PUBLICATIONS

SERGUEI V. S. PAKHOMOV


2015

Pakhomov, S., Marino, S., Banks, S., Bernick, C. (2015). Using Automatic Speech Recognition to Assess Spoken Responses to Cognitive Tests of Semantic Verbal Fluency. Speech Communication; 75:14-26.

Melton, G.B., Wang, Y., Arsoniadis, E., Pakhomov, S.V., Adam, T.J., Kwaan, M.R., Rothenberger, D.A., Chen, E.S. (2015). Analyzing Operative Note Structure in Development of a Section Header Resource. Studies in Health Technology and Informatics; 216:821-6.

Zheng, K., Vydiswaran, V.G., Liu, Y., Wang, Y., Stubbs, A., Uzuner, O., Gururaj, A.E., Bayer, S., Aberdeen, J., Rumshisky, A., Pakhomov, S., Liu, H., Xu, H. (2015). Ease of adoption of clinical natural language processing software: An evaluation of five systems. Journal of Biomedical Informatics; S1532-0464(15):00148-3.

Ahmed, G.F., Marino, S.E., Brundage, R.C., Pakhomov, S.V., Leppik, I.E., Cloyd, J.C., Clark, A., Birnbaum, A.K. (2015). Pharmacokinetic-pharmacodynamic modelling of intravenous and oral topiramate and its effect on phonemic fluency in adult healthy volunteers. British Journal of Clinical Pharmacology; 79(5):820-30.

Wang, Y., Pakhomov, S, Ryan, J.O., Melton, G.B. (2015). Domain adaption of parsing for operative notes. Journal of Biomedical Informatics; 54:1-9.

Manohar, N., Adam, T.J., Pakhomov, S.V., Melton, G.B., Zhang, R. (2015). Evaluation of Herbal and Dietary Supplement Resource Term Coverage. Studies in Health Technology and Informatics; 216:785-9.

Zhang, R., Adam, T.J., Simon, G., Cairelli, M.J., Rindflesch, T., Pakhomov, S., Melton, G.B. (2015). Mining Biomedical Literature to Explore Interactions between Cancer Drugs and Dietary Supplements. In Proceedings of the AMIA Joint Summits on Translational Science; 2015:69-73.

2014

Pakhomov, S., Jones, D.T., Knopman, D. (2014). Language Networks Associated with Computerized Semantic Indices. NeuroImage; 104:125-37.

Moon, S., Pakhomov, S., Liu, N., Ryan, J.O., Melton, G.B. (2014). A sense inventory for clinical abbreviations and acronyms created using clinical notes and medical dictionary resources. Journal of American Medical Informatics Association; 2014; 21:299-307.

Zhang, R., Cairelli, M., Fiszman, M., Rosemblat, G., Kilicoglu, H., Rindflesch, T., Pakhomov, S., Melton, G. (2014). Using Semantic Predications to Uncover Drug-Drug Interactions in Clinical Data. Journal of Biomedical Informatics; 49:134-147.

Pakhomov, S., Hemmy, L. (2014). A computational linguistic measure of clustering behavior on semantic verbal fluency task predicts risk of future dementia in the Nun Study. Cortex; 55:97-106.

Zhang, R., Cairelli, M., Fiszman, M., Kilicoglu, H., Rindflesch, TC, Pakhomov, S., Melton, GB. (2014). Exploiting literature-derived knowledge and semantics to identify potential prostate cancer drugs. Cancer Informatics; Supp.1:103-11.

Masanz. J., Pakhomov, S., Xu, H., Wu, S., Chute, C., Liu, H. (2014). Open Source Clinical NLP - More than Any Single System. In Proceedings of the American Medical Informatics Association Joint Summits on Translational Science.

McInnes, B., Pedersen, T., Liu, Y., Melton, G., Pakhomov, S. (2014). U-path: An undirected path-based measure of semantic similarity. In Proceedings of the American Medical Informatics Association Symposium, Washington, DC.

Bill, R.; Pakhomov, S., Chen, E., Winden, T., Carter, E., Melton, G. (2014). Automated Extraction of Family History Information from Clinical Notes. In Proceedings of the American Medical Informatics Association Symposium, Washington, DC.

Wang, Y., Pakhomov, S., Dale, J., Chen, E., Melton, G. (2014). Application of HL7/LOINC Document Ontology to a University-affiliated Integrated Health System Research Clinical Data Repository. In Proceedings of the American Medical Informatics Association Joint Summits on Translational Science.

Wang, Y., Pakhomov, S., Ryan, J., Melton, G. (2014). Semantic Role Labeling for Modeling Surgical Procedures in Operative Notes. In Proceedings of the American Medical Informatics Association Symposium, Washington, DC.

