Publications

  1. Wang Y, Mehrabi S, Sohn S, Atkinson EJ, Amin S, Liu H. Natural language processing of radiology reports for identification of skeletal site-specific fractures. BMC Med Inform Decis Mak. 2019 Apr 4; 19 (Suppl 3):73 Epub 2019 Apr 04
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  2. Wang Y, Sohn S, Liu S, Shen F, Wang L, Atkinson EJ, Amin S, Liu H. A clinical text classification paradigm using weak supervision and deep representation. BMC Med Inform Decis Mak. 2019 Jan 7; 19 (1):1 Epub 2019 Jan 07
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  3. Seol HY, Sohn S, Liu H, Wi CI, Ryu E, Park MA, Juhn YJ. Early Identification of Childhood Asthma: The Role of Informatics in an Era of Electronic Health Records. Front Pediatr. 2019; 7:113 Epub 2019 Apr 02
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  4. Chen D, Afzal N, Sohn S, Habermann EB, Naessens JM, Larson DW, Liu H. Postoperative bleeding risk prediction for patients undergoing colorectal surgery. Surgery. 2018 Dec; 164 (6):1209-1216 Epub 2018 July 20
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  5. Wu S, Liu S, Sohn S, Moon S, Wi CI, Juhn Y, Liu H. Modeling asynchronous event sequences with RNNs. J Biomed Inform. 2018 Jul; 83:167-177 Epub 2018 June 05
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  6. Wi CI, Krusemark EA, Voge G, Sohn S, Liu H, Liu H, Ryu E, Park MA, Castro-Rodriguez JA, Juhn YJ. Usefulness of asthma predictive index in ascertaining asthma status of children using medical records: An explorative study. Allergy. 2018 Jun; 73 (6):1276-1283 Epub 2018 Feb 07
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  7. Sohn S, Wi CI, Wu ST, Liu H, Ryu E, Krusemark E, Seabright A, Voge GA, Juhn YJ. Ascertainment of asthma prognosis using natural language processing from electronic medical records. J Allergy Clin Immunol. 2018 Jun; 141 (6):2292-2294.e3 Epub 2018 Feb 10
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  8. Afzal N, Mallipeddi VP, Sohn S, Liu H, Chaudhry R, Scott CG, Kullo IJ, Arruda-Olson AM. Natural language processing of clinical notes for identification of critical limb ischemia. Int J Med Inform. 2018 Mar; 111:83-89 Epub 2017 Dec 28
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  9. Kaur H, Sohn S, Wi CI, Ryu E, Park MA, Bachman K, Kita H, Croghan I, Castro-Rodriguez JA, Voge GA, Liu H, Juhn YJ. Automated chart review utilizing natural language processing algorithm for asthma predictive index. BMC Pulm Med. 2018 Feb 13; 18 (1):34
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  10. Wang Y, Wang L, Rastegar-Mojarad M, Moon S, Shen F, Afzal N, Liu S, Zeng Y, Mehrabi S, Sohn S, Liu H. Clinical information extraction applications: A literature review. J Biomed Inform. 2018 Jan; 77:34-49 Epub 2017 Nov 21
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  11. Wi CI, Sohn S, Ali M, Krusemark E, Ryu E, Liu H, Juhn YJ. Natural Language Processing for Asthma Ascertainment in Different Practice Settings. J Allergy Clin Immunol Pract. 2018 Jan - Feb; 6 (1):126-131 Epub 2017 June 19
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  12. Hong N, Wen A, Shen F, Sohn S, Liu S, Liu H, Jiang G. Integrating Structured and Unstructured EHR Data Using an FHIR-based Type System: A Case Study with Medication Data. AMIA Jt Summits Transl Sci Proc. 2018; 2017:74-83 Epub 2018 May 18
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  13. Wang Y, Mehrabi S, Sohn S, Atkinson E, Amin S, Liu H. Automatic extraction of major osteoporotic fractures from radiology reports using natural language processing Proceedings - 2018 IEEE International Conference on Healthcare Informatics Workshops, ICHI-W 2018. 2018; 64-5
  14. Hong N, Wen A, Mojarad MR, Sohn S, Liu H, Jiang G. Standardizing Heterogeneous Annotation Corpora Using HL7 FHIR for Facilitating their Reuse and Integration in Clinical NLP. AMIA Annu Symp Proc. 2018; 2018:574-583 Epub 2018 Dec 05
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  15. Rastegar-Mojarad M, Sohn S, Wang L, Shen F, Bleeker TC, Cliby WA, Liu H. Need of informatics in designing interoperable clinical registries. Int J Med Inform. 2017 Dec; 108:78-84 Epub 2017 Oct 10
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  16. Sohn S, Wang Y, Wi CI, Krusemark EA, Ryu E, Ali MH, Juhn YJ, Liu H. Clinical documentation variations and NLP system portability: a case study in asthma birth cohorts across institutions. J Am Med Inform Assoc. 2017 Nov 30 [Epub ahead of print]
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  17. Rastegar-Mojarad M, Lovely JK, Pankratz J, Sohn S, Ihrke DM, Merchea A, Larson DW, Liu H. Using unstructured data to identify readmitted patients 2017 IEEE International Conference on Healthcare Informatics (ICHI).2017;1-4.
