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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.
  • Yu Z, Nguyen T, Dhombres F, Johnson T, Bodenreider O. "Hybrid Topics" - Facilitating the Interpretation of Topics Through the Addition of MeSH Descriptors to Bags of Words. Stud Health Technol Inform. 2017;245:662-666.
  • Lindberg DA, Howe SE. "My flying machine was out of order". Trans Am Clin Climatol Assoc. 2009;120:99-111.
  • Yoo TS. 3D Medical Informatics: Information Science in Multiple Dimensions. In: Chen H, Fuller SS, Friedman C, Hersh W, editors. Medical Informatics: Knowledge Management and Data Mining in Biomedicine. New York: Springer Science. p. 333-58.
  • Felts RL, Narayan K, Estes JD, Shi D, Trubey CM, Fu J, Hartnell LM, Ruthel GT, Schneider DK, Nagashima K, Bess JW Jr, Bavari S, Lowekamp B, Bliss D, Lifson JD, Subramaniam S. 3D visualization of HIV transfer at the virological synapse between dendritic cells and T cells. Proc Natl Acad Sci U S A. 2010 Jul 27;107(30):13336-41. doi: 10.1073/pnas.1003040107. Epub 2010 Jul 12.
  • 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.
  • Rahman MM, Antani SK, Thoma GR. A Classification-Driven Similarity Matching Framework For Retrieval of Biomedical Images. 11th ACM International Conference on Multimedia Information Retrieval (MIR 2010). 2010:147-154.
  • Thomas SM, Overhage JM, Warvel J, McDonald CJ. A comparison of a printed patient summary document with its electronic equivalent: early results. Proc AMIA Symp. 2001:701-5.
  • Vreeman DJ, McDonald CJ. A comparison of Intelligent Mapper and document similarity scores for mapping local radiology terms to LOINC. AMIA Annu Symp Proc. 2006:809-13.
  • 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).
  • Kroth PJ, Dexter PR, Overhage JM, Knipe C, Hui SL, Belsito A, McDonald CJ. A computerized decision support system improves the accuracy of temperature capture from nursing personnel at the bedside. AMIA Annu Symp Proc. 2006:444-8.
  • McCray AT, Bodenreider O. A Conceptual Framework for the Biomedical Domain The Semantics of Relationships: An Interdisciplinary Perspective. Boston: Kluwer Academic Publishers. 2002;:181-198.
  • Bakker TA, Ryce AN, Logan RA, Tse T, Hutcherson LY. A Consumer Health Informatics (CHI) Toolbox: Challenges and Implications AMIA Annu Symp Proc. 2005:21-5
  • You D, Antani SK, Demner-Fushman D, Thoma GR. A Contour-based Shape Descriptor For Biomedical Image Classification and Retrieval. Proceedings of SPIE 2014, Vol. 9021, Document Recognition and Retrieval XXI. February 2014;9021.
  • Gong RH, Jenkins B, Sze RW, Yaniv Z. A cost effective and high fidelity fluoroscopy simulator using the image-guided surgery toolkit (IGSTK). In: Yaniv Z, Holmes DR III, editors. Medical Imaging 2014: Image-Guided Procedures, Robotic Interventions, and Modeling; 2014 Feb 15-20; San Diego. Proc. SPIE 9036; 2014 Mar 12:11 pages. DOI: 10.1117/12.2044112.
  • Sharp M, Bodenreider O, Wacholder N. A Framework for Characterizing Drug Information Sources AMIA Annu Symp Proc. 2008 Nov 6:662-6
  • Bodenreider O, Burgun A. A framework for comparing phenotype annotations of orthologous genes. Stud Health Technol Inform. 2010;160(Pt 2):1309-13.
  • Nagy DA, Haidegger T, Yaniv Z. A framework for semi-automatic fiducial localization in volumetric images. In: Linte CA, Yaniv Z, Fallavollita P, Abolmaesumi P, Holmes DR III, editors. Augmented Environments for Computer-Assisted Interventions 2014: Proceedings of 9th International AE-CAI Workshop; 2014 Sep 14; Boston. Lecture Notes in Computer Science vol. 8678. Springer; 2014. p. 138-48.
  • Jaeger S. A geomedical approach to Chinese medicine: The origin of the yin-yang symbol. Recent Advances in Theories and Practice of Chinese Medicine, Haixue Kuang (Ed.), ISBN: 978-953-307-903-5, InTech, 2012.
  • Kim E, Huang X, Tan G, Long LR, Antani S. A Hierarchical SVG Image Abstraction Layer for Medical Imaging Medical Imaging 2010: Advanced PACS-based Imaging Informatics and Therapeutic Applications. San Diego, California. March 2010;7628
  • 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.
  • Kilicoglu H, Rogers W. A Hybrid System for Extracting Chemical-Disease Relationships from Scientific Literature. 2015. BioCreative 5 Proceedings.
  • Bryant B, Sari-Sarraf H, Long LR, Antani SK. A Kernel Support Vector Machine Trained Using Approximate Global and Exhaustive Local Sampling. Proceedings of the 4th IEEE/ACM International Conference on Big Data Computing, Applications and Technologies (BDCAT) 2017, Austin, Texas, USA, December 2017. Pp. 267-8 DOI: https://doi.org/10.1145/3148055.3149206
  • 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.
  • 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.
  • Rodgers RPC, Sherwin Z. A Management System for Network Sharable Locally Installed Software: Merging RPM and the Depot Scheme under Solaris LISA XV: Proceedings of the Fifteenth Systems Administration Conference. 2001 Dec;: 267-272.
  • Lu C, Humphrey SM, Browne AC. A method for verifying a vector-based text classification system AMIA Annu Symp Proc. 2008 Nov 6:1030.
  • Karargyris A, Bourbakis N. A methodology for detecting blood-based abnormalities in wireless capsule endoscopy videos. BioInformatics and BioEngineering, 2008. BIBE 2008. 8th IEEE International Conference. 2008 Oct 8; pp 1-6. doi: 10.1109/BIBE.2008.4696806.
  • Biondich PG, Overhage JM, Dexter PR, Downs SM, Lemmon L, McDonald CJ. A modern optical character recognition system in a real world clinical setting: some accuracy and feasibility observations. Proc AMIA Symp. 2002:56-60.
  • You D, Antani SK, Demner-Fushman D, Thoma GR. A MRF Model for Biomedical Image Segmentation. CBMS 2014. May 2014.
  • Borovikov E, Zavorin I. A multi-stage document processing approach To Arabic text recognition. Guide to OCR for Arabic Scripts. 2012:55-78.
  • Xu T, Xin C, Long LR, Antani SK, Xue Z, Kim E, Huang X. A New Image Data Set and Benchmark for Cervical Dysplasia Classification Evaluation. Machine Learning in Medical Imaging: 6th International Workshop, MLMI 2015, LNCS 9352, pp. 26–35, 2015. DOI: 10.1007/978-3-319-24888-2 4.