Zhang, R., Pakhomov, S., Melton, GB. (2014). Longitudinal analysis of new information types in clinical notes. In Proceedings of the AMIA Joint Summits on Translational Science. 2014.

Zhang, R., Pakhomov, S., Lee, J., Melton, G. (2014). Using Language Models to Identify Relevant New Information in Inpatient Clinical Notes. In Proceedings of the American Medical Informatics Association Symposium, Washington, DC.

2013

Pakhomov, S., Marino, S., Birnbaum, AK, (2013). Quantification of Speech Dysfluency as a Marker of Medication-Induced Cognitive Impairment: An Application of Computerized Speech Analysis in Neuropharmacology. Computer Speech and Language. 27(1):116-134

Ryan, J., Pakhomov, S., Marino, S., Bernick, C., Banks, S. (2013). Computerized Analysis of a Verbal Fluency Test. Proceedings of the Assoication for Computational Linguistics (ACL) Symposium (Short paper).

Farri, O., Monsen, K., Pakhomov, S., Pieczkiewicz, D., Speedie, S., & Melton, G. (2013). Effects of Time Constraints on Clinician-Computer Interaction: A Study on Information Synthesis from EHR Notes. Journal of Biomedical Informatics; 46(6):1136-44.

Zhang, R., Pakhomov, S., Lee, J., Meltoon, G. (2013). Navigating Longitudinal Clinical Notes with an Automated Method for Detecting New Information. Proceedings of MedInfo Symposium, Copenhagen, Denmark.

Wang, Y., Pakhomov, S., Melton, G. (2013). Predicate Argument Structure Frames for Modeling Information in Operative Notes. Proceedings of MedInfo Symposium, Copenhagen, Denmark.

2012

Pakhomov, S., Hemmy, L., Lim, K. (2012). Automated Semantic Indices Related to Cognitive Function and Rate of Cognitive Decline. Neuropsychologia. 50(9):2165-2175.

Pakhomov, S., McInnes, B., Lamba, J., Liu, Y., Melton, G., Ghodke, Y., Bhise, N., Lamba, V., Birnbaum, AK. (2012). Using PharmGKB to train text mining approaches for identifying potential gene targets for pharmacogenomic studies. Journal of Biomedical Informatics; 45(5):862-869.

Marino, S. Pakhomov, S., Han, S., Anderson, K, Ding, M., Eberly, L. et al. (2012). The Effect of Topiramate Plasma Concentration on Linguistic Behavior, Verbal Recall and Working Memory. Epilepsy and Behavior; 24(3):365-372.

Moon S, Pakhomov S, Melton GB. (2012). 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.

Farri O, Pieckiewicz DS, Rahman AS, Adam TJ, Pakhomov SV, Melton GB. (2012). A Qualitative Analysis of EHR Clinical Document Synthesis by Clinicians. Proceedings of the American Medical Informatics Association Symposium. 2012:1211-20.

Wang Y, Pakhomov S, Burkart NE, Ryan JO, Melton GB. (2012). 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. (2012). Automated Assessment of Medical Training Evaluation Text. Proceedings of the American Medical Informatics Association Symposium. 2012:1459-68.

Liu Y, Bill R, Fiszman M, Rindflesch T, Pedersen T, Melton GB, Pakhomov SV. (2012). Using SemRep to Label Semantic Relations Extracted from Clinical Text. Proceedings of the American Medical Informatics Association Symposium. 2012:587-95.

Bill RW, Liu Y, McInnes BT, Melton GB, Pedersen T, Pakhomov S. (2012). Evaluating Semantic Relatedness and Similarity Measures with Standardized MedDRA Queries. Proceedings of the American Medical Informatics Association Symposium. 2012:43-50.

Farri O, Rahman A, Monsen KA, Zhang R, Pakhomov SV, Pieckiewicz DS, Speedie, SM, Melton GB. (2012). Impact of a prototype visualization tool for new information in EHR Clinical Documents. Applied Clinical Informatics; 3(4):404-18.

Liu, Y., McInnes, B., Pedersen, T., Melton, G.B., Pakhomov, S. (2012). Semantic Relatedness Study Using Second Order Co-Occurrence Vector Computed by Biomedical Corpora, UMLS and WordNet. In Proceedings of the 2nd ACM SIGHIT International Health Informatics Symposium (IHI 2012) (January, 2012). Miami, Florida. pp. 363-372.