  18. Wi CI, Sohn S, Rolfes MC, Seabright A, Ryu E, Voge G, Bachman KA, Park MA, Kita H, Croghan IT, Liu H, Juhn YJ. Application of a Natural Language Processing Algorithm to Asthma Ascertainment. An Automated Chart Review. Am J Respir Crit Care Med. 2017 Aug 15; 196 (4):430-437
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  19. Afzal N, Sohn S, Abram S, Scott CG, Chaudhry R, Liu H, Kullo IJ, Arruda-Olson AM. Mining peripheral arterial disease cases from narrative clinical notes using natural language processing. J Vasc Surg. 2017 Jun; 65 (6):1753-1761 Epub 2017 Feb 08
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  20. Sohn S, Larson DW, Habermann EB, Naessens JM, Alabbad JY, Liu H. Detection of clinically important colorectal surgical site infection using Bayesian network. J Surg Res. 2017 Mar; 209:168-173 Epub 2016 Oct 05
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  21. Afzal N, Sohn S, Scott CG, Liu H, Kullo IJ, Arruda-Olson AM. Surveillance of Peripheral Arterial Disease Cases Using Natural Language Processing of Clinical Notes. AMIA Jt Summits Transl Sci Proc. 2017; 2017:28-36 Epub 2017 July 26
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  22. Shen F, Sohn S, Rastegar-Mojarad M, Liu S, Pankratz JJ, Hatton MA, Sowada N, Shrestha OK, Shurson SL, Liu H. Populating Physician Biographical Pages Based on EMR Data. AMIA Jt Summits Transl Sci Proc. 2017; 2017:522-530 Epub 2017 July 26
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  23. Sohn S, Wi CI, Juhn YJ, Liu H. Analysis of Clinical Variations in Asthma Care Documented in Electronic Health Records Between Staff and Resident Physicians. Stud Health Technol Inform. 2017; 245:1170-1174
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  24. Li D, Wang Z, Wang L, Sohn S, Shen F, Murad MH, Liu H. A Text-Mining Framework for Supporting Systematic Reviews. Am J Inf Manag. 2016 Nov; 1 (1):1-9 Epub 2016 Aug 31
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  25. Wu ST, Wi C, Sohn S, Liu H, Juhn YJ. Staggered NLP-assisted refinement for Clinical Annotations of Chronic Disease Events, Language Resources and Evaluation Proceedings of the Tenth International Conference on Language Resources and Evaluation .2016;
  26. Shen F, Liu H, Sohn S, Larson DW, Lee Y. Predicate Oriented Pattern Analysis for Biomedical Knowledge Discovery. Intell Inf Manag. 2016 May; 8 (3):66-85
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  27. Afzal N, Sohn S, Abram S, Liu H, Kullo IJ, Arruda-Olson AM. Identifying Peripheral Arterial Disease Cases Using Natural Language Processing of Clinical Notes. IEEE EMBS Int Conf Biomed Health Inform. 2016 Feb; 2016:126-131 Epub 2016 Apr 21
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  28. Kaggal VC, Elayavilli RK, Mehrabi S, Pankratz JJ, Sohn S, Wang Y, Li D, Rastegar MM, Murphy SP, Ross JL, Chaudhry R, Buntrock JD, Liu H. Toward a Learning Health-care System - Knowledge Delivery at the Point of Care Empowered by Big Data and NLP. Biomed Inform Insights. 2016; 8 (Suppl 1):13-22 Epub 2016 June 23
