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  • Kim I, Thoma GR. Machine Learning with Selective Word Statistics for Automated Classification of Citation Subjectivity in Online Biomedical Articles. Proc. Int’l Conf. Artificial Intelligence (ICAI’17), pp. 201-207, Las Vegas, July 2017.
  • Rae A, Kim J, Le DX, Thoma GR. Main Content Detection in HTML Journal Articles. DocEng ’18: ACM Symposium on Document Engineering 2018, August 28–31, 2018, Halifax, NS, Canada. ACM, New York, NY, USA, 4 pages. https://doi.org/10.1145/3209280.3229115
  • 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.
  • Aronson AR, Mork JG, Neveol A, Shooshan SE, Demner-Fushman D. Methodology for Creating UMLS Content Views Appropriate for Biomedical Natural Language Processing AMIA Annu Symp Proc. 2008 Nov 6:21-5
  • Kayaalp M, Aronson AR, Humphrey SM, Ide NC, Tanabe LK, Smith LH, Demner-Fushman D, Loane RF, Mork JG, Bodenreider O. Methods for accurate retrieval of MEDLINE citations in functional genomics. The Twelfth Text Retrieval Conference (TREC 2003). 2003:441-50.
  • 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.
  • 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.
  • Xue Z, Rahman M, Antani SK, Long LR, Demner-Fushman D, Thoma GR. Modality Classification for Searching Figures in Biomedical Literature. Proceedings of the IEEE 29th International Symposium on Computer-Based Medical Systems, pp. 152-157, 2016. doi:10.1109/CBMS.2016.29.
  • Kim J, Le DX, Thoma GR. Naive Bayes and SVM Classifiers For Classifying Databank Accession Number Sentences From Online Biomedical Articles IS&T/SPIE's 22nd Annual Symposium on Electronic Imaging. San Jose, CA. January 2010;7534:75340U-1 - 8
  • Kim J, Le DX, Thoma GR. Naive Bayes Classifier for Extracting Bibliographic Information From Biomedical Online Articles Proc 2008 International Conference on Data Mining. Las Vegas, Nevada, USA. July 2008;II:373-8
  • Kim J, Thoma GR. Named Entity Recognition in Affiliations of Biomedical Articles Using Statistics and HMM Classifiers. The 2016 International Conference on Data Mining (DMIN2016), Las Vegas, USA, pp. 236-241, July, 2016.
  • Ben Abacha A, Long LR, Seco de Herrera AG, Antani SK, Wang K, Demner-Fushman D. Named Entity Recognition in Functional Neuroimaging Literature. BIBM 2017
  • Mork JG, Bodenreider O, Demner-Fushman D, Doagan RI, Lang F-M, Lu Z, Névéol A, Peters L, Shooshan SE, Aronson AR. NLM's I2B2 tool system description. Third i2b2 Workshop on Natural Language Processing Challenges for Clinical Records, November, San Francisco, 2009
  • Ben Abacha A, Demner-Fushman D. NLM_NIH at SemEval-2017 Task 3: from Question Entailment to Question Similarity for Community Question Answering. In Proceedings of the 11th International Workshop on Semantic Evaluation (SemEval@ACL) 2017: 349-352.
  • Ben Abacha A, Demner-Fushman D. On the role of question summarization and information source restriction in consumer health question answering. In Proceedings of the AMIA 2019 Informatics Summit, San Francisco, CA, USA, 2019.
  • Zou J, Le DX, Thoma GR. Online Medical Journal Article Layout Analysis Proc SPIE-IS&T Electronic Imaging 2007, SPIE Vol. 6500: 65000V (1-12)
  • Demner-Fushman D, Fung K, Do P, Boyce R, Goodwin T. Overview of the TAC 2018 Drug-Drug Interaction Extraction from Drug Labels Track. Proceedings of the Text Analysis Conference (TAC) 2018, Gaithersburg, MD, USA, November 13-14, 2018.
  • Le DX, Thoma GR. Page Layout Classification Technique for Biomedical Documents Proc. World Multiconference on Systems, Cybernetics and Informatics (SCI). 2000 Jul.;X: 348-52.
  • 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.
  • Walker FL, Thoma GR. Read it to Me! Proc. 21st National Online Meeting. 2000 May;: 473-83.
  • Mork JG, Demner-Fushman D, Schmidt SC, Aronson A. Recent Enhancements to the NLM Medical Text Indexer. BioASQ 2014.
  • Ben Abacha A, Demner-Fushman D. Recognizing Question Entailment for Medical Question Answering. AMIA Annu Symp Proc. 2017 Feb 10;2016:310-318. eCollection 2016.