Zhang, R., Pakhomov, S., Melton, G.B. (2012). Automated Identification of Relevant New Information in Clinical Narrative. In Proceedings of the 2nd ACM SIGHIT International Health Informatics Symposium (IHI 2012) (January, 2012). Miami, Florida.

2011

Pakhomov, S., Kaiser, E., Boley, D., Marino, S., Knopman, D., Birnbaum, A. (2011). Effects of age and dementia on temporal cycles in spontaneous speech fluency. Journal of Neurolinguistics; 24(6):619-635.

Pakhomov, S. and Kotlyar, M. (2011). Prosodic Correlates of Individual Physiological Response to Stress. In Proceedings of 12thAnnual Conference of the International Speech Communication Association (Interspeech) (Aug. 2011), Florence, Italy.

Pakhomov, S., Shah, N., Van Houten, H., Hanson, P., Smith, S. (2011). The Role of the Electronic Medical Record in the Assessment of Health Related Quality of Life. In Proceedings of the American Medical Informatics Symposium (November 2011), pp. 1080-8.

Zhang, R., Pakhomov, S., McInnes, B., Melton, G.B. (2011). Evaluating Measures of Redundancy in Clinical Texts. In Proceedings of the American Medical Informatics Symposium (November 2011), pp. 1612-20.

Moon, S.R., Pakhomov, S., Ryan, J., Melton, G.B. (2011). Automated Non-Alphanumeric Symbol Resolution in Clinical Text. In Proceedings of the American Medical Informatics Symposium (November 2011), pp. 979-86.

Wang, Y., Melton, G.B., Pakhomov, S. (2011). It’s about This and That: A Description of Anaphoric Expressions in Clinical Text. In Proceedings of the American Medical Informatics Symposium (November 2011), pp. 1471-80.

McInnes, B., Pedersen, T., Liu, Y., Pakhomov, S., Melton, G.B. (2011). Knowledge-based Method for Determining the Meaning of Ambiguous Biomedical Terms Using Information Content Measures of Similarity. In Proceedings of the American Medical Informatics Symposium (November 2011), pp. 895-904.

McInnes, B., Pedersen, T., Liu, Y., Pakhomov, S., Melton, G. (2011). Using Second-order Vectors in a Knowledge-based Method for Acronym Disambiguation. In Proceedings of the Fifteenth Conference on Computational Natural Language Learning (CoNLL 2011) (June 2011). Portland, OR, pp. 145-153.

2010

Pakhomov, S., Smith, G., Chacon, D., Feliciano, Y., Graff-Radford, N., Caselli, R., Knopman, D. (2010). Computerized analysis of speech and language to identify psycholinguistic correlates of fronto-temporal lobar degeneration. Cognitive and Behavioral Neurology; 23(3):165-177.

Pakhomov, S., Chacon, D., Wicklund, M., Gundel, J. (2010). Computerized Assessment of Syntactic Complexity in Alzheimer's Disease: a Case Study of Iris Murdoch's Writing. Behavioral Research Methods; 43(1):136-144.

Pakhomov, S. Shah, N., Penny Hanson, Balasubramaniam, S., Smith, S. (2010). Automated Monitoring of Aspirin Use in Populations at Risk for Cardiovascular Events. Informatics in Primary Care; 18(2):125-33.

Melton-Meaux,, Moon, R. McInness, B., Pakhomov. S. (2010). Automated Identification of Synonyms in Biomedical Acronym Sense Inventories. In proceedings of Louhi 02 Workshop at the North American Association of Computational Linguistics, Los Angeles, CA.

Pakhomov, S., Pedersen, T., McInnes, B., Melton, G., Ruggieri, A., Chute, C. (2010). Towards a framework for developing semantic relatedness reference standards. Journal of Biomedical Informatics; 44(2):251-265.

Pakhomov, S. McInnes, B., Adam, T., Liu, Y., Pedersen, T., Melton, G. (2010). Semantic Similarity and Relatedness between Clinical Terms: An Experimental Study. In Proceedings of the American Medical Informatics Symposium (November 2010), pp. 572-576.

2009

Pakhomov, S., Smith, G., Marino, S., Birnbaum, A., Graff-Radford, N., Caselli, R., Boeve, B., Knopman, D. (2009). A computerized technique to assess language use patterns in patients with frontotemporal dementia. Journal of Neurolinguistics. 23(2):127-144.

Melton-Meaux, G., Raman, N., Chen, E., Sarkar, I., Pakhomov, S., Madoff, R. (2009) Evaluation of Family History Information within Clinical Documents and Adequacy of HL7 Clinical Statement and Clinical Genomics Family History Models for Its Representation. Journal of American Medical Informatics Association; 17:337-340.