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  29. Wu ST, Wi CI, Sohn S, Liu H, Juhn YJ. Staggered NLP-assisted refinement for clinical annotations of chronic disease events Proceedings of the 10th International Conference on Language Resources and Evaluation, LREC 2016. 2016; 426-9
  30. Bielinski SJ, Pathak J, Carrell DS, Takahashi PY, Olson JE, Larson NB, Liu H, Sohn S, Wells QS, Denny JC, Rasmussen-Torvik LJ, Pacheco JA, Jackson KL, Lesnick TG, Gullerud RE, Decker PA, Pereira NL, Ryu E, Dart RA, Peissig P, Linneman JG, Jarvik GP, Larson EB, Bock JA, Tromp GC, de Andrade M, Roger VL. A Robust e-Epidemiology Tool in Phenotyping Heart Failure with Differentiation for Preserved and Reduced Ejection Fraction: the Electronic Medical Records and Genomics (eMERGE) Network. J Cardiovasc Transl Res. 2015 Nov; 8 (8):475-83 Epub 2015 July 21
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  31. Mehrabi S, Krishnan A, Sohn S, Roch AM, Schmidt H, Kesterson J, Beesley C, Dexter P, Max Schmidt C, Liu H, Palakal M. DEEPEN: A negation detection system for clinical text incorporating dependency relation into NegEx. J Biomed Inform. 2015 Apr; 54:213-9 Epub 2015 Mar 16
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  32. Jiang G, Sohn S, Zimmermann MT, Wang C, Liu H, Chute CG. Drug Normalization for Cancer Therapeutic and Druggable Genome Target Discovery. AMIA Jt Summits Transl Sci Proc. 2015; 2015:72-6 Epub 2015 Mar 25
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  33. Li D, Rastegar Mojarad M, Li Y, Sohn S, Mehrabi S, Komandur Elayavilli R, Yu Y, Liu H. A Frequency-based Strategy of Obtaining Sentences from Clinical Data Repository for Crowdsourcing. Stud Health Technol Inform. 2015; 216:1033-4
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  34. Shen F, Liu H, Sohn S, Larson DW, Lee Y. BmQGen: Biomedical query generator for knowledge discovery Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015. 2015; 1092-7.
  35. Li D, Rastegar-Mojarad M, Elayavilli RK, Wang Y, Mehrabi S, Yu Y, Sohn S, Li Y, Afzal N, Liu H. A frequency-filtering strategy of obtaining PHI-free sentences from clinical data repository BCB 2015 - 6th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics. 2015; 315-24.
  36. Mehrabi S, Sohn S, Li D, Pankratz JJ, Therneau T, St Sauver JL, Liu H, Palakal M. Temporal pattern and association discovery of diagnosis codes using deep learning Proceedings - 2015 IEEE International Conference on Healthcare Informatics, ICHI 2015. 2015; 408-16.
  37. Wu ST, Juhn YJ, Sohn S, Liu H. Patient-level temporal aggregation for text-based asthma status ascertainment. J Am Med Inform Assoc. 2014 Sep-Oct; 21 (5):876-84 Epub 2014 May 15
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  38. Sohn S, Clark C, Halgrim SR, Murphy SP, Chute CG, Liu H. MedXN: an open source medication extraction and normalization tool for clinical text. J Am Med Inform Assoc. 2014 Sep-Oct; 21(5):858-65. Epub 2014 Mar 17.
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  39. Khaleghi M, Isseh IN, Jouni H, Sohn S, Bailey KR, Kullo IJ. Family history as a risk factor for carotid artery stenosis. Stroke. 2014 Aug; 45: (8)2252-6.
