Natural Language Processing Laboratory | NLPL Publications

 

Recent Publications

A system for coreference resolution for the clinical narrative. Jiaping Zheng, Wendy W Chapman, Timothy A Miller, Chen Lin, Rebecca S Crowley, Guergana K Savova J Am Med Inform Assoc. amiajnl-2011-000599. Published Online First: 31 January 2012. doi:10.1136/amiajnl-2011-000599

All Publications

Chapman, Wendy; Savova, Guergana; Zheng, Jiaping; Castine, Melissa; Crowley, Rebecca. In Press. Anaphoric reference in clinical reports: characteristics of an annotated corpus. Journal of Biomedical Informatics.

Rea, Susan; Pathak, Jyotishman; Savova, Guergana; Oniki, Thomas; Westberg, Les; Beebe, Calvin; Tao, Cui; Parker, Craig; Haug, Peter; Huff, Stanley; Chute, Christopher. In Press. Building a robust, scalable and standards-driven infrastructure for secondary use of the EHR data. Journal of Biomedical Informatics.

Savova, Guergana; Olson, Janet; Murphy, Sean; Cafourek, Victoria; Couch, Fergus; Goetz, Matthew; Ingle, James; Suman, Vera; Chute, Christopher and Weinshilboum, Richard. 2011. The electronic medical record and drug response research: automated discovery of drug treatment patterns for endocrine therapy of breast cancer. Journal of American Medical Informatics Association.

Sohn, Sunghwan; Kocher, Jean-Pierre; Chute, Christopher; Savova, Guergana. 2011. Drug side effect extraction from clinical narratives of psychiatry and psychology patients. Journal of American Medical Informatics Association.

Zheng, Jiaping; Chapman, Wendy; Crowley, Rebecca and Savova, Guergana. 2011. Coreference resolution: a review of general methodologies and applications in the clinical domain. Journal of Biomedical Informatics. doi:10.1016/j.jbi.2011.08.006

Wu, Stephen; Kaggal, Vinod; Savova, Guergana; Liu, Hongfang; Dligach, Dmitriy; Zheng, Jiaping; Chapman, Wendy; Chute, Christopher. 2011. Generality and reuse in a common type system for clinical natural language processing. Managing Interoperability and Complexity in Health Systems (MIXHS 2011), In conjunction with the 20th ACM International conference on information and knowledge management. October 28, 2011. Glasgow, UK.

Chute, Christopher; Pathak, Jyoti; Savova, Guergana; Bailey Kent; Schor Marshall; Hart, Lacey; Beebe, Calvin and Huff, Stan. 2011. The SHARPn project on secondary use of electronic medical record data: progress, plans an possibilities. AMIA ann symp.

Chapman, Wendy; Nadkarni, Prakash; Hirschman, Lynette; D’Avolio, Leonard; Savova, Guergana; Uzuner, Ozlem. 2011. Overcoming barriers to NLP for clinical text: the role of shared tasks and the need for additional creative solutions. Journal of American Medical Informatics Association. 2011 -:1e4. doi:10.1136/amiajnl-2011-000465.

Cairns, Brian ; Nielsen, Rodney; Masanz, James; Martin, James; Palmer, Martha; Ward, Wayne; Savova, Guergana. 2011. The MiPACQ Clinical Question Answering System. AMIA Annual Symposium. Washington, DC.

Tao, Cui; Savova, Guergana; de Groen, Piet and Chute, Christopher. Semantic-Web based Annotation and Reasoning for Temporal Information in Clinical Narratives. In 2011 AMIA Joint Summit on Translational Science. March 9-11, 2011. San Francisco.

Savova, Guergana; Chapman, Wendy, Zheng, Jiaping and Crowley, Rebecca. 2011. Anaphoric relations in the clinical narrative: corpus creation. JAMIA. JAMIA doi:10.1136/amiajnl-2011-000108

Wilke, Russell; Xu, Hua; Denny, Joshua; Roden, Daniel; Krauss, Ronald M; McCarty, Catherine A; Davis, R; Skaar, Todd; Lamba Jatinder and Savova, Guergana. 2011. The emerging role of electronic medical records in pharamacogenomics. Journal of Clinical Pharmacology and Therapeutics.

Tao, Cui; Solbrig, Harold; Sharma, Deepak; Wei, Wei-Qi; Savova, Guergana and Chute, Christopher. 2010. Time-oriented question answering from clinical narratives using semantic-web techniques. International Semantic Web Conference. Shanghai, China.

Nielsen, Rodney; Masanz, James; Ogren, Philip; Ward, Wayne; Martin, James; Palmer, Martha; Savova, Guergana. 2010. An architecture for complex clinical question answering. 1st Annual ACM International Conference on Health Informatics (IHI 2010). Washington, DC.

Kullo, Iftikar; Fan, Jin; Pathak, Jyotishman; Savova, Guergana; Ali, Zeenat; Chute, Christopher. 2010. Leveraging informatics for genetic studies: use of the electronic medical record to enable a genome-wide association study of peripheral arterial disease. JAMIA. DOI:10.1136/jamia.2010.004366.