  • Yoo TS, Ackerman MJ. A New Research Program in Medical Image Processing. In: Westwood JD, Hoffman HM, Mogel GT, Robb RA, Stredney D, editors. Stud Health Technol Inform [Studies in Health Technology and Informatics] -- Proceedings of Medicine Meets Virtual Reality 2000;70:385-91. Amsterdam: IOS Press.
  • 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.
  • Cheng B, Stanley RJ, Antani SK, Thoma GR. A Novel Computational Intelligence-based Approach For Medical Image Artifacts Detection Proceedings of the 2010 International Conference on Artificial Intelligence and Pattern Recognition. Orlando, FL. July 2010:113-20
  • Rajaraman S, Candemir S, Xue Z, Alderson P, Kohli M, Abuya J, Thoma GR, Antani SK. A novel stacked generalization of models for improved TB detection in chest radiographs. Proc. IEEE Engineering in Medicine and Biology Conference (EMBC 2018), Honolulu, Hawaii, 2018. pp. 718-721.
  • Rajaraman S, Candemir S, Xue Z, Alderson P, Thoma G, Antani SK. A Novel Stacked Model Ensemble for Improved TB Detection in Chest Radiographs. In Santosh KC et al. (Eds.). Medical Imaging: Artificial Intelligence, Image Recognition, and Machine Learning Techniques. (pp. 1-26). New York, NY: CRC Press, Taylor & Francis Group.
  • Liu J, Subramanian K, Yoo TS. A Phantom Design for Validating Colonoscopy Tracking. Proc. SPIE 8315, Medical Imaging 2012: Computer-Aided Diagnosis, 83151N (23 February 2012); doi: 10.1117/12.912395; http://dx.doi.org/10.1117/12.912395
  • 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
  • Bodenreider O, Coban ZH, Doganay MC, Erdem E, Kosucu H. A preliminary report on answering complex queries related to drug discovery using answer set programming. Proceedings of the 3rd International Workshop on Applications of Logic Programming to the (Semantic) Web and Web Services (ALPSWS2008), 2008: p. 85-90 (electronic proceedings: http://ceur-ws.org/Vol-434/).
  • Tulpule B, Hernes DL, Srinivasan Y, Mitra S, Sriraja Y, Nutter BS, Phillips B, Long RL, Ferris DG. A Probabilistic Approach to Segmentation and Classification of Neoplasia in Uterine Cervix Images Using Color and Geometric Features SPIE Medical Imaging, February 2005; San Diego, CA; vol. 5748:995-1003
  • Zhan Zhang, Ackerman MJ, Jixing Li. A Prototype Colon Straightening System for Polyp Detection. Proceedings of 17th IEEE Symposium on Computer-Based Medical Systems (CBMS); 2004 Jun 24-25; Bethesda, Maryland:548-52. DOI: 10.1109/CBMS.2004.1311772.
  • Rossi E, Fontelo P, Ackerman M, Pozzi G, Marceglia S. A Prototype of Mobile app/EHR Communication through Standards for Home Treatment of Transcranial Direct Current Stimulation. International Conference on Healthcare Informatics (ICHI), Dallas TX, 2015. 310-315.
  • 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.
  • Osborne R, Aronson A, Cohen K. A repository of semantic types in the MIMIC II database clinical notes. BioNLP 2014. pp. 93-97.
  • You D, Simpson M, Antani SK, Demner-Fushman D, Thoma GR. A robust pointer segmentation in biomedical images toward building a visual ontology for biomedical article retrieval. Proc. SPIE 8658, Document Recognition and Retrieval XX, 86580Q (February 4, 2013); doi:10.1117/12.2005934.
  • Bodenreider O. A Semantic Navigation Tool for the UMLS AMIA Annu Symp Proc. 2000;: 971.
  • Nelson SJ, Brown SH, Erlbaum MS, Olson N, Powell T, Carlsen B, Carter J, Tuttle MS, Hole WT. A semantic normal form for clinical drugs in the UMLS: early experiences with the VANDF. Proc AMIA Symp. 2002:557-61.
  • 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.
  • Liu J, Subramanian K, Yoo T, Van Uitert R. A Stable Optic-flow Based Method for Tracking Colonoscopy Images. Proceedings of MMBIA 2008, the IEEE Computer Society Workshop on Mathematical Methods in Biomedical Image Analysis; 2008 Jun 23-28; Anchorage, Alaska. DOI: 10.1109/CVPRW.2008.4562990.
  • 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 K, Locatis CN, Liu WL. A Study of Higher Quality Video Applications on Access Grid (Presentation). Proceedings of 2008 Access Grid Retreat; 2008 May 28-30; Simon Fraser University, Vancouver, Canada. http://www.accessgrid.org/retreat/2008/abstracts/zhang.pdf.
  • Thomas SM, Mamlin B, Schadow G, McDonald CJ. A successful technique for removing names in pathology reports using an augmented search and replace method. Proc AMIA Symp. 2002:777-81.
  • 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.
  • Zeng Q, Kin E, Crowell J, Tse T. A Text Corpora-Based Estimation of the Familiarity of Health Terminology ISBMD, Aveiro, Portugal, 10-11 November 2005:184-92.
  • Guler, O, Yaniv Z. A tutorial on image guided therapy. Chapter 11 in: Birkfellner W, editor. Applied Medical Image Processing, Second Edition: A Basic Course. London: CRC Press; 2014. ISBN: 9781466555570.
  • Rahman MM, Antani SK, Demner-Fushman D, Thoma GR. A visual concept-based interactive biomedical image retrieval using entropy and spatial information. Proc. SPIE. 9418, Medical Imaging 2015: PACS and Imaging Informatics: Next Generation and Innovations, 94180U. (March 17, 2015) doi: 10.1117/12.2081456.
  • Crowell J, Zeng QT, Tse T. A Web Application to Support Consumer Health Vocabulary Development AMIA Annu Symp Proc. 2005:932
  • Xue Z, Long R, Antani SK, Thoma GR. A Web-accessible Content-based Cervicographic Image Retrieval System Proc SPIE Medical Imaging 2008. April 2008;6919:691907-1-9
  • Fontelo P, Nahin A, Liu F, Kim G, Ackerman MJ. Accessing MEDLINE/PubMed with Handheld Devices: Developments and New Search Portals. Proceedings of 38th Hawaii International Conference on System Sciences; 2005 Jan 3-6; Big Island, Hawaii; Track 6:158b. DOI Bookmark: http://doi.ieeecomputersociety.org/10.1109/HICSS.2005.64.
  • Liu J, Subramanian K, Yoo TS. Accurate motion parameter estimation for colonoscopy tracking using a regression method. In: Karssemeijer N, Summer RM, editors. Proceedings of SPIE Medical Imaging 2010: Computer-Aided Diagnosis; 2010 Feb 13-18; San Diego;7624:11 pages. DOI: 10.1117/12.844433.
