NLP/IE Publications

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Recent papers

2017

2017

  • Mattar A, Carlston D, Sariol G, Yu T, Almustafa A, Melton GB, Ahmed A. The prevalence of obesity documentation in Primary Care Electronic Medical Records. Are we acknowledging the problem? Applied Clinical Informatics. 2017 Jan 25;8(1):67-79. doi: 10.4338/ACI-2016-07-RA-0115. PMID: 28119990. 
  • Sun D, Sarda G, Skube SJ, Blaes A, Zhang R, Melton GB. A Study on Phenotyping and Visualizing Black Box Warnings of Antineoplastic Breast Cancer Medications. American Medical Informatics Association Joint Summits Translational Science Proceedings. 2017: 392-393.
  • Hultman G, McEwan R, Pakhomov S, Skube SJ, Melton GB. Usability Testing of a Clinical Document Search Engine for Researchers. American Medical Informatics Association Joint Summits Translational Science Proceedings. 2017: 348-349.
  • Arsoniadis EG, Ho YY, Melton GB, Madoff RD, Le C, Kwaan MR. African American and Short-Term Outcomes after Surgery for Crohn’s Disease: An ACS-NSQIP Analysis. J Crohns Colitis. 2017 Apr 1;11(4):468-473. doi: 10.1093/ecco-jcc/jjw175. PMID: 27683803.
  • Hu Z, Melton GB, Arsoniadis EG, Wang Y, Kwaan MR, Simon GJ. Strategies for handling missing clinical data for automated surgical site infection detection from the electronic health record. J Biomed Inform. 2017 Apr;68:112-120. Doi:10.1016/j.jbi.2017.03.009. PMID: 28323112.
  • Rajamani S, Chen ES, Lindemann E, Aldekhyyel R, Wang Y, Melton GB. Representation of occupational information across resources and validation of the occupational data for health model. J Am Med Inform Assoc. 22 Apr 2017. doi: 10.1093/jamia/ocx035
  • Lindemann E, Chen ES, Rajamani S, Manohar N, Wang Y, Melton GB. Assessing the Representation of Occupation Information in Free-Text Clinical Documents Across Multiple Sources. Studies in Health Technology and Informatics (MedInfo 2017). Accepted.
  • Rizvi RF, Marquard JL, Seywerd MA, Adam TJ, Elison JT, Hultman GM, Harder KA, Melton GB. Usability Evaluation of an EHR’s Clinical Notes Interface from Attendings and Residents Perspectives-An Exploratory Study. Studies in Health Technology and Informatics (MedInfo 2017). Accepted.
  • Skube SJ, Hu Z, Arsoniadis EG, Simon GJ, Wick EC, Ko CY, Melton GB. Characterizing Surgical Site Infection Signals in Clinical Notes. Studies in Health Technology and Informatics (MedInfo 2017). Accepted. 
  • Arsoniadis EG, Skube SJ, Bjerke TM, Jarabek B, Melton GB. Assessing Provider-Generated Free-Text Quality in EHR-Integrated Handoff Notes. Studies in Health Technology and Informatics (MedInfo 2017). Accepted.
  • Zhang R, Pakhomov SVS, Arsoniadis EG, Lee JT, Wang Y, Melton GB. Detecting clinically relevant new information in clinical notes across specialties and settings. BMC Medical Informatics and Decision Making. 2017: 17(suppl2):68.
  • Lindemann EA, Chen ES, Wang Y, Skube SJ, Melton GB. Representation of Social History Factors Acrsos Age Groups: A Topic Analysis of Free-Text Social Documentation. Proceedings of the American Medical Informatics Association Symposium. 2017. Accepted.
  • Sun D, Simon GJ, Skube S, Blaes AH, Melton GB, Zhang R. Causal Phenotyping for Susceptibility to Cardiotoxicity from Antineoplastic Breast Cancer Medications. Proceedings of the American Medical Informatics Association Symposium. 2017. Accepted.
  • Winden TJ, Chen ES, Wang Y, Lindemann E, Melton GB. Residence, Living Situation, and Living Conditions Information Documentation in Clinical Practice. Proceedings of the American Medical Informatics Association Symposium. 2017. Accepted. 