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  40. Liu H, Sohn S, Murphy S, Lovely J, Burton M, Naessens J, Larson DW. Facilitating post-surgical complication detection through sublanguage analysis. AMIA Jt Summits Transl Sci Proc. 2014; 2014:77-82 Epub 2014 Apr 07
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  41. Sohn S, Liu H. Analysis of medication and indication occurrences in clinical notes. AMIA Annu Symp Proc. 2014; 2014:1046-55 Epub 2014 Nov 14
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  42. Pathak J, Bailey KR, Beebe CE, Bethard S, Carrell DC, Chen PJ, Dligach D, Endle CM, Hart LA, Haug PJ, Huff SM, Kaggal VC, Li D, Liu H, Marchant K, Masanz J, Miller T, Oniki TA, Palmer M, Peterson KJ, Rea S, Savova GK, Stancl CR, Sohn S, Solbrig HR, Suesse DB, Tao C, Taylor DP, Westberg L, Wu S, Zhuo N, Chute CG. Normalization and standardization of electronic health records for high-throughput phenotyping: the SHARPn consortium. J Am Med Inform Assoc. 2013 Dec; 20 (e2):e341-8 Epub 2013 Nov 04
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  43. Wu ST, Sohn S, Ravikumar KE, Wagholikar K, Jonnalagadda SR, Liu H, Juhn YJ. Automated chart review for asthma cohort identification using natural language processing: an exploratory study. Ann Allergy Asthma Immunol. 2013 Nov; 111 (5):364-9 Epub 2013 Aug 12
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  44. Sohn S, Wagholikar KB, Li D, Jonnalagadda SR, Tao C, Komandur Elayavilli R, Liu H. Comprehensive temporal information detection from clinical text: medical events, time, and TLINK identification. J Am Med Inform Assoc. 2013 Sep-Oct; 20: (5)836-42.
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  45. Sohn S, Clark C, Halgrim SR, Murphy SP, Jonnalagadda SR, Wagholikar KB, Wu ST, Chute CG, Liu H. Analysis of cross-institutional medication description patterns in clinical narratives. Biomed Inform Insights. 2013; 6 (Suppl 1):7-16 Epub 2013 June 24
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  46. Wagholikar K, Sohn S, Wu S, Kaggal V, Buehler S, Greenes RA, Wu TT, Larson D, Liu H, Chaudhry R, Boardman L. Workflow-based Data Reconciliation for Clinical Decision Support: Case of Colorectal Cancer Screening and Surveillance. AMIA Summits Transl Sci Proc. 2013; 2013:269-73. Epub 2013 Mar 18.
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  47. Sohn S, Ye Z, Liu H, Chute CG, Kullo IJ. Identifying Abdominal Aortic Aneurysm Cases and Controls using Natural Language Processing of Radiology Reports. AMIA Summits Transl Sci Proc. 2013; 2013:249-53. Epub 2013 Mar 18.
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  48. Liu H, Bielinski SJ, Sohn S, Murphy S, Wagholikar KB, Jonnalagadda SR, Ravikumar KE, Wu ST, Kullo IJ, Chute CG. An information extraction framework for cohort identification using electronic health records. AMIA Summits Transl Sci Proc. 2013; 2013:149-53. Epub 2013 Mar 18
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  49. Li DC, Ning X, Sohn S, Chute CG, Cohen K, Liu H. Incorporating Topic Modeling Features For Clinical Concept Assertion Classification. The Proc of the 5th International Symposium on Languages in Biology and Medicine. 2013.
  50. Liu H, Wagholikar K, Jonnalagadda S, Sohn S. MedTagger for concept mention detection and normalization. In Proceedings of ShARe/CLEF eHealth Evaluation. 2013.
  51. Liu H, Wagholikar K, Jonnalagadda S, Sohn S. Integrated cTAKES for concept mention detection and normalization. CEUR Workshop Proceedings. 2013; 1179.
  52. Sohn S, Clark C, Halgrim S, et al. Analysis of Cross-Institutional Medication Information Annotation in Clinical Notes. Computational Semantics in Clinical Text Workshop Potsdam, Germany. 2013.
  53. Jonnalagadda SR, Li D, Sohn S, Wu ST, Wagholikar K, Torii M, Liu H. Coreference analysis in clinical notes: a multi-pass sieve with alternate anaphora resolution modules. J Am Med Inform Assoc. 2012 Sep-Oct; 19 (5):867-74 Epub 2012 June 16
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  54. Liu H, Wu ST, Li D, Jonnalagadda S, Sohn S, Wagholikar K, Haug PJ, Huff SM, Chute CG. Towards a semantic lexicon for clinical natural language processing. AMIA Annu Symp Proc. 2012; 2012:568-76 Epub 2012 Nov 03
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  55. Wagholikar K, Sohn S, Wu S, Kaggal V, Buehler S, Greenes R, Wu TT, Larson D, Liu H, Chaudhry R, Boardman L. Clinical decision support for colonoscopy surveillance using natural language processing. Proceedings - 2012 IEEE 2nd Conference on Healthcare Informatics, Imaging and Systems Biology, HISB 2012. 2012:12-21.