  • Hole WT, Carlsen BA, Tuttle MS, Srinivasan S, Lipow SS, Olson NE, Sheretz DD, Humphreys BL. Achieving "source transparency" in the UMLS Metathesaurus. Stud Health Technol Inform. 2004;107(Pt 1):371-5.
  • Fung K, Xue Z, Ameye F, Gutierrez AR, D'Have A. Achieving Logical Equivalence between SNOMED CT and ICD-10-PCS Surgical Procedures. AMIA Annu Symp Proc. 2018 Apr 16;2017:724-733. eCollection 2017.
  • Morse BS, Liu W, Yoo TS, Subramanian KR. Active contours using a constraint-based implicit representation. Proceedings of IEEE Computer Society Conference on Computer Vision and Pattern Recognition (CVPR); 2005 Jun 20-25; San Diego. 285-92. DOI: 10.1109/CVPR.2005.59.
  • Cimino JJ, Remennick L. Adapting a Clinical Data Repository to ICD-10-CM through the use of a Terminology Repository. AMIA Annu Symp Proc. 2014 Nov 14;2014:405-13. eCollection 2014.
  • Rosemblat G, Tse T, Gemoets D. Adapting A Monolingual Consumer Health System for Cross-Language Information Retrieval Advances in Knowledge Organization, Proceedings of the Eighth International ISKO Conference. 2004 July;9:315-321.
  • Zweigenbaum P, Demner-Fushman D. Advanced Literature-Mining Tools. In Edwards D, Stajich J, and Hansen D. (Editors). Bioinformatics: Tools and Applications. Springer 2009.
  • Yoo TS. Advances Toward Understanding of Multimodal Volume Data. Proceedings of High Care 2000: Innovations in Medicine; 2000 Feb 25-27; Ruhr University, Bochum, Germany.
  • Xiaocheng L, Prettyman M, Antonucci R. Agent-based system expansion and integration in HSTAT. Proceedings of the Fourth World Multiconference on Systemics, Cybernetics, and Informatics (SCI2000). July 2000.
  • Almubarak H, Guo P, Stanley RJ, Long LR, Antani SK, Thoma GR. Algorithm Enhancements for Improvement of Localized Classification of Uterine Cervical Cancer Digital Histology Images. in Handbook of Research on Emerging Perspectives on Healthcare Information Systems and Informatics,. IGI Global (Hershey, PA).
  • Zhang S, Bodenreider O, Kantz N. Aligning Anatomical Ontologies: The Role of Complex Structural Rules IIAS-Transactions on Systems Research and Cybernetics - Proc InterSymp 2006;VI(2):27-32.
  • 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
  • Zhang S, Bodenreider O. Aligning Representations of Anatomy Using Lexical and Structural Methods AMIA Annu Symp Proc. 2003 Nov;:753-757.
  • Mrabet Y, Vougiouklis P, Kilicoglu H, Gardent C, Demner-Fushman D, Hare J, Simperl E. Aligning Texts and Knowledge Bases with Semantic Sentence Simplification. WebNLG 2016.
  • Zhang S, Bodenreider O. Alignment of Multiple Ontologies of Anatomy: Deriving Indirect Mappings from Direct Mappings to a Reference AMIA Annu Symp Proc 2005:864-868
  • Peters L, Kapusnik-Uner JE, Nguyen T, Bodenreider O. An approximate matching method for clinical drug names. AMIA Annu Symp Proc. 2011;2011:1117-26. Epub 2011 Oct 22.
  • Zhang K, Locatis CN, Liu WL. An Enhanced Shared Browser for the Access Grid. Proceedings of Access Grid 2006; 2006 May 15-17; Michigan Information and Technology Center, Ann Arbor.
  • Zhang K, Locatis CN, Liu WL. An Enhanced Shared Presentation Tool for the Access Grid (Presentation). Proceedings of Access Grid 2007; 2007 May 14-16; Chicago.
  • 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.
  • Pearson G, Gill MJ. An Evaluation of Motion JPEG 2000 for Video Archiving. Proc. Archiving 2005. Washington, D.C. April 2005:237-43.
  • 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.
  • Marcelo AB, Fontelo P. An Evaluation of the Usability of Accessing MEDLINE over Short Messaging System. In: Kuhn KA, Warren JR, Leong T-Y, editors. Stud Health Technol Inform [Studies in Health Technology and Informatics] -- MEDINFO 2007: Proceedings of the 12th World Congress on Health (Medical) Informatics -- Building Sustainable Health Systems; 2007 Aug 20-24; Brisbane, Australia:235-6. IOS Press.
  • Sahoo S, Bodenreider O, Zeng K, Sheth AP. An Experiment in Integrationg Large Biomedical Knowledge Resources with RDF: Application to Associating Genotype and Phenotype Information Proc Workshop on Health Care and Life Sciences Data Integration for the Semantic Web at WWW2007 (electronic proceedings: http://www2007.org/workshops/paper_149.pdf)
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  • Rahman MM, You D, Simpson M. An interactive image retrieval framework for biomedical articles based on visual region-of-interest (ROI) identification and classification [Abstract]. The 2nd IEEE Conference on Healthcare Informatics, Imaging, and Systems Biology Analyzing Big Data for Healthcare and Biomedical Sciences (HISB 2012). La Jolla, CA. September 2012.
  • Caban JJ, Rheingans P, Yoo TS. An MRF-based Statistical Deformation Model for Morphological Image Analysis. IEEE Computer Society Workshop on Mathematical Models in Biomedical Image Analysis (MMBIA); 2010 Jun 14; San Francisco:31-8.
  • Xue Z, Antani SK, Long LR, Thoma GR. An online segmentation tool for cervicographic image analysis. ACM International Health Informatics Symposium, IHI 2010, Arlington, VA, USA, November 11 - 12, 2010, Proceedings; 01/2010.
  • Resnick MP, Ripple AM, Auston I, Rindflesch TC. An Ontology for Public Health to Support Enhanced Information Retrieval AMIA Annu Symp Proc. 2010
  • Bergun A, Bodenreider O. An ontology of chemical entities helps identify dependence relations among Gene Ontology terms Proc SMBM-2005
  • Banez RJ, Sarmiento R, Marcelo A, Fontelo P, Du B. An SMS Appointment Reminder System for Prenatal Care in Urban Health Care Centers in the Philippines. Telemed J E Health;16(S1):S-38. American Telemedicine Association 15th Annual International Meeting and Exposition; 2010 May 16-18; San Antonio, Texas.
  • Grannis SJ, Overhage JM, Hui S, McDonald CJ. Analysis of a probabilistic record linkage technique without human review. AMIA Annu Symp Proc. 2003:259-63.
  • 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
  • Kury F, Baik SH, McDonald CJ. Analysis of Healthcare Cost and Utilization in the First Two Years of the Medicare Shared Savings Program Using Big Data from the CMS Enclave. AMIA Annu Symp Proc. 2017 Feb 10;2016:724-733. eCollection 2016.