2016

2016

  • Winden TJ, Chen ES, Melton GB. Representing Residence, Living Situation, and Living Conditions: An Evaluation of Terminologies, Standards, Guidelines, and Measures/Surveys. Proceedings of the American Medical Informatics Association Symposium. 2016: 2072-81.
  • Aldekhyyel R, Chen ES, Rajamani S, Wang Y, Melton GB. Content and Quality of Free-Text Occupation Documentation in the Electronic Health Record. Proceedings of the American Medical Informatics Association Symposium. 2016: 1708-16. ** Manuscript winner of the AMIA Student Paper Competition (1st place)
  • Wang Y, Chen ES, Pakhomov S, Melton GB. Investigating Longitudinal Tobacco Use Information from Social History and Clinical Notes in the Electronic Health Record. Proceedings of the American Medical Informatics Association Symposium. 2016: 1209-18.
  • Hu Z, Melton GB, Moeller ND, Arsoniadis EG, Wang Y, Kwaan MR, Jensen EH, Simon GJ. Accelerating Chart Review Using Automated Methods on Electronic Health Record Data for Postoperative Complications. Proceedings of the American Medical Informatics Association Symposium. 2016: 1822-31.
  • Finley GP, Pakhomov S, McEwan R, Melton GB. Towards Comprehensive Clinical Abbreviation Disambiguation Using Machine-Labeled Training Data. Proceedings of the American Medical Informatics Association Symposium. 2016: 560-9.
  • Hultman G, Marquard J, Arsoniadis E, Mink PJ, Rizvi R, Ramer T, Khairat S, Fickau K, Melton GB. Usability Testing of Two Ambulatory EHR Navigators. Applied Clinical Informatics. 2016. 7(2): 502-15.
  • Rizvi R, Harder K, Hultman G, Adam TJ, Kim K, Pakhomov S, Melton GB. A comparative observational study of inpatient clinical note entry and reading/retrieval styles adopted by physicians. International Journal of Medical Informatics. 2016 Jun;90:1-11. doi: 10.1016/j.ijmedinf.2016.02.011. Epub 2016 Mar 2. PMID: 27103191.
  • Knoll B, Melton G, Liu H, Xu H, Pakhomov S. "Using Synthetic Clinical Data to Train an HMM-Based POS Tagger."  Proceedings of the IEEE International Conference on Biomedical and Health Informatics. 2016. 252-5.
  • Wang Y, Chen ES, Leppik I, Pakhomov S, Sarkar IN, Melton GB. Identifying Family History and Substance Use Associations for Adult Epilepsy from the Electronic Health Record. American Medical Informatics Association Joint Summits Translational Science Proceedings. 2016. 250-9. * This paper was nominated for “Best Paper” for the AMIA Clinical Research Informatics Summits.
  • McEwan R, Melton GB, Knoll BC, Wang Y, Hultman G, Dale JL, Meyer T, Pakhomov S. NLP-PIER: A Scalable Natural Language Processing, Indexing, and Searching Architecture for Clinical Notes. American Medical Informatics Association Joint Summits Translational Science Proceedings. 2016. 150-9. 

