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  • Lin J, Demner-Fushman D. "Bag of words" is not enough for strength of evidence classification AMIA Annu Symp Proc. 2005:1031.
  • 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.
  • 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.
  • 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.
  • Mao S, Kim J, Thoma G. A Dynamic Feature Generation System for Automated Metadata Extraction in Preservation of Digital Materials Proc. International Workshop on Document Image Analysis for Libraries (DIAL2004). 2004 Jan;: 225-32.
  • Chachra S, Ben Abacha A, Shooshan SE, Rodriguez L, Demner-Fushman D. A Hybrid Approach to Generation of Missing Abstracts in Biomedical Literature. Proceedings of COLING 2016, the 26th International Conference on Computational Linguistics: Technical Papers: 1093-1100.
  • Simpson M, Ford G, Antani S, Demner-Fushman D, Thoma GR. A Lightweight Statistics Package for Interactive Publications Poster at 20th NIH Research Festival (TECH-15), September 2007, National Institutes of Health
  • Rance B, Doughty E, Demner-Fushman D, Kann MG, Bodenreider O. A mutation-centric approach to identifying pharmacogenomic relations in text. J Biomed Inform. 2012 Oct;45(5):835-41. doi: 10.1016/j.jbi.2012.05.003. Epub 2012 Jun 7.
  • 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.
  • Demner-Fushman D, Seckman C, Fisher C, Hauser SE, Clayton J, Thoma GR. A prototype system to support evidence-based practice AMIA Annu Symp Proc. 2008 Nov 6:151-5.
  • Cohen T, Roberts K, Gururaj AE, Chen X, Pournejati S, Alter G, Hersh WR, Demner-Fushman D, Ohno-Machado L, Lu H. A publicly available benchmark for biomedical dataset retrieval: the reference standard for the 2016 bioCADDIE dataset retrieval challenge. Database (Oxford). 2017 Jan 1;2017. doi: 10.1093/database/bax061.
  • Zhang X, Zou J, Le DX, Thoma GR. A Semi-supervised Learning Method to Classify Grant Support Zone in Web-based Medical Articles Proc SPIE Electronic Imaging Science and Technology, Document Recognition and Retrieval. January 2009;7247:7247 OW(1-8)
  • Abhyankar S, Demner-Fushman D. A simple method to extract key maternal data from neonatal clinical notes. AMIA Annu Symp Proc. 2013 Nov 16;2013:2-9. eCollection 2013.
  • Zhang X, Zou J, Le DX, Thoma GR. A Stacked Sequential Learning Method For Investigator Name Recognition From Web-based Medical Articles 17th Document Recognition and Retrieval Conference (SPIE-DR&R). San Jose, CA. January 2010;7534:753404-7
  • 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.
  • Callaghan F, Demner-Fushman D, Abhyankar S, McDonald CJ. Addressing errors in a retrospective observational ICU database [poster]. AMIA 2011 Fall Symposium.
  • Zweigenbaum P, Demner-Fushman D. Advanced Literature-Mining Tools. In Edwards D, Stajich J, and Hansen D. (Editors). Bioinformatics: Tools and Applications. Springer 2009.
  • Callaghan F, Jackson MT, Demner-Fushman D, Abhyankar S, McDonald C. Analysis of data that has been extracted from free-text using natural language processing: a likelihood model for misclassification with an application to medical informatics. International Conference on Advances in Interdisciplinary Statistics and Combinatorics (AISC2012), Greensboro, NC, October 2012
  • 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.
  • Demner-Fushman D, Lin J. Answer Extraction, Semantic Clustering, and Extractive Summarization for Clinical Question Answering Proc COLING/ACL 2006. July 2006, Sydney, Australia
  • Demner-Fushman D, Lin J. Answering Clinical Questions with Knowledge-based and Statistical Techniques Computational Linguistics. 2007 Jan;33(1):63-103
  • Lasko TA, Hauser SE. Approximate String Matching Algorithms for Limited-Vocabulary OCR Output Correction Proc. SPIE, Document Recognition and Retrieval VIII. 2001 Jan;4307:232-40.
  • Misra D, Mao S, Rees J, Thoma GR. Archiving a Historic Medico-legal Collection: Automation and Workflow Customization Proc IS&T Archiving 2007. Arlington, Virginia, May 2007; 157-61
  • Kim I, Thoma GR. Automated Classification of Author’s Sentiments in Citation Using Machine Learning Techniques: A Preliminary Study. Proc. the 2015 IEEE Conf. Computational Intelligence in Bioinformatics and Computational Biology (CIBCB 2015), Niagara Falls, Canada, Aug. 12-15, 2015.
  • 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.
  • Kim I, Le DX, Thoma GR. Automated Cleanup Processing for Extracting Bibliographic Data from Biomedical Online Journals In: Callaos N, Lesso W, editors. SCI 2005. Proc. 9th World Multiconference on Systemics, Cybernetics and Informatics; 2005 Jul 10-13; Vol. 4; Orlando (FL): International Institute of Informatics and Systemics; c2005. 401-5
  • Thoma GR, Ford G. Automated Data Entry System: Performance Issues Proc. SPIE: Document Recognition and Retrieval IX. 2002 Jan;4670: 181-90.