  • Grannis SJ, Overhage JM, McDonald CJ. Analysis of identifier performance using a deterministic linkage algorithm. Proc AMIA Symp. 2002:305-9.
  • Bodenreider O, Rodriguez L. Analyzing U.S. prescription lists with RxNorm and the ATC/DDD Index. AMIA Annu Symp Proc. 2014 Nov 14;2014:297-306. eCollection 2014.
  • Yoo TS, Morse B, Subramanian KR, Rheingans P, Ackerman MJ. Anatomical Modeling from Unstructured Samples Using Variational Implicit Surfaces. In: Westwood JD, Hoffman HM, Mogel GT, Stredney D, Robb RA, editors. Stud Health Technol Inform [Studies in Health Technology and Informatics] -- Proceedings of Medicine Meets Virtual Reality 2001;81:594-600. Amsterdam: IOS Press.
  • Ackerman MJ. Anatomy in the Digital Age. In: Rifkin BA, Ackerman MJ. Human Anatomy: From the Renaissance to the Digital Age. 2006 May 2. New York: Abrams. p. 318-329.
  • You D, Simpson M, Antani SK, Demner-Fushman D, Thoma GR. Annotating image ROIs with text descriptions for multimodal biomedical document retrieval. Proc. SPIE 8658, Document Recognition and Retrieval XX, 86580Q (February 4, 2013); doi:10.1117/12.2005934; http://dx.doi.org/10.1117/12.2005934.
  • 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.
  • 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.
  • Roberts K, Masterton K, Kilicoglu H, Fiszman M, Demner-Fushman D. Annotating Question Decomposition on Complex Medical Questions. LREC 2014.
  • Roberts K, Masterton K, Fiszman M, Kilicoglu H, Demner-Fushman D. Annotating Question Types for Consumer Health Questions. LREC 2014, BioTxtM workshop.
  • Demner-Fushman D, Shooshan SE, Rodriguez L, Antani SK, Thoma GR. Annotation of Chest Radiology Reports for Indexing and Retrieval. Multimodal Retrieval in the Medical Domain 2015 (MRMD 2015), Vienna, Austria, March 29, 2015
  • Demner-Fushman D, Lin J. Answer Extraction, Semantic Clustering, and Extractive Summarization for Clinical Question Answering Proc COLING/ACL 2006. July 2006, Sydney, Australia
  • Bodenreider O. API: NDF-RT
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  • Gandhi T, Kasturi R, Antani S. Application of Planar Motion Segmentation for Scene Text Extraction Proc. of the 15th IEEE International Conference of Pattern Recognition. 2000 Sept.;1:1831-4.
  • Yaniv Z, Linte CA. Applications of Augmented Reality in the Operating Room. Chapter 19 in Fundamentals of Wearable Computers and Augmented Reality, 2nd ed. CRC Press, 2015.
  • Guan Y, Li M, Jaeger S, Lure F, Raptopoulos V, Lu P, Folio LR, Candemir S, Antani SK, Siegelman J, Li J, Wu T, Thoma GR, Qu S. Applying Artificial Intelligence and Radiomics for Computer Aided Diagnosis and Risk Assessment in Chest Radiographs. 2nd Conference on Machine Intelligence in Medical Imaging (CMIMI) of the Society for Imaging Informatics in Medicine (SIIM), Poster, 2017.
  • Peters LB, Bodenreider O. Approaches to Supporting the Analysis of Historical Medication Datasets with RxNorm. AMIA Annu Symp Proc. 2015 Nov 5;2015:1034-41. eCollection 2015.
  • 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
  • Rindflesch TC, Bean CA, Sneiderman CA. Argument Identification for Arterial Branching Predications Asserted in Cardiac Catheterization Reports Proc AMIA Symp. 2000:704-8.
  • Ruch P, Tbahriti I, Bobeill J, Aronson AR. Argumentative Feedback: A Linguistically-motivated Term Expansion for Information Retrieval Proc COLING/ACL 2006, 675-82
  • 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
  • KC S, Naved A, Roy PP, Wendling L, Antani SK, Thoma GR. Arrowhead detection in biomedical images. Proceedings IS&T Electronic Imaging, Document Recognition and Retrieval XXIII, 2016, pp. 1-7.
  • 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.
  • Rajaraman S, Sornapudi S, Kohli M, Antani SK. Assessment of an ensemble of machine learning models toward abnormality detection in chest radiographs. Proc. IEEE Engineering in Medicine and Biology Conference (EMBC), Berlin, Germany, 23 – 27 July 2019. pp. 3689 – 3692.
  • Ganesan P, Rajaraman S, Long LR, Ghoraani B, Antani SK. Assessment of Data Augmentation Strategies Toward Performance Improvement of Abnormality Classification in Chest Radiographs. Proc. IEEE Engineering in Medicine and Biology Conference (EMBC), Berlin, Germany, 23 – 27 July 2019. pp. 841 – 844.
  • Lindberg, DAB, Ash JS (Interviewer and Editor), Sittig DF (Interviewer and Editor), Goodwin RM (Editor). At the helm of the world's largest biomedical library: 2005 Interviews with Donald A.B. Lindberg, MD Conversations with Medical Informatics Pioneers: An oral history project.
  • Wang Y, Wei D, Xu J, Elhanan G, Perl Y, Halper M, Chen Y, Spackman KA, Hripcsak G. Auditing complex concepts in overlapping subsets of SNOMED. AMIA Annu Symp Proc. November 2008:273-7.
  • Mougin F, Bodenreider O. Auditing the NCI Thesaurus with Semantic Web Technologies AMIA Annu Symp Proc. 2008 Nov 6:500-4
  • Linte CA, Yaniv Z, Fallavollita P, Abolmaesumi P, Holmes DR III, editors. Augmented Environments for Computer-Assisted Interventions 2014: 9th International AE-CAI Workshop. Held in conjunction with MICCAI 2014. 2014 Sep 14; Boston. Lecture Notes in Computer Science, vol. 8678. Springer; 2014. 149 pages.
  • 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.
  • 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
  • Mamlin BW, Heinze DT, McDonald CJ. Automated extraction and normalization of findings from cancer-related free-text radiology reports. AMIA Annu Symp Proc. 2003:420-4.
  • 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 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
  • Vreeman DJ, McDonald CJ. Automated mapping of local radiology terms to LOINC. AMIA Annu Symp Proc. 2005:769-73.
  • 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
  • Hauser SE, Le DX, Thoma GR. Automated Zone Correction in Bitmapped Document Images SPIE: Document Recognition and Retrieval VII. 2000 Jan;3976: 248-58.
  • 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.
  • 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
  • Rodriguez LM, Fushman DD. Automatic Classification of Structured Product Labels for Pregnancy Risk Drug Categories, a Machine Learning Approach. AMIA Annu Symp Proc. 2015 Nov 5;2015:1093-102. eCollection 2015.