McInnes, B., Pedersen, T., and Pakhomov, S. (2009). UMLS-Interface and UMLS-Similarity: Open Source Software for Measuring Paths and Semantic Similarity. To appear in Proceedings of the American Medical Informatics Symposium (November 2009). San Francisco, CA.

Melton-Meaux, G., Raman, N., Chen, E., Sarkar, I., Pakhomov, S., Madoff, R. (2009). Evaluation of Family History Information within Clinical Documents and Adequacy of HL7 Clinical Statement and Clinical Genomics Family History Models for Its Representation. In Proceedings of the American Medical Informatics Symposium (November 2009).

2008

Schommer, JC., Worley, MM., Kjos, AL., Pakhomov, S., Schondelmeyer, SW. (2008). A Thematic Analysis for How Patients, Prescribers, Experts, and Patient Advocates View the Prescription Choice Process. Research in Social and Administrative Pharmacy; 5(2):154-169.

Pakhomov, S., Jacobsen, S., Chute, C., & Roger, V. (2008). Agreement between Patient-reported Symptoms and their Documentation in the Medical Record. American Journal of Managed Care; 14(8):530-539.

Pakhomov, S., Shah, N., Hanson, P., Balasubramaniam, S., & Smith, S. (2008). Automatic Quality of Life Prediction Using Electronic Medical Records. In Proceedings of the American Medical Informatics Association Annual Symposium, November 2008, Washington, DC, pp. 545-549.

Pakhomov, S., Richardson, J., Finholt-Daniel, M., & Sales, G. (2008). Forced-alignment and Edit-Distance Scoring for Vocabulary Tutoring. In Proceedings of Text Speech and Dialogue (TSD) Conference, September 2008, Brno, Czech Republic, (Lecture Notes in Artificial Intelligence): 443-450.

2007

Pakhomov, S., Bjornsen, S., Hanson, P., & Smith, S. (2007). Quality Performance Measurement Using the Text of Electronic Medical Records. Medical Decisions Making; 28(4):462-470.

Pakhomov, S., Hanson, P., Bjornsen, S., & Smith, S. (2007). Automatic Classification of Foot Examination Findings using Statistical Natural Language Processing and Machine Learning Journal of the American Medical Informatics Association; 15(2):198-202.

Pakhomov, S., Hemingway, H., Weston, S., Jacobsen, S., Rodeheffer, R., & Roger, V. (2007). Epidemiology of Angina Pectoris: Role of Natural Language Processing of the Medical Record. American Heart Journal; 153(4):666-673.

Pakhomov, S., Weston, S., Jacobsen, S., Chute, C., Meverden, R., & Roger, V. (2007). Electronic Medical Records for Clinical Research: Application to the Identification of Heart Failure. American Journal of Managed Care; 13:281-288.

McInnes, B. Pedersen, T. & Pakhomov. S. (2007). Determining the Syntactic Structure of Medical Terms in Clinical Notes. In Proceedings of the BioNLP workshop at the Association for Computational Linguistics Symposium, June 2007, Prague, Czech Republic, pp. 9-16.

2006

Bursi, F, Weston, SA, Redfield, MM, Jacobsen, SJ, Pakhomov, S, Nkomo, VT, Meverden, RA, Roger, VL. (2006). Systolic and Diastolic Heart Failure in the Community. JAMA; 296(18):2209-2216.

Pakhomov, S, Buntrock, J, Chute, CG. (2006). Improving the efficiency of manual classification of clinical diagnoses with example-based and machine learning techniques. Journal of American Medical Informatics Association;13:516-525.

Pedersen, T, Pakhomov, S, Patwardhan, S. (2006). Measures of Semantic Similarity and Relatedness in the Biomedical Domain. Journal of Biomedical Informatics; 40(3):288-299.

Pakhomov, S. and Chute, C. (2006). A Hybrid Approach to Determining Modification of Clinical Diagnoses. In Proceedings of the American Medical Informatics Association Annual Symposium; pp. 609-613.

Joshi, M., Pakhomov, S., Pedersen, T. and Chute, C. (2006). Supervised Acronym Disambiguation in Clinical Discourse. In Proceedings of the American Medical Informatics Association Annual Symposium; pp. 589-593.

2005

Pakhomov, S., Coden, A., & Chute, C. G. (2005). Developing a Corpus of Clinical Notes Manually Annotated for Part-of-Speech. International Journal of Medical Informatics (Special Issue on Natural Language Processing in Biomedical Applications, 75(6):418-29).