  • Roberts K, Rodriguez L, Shooshan SE, Demner-Fushman D. Resource Classification for Medical Questions. AMIA Annu Symp Proc. 2017 Feb 10;2016:1040-1049. eCollection 2016.
  • Sneiderman C, Demner-Fushman D, Fiszman M, Rindflesch TC. Semantic Characteristics of MEDLINE Citations Useful for Therapeutic Decision-making AMIA Annu Symp Proc. 2005:1117.
  • Sneiderman C, Demner-Fushman D, Fiszman M, Rosemblat G, Lang FM, Norwood D, Rindflesch TC. Semantic Processing to Enhance Retrieval of Diagnosis Citations from Medline AMIA Annu Symp Proc. 2006:1104
  • Chen S, Mao S, Thoma GR. Simultaneous Layout Style and Logical Entity Recognition in a Heterogeneous Collection of Documents Proc ICDAR2007. Curitiba, Brazil; September 2007, pp. 118-22
  • Demner-Fushman D, Lin J. Situated Question Answering in the Clinical Domain: Selecting the Best Drug Treatment for Diseases Proc COLING/ACL 2006 Workshop on Task-Focused Summarization and Question Answering, July 2006, Sydney, Australia
  • Thoma GR, Ford G, Demner-Fushman D, Antani SK, Chung M. Software: Panorama
  • Mao S, Kanungo T. Stochastic Language Models for Automatic Acquisition of Lexicons from Printed Bilingual Dictionaries Document Layout Interpretation and Its Application. 2001.
  • Zou J, Le DX, Thoma GR. Structure and Content Analysis for HTML Medical Articles: A Hidden Markov Model Approach Proc August 2007 ACM Symposium on Document Engineering. pp. 199-201
  • Demner-Fushman D, Abhyankar S. Syntactic-semantic frames for clinical cohort identification queries. Data Integration in the Life Sciences (DILS) June 2012, LNBI 7348 proceedings. Lecture Notes in Computer Science. 2012;7348:100-112
  • Demner-Fushman D, Abhyankar S. Syntactic-semantic question frames for cohort identification. The 2012 Joint Summits on Translational Science. San Francisco, CA. March 2012.
  • Misra D, Seamans J, Thoma GR. Testing the Scalability of a DSpace-based Archive Proc. IS&T Archiving 2008. Bern, Switzerland. June 2008:36-40
  • Mrabet Y, Kilicoglu H, Demner-Fushman D. TextFlow: A Text Similarity Measure based on Continuous Sequences. Proceedings of the 55th Annual Meeting of the Association for Computational Linguistics, 2017, Vancouver, Canada, July 30 - August 4, Volume
  • Lin J, Demner-Fushman D. The Role of Knowledge in Conceptual Retrieval: A Study in the Domain of Clinical Medicine Proc SIGIR 2006, pages 99-106, August 2006, Seattle, Washington
  • Roberts K, Demner-Fushman D. Toward a Natural Language Interface for EHR Questions. AMIA Jt Summits Transl Sci Proc. 2015 Mar 25;2015:157-61. eCollection 2015.
  • Kilicoglu H, Demner-Fushman D, Rindflesch TC, Wilczynski NL, Haynes RB. Toward Automatic Recognition of High Quality Clinical Evidence. AMIA Annu Symp Proc. 2008 Nov 6:368
  • Mao S, Nie L, Thoma GR. Unsupervised Style Classification of Document Page Images Proc IEEE International Conference on Image Processing, September 2005, Genova, Italy; Vol. II: 510-13
  • Misra D, Thoma GR. Use of descriptive metadata as a knowledgebase for analyzing data in large textual collections. Proc. IS&T Archiving 2013. Washington D.C. Proc. IS&T Archiving 2013. Washington D.C. pg 193-199.
  • De Herrera A, Schaer R, Antani SK, Müller H. Using Crowdsourcing for Multi-label Biomedical Compound Figure Annotation. In: Carneiro G. et al. (eds) Deep Learning and Data Labeling for Medical Applications. LABELS 2016, DLMIA 2016. Lecture Notes in Computer Science, vol 10008. Springer, Cham
  • Kim J, Lobuglio PS, Thoma GR. Visualization of Statistics from MEDLINE. 2016 IEEE 29th International Symposium on Computer-Based Medical Systems (CBMS 2016), Dublin and Belfast, Ireland, pp. 290-291, June, 2016.
  • Walker FL, Thoma GR. Web-Based Document Image Processing Proc. SPIE: Internet Imaging. 2000 Jan;:268-77.

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