  • Bodenreider O, Mougin F, Burgun A. Automatic Determination of Anti-coagulation Status with NDF-RT Proceedings of the 13th ISMB'2010 SIG meeting Bio-ontologies 2010:140-143
  • Lotenberg S, Gordon S, Long LR, Antani SK, Jeronimo J, Greenspan H. Automatic Evaluation of Uterine Cervix Segmentations Proc. SPIE Medical Imaging 2007. Vol. 6515: 65151J-1-12.
  • Roberts K, Rodriguez L, Shooshan SE, Demner-Fushman D. Automatic Extraction and Post-coordination of Spatial Relations in Consumer Language. AMIA Annu Symp Proc. 2015 Nov 5;2015:1083-92. eCollection 2015.
  • 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
  • Xue Z, Long LR, Antani SK, Thoma GR. Automatic Extraction of Mosaic Patterns In Uterine Cervix Images 23rd IEEE International Symposium on Computer-Based Medical Systems (CBMS) 2010. Perth, Australia. October 2010:273-8.
  • Candemir S, Jaeger S, Lin W, Xue Z, Antani SK, Thoma GR. Automatic heart localization and radiographic index computation in chest x-rays. Proc. SPIE. 9785, Medical Imaging 2016: Computer-Aided Diagnosis, 978517. DOI: 10.1117/12.2217209.
  • Caban JJ, Rosebrock A, Yoo TS. Automatic identification of prescription drugs using shape distribution models. In: 19th IEEE International Conference on Image Processing (ICIP); 2012 Sep 30-Oct 3; Lake Buena Vista, Florida. p. 1005-8. DOI: 10.1109/ICIP.2012.6467032
  • You D, Antani SK, Demner-Fushman D, Rahman MM, Govindaraju V, Thoma GR. Automatic identification of ROI in figure images toward improving hybrid (text and image) biomedical document retrieval. Proceedings of SPIE Electronic Imaging Science and Technology, Document Retrieval and Recognition XVIII. San Francisco, CA. January 2011;7874:78740K.
  • 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.
  • 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.
  • Yao J, Antani S, Long LR, Thoma GR, Zhang Z. Automatic Medical Image Annotation and Retrieval Using SECC Proc CBMS 2006, June 2006, Salt Lake City, Utah; 105-10
  • Mougin F, Burgun A, Bodenreider O, Chabalier J, Loreal O, Le Beux P. Automatic Methods for Integrating Biomedical Data Sources in a Mediator-Based System Proc DILS 2008. Berlin Heidelberg New York: Springer; 2008. p. 61-76
  • Xue Z, Antani SK, Long LR, Thoma GR. Automatic multi-label annotation of abdominal CT images using CBIR. Proc. SPIE 10138, Medical Imaging 2017: Imaging Informatics for Healthcare, Research, and Applications, 1013807 (March 13, 2017); doi:10.1117/12.2254368.
  • KC S, Vajda S, Antani SK, Thoma GR. Automatic Pulmonary Abnormality Screening using Thoracic Edge Map. IEEE, 28th International Symposium on Computer-Based Medical Systems (CBMS), pp. 360-361, 2015.
  • 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
  • Cheng B, Antani SK, Stanley J, Demner-Fushman D, Thoma GR. Automatic segmentation of subfigure image panels for multimodal biomedical document retrieval. Proceeding of: Document Recognition and Retrieval XVIII - DRR 2011, 18th Document Recognition and Retrieval Conference, part of the IS&T-SPIE Electronic Imaging Symposium, San Jose, CA, USA, January 24-29, 2011, Proceedings.
  • Mao S, Kanungo T. Automatic Training of Page Segmentation Algorithms: An Optimization Approach International Conference on Pattern Recognition. 2000 Sept.;:531-534.
  • Jaeger S, Karargyris A, Candemir S, Folio L, Siegelman J, Callaghan FM, Xue Z, Palaniappan K, Singh RK, Antani SK, Thoma GR, Wang Y, Lu P, McDonald CJ. Automatic tuberculosis screening using chest radiographs. IEEE Trans Med Imaging. 2014 Feb;33(2):233-45. doi: 10.1109/TMI.2013.2284099. Epub 2013 Oct 1.
  • 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
  • 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.
  • 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.
  • Demner-Fushman D, Antani S, Thoma GR. Automatically Finding Images for Clinical Decision Support Proc of IEEE DM-Med 2007. Omaha, NE, October 2007, pp. 139-144
  • Rahman MM, Antani SK, Thoma GR. Bag of Keypoints-Based Biomedical Image Search With Affine Covariant Region Detection and Correlation-Enhanced Similarity Matching. 23rd IEEE International Symposium on Computer-Based Medical Systems (CBMS ) 2010. Perth, Australia. October 2010:261-6.
  • 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.
  • Kroth PJ, Belsito A, Overhage JM, McDonald CJ. Bedside vital signs capture for the non-ICU setting--an open source, PC-based solution. Proc AMIA Symp. 2001:344-8.
  • 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.
  • 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
  • Tran EEH, Kuybeda O, Bartesaghi A, Milne JLS, Subramaniam S. Binding of Neutralizing Antibodies Results in Distinct Quaternary Conformations of Trimeric HIV-1 Envelope Glycoproteins. Biophysical Society 57th Annual Meeting; 2013 Feb 2-6; Philadelphia.
  • Zweigenbaum P, Demner-Fushman D. Bioinformatics: Tools and Applications. Springer 2009.
  • He Y, Kayaalp M. Biological Entity Recognition with Conditional Random Fields AMIA Annu Symp Proc. 2008 Nov 6:293-7
  • You D, Antani S, Demner-Fushman D, Rahman MM, Govindarju V, Thoma GR. Biomedical Article Retrieval Using Multimodal Features and Image Annotations In Region-based CBIR. Document Recognition and Retrieval XVII. Edited by Likforman-Sulem, Laurence; Agam, Gady. Proceedings of the SPIE. San Jose, CA. January 2010;7534:75340V-75340V-12.
  • Rahman MM, Antani SK, Demner-Fushman D, Thoma GR. Biomedical image representation and classification using an entropy-weighted probabilistic concept feature space. Proc. SPIE. 9039. Medical Imaging 2014: PACS and Imaging Informatics: Next Generation and Innovations. 90390G.
  • Rahman MM, Antani SK, Thoma GR. Biomedical Image Retrieval In a Fuzzy Feature Space With Affine Region Detection and Vector Quantization of a Scale-Invariant Descriptor. 6th International Symposium on Visual Computing (ISVC) 2010. Las Vegas, NV. November 2010.
  • Cohen KB, Demner-Fushman D. Biomedical Natural Language Processing John Benjamins Publishing Company, 2014. DOI: 10.1075/nlp.11
  • Bodenreider O. Biomedical Ontologies in Action: Role in Knowledge Management, Data Integration and Decision Support. Geissbuhler A, Kulikowski C, editors. IMIA Yearbook of Medical Informatics 2008. Methods Inf Med, 2008. 47(Suppl 1): p. 67-79.