Pakhomov, S., Buntrock, J., & Chute, C. G. (2005). Prospective Recruitment of Patients with Congestive Heart Failure using an Ad-hoc Binary Classifier. Journal of Biomedical Informatics; 38(2):145-153.

Coden, A., Pakhomov, S., Ando, R., Duffy, P., & Chute, C. G. (2005). Domain-specific language models and lexicons for tagging. Journal of Biomedical Informatics; 38(2):422-430.

Rindflesch, T. C., Pakhomov, S., Fiszman, M., Kilicoglu, H., & Sanches, V. (2005). Medical Facts to Support Inferencing in Natural Language Processing. In Proceedings of the American Medical Informatics Association Annual Symposium, Washington, DC.

Kogan, Y., Collier, N., Pakhomov, S., & Krauthammer, M. (2005). Towards Semantic Role Labeling & IE in the Medical Literature. In Proceedings of the American Medical Informatics Association Annual Symposium, Washington, DC.

Pakhomov, S., Pedersen, T., & Chute, C. G. (2005). Abbreviation and Acronym Disambiguation in Clinical Discourse. In Proceedings of the American Medical Informatics Association Annual Symposium, Washington, DC.

Pakhomov, S., Buntrock, J., & Duffy, P. (2005). High Throughput Modularized NLP System for Clinical Text (Interactive Poster). In Proceedings of the 43rd Annual Meeting of the Association for Computational Linguistics, Ann Arbor, MI.

2004

Pakhomov, S., Coden, A., & Chute, C. G. (2004). Creating a Test Corpus of Clinical Notes Manually Tagged for Part-of-Speech Information (Poster). Biomedical NLP Workshop at Computational Linguistics Conference: Geneva, Switzerland. ( PDF )

Pakhomov, S., Buntrock, J., & Chute, C. G. (2004). Using Compound Codes for Automatic Classification of Clinical Diagnoses. In Proceedings of the Medinfo, San Francisco, CA. ( PDF )

Ruggieri, A., & Pakhomov, S. (2004). A Corpus Driven Approach Applying the 'Frame Semantic' Method for Modeling Functional Status Terminology. In Proceedings of the Medinfo, San Francisco, CA. ( PDF )

Thomson-McInness, B., Pakhomov, S., Pedersen, T., & Chute, C. G. (2004). Automating Spelling Correction Tools Using Bigram Statistics. Medinfo Symposium: San Francisco, CA.

2003

Pakhomov, S., Buntrock, J., & Chute, C. G. (2003). Identification of Patients with Congestive Heart Failure Using a Binary Classifier. In Proceedings of the Biomedical NLP Workshop at the 41st Meeting of the Association for Computational Linguistics, Sapporo, Japan. ( PDF )

Bodenreider, O., & Pakhomov, S. (2003). Exploring Adjectival Modification in Biomedical Terms across Two Genres. In Proceedings of the Biomedical NLP Workshop at the 41st Meeting of the Association for Computational Linguistics, Sapporo, Japan. ( PDF )

2002

Pakhomov, S., Ruggieri, A., & Chute, C. G. (2002). Maximum Entropy Modeling for Mining Patient Medication Status from Free Text. In Proceedings of the American Medical Informatics Association Symposium, San Antonio, TX. ( PDF )

Pakhomov, S. (2002). Semi-Supervised Maximum Entropy Based Approach to Acronym and Abbreviation Normalization in Medical Texts. In Proceedings of the 40th Meeting of the Association for Computational Linguistics, Philadelphia, PA. ( PDF )

2001

Pakhomov. S. (2001). Hesitations and Cognitive Status of Noun Phrase Referents in Spontaneous Discourse. (PhD Thesis) University of Minnesota. ( PDF )

Pakhomov, S., Schonwetter, M., & Bachenko, J. (2001). Generating Training Data for Medical Dictations. In Proceedings of the The 2nd Meeding of the North American Chapter of the Association for Computational Linguistics, Pittsburgh, PA. ( PDF )

2000

Pakhomov, S., Schonwetter, M and Bachenko, J. (2000). Dynamic Partial Transcription Recycling System. (Demonstration) In Proceedings of the ANLP/NAACL 2000 Symposium, Seattle, WA. ( PDF )

1999

Pakhomov, S. (1999). Modeling Filled Pauses in Medical Dictations (Student Paper). In Proceedings of the 37th Annual Meeting of the Association for Computational Linguistics, College Park, MD. ( PDF )

Pakhomov, S., & Savova, G. (1999). Filled Pause Distribution and Modeling in Quasi-spontaneous Speech. In Proceedings of the Disfluency Workshop at International Congress of Phonetic Sciences, Berkely, CA. ( PDF )

 


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