• Divita G, Rosemblat G, Browne AC. Building a medical Spanish lexicon. AMIA Annu Symp Proc. 2007 Oct 11:941.

  Abstract | PMID:  18694041

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• Lu C, Demner-Fushman D. Improving Spelling Correction with Consumer Health Terminology Improving Spelling Correction with Consumer Health Terminology AMIA 2018 Annual Symposium, San Francisco, CA, November 3-7, 2018, p. 2053.

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• Kayaalp M. Modes of De-identification. AMIA Annu Symp Proc. 2018 Apr 16;2017:1044-1050. eCollection 2017.

  Abstract | pub9526.pdf | PMID:  29854172 | PMCID:  PMC5977668

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• Rodriguez L, Morrison SM, Greenberg K, Demner-Fushman D. Mining the literature for genes associated with placenta-mediated maternal diseases. AMIA Annu Symp Proc. 2018 Apr 16;2017:1498-1506. eCollection 2017.

  Abstract | pub9572.pdf | PMID:  29854219 | PMCID:  PMC5977710

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• Lu C, Tormey D, McCreedy L, Browne AC. Enhancing LexSynonym Features in the Lexical Tools AMIA 2017 Annual Symposium, Washington, DC, November 04-08, 2017, p. 2090

  Abstract | pub9775.pdf

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• Bhupatiraju R, Fung K, Bodenreider O. MetaMapLite in Excel: Biomedical named-entity recognition for non-technical users. Stud Health Technol Inform (Proc Medinfo): 1252.

  Abstract | PMID:  29295337 | PMCID:  PMC5884681

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• Lu C, Tormey D, McCreedy L, Browne AC. Generating A Distilled N-Gram Set: Effective Lexical Multiword Building in the SPECIALIST Lexicon. The 10th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2017), Vol(5): HEALTHINF, PORTO, Portugal, February 21-23, 2017, p. 77-87.

  Abstract | pub9575.pdf

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• 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

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• 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

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• Kilicoglu H. Inferring Implicit Causal Relationships in Biomedical Literature. Proc 15th Workshop on Biomedical Natural Language Processing. Pages 46-55. 2016.

  Abstract | pub9441.pdf

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• Demner-Fushman D, Elhadad N. Aspiring to Unintended Consequences of Natural Language Processing: A Review of Recent Developments in Clinical and Consumer-Generated Text Processing. IMIA Yearbook of Medical Informatics 2016.

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• Mrabet Y, Kilicoglu H, Demner-Fushman D. Unsupervised Ranking of Knowledge Bases for Named Entity Recognition. ECAI 2016, The Hague, The Netherlands, 1248-1255.

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• Kilicoglu H, Ben Abacha A, Mrabet Y, Roberts K, Rodriguez L, Shooshan SE, Demner-Fushman D. Annotating named entities in consumer health questions. LREC,23-28 May 2016, Portorož.

  Abstract | pub9349.pdf

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• Kilicoglu H, Fiszman M, Roberts K, Demner-Fushman D. An Ensemble Method for Spelling Correction in Consumer Health Questions. AMIA Annu Symp Proc. 2015 Nov 5;2015:727-36. eCollection 2015.

  Abstract | PMID:  26958208 | PMCID:  PMC4765565

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• 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

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• Wei W, Demner-Fushman D, Wang S, Jiang X, Ohno-Machado L. Ranking Medical Subject Headings using a factor graph model. AMIA Jt Summits Transl Sci Proc. 2015 Mar 23;2015:56-63. eCollection 2015.

  Abstract | pub9268.pdf | PMID:  26306236 | PMCID:  PMC4525219

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• Browne AC, Kayaalp M, Dodd Z, Sagan, P, McDonald CJ. The Challenges of Creating a Gold Standard for De-identification Research. AMIA Annu Symp Proc. 2014 Nov 14;2014:353-8. eCollection 2014.

  Abstract | pub8927.pdf | PMID:  25954338 | PMCID:  PMC4420002

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• Culbertson A, Fiszman M, Shin D, Rindflesch TC. Semantic processing to identify adverse drug event information from black box warnings. AMIA Annu Symp Proc. 2014 Nov 14;2014:442-8. eCollection 2014.

  Abstract | PMID:  25954348 | PMCID:  PMC4419903

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• Huser, V, Kayaalp M, Dodd Z, Cimino J. Piloting a deceased subject integrated data repository and protecting privacy of relatives. AMIA Annu Symp Proc. 2014 Nov 14;2014:719-28. eCollection 2014.

  Abstract | pub8928.pdf | PMID:  25954378 | PMCID:  PMC4420001

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• 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

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• Ozturk S, Kayaalp M, McDonald CJ. Visualization of patient prescription history data in emergency care. AMIA Annu Symp Proc. 2014 Nov 14;2014:963-8. eCollection 2014.

  Abstract | PMID:  25954404 | PMCID:  PMC4419971

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• 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 | URL:  http://knowledge.amia.org/56638-amia-1.1540970/t-004-1.1544972/f-004-1.1544973/a...

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• Winnenburg R, Bodenreider O. Desiderata for an authoritative representation of MeSH in RDF. AMIA Annu Symp Proc 2014:1218-1227.