  • Simpson MS, Demner-Fushman D. Biomedical Text Mining: A Survey of Recent Progress. In Charu C. Aggarwal and ChengXiang Zhai, Editors. Mining Text Data. (Springer) 2011.
  • Xue Z, Antani SK, Long LR, Demner-Fushman D, Thoma GR. Body Segment Classification for Visible Human Cross Section Slices. IEEE 27th International Symposium on Computer-Based Medical Systems (CBMS), New York, NY, May 2014: pp. 199-204
  • Antani S, Long LR, Thoma GR. Bridging the Gap: Enabling CBIR in Medical Applications Proc IEEE CBMS. Jyvaskyla, Finland. June 2008:4-6
  • 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.
  • Bodenreider O, Peters L, Nguyen T. Browser and application programming interfaces for drug information sources. AMIA Annu Symp Proc, 2011: p. 2129.
  • Divita G, Rosemblat G, Browne AC. Building a medical Spanish lexicon. AMIA Annu Symp Proc. 2007 Oct 11:941.
  • Campbell JR, Xu J, Fung K. Can SNOMED CT fulfill the vision of a compositional terminology? Analyzing the use case for problem list. AMIA Annu Symp Proc. 2011;2011:181-8. Epub 2011 Oct 22.
  • Kury F, Baik SH, McDonald CJ. Cardioprotective Drugs and Incident Dementias in Medicare's Big Data. AMIA 2017.
  • McKnight L, Srinivasan P. Categorization of sentence types in medical abstracts. AMIA Annu Symp Proc. 2003:440-4.
  • Chang Y, Antani S, Lee DJ, Gledhill K, Long LR, Christensen P. CBIR of Spine X-ray Images on Inter-vertebral Disc Space and Shape Profiles Proc IEEE CBMS. Jyvaskyla, Finland. June 2008:224-9.
  • Kayaalp M, Browne AC, Sagan P, McGee T, McDonald CJ. Challenges and Insights in Using HIPAA Privacy Rule for Clinical Text Annotation. AMIA Annu Symp Proc. 2015 Nov 5;2015:707-16. eCollection 2015.
  • Srinivasan Y, Nutter BS, Mitra SD, Yang S, Phillips B, Long LR. Challenges in Automated Detection of Cervical Intraepithelial Neoplasia Proc SPIE Medical Imaging 2007. Vol. 6514: 65140F-1-11
  • Hruby GW, Boland MR, Cimino J, Gao J, Wilcox AB, Hirschberg J, Weng C. Characterization of the biomedical query mediation process. AMIA Jt Summits Transl Sci Proc. 2013 Mar 18;2013:89-93. eCollection 2013.
  • Cimino JJ, Huser V. Characterization of the Context of Drug Concepts in Research Protocols: An Empiric Study to Guide Ontology Development. AMIA Annu Symp Proc. 2015 Nov 5;2015:441-7. eCollection 2015.
  • Xue Z, You D, Candemir S, Jaeger S, Antani SK, Long LR, Thoma GR. Chest X-ray Image View Classification The 28th IEEE International Symposium on Computer-Based Medical Systems
  • Jaeger S. Chest X-ray Screening System: Segmentation Module – v3
  • Dangi S, Linte C, Yaniv Z. Cine cardiac MRI slice misalignment correction towards full 3D left ventricle segmentation SPIE Medical Imaging: Image-Guided Procedures, Robotic Interventions, and Modeling, Houston, Texas, in press.
  • Zohora FT, Antani SK, Santosh KC. Circle-like foreign element detection in chest x-rays using normalized cross-correlation and unsupervised clustering. Proc. SPIE 10574, Medical Imaging 2018: Image Processing, 105741V (2 March 2018); doi: 10.1117/12.2293739; doi.org/10.1117/12.2293739.
  • Bodenreider O. Circular hierarchical relationships in the UMLS: etiology, diagnosis, treatment, complications and prevention. Proc AMIA Symp. 2001:57-61.
  • Morid MA, Jonnalagadda S, Fiszman M, Raja K, Del Fiol G. Classification of Clinically Useful Sentences in MEDLINE. AMIA Annu Symp Proc. 2015 Nov 5;2015:2015-24. eCollection 2015.
  • Xue Z, Antani SK, Long LR, Demner-Fushman D, Thoma GR. Classification of CT Figures in Biomedical Articles Based on Body Segments. 2013 IEEE International Conference on Healthcare Informatics (ICHI), pp.264,268, 9-11 Sept. 2013. doi: 10.1109/ICHI.2013.17.
  • Xue Z, You D, Antani SK, Long LR, Demner-Fushman D, Thoma GR. Classification of Visual Signs in Abdominal CT Image Figures in Biomedical Literature. Proc. SPIE. 9039. Medical Imaging 2014: PACS and Imaging Informatics: Next Generation and Innovations. 90390T.
  • Lu C, Payne A, Demner-Fushman D. Classification Types: A New Feature in the SPECIALIST Lexicon MIA 2019 Annual Symposium, Washington, DC, November 16-20, 2019.
  • Bergun A, Bodenreider O, Mougin F. Classifying diseases with respect to anatomy: a study in SNOMED CT AMIA Annu Symp Proc. 2005:91-5
  • Mamlin BW, Overhage JM, Tierney WM, Dexter PR, McDonald CJ. Clinical decision support within the Regenstrief Medical Record System [Book//chapter] Health Informatics, Berner, Eta S. (Ed.) 2nd ed., 2007, 190-21.
  • Kawamoto K, Jacobs J, Welch BM, Huser V, Paterno MD, Del Fiol G, Shields D, Strasberg HR, Huag PJ, Liu Z, Jenders RA, Rowed DW, Chertcoff D, Fehre K, Adlassnig KP, Curtis C. Clinical information system services and capabilities desired for scalable, standards-based, service-oriented decision support: consensus assessment of the Health Level 7 clinical decision support Work Group. AMIA Annu Symp Proc. 2012;2012:446-55. Epub 2012 Nov 3.
  • Lussier YA, Bodenreider O. Clinical Ontologies for Discovery Applications In: Baker CJO, Cheung K-H, editors. Semantic Web: Revolutionizing knowledge discovery in the life sciences. New York: Springer; 2007. p. 101-119.
  • Weiner M, Schadow G, Lindbergh D, Warvel J, Abernathy G, Perkins SM, Fyffe J, Dexter PR, McDonald CJ. Clinicians' and patients' experiences and satisfaction with unscheduled, nighttime, Internet-based video conferencing for assessing acute medical problems in a nursing facility. AMIA Annu Symp Proc. 2003:709-13.
  • Liang Z, Powell A, Ersoy I, Poostchi M, Silamut K, Palaniappan K, Guo P, Hossain M, Antani SK, Maude R, Huang J, Jaeger S, Thoma GR. CNN-Based Image Analysis for Malaria Diagnosis. IEEE International Conference on Bioinformatics & Biomedicine (BIBM), Shenzhen, China, 2016.
