| National Library of Medicine

Sarrouti M, Quatik EL, Alaoui S. SemBioNLQA: A semantic biomedical question answering system for retrieving exact and ideal answers to natural language questions. Artif Intell Med. 2020 Jan;102:101767. doi: 10.1016/j.artmed.2019.101767. Epub 2019 Nov 28.

Abstract | PMID: 31980104

Abstract

Lu C, Aronson, AR, Shooshan SE, Demner-Fushman D. Spell checker for consumer language (CSpell). J Am Med Inform Assoc. 2019 Jan 21. doi: 10.1093/jamia/ocy171. [Epub ahead of print]

Abstract | PMID: 30668712

Abstract

Lau JJ, Gayen S, Ben Abacha A, Demner-Fushman D. A dataset of clinically generated visual questions and answers about radiology images. Sci Data. 2018 Nov 20;5:180251. doi: 10.1038/sdata.2018.251.

Abstract | PMID: 30457565 | PMCID: PMC6244189

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Kilicoglu H, Ben Abacha A, Mrabet Y, Shooshan SE, Rodriguez L, Masterton K, Demner-Fushman D. Semantic annotation of consumer health questions. BMC Bioinformatics. 2018 Feb 6;19(1):34. doi: 10.1186/s12859-018-2045-1.

Abstract | PMID: 29409442 | PMCID: PMC5802048

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Demner-Fushman D. A dataset of 200 structured product labels annotated for adverse drug reactions. Sci Data. 2018 Jan 30;5:180001. doi: 10.1038/sdata.2018.1.

Abstract | PMID: 29381145 | PMCID: PMC5789866

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Zhang, K, Demner-Fushman D. Automated classification of eligibility criteria in clinical trials to facilitate patient-trial matching for specific patient populations. J Am Med Inform Assoc. 2017 Jul 1;24(4):781-787. doi: 10.1093/jamia/ocw176.

Abstract | PMID: 28339690 | PMCID: PMC6080677

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Mork JG, Aronson A, Demner-Fushman D. 12 years on - Is the NLM medical text indexer still useful and relevant? J Biomed Semantics. 2017 Feb 23;8(1):8. doi: 10.1186/s13326-017-0113-5.

Abstract | PMID: 28231809 | PMCID: PMC5324252

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Demner-Fushman D, Rogers W, Aronson A. MetaMap Lite: an evaluation of a new Java implementation of MetaMap. J Am Med Inform Assoc. 2017 Jul 1;24(4):841-844. doi: 10.1093/jamia/ocw177.

Abstract | PMID: 28130331

Abstract

Deardorff A, Masterton K, Roberts K, Kilicoglu H, Demner-Fushman D. A protocol-driven approach to automatically finding authoritative answers to consumer health questions in online resources. JASIST, 68(7): 1724-1736. doi: 10.1002/asi.23806.

Abstract

De Herrera A, Schaer R, Bromuri S, Müller H. Overview of the ImageCLEF 2016 Medical Task. CLEF working notes 2016, CEUR, 2016.

Abstract | pub9419.pdf

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Wei W, Marmor R, Singh S, Wang S, Demner-Fushman D, Kuo TT, Hsu CN, Ohno-Machado L. Finding Related Publications: Extending the Set of Terms Used to Assess Article Similarity. AMIA Jt Summits Transl Sci Proc. 2016 Jul 20;2016:225-34. eCollection 2016.

Abstract | PMID: 27570676 | PMCID: PMC5001748

Abstract

Ben Abacha A, Demner-Fushman D. Meta-Learning with Selective Data Augmentation for Medical Entity Recognition. International Journal of Computational Linguistics and Applications (IJCLA) 7(2): 167-182 (2016)

Abstract | 1_IJCLA.pdf

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Roberts K, Demner-Fushman D. Interactive use of online health resources: a comparison of consumer and professional questions. J Am Med Inform Assoc. 2016 Jul;23(4):802-11. doi: 10.1093/jamia/ocw024. Epub 2016 May 4.

Abstract | pub9363.pdf | PMID: 27147494 | PMCID: PMC4926747

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Demner-Fushman D, Kilicoglu H. Dataset: CHQA Named Entity Dataset

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Demner-Fushman D, Roberts K. Dataset: Question Decomposition Data

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Demner-Fushman D, Roberts K. Dataset: Question Type Data

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Roberts K, Shooshan SE, Rodriguez L, Abhyankar S, Kilicoglu H, Demner-Fushman D. The role of fine-grained annotations in supervised recognition of risk factors for heart disease from EHRs. J Biomed Inform. 2015 Dec;58 Suppl:S111-9. doi: 10.1016/j.jbi.2015.06.010. Epub 2015 Jun 26.

Abstract | pub9188.pdf | PMID: 26122527 | PMCID: PMC4988795

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Roberts K, Simpson M, Demner-Fushman D, Voorhees E, Hersh W. State-of-the-art in biomedical literature retrieval for clinical cases: A survey of the TREC 2014 CDS Track. Inf Retrieval J. 2015.

Abstract | pub9284.pdf

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Roberts K, Kilicoglu H, Fiszman M, Demner-Fushman D. Decomposing consumer health questions. BioNLP 2014.