  56. Sohn S, Murphy SP, Jonnalagadda SR, Wagholikar K, Wu ST, Chute CG, Liu H, Halgrim S. Systematic analysis of cross-institutional medication description patterns in clinical notes. Proceedings - 2012 IEEE 2nd Conference on Healthcare Informatics, Imaging and Systems Biology, HISB 2012. 2012:118.
  57. Sohn S, Wu S, Chute CG. Dependency Parser-based Negation Detection in Clinical Narratives. AMIA Jt Summits Transl Sci Proc. 2012; 2012:1-8 Epub 2012 Mar 19
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  58. Sohn S, Torii M, Li D, Wagholikar K, Wu S, Liu H. A hybrid approach to sentiment sentence classification in suicide notes. Biomed Inform Insights. 2012; 5 (Suppl. 1):43-50 Epub 2012 Jan 30
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  59. Sohn S, Kocher JP, Chute CG, Savova GK. Drug side effect extraction from clinical narratives of psychiatry and psychology patients. J Am Med Inform Assoc. 2011 Dec; 18 Suppl 1:i144-9 Epub 2011 Sept 21
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  60. Jonnalagadda S, Li D, Sohn S, Wu S, Wagholikar K, Torii M, Liu H. Coreference analysis in clinical notes: A multi-pass sieve with alternate anaphora resolution modules. Proceedings of the i2b2/VA/Cincinnati. 2011 Nov.
  61. Wu S, Wagholikar K, Sohn S, Kaggal V, Liu H. Empirical ontologies for cohort identification. NIST Special Publication. 2011.
  62. Sohn S, Murphy SP, Masanz JJ, Kocher JP, Savova GK. Classification of medication status change in clinical narratives. AMIA Annu Symp Proc. 2010 Nov 13; 2010:762-6
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  63. Savova GK, Masanz JJ, Ogren PV, Zheng J, Sohn S, Kipper-Schuler KC, Chute CG. Mayo clinical Text Analysis and Knowledge Extraction System (cTAKES): architecture, component evaluation and applications. J Am Med Inform Assoc. 2010 Sep-Oct; 17 (5):507-13
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  64. Sohn S, Savova GK. Mayo clinic smoking status classification system: extensions and improvements. AMIA Annu Symp Proc. 2009 Nov 14; 2009:619-23
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  65. Sohn S, Comeau DC, Kim W, Wilbur J. Term Based Active Learning for Naive Bayes Document Classification. The Open Information Systems Journal.2009;3:54-67.
  66. Sohn S, Corneau DC, Kim W, Wilbur, WJ. Abbreviation Definition Identification Based on Automatic Precision Estimates. BMC Bioinformatics. 2008; Vol 9:402.
  67. Sohn S, Kim W, Corneau DC, Wilbur WJ. Optimal Training Sets for Bayesian Predication of MeSH Assignment. Journal of American Medical Informatics Association, 546-553,. 2008; Vol 15: (4)
  68. Sohn S, Dagli CH. Ensemble of Evolving Neural Networks in Classification. Neural Processing Letters. 2004; Vol 19(3):191-203.
  69. Sohn S, Dagli CH. Combining Evolving Neural Network Classifiers Using Bagging. Proc. of IEEE International Joint Confernece on Neural Networks. 2003 Jul; Vol 4:3218-22.
  70. Sohn S, Dagli CH. Evolving Multiple Neural Networks. Intelligent Engineering Systems through Artificial Neural Networks. 2002 Nov; 12:9-14.
  71. Sohn S, Dagli CH. Adaptable multiple neural networks using evolutionary computation. Proc. of SPIE - Applications and Science of Computational Intelligency V. 2002 Apr; Vol 4739:141-9.
  72. Sohn S, Dagli CH. Sample Selection Through Class Probability and Possibility in Support Vector Machines. Intelligent engineering Systmes through Artificial Neural Networks. 2001 Nov; 11.
  73. Keller JM, Gader PD, Sohn S, Caldwell CW. Soft counting networks for bone marrow differentials. Proc. of IEEE International Conference on Systems, Man and Cybernetics. 2001 Oct; Vol 5:3425-28.
  74. Sohn S, Dagli CH. Advantages of using fuzzy class memberships in self-organization map and support vector machines. Proc. of International Joint Conference on Neural Networks. 2001 Jul; Vol 3:1886-90.
  75. Sohn S, Dagli CH. Self-organizing map with fuzzy class memberships. Proc. of SPIE - Applications and Science of Computational Intelligence V. 2001 Apr; Vol 4390:150-7.