  • Biondich PG, Downs SM, Carroll AE, Shiffman RN, McDonald CJ. Collaboration between the medical informatics community and guideline authors: fostering HIT standard development that matters. AMIA Annu Symp Proc. 2006:36-40.
  • Zhang X, Zou J, Le DX, Thoma GR. Combining Discriminative SVM models for the Improved Recognition of Investigator Names in Medical Articles. Proceedings of SPIE Volume 8658, Document Recognition and Retrieval XX, IS&T/SPIE Electronic Imaging 2013.
  • Zou J, Le DX, Thoma GR. Combining DOM Tree and Geometric Layout Analysis for Online Medical Journal Article Segmentation Proc JCDL, June 2006, Chapel Hill, NC; 119-28
  • Demner-Fushman D, Antani SK, Simpson M, Thoma GR. Combining Medical Domain Ontological Knowledge and Low-level Image Features for Multimedia Indexing Procf OntoImage 2008, part of LREC 2008. Marrakech, Morrocco. May 2008:CDROM Proceedings
  • 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.
  • Fiszman M, Bray B, Shin D, Kilicoglu H, Bennett GC, Bodenreider O, Rindflesch TC. Combining relevance assignment with quality of the evidence to support guideline development. Stud Health Technol Inform. 2010;160(Pt 1):709-13.
  • 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
  • Hristovski D, Kastrin A, Peterlin B, Rindflesch TC. Combining Semantic Relations and DNA Microarray Data for Novel Hypotheses Generation Lecture Notes in Bioinformatics. Springer
  • Mao S, Mansukhani P, Thoma GR. Combining Static Classifiers and Class Syntax Models for Logical Entity Recognition in Scanned Historical Documents Proc IEEE CVPR, Minneapolis, Minnesota, June 2007, pp. 1-8.
  • Kim J, Le DX, Thoma GR. Combining SVM Classifiers to Identify Investigator Name Zones in Biomedical Articles. IS&T/SPIE’s 22nd Annual Symposium on Electronic Imaging. San Francisco, CA, January 2012; 8297.
  • Bodenreider O. Comment les Usagers Accedent a l'Information Medicale Aux USA: l'Exemple de MEDLINEplus [How Consumers Access Health Information in the USA: The MEDLINEplus Example] Innovation et Technologie en Biologie et Medecine. 2000;21(5):286-90.
  • Xue Z, Antani SK, Long LR, Thoma GR. Comparative Performance Analysis of Cervix ROI Extraction and Specular Reflection Removal Algorithms for Uterine Cervix Image Analysis Proc SPIE Medical Imaging 2007. Vol. 6512: 65124I-1-9
  • Rajaraman S, Antani SK, Candemir S, Xue Z, Abuya J, Kohli M, Alderson P, Thoma GR. Comparing deep learning models for population screening using chest radiography. Proc. SPIE 10575, Medical Imaging 2018: Computer-Aided Diagnosis, 105751E (27 February 2018).
  • Mougin F, Burgun A, Bodenreider O. Comparing Drug-class Membership in ATC and NDF-RT Proc IHI 2012 2012:437-443
  • Geller J, Morrey CP, Xu J, Halper M, Elhanan G, Perl Y, Hripcsak G. Comparing inconsistent relationship configurations indicating UMLS errors. AMIA Annu Symp Proc. 2009 Nov 14;2009:193-7.
  • Mortensen J, Bodenreider O. Comparing Pharmacologic Classes in NDF-RT and SNOMED CT. Proc SMBM 2010:119-124.
  • Bodenreider O. Comparing SNOMED CT and the NCI Thesaurus through Semantic Web Technologies Proc. KR-MED 2008
  • Bodenreider O, Zhang S. Comparing the Representation of Anatomy in the FMA and SNOMED CT AMIA Annu Symp Proc. 2006:46-50
  • Mougin F, Bodenreider O. Comparing Two Approaches to Eliminating Cycles in Terminological Systems Proc RFIA 2006
  • 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.
  • Wei D, Wang Y, Perl Y, Xu J, Halper M, Spackman KA. Complexity measures to track the evolution of a SNOMED hierarchy. AMIA Annu Symp Proc. 2008 Nov 6:778-82.
  • Thamizhvani TR, Lakshmanan S, Rajaraman S. Computer Aided Diagnosis of Skin Tumours from Dermal Images. Hemanth D., Smys S. (eds) Computational Vision and Bio Inspired Computing. Lecture Notes in Computational Vision and Biomechanics, vol 28. Springer, Cham
  • Morris J, Yoo TS, Chen D, Burgess J, Richardson AC. Computer Assisted Pedicle Screw Trajectory Guidance Using Fused Deposition Modeling. Abstract in Computer Assisted Surgery. 2001.
  • Christensen JD, Hutchins GC, McDonald CJ. Computer automated detection of head orientation for prevention of wrong-side treatment errors. AMIA Annu Symp Proc. 2006:136-40.
  • Tang P, McDonald CJ. Computer-Based Patient-Record Systems - Chapter 9. In Shortliffe E, Perreault L, eds. Medical Informatics. New York: springer. 2001:327-358. DOI: 10.1007/978-0-387-21721-5_9.
  • Ackerman MJ, Banvard RA, guest editors. Computerized Medical Imaging and Graphics;24(3). Elsevier; 2000.
  • Kho A, Dexter P, Warvel J, Commiskey M, Wilson S, McDonald CJ. Computerized reminders to improve isolation rates of patients with drug-resistant infections: design and preliminary results. AMIA Annu Symp Proc. 2005:390-4.
  • Weiner M, Schadow G, Lindbergh D, Warvel J, Abernathy G, Perkins SM, Dexter PR, McDonald CJ. Conducting a study of Internet-based video conferencing for assessing acute medical problems in a nursing facility. Proc AMIA Symp. 2002:874-8.
  • Uy RC, Sarmiento RF, Gavino A, Fontelo P. Confidence and Information Access in Clinical Decision-Making: An Examination of the Cognitive Processes that affect the Information-seeking Behavior of Physicians. AMIA Annu Symp Proc. 2014 Nov 14;2014:1134-40. eCollection 2014.
  • 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.
  • Gordon S, Zimmerman G, Long LR, Antani S, Jeronimo J, Greenspan H. Content Analysis of Uterine Cervix Images: Initial Steps Towards Content Based Indexing and Retrieval of Cervigrams Proc of SPIE Vol. 6144 61444U-7
  • De Herrera A, Long LR, Antani SK. Content-Based fMRI Brain Maps Retrieval. International Conference on Brain and Health Informatics, Omaha, NE, USA, October 13-16, 2016.
  • Long LR, Antani SK, Thoma GR, Deserno TM. Content-based Image Retrieval For Advancing Medical Diagnostics, Treatment, and Education New Technologies for Advancing Healthcare and Clinical Practices. June 2011:1-17.