  • Le DX, Thoma GR. Automated Document Labeling for Web-Based Online Medical Journals Proc. 7th World Multiconference on Systemics, Cybernetics and Informatics. 2003 July;II: 411-15.
  • Kim I, Le DX, Thoma GR. Automated identification of biomedical article type using support vector machines. Proc. 18th SPIE Document Recognition and Retrieval, 7874:787403 (1-9), San Francisco, January 2011.
  • Kim I, Thoma GR. Automated Identification of Potential Conflict-of-Interest in Biomedical Articles Using Hybrid Deep Neural Network. Proc. 14th Int’l Conf. Machine Learning and Data Mining (MLDM 2018), LNAI 10934, pp. 99-112, Newark, NJ, July 2018.
  • Kim I, Thoma GR. Automated Identification of Potential Conflict-of-Interest in Biomedical Articles Using Hybrid Deep Neural Network. Proc. 14th Int’l Conf. Machine Learning and Data Mining (MLDM 2018), LNAI 10934, pp. 99-112, Newark, NJ, July 2018.
  • Kim J, Le DX, Thoma GR. Automated Labeling Algorithms for Biomedical Document Images Proc. 7th World Multiconference on Systemics, Cybernetics and Informatics. 2003 July;V: 352-57.
  • Kim J, Le DX, Thoma GR. Automated Labeling in Document Images Proc. SPIE, Document Recognition and Retrieval VIII. 2001 Jan;4307:111-22.
  • Kim J, Le DX, Thoma GR. Automated Labeling of Bibliographic Data Extracted from Biomedical Online Journals Proc. SPIE Electronic Imaging. 2003 Jan;5010: 47-56.
  • Kim J, Le DX, Thoma GR. Automated Labeling Of Biomedical Online Journal Articles In: Callaos N, Lesso W, editors. SCI 2005. Proc 9th World Multiconference on Systemics, Cybernetics and Informatics; 2005 Jul 10-13; Vol. 4; Orlando (FL): International Institute of Informatics and Systemics; c2005. 406-11
  • Le DX, Tran LQ, Chow J, Kim J, Hauser SE, Moon CW, Thoma GR. Automated Medical Citation Records Creation for Web-Based Online Journals Proc. 14th IEEE Symposium on Computer-Based Medical Systems: IEEE Computer Society. 2001.
  • Thoma GR, Mao S, Misra D. Automated Metadata Extraction to Preserve the Digital Contents of Biomedical Collections Proc VIIP 2005. September 2005. Benidorm, Spain; 214-19
  • Kim I, Le DX, Thoma GR. Automated method for extracting "citation sentences" from online biomedical articles using SVM-based text summarization technique. Proc. the 2014 IEEE Int'l Conf. on Systems, Man, and Cybernetics (SMC 2014), pp. 2006-2011, San Diego, October, 2014
  • Hauser SE, Le DX, Thoma GR. Automated Zone Correction in Bitmapped Document Images SPIE: Document Recognition and Retrieval VII. 2000 Jan;3976: 248-58.
  • Kim J, Le DX, Thoma GR. Automatic Extraction of Bibliographic Information from Biomedical Online Journal Articles Using a String Matching Algorithm Proc IEEE CBMS, June 2006, Salt Lake City, Utah; 905-10
  • 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
  • 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.
  • Mao S, Kanungo T. Automatic Training of Page Segmentation Algorithms: An Optimization Approach International Conference on Pattern Recognition. 2000 Sept.;:531-534.
  • Demner-Fushman D, Karpinski J, Thoma GR. Automatically building a repository to support evidence-based practice. Proceedings of the 2nd Workshop on Building and evaluating resources for biomedical text mining (BioTxtM 2010), 7th Language Resources and Evaluation Conference (LREC 2010). Valetta, Malta. May 2010.
  • 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.
  • Le DX, Thoma GR. Automatically Creating Biomedical Bibliographic Records from Printed Volumes of Old Indexes In: Callaos N, Lesso W, editors. SCI 2005. Proc 9th World Multiconference on Systemics, Cybernetics and Informatics; 2005 Jul 10-13; Vol. 3, Computer Science and Engineering. Orlando (FL): International Institute of Informatics and Systemics; c2005. 267-74
  • Demner-Fushman D, Few B, Hauser SE, Thoma GR. Automatically Identifying Health Outcome Information in MEDLINE Records J Am Med Inform Assoc. 2006 Jan-Feb;13(1):52-60. Epub 2005 Oct 12.
  • Kilicoglu H, Demner-Fushman D. Bio-SCoRes: A Smorgasbord Architecture for Coreference Resolution in Biomedical Text. PLoS One. 2016 Mar 2;11(3):e0148538. doi: 10.1371/journal.pone.0148538. eCollection 2016.
  • Cohen KB, Demner-Fushman D. Biomedical Natural Language Processing John Benjamins Publishing Company, 2014. DOI: 10.1075/nlp.11
  • Pearson G, Moon CW. Bridging Two Biomedical Journal Databases with XML - A Case Study. Proc. 14th IEEE Symposium on Computer-Based Medical Systems: IEEE Computer Society. 2001 Jul;:309-14.

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