2015

2015

  • Zhang R, Manohar N, Arsoniadis E, Wang Y, Adam TJ, Pakhomov SV, Melton GB. Evaluating Term Coverage of Herbal and Dietary Supplements in Electronic Health Records. Proceedings of the American Medical Informatics Association Symposium. 2015: 1361-70. PMID: 26958277
  • Wang Y, Chen ES, Pakhomov S, Arsoniadis E, Carter EW, Lindemann E, Sarkar IN, Melton GB.  Automated Extraction of Substance Use Information from Clinical Texts. Proceedings of the American Medical Informatics Association Symposium. 2015: 2121-30. PMID: 26958312
  • Carter EW, Sarkar IN, Melton GB, Chen EC. Representation of Drug Use in Biomedical Standards, Clinical Text, and Research Measures. Proceedings of the American Medical Informatics Association Symposium. 2015: 376-85. PMID: 26958169
  • Chen ES, Melton GB, Wasserman RC, Rosenau PT, Howard DB, Sarkar IN. Mining and Visualizing Family History Associations in the Electronic Health Record: A Case Study for Pediatric Asthma. Proceedings of the American Medical Informatics Association Symposium. 2015: 396-405. PMID: 26958171
  • Melton GB, Wang Y, Arsoniadis E, Pakhomov SVS, Adam TJ, Kwaan MR, Rothenberger DA, Chen ES. Analyzing Operative Note Structure in Development of a Section Header Resource. Studies in Health Technology and Informatics (MedInfo 2015). 2015;216:821-6. PMID: 26262166.
  • Manohar N, Adam TJ, Pakhomov S, Melton GB, Zhang R. Evaluation of herbal and nutritional supplement resource term coverage. Studies in Health Technology and Informatics (MedInfo 2015). 2015;216:785-9. PMID: 26262159.
  • Arsoniadis E, Tambyraja R, Khairat S, Jahansouz C, Scheppmann D, Kwaan MR, Melton GB. Characterizing Patient-Generated Clinical Data and Associated Implications for Electronic Health Records. Studies in Health Technology and Informatics (MedInfo 2015). 2015;216:158-62. PMID: 26262030.
  • Zhen H, Simon GJ, Arsoniadis EG, Wang Y, Kwaan MR, Melton GB. Automated Detection of Postoperative Surgical Site Infections Using Supervised Methods with Electronic Health Record Data. Studies in Health Technology and Informatics (MedInfo 2015). 2015;216:706-10. PMID: 26262143.
  • Moon S, McInnes B, Melton GB. Challenges and practical approaches with word sense disambiguation of acronyms and abbreviations in the clinical domain. Healthc Inform Res. 2015 Jan;21(1):35-42. doi: 10.4258/hir.2015.21.1.35. Epub 2015 Jan 31. PMID: 25705556.
  • Zhang R, Adam T, Simon G, Cairelli M, Rindflesch T, Pakhomov S, Melton GB. Mining Biomedical Literature to Explore Interactions between Cancer Drugs and Dietary Supplements. American Medical Informatics Association Joint Summits Translational Science Proceedings. 2015 Mar 23;2015:69-73. PMID: 26306241. *Manuscript nominated for best paper for the AMIA Translational Bioinformatics Meeting. 
  • Wang Y, Pakhomov S, Ryan JO, Melton GB. Domain Adaption of Parsing for Operative Notes. Journal of Biomedical Informatics. 2015 Apr;54:1-9. doi: 10.1016/j.jbi.2015.01.016. Epub 2015 Feb 7. PMID: 25661593.
  • Winden TJ, Chen ES, Wang, Y, Sarkar IN, Carter EW, Melton GB. Towards the Standardized Documentation of E-Cigarette Use in the Electronic Health Record for Population Health Surveillance and Research. American Medical Informatics Association Joint Summits Translational Science Proceedings. 2015 Mar 25;2015:199-203. PMID: 26306269.
  • Rajamani S, Chen ES, Akre M, Wang Y, Melton GB. Assessing the Adequacy of the HL7/LOINC Document Ontology Role Axis. Journal of the American Medical Informatics Association. 2015 22 (3): 615-620 doi: 10.1136/amiajnl-2014-003100. PMID: 25352569.
  • Chen ES, Carter EW, Winden TJ, Sarkar IN, Wang Y, Melton GB. Multi-Source Development of an Integrated Model for Family Health History. Journal of the American Medical Informatics Association. 2015 22 (3): 615-620. doi: 10.1136/amiajnl-2014-003100. PMID: 25336591.

