch P, Luan X, Prettyman M, Mericle L, Borkmann E, Schlaifer J. An evaluation of new and old similarity ranking algorithms. Proceedings of the International Conference on Information Technology: Coding and Computing (ITCC’04). 2004;2:148.
    Abstract | pub2004-079.pdf
  • Resnick MP, Ripple AM, Auston I, Rindflesch TC. An Ontology for Public Health to Support Enhanced Information Retrieval AMIA Annu Symp Proc. 2010
    Abstract | pub2010031.pdf
  • Roberts K, Demner-Fushman D. Annotating Logical Forms for EHR Questions. Proceedings of the Language Resources and Evaluation Conference, LREC,23-28 May 2016, Portorož.
    Abstract | http://www.lrec-conf.org/proceedings/lrec2016/pdf/152_Paper.pdf
  • Demner-Fushman D, Lin J. Answer Extraction, Semantic Clustering, and Extractive Summarization for Clinical Question Answering Proc COLING/ACL 2006. July 2006, Sydney, Australia
    Abstract | pub2006031.pdf
  • Rindflesch TC, Bean CA, Sneiderman CA. Argument Identification for Arterial Branching Predications Asserted in Cardiac Catheterization Reports Proc AMIA Symp. 2000:704-8.
    Abstract | pub2000018.pdf | PMID:  11079975 | PMCID:  PMC2243725
  • Ruch P, Tbahriti I, Bobeill J, Aronson AR. Argumentative Feedback: A Linguistically-motivated Term Expansion for Information Retrieval Proc COLING/ACL 2006, 675-82
    Abstract | pub2006071.pdf
  • Kilicoglu H, Fiszman M, Rosemblat G, Marimpietri S, Rindflesch TC. Arguments of Nominals in Semantic Interpretation of Biomedical Text BioNLM Workshop Proc, Assoc. for Computational Linguistics 2010
    Abstract | pub2010030k.pdf
  • Jimeno-Yepes A, Mork J, Demner-Fushman D, Aronson AR. Automatic algorithm selection for MeSH Heading indexing based on meta-learning. International Symposium on Languages in Biology and Medicine, Singapore, December, 2011.
    Abstract | pub2011-110.pdf | http://ii.nlm.nih.gov/MTI_ML/index.shtml
  • Bangalore AK, Divita G, Humphrey SM, Browne AC, Thorn KE. Automatic Categorization of Google Search Results for Medical Queries using JDI Medinfo 2007: Proc. of the 11th World Congress on Health (Medical) Informatics
    Abstract
  • Névéol A, Mork JG, Aronson AR. Automatic indexing of specialized documents: using generic vs. domain-specific document representations. Proc 2007 Workshop BioNL'07, 183-92.
    Abstract | pub2007036.pdf
  • Humphrey S, Rindflesch TC, Aronson AR. Automatic Journal Descriptor Indexing Extended to Indexing by UMLS Semantic Type Using the Cosine Document Similarity Measure. Proc. of the 11th SIG/CR Classification Research Workshop. 2000;103-16.
    Abstract | pub2000056.pdf
  • Apostolova E, Channin DS, Demner-Fushman D, Furst J, Lytinen S, Raicu D. Automatic segmentation of clinical texts. 2009 Annual International Conference of the IEEE Engineering in Medicine and Biology Society, Minneapolis, MN, 2009, pp. 5905-5908. doi: 10.1109/IEMBS.2009.5334831
    Abstract | PMID:  19965054
  • Roberts K, Kilicoglu H, Fiszman M, Demner-Fushman D. Automatically classifying question types for consumer health questions. AMIA Annu Symp Proc. 2014 Nov 14;2014:1018-27. eCollection 2014.
    Abstract | pub8972.pdf | PMID:  25954411 | PMCID:  PMC4420005 | http://knowledge.amia.org/56638-amia-1.1540970/t-004-1.1544972/f-004-1.1544973/a...
  • Mishra R, Del Fiol G, Kilicoglu H, Jonnalagadda S, Fiszman M. Automatically extracting clinically useful sentences from UpToDate to support clinicians' information needs. AMIA Annu Symp Proc. 2013 Nov 16;2013:987-92. eCollection 2013.
    Abstract | pub8952.pdf | PMID:  24551389 | PMCID:  PMC3900230
  • Jonnalagadda SR, Del Fiol G, Medlin R, Weir C, Fiszman M, Mostafa J, Liu H. Automatically extracting sentences from Medline citations to support clinicians' information needs. J Am Med Inform Assoc. 2013 Sep-Oct;20(5):995-1000. doi: 10.1136/amiajnl-2012-001347. Epub 2012 Oct 25.
    Abstract | pub7003.pdf | PMID:  23100128 | PMCID:  PMC3756259
  • Kayaalp M. Bayesian Methods for Diagnosing Physiological Conditions of Human Subjects from Multivariate Time Series Biosensor Data Physiological Data Modeling Contest, the Twenty-First International Conference on Machine Learning (ICML), 2004 July.
    Abstract | pub2004022.pdf
  • Névéol A, Zeng K, Bodenreider O. Besides precision & recall: exploring alternative approaches to evaluating an automatic indexing tool for MEDLINE. AMIA Annu Symp Proc. 2006:589-93.