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• Zhang GQ, Zhu W, Sun M, Tao S, Bodenreider O, Cui L. MaPLE: A MapReduce Pipeline for Lattice-based Evaluation and Its Application to SNOMED CT. Proc IEEE Int Conf Big Data. 2014 Oct;2014:754-759.

  Abstract | PMID:  25705725 | PMCID:  PMC4334137

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• Kilicoglu H, Demner-Fushman D. Coreference Resolution for Structured Drug Product Labels Proceedings of BioNLP 2014. pp. 44-53.

  Abstract | pub8919.pdf

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• Roberts K, Masterton K, Kilicoglu H, Fiszman M, Demner-Fushman D. Annotating Question Decomposition on Complex Medical Questions. LREC 2014.

  Abstract | pub7076.pdf

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• Roberts K, Masterton K, Fiszman M, Kilicoglu H, Demner-Fushman D. Annotating Question Types for Consumer Health Questions. LREC 2014, BioTxtM workshop.

  Abstract | pub7077.pdf

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• Cohen T, Widdows D, Rindflesch TC. Expansion-by-analogy: A vector symbolic approach to semantic search. AAAI-Fall 2014 Symposium on Quantum Informatics for Cognitive, Social, and Semantic Processes.

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• Kastrin A, Rindflesch TC, Hristovski D. Link prediction on the Semantic MEDLINE Network. Proceedings of the 17th International conference on Discovery Science.

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• Mork JG, Demner-Fushman D, Schmidt SC, Aronson A. Recent Enhancements to the NLM Medical Text Indexer. BioASQ 2014.

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• Osborne R, Aronson A, Cohen K. A repository of semantic types in the MIMIC II database clinical notes. BioNLP 2014. pp. 93-97.

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• Kilicoglu H, Fiszman M, Demner-Fushman D. Interpreting Consumer Health Questions: The Role of Anaphora and Ellipsis. Proceedings of BioNLP 2013. Pages 54-62.

  Abstract | pub7057.pdf

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• Cairelli MJ, Miller CM, Fiszman M, Workman TE, Rindflesch TC. Semantic MEDLINE for discovery browsing: using semantic predications and the literature-based discovery paradigm to elucidate a mechanism for the obesity paradox. AMIA Annu Symp Proc. 2013 Nov 16;2013:164-73. eCollection 2013.

  Abstract | PMID:  24551329 | PMCID:  PMC3900170

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• Demner-Fushman D, Mork JG, Aronson AR. Mining MEDLINE for problems associated with vitamin D. AMIA Annu Symp Proc. 2013 Nov 16;2013:300-8. eCollection 2013.

  Abstract | PMID:  24551339 | PMCID:  PMC3900180

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• 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

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• 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

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• 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

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• Le T, Rance B, Bodenreider O. Network visualization of UMLS source vocabularies using semantic groups. AMIA Annu Symp Proc, 2013: p. 90

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• 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

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• Winnenburg R, Rodriguez L, Callaghan F, Sorbello A, Szarfman A, Bodenreider O. Aligning Pharmacologic Classes Between MeSH and ATC. 4th International Conference on Biomedical Ontology · ICBO 2013

  Abstract | pub9580.pdf

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• Gallagher ME. Improving Software Sustainability: Lessons Learned from Profiles in Science. Archiving. 2013;2013:74-79.

  Abstract | a2013001.pdf | PMID:  25267934 | PMCID:  PMC4176707

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• Jimeno Yepes AJ, Mork JG, Aronson A. Identifying Publication Types Using Machine Learning. BioASQ Workshop 2013.

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• Mork JG, Jimeno Yepes A, Aronson A. The NLM Medical Text Indexer System for Indexing Biomedical Literature. BioASQ 2013.

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• Gallagher ME, Moffatt C. The Profiles in Science Digital Library: Behind the Scenes. Proc ACM/IEEE Joint Conf Digit Libr. 2012: 433–434. doi: 10.1145/2232817.2232928.

  Abstract | pub2012016.pdf | PMCID:  PMC3609548

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• Lu C, Browne AC. Development of Sub-Term Mapping Tools (STMT) AMIA 2012 Annual Symposium, Chicago, IL, November 3-7, 2012

  Abstract | pub2012017.pdf

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• Tse T, Zarin D, Williams R, Ide N. The role and importance of clinical trial registries and results databases In: Gallin JI, Ognibene FP, eds, Principles and Practice of Clinical Research. 3rd ed. Amsterdam: Academic Press; 2012: 171-81.

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• Jimeno-Yepes A, Aronson AR. Knowledge-based and knowledge-lean methods combined in unsupervised word sense disambiguation. Proc 2nd ACM SIGHIT International Health Informatics (IHI) Symposium 2012, 733-736.

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• Jimeno-Yepes A, Mork JG, Wilkowski B, Demner-Fushman D, Aronson AR. MEDLINE MeSH indexing: lessons learned from machine learning and future directions. Proc IHI 2012, 737-742.

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• Jimeno-Yepes A, Wilkowski B, Mork JG, Demner-Fushman D, Aronson AR. MeSH indexing: machine learning and lessons learned. ACM SIGHIT International Health Informatics Symposium, Miami, FL, USA, 2012.

  Abstract | pub2012-064.pdf

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• 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 | URL:  http://ii.nlm.nih.gov/MTI_ML/index.shtml

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