2014

2014

  • McInnes B, Pedersen T, Liu Y, Melton GB, Pakhomov SV. U-path: An undirected path-based measure of semantic similarity. Proceedings of the American Medical Informatics Association Symposium. 2014. 882-91.
  • Chen ES, Carter EW, Sarkar IN, Winden TJ, Melton GB. Examining the Use, Contents, and Quality of Free-Text Tobacco Use Documentation in the Electronic Health Record. Proceedings of the American Medical Informatics Association Symposium. 2014. 366-74.
  • Rajamani S, Chen ES, Wang Y, Melton GB. Extending the HL7/LOINC Document Ontology Settings of Care. Proceedings of the American Medical Informatics Association Symposium. 2014. 994-1001.
  • Zhang R, Pakhomov SV, Lee JT, Melton GB. Using Language Models to Identify Relevant New Information in Inpatient Clinical Notes. Proceedings of the American Medical Informatics Association Symposium. 2014. 1268-76.
  • Bill R, Pakhomov S, Chen ES, Winden TJ, Carter EW, Melton GB. Automated Extraction of Family History Information from Clinical Notes. Proceedings of the American Medical Informatics Association Symposium. 2014. 1709-17.
  • Zhang R, Cairelli MJ, Fiszman M, Kilicoglu H, Rindflesch TC, Pakhomov SV, Melton GB. Exploiting Literature-Derived Knowledge and Semantics to Identify Potential Prostate Cancer Drugs. Cancer Informatics. 2014 Oct 14;13(Suppl 1):103-11. doi: 10.4137/CIN.S13889.
  • Zhang R, Pakhomov S, Melton GB. Longitudinal Analysis of New Information Types in Clinical Notes. American Medical Informatics Association Joint Summits Translational Science Proceedings. 2014. 232-7. *Manuscript selected finalist in AMIA Student Paper Competition 
  • Wang Y, Pakhomov S, Dale JL, Chen ES, Melton GB. Application of HL7/LOINC Document Ontology to a University-Affiliated Integrated Health System Research Clinical Data Repository. American Medical Informatics Association Joint Summits Translational Science Proceedings. 2014. 231-5.
  • Zhang R, Cairelli MJ, Fiszman M, Rosemblat G, Kilicoglu H, Rindflesch TC, Pakhomov SV, Melton GB. “Using Semantic Predications to Uncover Drug-Drug Interactions in Clinical Data.” Journal of Biomedical Informatics. 2014 Jan 19. pii: S1532-0464(14)00005-7. doi: 10.1016/j.jbi.2014.01.004. [Epub ahead of print]. PMID: 24448204.

2013

2013

  • Farri O, Monsen KA, Pakhomov SV, Pieczkiewicz DS, Speedie SM, Melton GB. Effects of time constraints on clinician-computer interaction: A study on information synthesis from EHR clinical notes. J Biomed Inform. 2013 Sep; [Epub ahead of print].
  • Farri O, Rahman A, Monsen KA, Zhang R, Pakhomov S, Pieczkiewicz DS, Speedie SM, Melton GB. Impact of a prototype visualization tool for new information in EHR clinical documents. Applied Clinical Informatics. 2012;3(4): 404-418.
  • Moon S, Pakhomov S, Liu N, Ryan JO, Melton GB. A sense inventory for clinical abbreviations and acronyms created using clinical notes and medical dictionary resources. J Am Med Inform Assoc. 2013 Jun; [Epub ahead of print].
  • Wang Y, Pakhomov S, Melton GB. Predicate argument structure frames for modeling information in operative notes. Stud Health Technol Inform. 2013; 192:783-7.(Manuscript selected as a Student Paper Competition Finalist at MedInfo)
  • Zhang R, Pakhomov S, Lee JT, Melton GB. Navigating longitudinal clinical notes with an automated method for detecting new information. Stud Health Technol Inform. 2013;192:754-8. (Manuscript selected as a Student Paper Competition Finalist at MedInfo)