    Abstract | pub2006057.pdf | PMID:  17238409 | PMCID:  PMC1839480
  • Kim H, Goryachev S, Rosemblat G, Browne A, Keselman A, Zeng-Treitler Q. Beyond Surface Characteristics: A New Health Text-specific Readability Measurement AMIA Annu Symp Proc. 2007 Oct 11:418-22
    Abstract | PMID:  18693870 | PMCID:  PMC2655856
  • He Y, Kayaalp M. Biological Entity Recognition with Conditional Random Fields AMIA Annu Symp Proc. 2008 Nov 6:293-7
    Abstract | PMID:  18999272 | PMCID:  PMC2656029
  • Divita G, Rosemblat G, Browne AC. Building a medical Spanish lexicon. AMIA Annu Symp Proc. 2007 Oct 11:941.
    Abstract | PMID:  18694041
  • Kayaalp M, Browne AC, Dodd Z, Sagan P, McDonald CJ. Clinical Text De-Identification Research September 2013 Technical Report to the LHNCBC Board of Scientific Counselors
    Abstract | 6932.pdf
  • Mrabet Y, Kilicoglu H, Roberts K, Demner-Fushman D. Combining Open-domain and Biomedical Knowledge for Topic Recognition in Consumer Health Questions. AMIA Annu Symp Proc. 2017 Feb 10;2016:914-923. eCollection 2016.
    Abstract | pub9458.pdf | PMID:  28269888 | PMCID:  PMC5333243
  • Demner-Fushman D, Humphrey SM, Ide NC, Loane RF, Mork J, Ruch P, Ruiz ME, Smith LH, Wilbur WJ, Aronson AR. Combining Resources to Find Answers to Biomedical Questions Proc TREC 2007, 205-14
    Abstract | pub2007061.pdf
  • Mortensen J, Bodenreider O. Comparing Pharmacologic Classes in NDF-RT and SNOMED CT. Proc SMBM 2010:119-124.
    Abstract
  • Yepes AJ, Mork JG, Demner-Fushman D, Aronson AR. Comparison and combination of several MeSH indexing approaches. AMIA Annu Symp Proc. 2013 Nov 16;2013:709-18. eCollection 2013.
    Abstract | PMID:  24551371 | PMCID:  PMC3900212
  • Jung B, Lee S, Fontelo P, Liu F, Kim S. Construction of Korean Version PICO Linguist and BabelMeSH. Korean Society of Medical Informatics (KOSMI) Fall Congress Proceedings 2007.
    Abstract | pub2007072.pdf
  • Lu C, Browne AC. Converting Unicode Lexicon and Lexical Tools for ASII NLP Applications AMIA Annu Symp Proc 2011:1870.
    Abstract | pub2011070.pdf
  • Rosemblat G, Graham L. Cross-Language Search in a Monolingual Health Information System: Flexible Designs and Lexical Processes Proc ISKO, pages 173-182, Vienna, Austria, July 2006.
    Abstract | pub2006015.pdf
  • Kayaalp M, Browne AC, Dodd Z, Sagan P, McDonald CJ. De-identification of Address, Date, and Alphanumeric Identifiers in Narrative Clinical Reports. AMIA Annu Symp Proc. 2014 Nov 14;2014:767-76. eCollection 2014.
    Abstract | pub8926.pdf | PMID:  25954383 | PMCID:  PMC4419982
  • Goodwin T, Demner-Fushman D. Deep Learning from Incomplete Data: Detecting Imminent Risk of Hospital-acquired Pneumonia in ICU Patients. Proceedings of the AMIA 2019 Annual Symposium, Washington, DC, USA, November 17-20, 2019.
    Abstract | pub9980.pdf
  • Winnenburg R, Bodenreider O. Desiderata for an authoritative representation of MeSH in RDF. AMIA Annu Symp Proc 2014:1218-1227.
    Abstract
  • Bodenreider O, Burgun A. Desiderata for an Ontology of Diseases for the Annotation of Biological Datasets Proc ICBO 2009:39-42
    Abstract | pub2009023.pdf
  • Bernhardt PJ, Humphrey SM, Rindflesch TC. Determining Prominent Subdomains in Medicine. AMIA Annu Symp Proc. 2005:46-50.
    Abstract | pub2005052.pdf | PMID:  16778999 | PMCID:  PMC1560510
  • Weeber M, Mork JG, Aronson AR. Developing a Test Collection for Biomedical Word Sense Disambiguation Proc AMIA Symp. 2001:746-50.
    Abstract | pub2001054.pdf | PMID:  11825285 | PMCID:  PMC2243574
  • Lu C, Browne AC. Development of Sub-Term Mapping Tools (STMT) AMIA 2012 Annual Symposium, Chicago, IL, November 3-7, 2012
    Abstract | pub2012017.pdf
  • Lu C, Divita G, Browne AC. Development of Visual Tagging Tool AMIA Annu Symp Proc 2010:1156.
    Abstract | pub2010065.pdf
  • Workman E, Weir, C, Rindflesch TC. Differentiating Sense through Semantic Interaction Data. AMIA Annu Symp Proc. 2017 Feb 10;2016:1238-1247. eCollection 2016.
    Abstract | PMID:  28269921 | PMCID:  PMC5333208
  • Hole WT, Srinivasan S. Discovering Missed Synonymy in a Large Concept-Orientated Methathesaurus AMIA Annu Symp Proc. 2000;():354-8.
    Abstract | pub2000043.pdf | PMID:  11079904
  • Divita G, Browne AC, Loanne R. dTagger: A POS Tagger AMIA Annu Symp Proc. 2006:200-3
    Abstract | pub2006041.pdf | PMID:  17238331 | PMCID:  PMC1839340

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