Maradit-Kremers, Hilal; Myasoedova, Elena; Crowson, Cynthia; Savova, Guergana; Gabriel, Sherine; Matteson, Eric. 2010. The Rochester epidemiology project: exploiting the capabilities for population-based research in rheumatic diseases. Rheumatology. doi:10.1093/rheumatology/keq199.

Sohn, Sunghwan; Murphy, Sean; Masanz, James; Kocher, Jean-Pierre; Savova, Guergana. 2010. Classification of medication status change in clinical narratives. AMIA Fall symposium.

Savova, Guergana; Fan, Jin; Ye, Zi; Murphy, Sean; Zheng, Jiaping; Chute, Christopher and Kullo, Iftikhar. 2010. Discovering peripheral arterial disease cases from radiology notes using natural language processing. AMIA Fall symposium.

Tao, Cui; Wei, Wei-Qi; Savova, Guergana; Chute, Christopher. 2010. A semantic web ontology for temporal relation inferencing in clinical narratives. AMIA Fall symposium.

Liu, Kaihong; Chapman, Wendy; Savova, Guergana; Chute, Christopher; Sioutos, Nicholas; Crowley, Rebecca. 2010. Effectiveness of Lexico-Syntactic Pattern Matching for Ontology Enrichment with Clinical Documents. Methods of Information in Medicine.

Savova, Guergana; Masanz, James; Ogren, Philip; Zheng, Jiaping; Sohn, Sunghwan; Kipper-Schuler, Karin and Chute, Christopher. 2010. Mayo Clinical Text Analysis and Knowledge Extraction System (cTAKES): architecture, component evaluation and applications. JAMIA 2010;17:507-513 doi:10.1136/jamia.2009.001560

Cheng, Lionel; Zheng, Jiaping; Savova, Guergana and Erickson, Bradley. 2010. Discerning tumor status from unstructured MRI reports – completeness of information in existing reports and utility of natural language processing. Journal of Digital Imaging of the Society of Imaging Informatics in Medicine, ISSN: 0897-1889: 23(2), 119-133. PMID: 19484309. (Best paper 2010 award of the Journal of Digital Imaging).

Sohn, Sunghwan and Savova, Guergana. 2009. Mayo Clinic smoking status classification system. Proc. AMIA, Nov. 2009.

Savova, Guergana; Bethard, Steven; Styler, Will; Martin, James; Palmer, Martha; Masanz, James; Ward, Wayne. 2009. Towards temporal relation discovery from the clinical narrative. Proc. AMIA, Nov. 2009. p. 568–572

Coden, Anni; Savova, Guergana; Sominsky, Igor; Tanenblatt, Michael; Masanz, James; Schuler, Karin; Cooper, James; Guan, Wei and de Groen, Piet. 2009. Automatically extracting cancer disease characteristics from pathology reports into a cancer disease knowledge model. Journal of Biomedical Informatics 42 (2009), pp. 937-949. doi:10.1016/j.jbi.2008.12.005  

Kim H, Harris MR, Savova GK, Chute CG. 2008. The first step toward data reuse: disambiguating concept representation of the locally developed ICU nursing flowsheets.  Computers and Information in Nursing 26(5):282-9. PMID: 18769183

Li, Dingcheng; Schuler, Karin and Savova, Guergana. 2008. A Comparison between CRFs and SVMs in Disorder Named Entity Recognition in Clinic Texts. Intelligent Data Analysis in Biomedicine and Pharmacology (IDAMAP) 2008. A colloquium in conjunction with the American Medical Informatics Association Annual Symposium 2008 in Washington, DC, USA: 57-62.

Savova, Guergana; Clark, Cheryl; Zheng, Jiaping; Cohen, Bretonnel K.; Murphy, Sean; Wellner, Ben; Harris, David; Lazo, Marcia; Aberdeen, John; Hu, Qian; Chute, Christopher and Hirschman, Lynette. 2008. The Mayo/MITRE system for discovery of obesity and its comorbidities. In The Second i2b2 Workshop on Challenges in Natural Language Processing for Clinical Data. Washington, DC.

Meystre, Stephane M; Savova, Guergana K; Kipper-Schuler, Karin C. and Hurdle, John E. 2008. Extracting Information from Textual Documents in the Electronic Health Record: A Review of Recent Research. IMIA Yearbook of Medical Informatics 2008. Methods Inf Med 2008; 47 Suppl 1: 128-144. PMID: 18660887

Savova, Guergana; Coden, Anni; Sominsky, Igor; Johnson, Rie; Ogren, Philip; de Groen, Piet and Chute, Christopher. 2008. Word sense disambiguation across two domains: biomedical literature and clinical notes. Journal of Biomedical Informatics. 2008 Dec;41(6):1088-100. Epub 2008 Mar 4. PMID: 18375190

Savova, Guergana; Kipper-Schuler, Karin; Buntrock, James and Chute, Christopher. 2008. UIMA-based clinical information extraction system. Language Resources and Evaluation Conference, LREC 2008: Towards enhanced interoperability for large HLT systems: UIMA for NLP: 39-43. http://watchtower.coling.uni-jena.de/~coling/uimaws_lrec2008/

Ogren, Philip; Savova, Guergana and Chute, Christopher. 2008. Constructing evaluation corpora for automated clinical named entity recognition. Language Resources and Evaluation Conference, Proc LREC 2008: 3143-3150. http://www.lrec-conf.org/proceedings/lrec2008/. Marakesh, Morrocco.