Abstract | pub7078.pdf

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Apostolova E, You D, Xue Z, Antani SK, Demner-Fushman D, Thoma GR. Image Retrieval From Scientific Publications: Text and Image Content Processing To Separate Multipanel Figures. JASIST (Journal of the American Society for Information Science and Technology), 64(5):893–908, 2013.

Abstract | published_asi22810.pdf

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Demner-Fushman D, Antani SK, Simpson M, Thoma GR. Design and Development of a Multimodal Biomedical Information Retrieval System JCSE. June 2012;6(2):168-177.

Abstract | pub2012019.pdf

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Jimeno-Yepes A, Mork J, Demner-Fushman D, Aronson AR. A one-size-fits-all indexing method does not exist: automatic selection based on meta-learning. JCSE, vol. 6, no. 2, pp.151-160, 2012.

Abstract | pub-2012-048.pdf | URL: http://jcse.kiise.org/PublishedPaper/topic_abstract.asp?idx=134

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Stanley RJ, De S, Demner-Fushman D, Antani SK, Thoma GR. An image feature-based approach to automatically find images for application to clinical decision support. Comput Med Imaging Graph. 2011 Jul;35(5):365-72. doi: 10.1016/j.compmedimag.2010.11.008. Epub 2010 Dec 8.

Abstract | PMID: 21144707 | PMCID: PMC3084330

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Zhang X, Zou J, Le DX, Thoma GR. A structural SVM approach for reference parsing. BMC Bioinformatics. 2011 Jun 9;12 Suppl 3:S7. doi: 10.1186/1471-2105-12-S3-S7.

Abstract | PMID: 21658294 | PMCID: PMC3111593

Abstract

Mork JG, Bodenreider O, Demner-Fushman D, Dogan RI, Lang FM, Lu Z, Névéol A, Peters L, Shooshan SE, Aronson AR. Extracting Rx information from clinical narrative. J Am Med Inform Assoc. 2010 Sep-Oct;17(5):536-9. doi: 10.1136/jamia.2010.003970.

Abstract | pub2010047.pdf | PMID: 20819859 | PMCID: PMC2995679

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Demner-Fushman D, Mork JG, Shooshan SE, Aronson AR. UMLS content views appropriate for NLP processing of the biomedical literature vs. clinical text. J Biomed Inform. 2010 Aug;43(4):587-94. doi: 10.1016/j.jbi.2010.02.005. Epub 2010 Feb 10.

Abstract | pub2009040.pdf | PMID: 20152935 | PMCID: PMC2890296

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Demner-Fushman D, Simpson M, Antani S, Thoma GR. Annotation and retrieval of clinically relevant images. Int J Med Inform. 2009 Dec;78(12):e59-67. doi: 10.1016/j.ijmedinf.2009.05.003. Epub 2009 Jul 9.

Abstract | pub2009025.pdf | PMID: 19546026 | PMCID: PMC2783743

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Fiszman M, Demner-Fushman D, Kilicoglu H, Rindflesch TC. Automatic summarization of MEDLINE citations for evidence-based medical treatment: a topic-oriented evaluation. J Biomed Inform. 2009 Oct;42(5):801-13. doi: 10.1016/j.jbi.2008.10.002. Epub 2008 Nov 5.

Abstract | PMID: 19022398 | PMCID: PMC2776079

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Deserno TM, Antani S, Long LR. Ontology of gaps in content-based image retrieval. J Digit Imaging. 2009 Apr;22(2):202-15. doi: 10.1007/s10278-007-9092-x. Epub 2008 Feb 1.

Abstract | pub2009030.pdf | PMID: 18239964 | PMCID: PMC3043678

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Hsu W, Antani SK, Long LR, Neve L, Thoma GR. SPIRS: a Web-based image retrieval system for large biomedical databases. Int J Med Inform. 2009 Apr;78 Suppl 1:S13-24. doi: 10.1016/j.ijmedinf.2008.09.006. Epub 2008 Nov 8.

Abstract | PMID: 18996737 | PMCID: PMC2693318

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Kilicoglu H, Demner-Fushman D, Rindflesch TC, Wilczynski NL, Haynes RB. Towards Automatic Recognition of Scientifically Rigorous Clinical Research Evidence J Am Med Inform Assoc. 2009 Jan-Feb;16(1):25-31. Epub 2008 Oct 24.

Abstract | PMID: 18952929 | PMCID: PMC2605595

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Lee DJ, Antani S, Chang Y, Long LR, Christensen P, Jeronimo J. CBIR of Spine X-ray Images On Inter-vertebral Disc Space and Shape Profiles Using Feature Ranking and Voting Consensus. Data & Knowledge Engineering, Special Issue on Knowledge Discovery in Medicine. 2009.

Abstract | pub2009032.pdf

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Demner-Fushman D, Antani SK, Simpson M. Web Interface: Open-I

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Deserno TM, Antani S, Long LR. Content-based image retrieval for scientific literature access. Methods Inf Med. 2009;48(4):371-80. doi: 10.3414/ME0561. Epub 2009 Jul 20.

Abstract | pub2009029.pdf | PMID: 19621115

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Sneiderman CA, Demner-Fushman D, Fiszman M, Ide NC, Rindflesch TC. Knowledge-Based Methods to Help Clinicians Find Answers in MEDLINE. J Am Med Inform Assoc. 2007 Nov-Dec;14(6):772-80. Epub 2007 Aug 21.

Abstract | PMID: 17712086 | PMCID: PMC2213491

Abstract

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