  • Lu C, Browne AC. Converting Unicode Lexicon and Lexical Tools for ASII NLP Applications AMIA Annu Symp Proc 2011:1870.
  • Almubarak HA, Stanley RJ, Long LR, Antani SK, Thoma GR, Zuna R, Frazier SR. Convolutional Neural Network Based Localized Classification of Uterine Cervical Cancer Digital Histology Images. Procedia Computer Science, Volume 114, 2017, Pages 281-287, ISSN 1877-0509, https://doi.org/10.1016/j.procs.2017.09.044.
  • Kilicoglu H, Demner-Fushman D. Coreference Resolution for Structured Drug Product Labels Proceedings of BioNLP 2014. pp. 44-53.
  • Lin M-C, Vreeman DJ, McDonald CJ, Huff SM. Correctness of Voluntary LOINC Mapping for Laboratory Tests in Three Large Institutions. AMIA Annu Symp Proc. 2010 Nov 13;2010:447-51.
  • Yaniv Z, Güler Ö, Gong RH. Cost Effective Simulation; A Mixed Reality Approach. Ch. 10 in Mixed and Augmented Reality in Medicine.
  • Potter M, Yaniv Z. Cost-effective surgical registration using consumer depth cameras . Proc. SPIE 9786, Medical Imaging 2016: Image-Guided Procedures, Robotic Interventions, and Modeling, 97861W (March 24, 2016); doi:10.1117/12.2217515
  • Winnenburg R, Bodenreider O. Coverage of phenotypes in standard terminologies. Joint Bio-Ontologies and BioLINK ISMB'2014 SIG session "Phenotype Day" 2014:41-44. 
  • Fung KW, Richesson R, Bodenreider O. Coverage of rare disease names in standard terminologies and implications for patients, providers, and research. AMIA Annu Symp Proc. 2014 Nov 14;2014:564-72. eCollection 2014.
  • Buchanan BG, Chapman W, Cooper GF, Hanbury P, Kayaalp M, Ramachandran M, Saul M. Creating a Software Tool for the Clinical Researcher -- the IPS System Proc AMIA Symp. 2002: : 1210.
  • 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.
  • Thoma GR, Razi A, Seamans J, Strupp-Adams A, Edwards L, Gao J, Ledoux MT. Dataset: AnatQuest
  • Demner-Fushman D, Kilicoglu H. Dataset: CHQA Named Entity Dataset
  • McDonald CJ, Abhyankar S, Taft L. Dataset: common units of measure - subset of the Unified Code for Units of Measure.
  • Fung KW. Dataset: CORE problem list of SNOMED CT.
  • Fung KW. Dataset: ICD-9-CM to SNOMED CT Map
  • McDonald C. Dataset: LOINC Panels and Forms file
  • McDonald CJ, Vreeman D, Goodwin RM. Dataset: LOINC Top 2000+ Lab Observations and Mapper's Guide
  • McDonald C, Vreeman D, Goodwin RM. Dataset: LOINC Top 300+ Lab Orders
  • Abhyankar S, Goodwin RM, Zuckerman AE, McDonald CJ. Dataset: newborn screening LOINC codes (AHIC panel).
  • Abhyankar S, Goodwin RM, Zuckerman AE, McDonald CJ. Dataset: Newborn screening LOINC panel.
  • Abhyankar S, Goodwin RM, Zuckerman A, McDonald CJ. Dataset: newborn screening results annotated example HL7 electronic message guidance (v 5.2).
  • Fung KW. Dataset: Nursing Problem List Subset of SNOMED CT
  • Demner-Fushman D, Roberts K. Dataset: Question Decomposition Data
  • Demner-Fushman D, Roberts K. Dataset: Question Type Data
  • Fung KW. Dataset: SNOMED CT route of administration subset.
  • Fung K. Dataset: SNOMED CT to ICD-10 Cross Map
  • Fung K. Dataset: SNOMED CT to ICD-10-CM Map
  • Kilicoglu H. Dataset: Sortal Anaphora Dataset
  • Kilicoglu H. Dataset: Structured Drug Product Label (SPL) Coreference Dataset
  • Ackerman MJ. Dataset: Visible Human Project reference data sets.
  • Botti G, Bodenreider O, Burgun A, Le Beux P, Fieschi M. De la Classification à la Connaissance des Maladies: Une Réflexion à Partir de la Classification Internationale des Maladies [From Classification to Knowledge About Diseases: Thoughts about the International Classification of Diseases] Innovation et Technologie en Biologie et Médecine. 2000;21(5):291-97.
  • 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.
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  • Ben Abacha A. NLM_NIH at TREC 2016 Clinical Decision Support Track. Proceedings of TREC 2016, the 25th Text Retrieval Conference, Gaithersburg, MD, USA, November 2016.
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  • Bodenreider O, Aubry M, Burgun A. Non-Lexical Approaches to Identifying Associative Relations in the Gene Ontology Pac Symp Biocomput. 2005:91-102
  • Candemir S, Antani SK, Xue Z, Thoma GR. Novel Method for Storyboarding Biomedical Videos for Medical Informatics. 30th IEEE International Symposium on Computer-Based Medical Systems
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  • 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.
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  • Walker FL, Gallagher ME, Thoma GR. PDF File Migration to PDF/A: Technical Considerations. Proc IS&T Archiving 2007. Arlington, Virginia, May 2007; 6-11.
  • Ganesan P, Xue Z, Singh S, Long LR, Ghoraani B, Antani SK. Performance Evaluation of a Generative Adversarial Network for Deblurring Mobile-phone Cervical Images. Proc. IEEE Engineering in Medicine and Biology Conference (EMBC), Berlin, Germany, 23 – 27 July 2019. pp. 4487 – 4490.
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  • Yaniv Z. Registration for Orthopaedic Interventions. Chapter 3 in: Zheng G, Li S, editors. Computational Radiology for Orthopaedic Interventions: Lecture Notes in Computational Vision and Biomechanics. Springer International Publishing; c2016. p. 41-70.
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  • Bangalore AK, Sood AK. Securing web servers using self-cleansing intrusion tolerance (SCIT). 2009 Second International Conference on Dependability. 2009:60-5.
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  • Karargyris A, Antani SK, Thoma GR. Segmenting anatomy in chest x-rays for tuberculosis screening. Conf Proc IEEE Eng Med Biol Soc. 2011;2011:7779-82. doi: 10.1109/IEMBS.2011.6091917.
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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.
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  • Kakadiaris IA, Chen D, Miller MJ, Loftin RB, Patrick C. Simulation-based determination of breast tissue engineering design patterns. Third Biennial Tissue Engineering Society International Meeting; 2000 Nov 30-Dec 3; Orlando, Florida.
  • 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
  • Fung K, Berglund D, Scichilone R, Brear H, Giannangelo K. SNOMED CT to ICD-10 mapping project update - a joint task for IHTSDO and WHO-FIC. Meeting of the WHO Collaborating Centers for the Family of International Classifications. October 2009.
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