2012

2012

  • Bill R, Liu Y, McInnes B, Melton GB, Pakhomov S. Evaluating semantic relatedness and similarity measures with standardized MedDRA queries. Proceedings of the American Medical Informatics Association Symposium. 2012: 43-50.
  • Liu Y, Bill R, Fiszman M, Rindflesch T, Pedersen T, Melton GB, Pakhomov S. Using SemRep to label semantic relations extracted from clinical text. Proceedings of the American Medical Informatics Association Symposium. 2012: 587-95.
  • Liu Y, McInnes B, Pedersen T, Melton GB, Pakhomov S. Semantic Relatedness Study Using Second Order Co-occurrence Vectors Computed from Biomedical Corpora, UMLS and WordNet. 2nd ACM SIGHIT International Health Informatics (IHI) Symposium. 2012: 363-71.
  • Moon S, Pakhomov S, Melton GB, Automated Disambiguation of Acronyms and Abbreviations in Clinical Texts: Window and Training Size Considerations. Proceedings of the American Medical Informatics Association Symposium. 2012: 3010-9.
  • Pakhomov S, McInnes BT, Lamba J, Liu Y, Melton GB, Ghodke Y, Bhise N, Lamba V, Birnbaum AK. Using PharmGKB to train text mining approaches for identifying potential gene targets for pharmacogenomic studies. Journal of Biomedical Informatics. 2012 Oct; 45(5): 862-9.
  • Wang Y, Pakhomov S, Burkart NE, Ryan JO, Melton GB. A Study of Actions in Operative Notes. Proceedings of the American Medical Informatics Association Symposium. 2012: 1431-40.
  • Zhang R, Pakhomov S, Gladding S, Aylward M, Borman-Shoap E, Melton GB. Automated Assessment of Medical Training Evaluation Text. Proceedings of the American Medical Informatics Association Symposium. 2012: 1459-68.
  • Zhang R, Pakhomov S, Melton GB. Automated identification of relevant new information in clinical narrative. 2nd ACM SIGHIT International Health Informatics (IHI) Symposium. 2012: 837-41.

2011

2011

  • McInnes B, Pederson T, Liu Y, Melton GB, Pakhomov S. Knowledge-based Method for Determining the Meaning of Ambiguous Biomedical Terms Using Information Content. Proceedings of American Medical Informatics Association Symposium. 2011:895-904.
  • McInnes B, Pedersen T, Liu Y, Melton GB, Pakhomov S. Using Second-Order Vectors in a Knowledge-Based Method for Acronym Disambiguation. Proceedings of the 15th Conference of Computational Natural Language Learning. 2011:145-153.
  • Moon S, Pakhomov S, Ryan J, Melton GB. Automated Non-Alphanumeric Symbol Resolution in Clinical Texts. Proceedings of the American Medical Informatics Association Symposium. 2011:979-86.
  • Pakhomov SV, Shah ND, Van Houten HK, Hanson PL, Smith SA. The role of the electronic medical record in the assessment of health related quality of life. Proceedings of the American Medical Informatics Association Symposium. 2011:1080-8.
  • Wang Y, Melton GB, Pakhomov S. It’s about this and that: A Description of Anaphoric Expressions in Clinical Text. Proceedings of the American Medical Informatics Association Symposium. 2011:1471-80.
  • Zhang R, Pakhomov S, McInnes B, Melton GB. Evaluating measures of redundancy in clinical text. Proceedings of the American Medical Informatics Association Symposium. 2011:1612-20.

2010

2010

  • Melton GB, Moon S, McInnes B, Pakhomov S. Automated identification of synonyms in biomedical acronym sense inventories. Louhi 2010: Workshop on Text and Datamining of Health Documents. 2010:46-52.
  • Melton GB, Raman N, Chen ES, Sarkar IN, Pakhomov S, Madoff RD. Evaluation of Family History Information within Clinical Documents and Adequacy of HL7 Clinical Statement and Clinical Genomics Family History Models for Its Representation, A Case Report. Journal of the American Medical Informatics Association. 2010 May 1;17(3):337-40.
  • Melton GB, Westra BL, Raman N, Monsen KA, Kerr MJ, Hart CH, Solomon DA, Timm JE. Informing Standard Development and Understanding User Needs with Omaha System Signs and Symptoms Text Entries in Community-Based Care Settings. Proceedings of the American Medical Informatics Association Symposium. 2010:512-516.
  • Pakhomov S, McInnes B, Adam T, Liu Y, Pedersen T, Melton GB. Semantic Similarity and Relatedness of Clinical Terms. Proceedings of the American Medical Informatics Association Symposium. 2010:572-576.
  • Pakhomov SV, Pedersen T, McInnes B, Melton GB, Ruggieri A, Chute, CG. Towards a Framework for Developing Semantic Relatedness Reference Standards. Journal of Biomedical Informatics. 2011 April 44(2):251-65. 2010 Oct 31.