Kipper-Schuler, Karin; Kaggal, Vinod; Masanz, James and Savova, Guergana. 2008. System evaluation on a named entity corpus from clinical notes. Language Resources and Evaluation Conference, LREC 2008: 3001-3007. http://www.lrec-conf.org/proceedings/lrec2008/. Marakesh, Morrocco.

Savova, Guergana; Ogren, Philip; Duffy, Patrick; Buntrock, James and Chute, Christopher. 2008. Mayo Clinic System for patient smoking status classification. J Am Med Inform Assoc. 2008; 15(1):25-8. PMID: 17947622

Coden, Anni; Savova, Guergana; Buntrock, Jim; Sominsky, Igor; Ogren, Philip; Chute, Christopher and de Groen, Piet. 2007. Text analysis integration into a medical information retrieval system: challenges related to word sense disambiguation. In Medinfo 2007: Proceeding of the 12th World Congress on Health (Medical) Informatics; Building Sustainable Health Systems; pp. 2218-2219.

Kim, Hyeoneui; Harris, Marcelline; Savova, Guergana, Speedie, Stuart and Chute, Christopher. 2007. Toward Near Real-Time Acuity Estimation: A Feasibility Study. Journal of Nursing Research. July/August 2007, 56(4):288-294.PMID: 17625469

Savova, Guergana; Ogren, Philip; Duffy, Patrick; Buntrock, James and Chute, Christopher. 2006. Mayo Clinic NLP System for patient smoking status identification. I2b2 Workshop on Challenges in Natural Language Processing for Clinical Data. 10-11 November. Washington, DC.

Savova, Guergana; Therneau, Terry and Chute, Christopher. 2006. Cluster stopping rules for word sense discrimination. European Chapter of the Association for Computational Linguistics (EACL). Workshop: Making sense of sense – bringing computational linguistics and psycholinguistics together: 9-17.

Kim H; Harris MR; Savova G and Chute G. 2006. Content coverage of SNOMED-CT toward the ICU nursing flowsheets and the acuity indicators. Studies in Health Technology and Informatics 2006; 122:722-6.PMID: 17102358

Watters, Shana; McKoskey, David; Miller, Timothy; Thomson, Bridget; Boley, Daniel; Gini, Maria; Schuler, William; Polukeyeva, Anja; Gundel, Jeanette; Pakhomov, Sergey; Savova, Guergana. 2005. Using volunteers to annotate biomedical corpora for anaphora resolution. American Association of Artificial Intelligence Spring Symposium on Knowledge Collection from Volunteer Contributors (KCVC’05). San Francisco, March, 2005: 117-121.

Harris, Marcelline; Savova, Guergana; Johnson, Thomas and Chute, Christopher.  2003.  A term-extraction tool for expanding content in the domain of functioning, disability and health: proof of concept.  Journal of Biomedical Informatics. 36(2003) 250-259.PMID: 14643720

Savova, Guergana; Harris, Marcelline; Johnson, Thomas; Pakhomov, Sergey and Chute, Christopher.  2003.  A data-driven approach for extracting "the most specific term" for ontology development.  Proc. American Medical Informatics Association. Washington, DC. 2003; 579-583. PMID: 14728239

Harris, Marcelline; Kim, Hyeoneui; Rhudy, Lori; Savova, Guergana and Chute, Christopher. 2003.  Testing the generalizability of the ISO model for nursing diagnoses. Proc. American Medical Informatics Association. Washington, DC. 2003; 274-278. PMID: 14728177

Savova, Guergana and Bachenko, Joan.  2003.  Prosodic features of four types of disfluencies.  Proc. Disfluency in Spontaneous Speech (DiSS'03).  Goteborg University, Sweden. In DiSS'03: 91-94.

Savova, Guergana and Bachenko, Joan.  2003.  Designing for errors: similarities and differences of disfluency rates and prosodic characteristics across domains.  Proc. Eurospeech.  8th European conference in Speech Communication and Technology.  Geneva, Switzerland. In EUROSPEECH-2003, 229-232.

Savova, Guergana, Schonwetter, Michael and Pakhomov, Sergey. 2000.  Improving language model perplexity and recognition accuracy for medical dictations via within-domain interpolation with literal and semi-literal corpora.  Proceedings of International Conference for Spoken Language Processing. Beijing, China. In ICSLP-2000, vol.1, 206-209. http://www.isca-speech.org/archive/icslp_2000/i00_1206.html

Pakhomov, Sergey and Savova, Guergana. 1999. Filled pause distribution and modeling in quasi-spontaneous speech. Proceedings of the Disfluency Workshop at the International Congress of Phonetic Sciences 1999, San Francisco, CA: 31-34.