Research

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Guergana Savova, PhD

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Lab:
Natural Language Processing Laboratory
Program:
Computational Health Informatics Program (CHIP)
Department:
Medicine Research
Hospital Title:
Associate Scientific Researcher
Academic Title:
Assistant Professor, Harvard Medical School
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Publications

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  1. Hochheiser H, Castine M, Harris D, Savova G, Jacobson RS. An information model for computable cancer phenotypes. BMC Med Inform Decis Mak. 2016 Sep 15; 16(1):121.
  2. Lingren T, Chen P, Bochenek J, Doshi-Velez F, Manning-Courtney P, Bickel J, Wildenger Welchons L, Reinhold J, Bing N, Ni Y, Barbaresi W, Mentch F, Basford M, Denny J, Vazquez L, Perry C, Namjou B, Qiu H, Connolly J, Abrams D, Holm IA, Cobb BA, Lingren N, Solti I, Hakonarson H, Kohane IS, Harley J, Savova G. Electronic Health Record Based Algorithm to Identify Patients with Autism Spectrum Disorder. PLoS One. 2016; 11(7):e0159621.
  3. Lingren T, Thaker V, Brady C, Namjou B, Kennebeck S, Bickel J, Patibandla N, Ni Y, Van Driest SL, Chen L, Roach A, Cobb B, Kirby J, Denny J, Bailey-Davis L, Williams MS, Marsolo K, Solti I, Holm IA, Harley J, Kohane IS, Savova G, Crimmins N. Developing an Algorithm to Detect Early Childhood Obesity in Two Tertiary Pediatric Medical Centers. Appl Clin Inform. 2016 Jul 20; 7(3):693-706.
  4. Mowery DL, South BR, Christensen L, Leng J, Peltonen LM, Salanterä S, Suominen H, Martinez D, Velupillai S, Elhadad N, Savova G, Pradhan S, Chapman WW. Normalizing acronyms and abbreviations to aid patient understanding of clinical texts: ShARe/CLEF eHealth Challenge 2013, Task 2. J Biomed Semantics. 2016 Jul 01; 7:43.
  5. Ananthakrishnan AN, Cagan A, Cai T, Gainer VS, Shaw SY, Savova G, Churchill S, Karlson EW, Kohane I, Liao KP, Murphy SN. Comparative Effectiveness of Infliximab and Adalimumab in Crohn's Disease and Ulcerative Colitis. Inflamm Bowel Dis. 2016 Apr; 22(4):880-5.
  6. Dligach D, Miller T, Savova GK. Semi-supervised Learning for Phenotyping Tasks. AMIA Annu Symp Proc. 2015; 2015:502-11.
  7. Liao KP, Ananthakrishnan AN, Kumar V, Xia Z, Cagan A, Gainer VS, Goryachev S, Chen P, Savova GK, Agniel D, Churchill S, Lee J, Murphy SN, Plenge RM, Szolovits P, Kohane I, Shaw SY, Karlson EW, Cai T. Methods to Develop an Electronic Medical Record Phenotype Algorithm to Compare the Risk of Coronary Artery Disease across 3 Chronic Disease Cohorts. PLoS One. 2015; 10(8):e0136651.
  8. Kimia AA, Savova G, Landschaft A, Harper MB. An Introduction to Natural Language Processing: How You Can Get More From Those Electronic Notes You Are Generating. Pediatr Emerg Care. 2015 Jul; 31(7):536-41.
  9. Liao KP, Cai T, Savova GK, Murphy SN, Karlson EW, Ananthakrishnan AN, Gainer VS, Shaw SY, Xia Z, Szolovits P, Churchill S, Kohane I. Development of phenotype algorithms using electronic medical records and incorporating natural language processing. BMJ. 2015 Apr 24; 350:h1885.
  10. Haug PJ, Wu X, Ferraro JP, Savova GK, Huff SM, Chute CG. Developing a section labeler for clinical documents. AMIA Annu Symp Proc. 2014; 2014:636-44.
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  12. Pradhan S, Elhadad N, South BR, Martinez D, Christensen L, Vogel A, Suominen H, Chapman WW, Savova G. Evaluating the state of the art in disorder recognition and normalization of the clinical narrative. J Am Med Inform Assoc. 2015 Jan; 22(1):143-54.
  13. Carrell DS, Halgrim S, Tran DT, Buist DS, Chubak J, Chapman WW, Savova G. Carrell et al. respond to "Observational research and the EHR". Am J Epidemiol. 2014 Mar 15; 179(6):762-3.
  14. Carrell DS, Halgrim S, Tran DT, Buist DS, Chubak J, Chapman WW, Savova G. Using natural language processing to improve efficiency of manual chart abstraction in research: the case of breast cancer recurrence. Am J Epidemiol. 2014 Mar 15; 179(6):749-58.
  15. Xia Z, Secor E, Chibnik LB, Bove RM, Cheng S, Chitnis T, Cagan A, Gainer VS, Chen PJ, Liao KP, Shaw SY, Ananthakrishnan AN, Szolovits P, Weiner HL, Karlson EW, Murphy SN, Savova GK, Cai T, Churchill SE, Plenge RM, Kohane IS, De Jager PL. Modeling disease severity in multiple sclerosis using electronic health records. PLoS One. 2013; 8(11):e78927.
  16. 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.
  17. Dligach D, Bethard S, Becker L, Miller T, Savova GK. Discovering body site and severity modifiers in clinical texts. J Am Med Inform Assoc. 2014 May-Jun; 21(3):448-54.
  18. McMurry AJ, Fitch B, Savova G, Kohane IS, Reis BY. Improved de-identification of physician notes through integrative modeling of both public and private medical text. BMC Med Inform Decis Mak. 2013 Oct 02; 13:112.
  19. Lin C, Karlson EW, Canhao H, Miller TA, Dligach D, Chen PJ, Perez RN, Shen Y, Weinblatt ME, Shadick NA, Plenge RM, Savova GK. Automatic prediction of rheumatoid arthritis disease activity from the electronic medical records. PLoS One. 2013; 8(8):e69932.
  20. Ananthakrishnan AN, Cagan A, Gainer VS, Cai T, Cheng SC, Savova G, Chen P, Szolovits P, Xia Z, De Jager PL, Shaw SY, Churchill S, Karlson EW, Kohane I, Plenge RM, Murphy SN, Liao KP. Normalization of plasma 25-hydroxy vitamin D is associated with reduced risk of surgery in Crohn's disease. Inflamm Bowel Dis. 2013 Aug; 19(9):1921-7.
  21. Ananthakrishnan AN, Cai T, Savova G, Cheng SC, Chen P, Perez RG, Gainer VS, Murphy SN, Szolovits P, Xia Z, Shaw S, Churchill S, Karlson EW, Kohane I, Plenge RM, Liao KP. Improving case definition of Crohn's disease and ulcerative colitis in electronic medical records using natural language processing: a novel informatics approach. Inflamm Bowel Dis. 2013 Jun; 19(7):1411-20.
  22. Liu K, Mitchell KJ, Chapman WW, Savova GK, Sioutos N, Rubin DL, Crowley RS. Formative evaluation of ontology learning methods for entity discovery by using existing ontologies as reference standards. Methods Inf Med. 2013; 52(4):308-16.
  23. Albright D, Lanfranchi A, Fredriksen A, Styler WF, Warner C, Hwang JD, Choi JD, Dligach D, Nielsen RD, Martin J, Ward W, Palmer M, Savova GK. Towards comprehensive syntactic and semantic annotations of the clinical narrative. J Am Med Inform Assoc. 2013 Sep-Oct; 20(5):922-30.
  24. Ananthakrishnan AN, Gainer VS, Cai T, Perez RG, Cheng SC, Savova G, Chen P, Szolovits P, Xia Z, De Jager PL, Shaw S, Churchill S, Karlson EW, Kohane I, Perlis RH, Plenge RM, Murphy SN, Liao KP. Similar risk of depression and anxiety following surgery or hospitalization for Crohn's disease and ulcerative colitis. Am J Gastroenterol. 2013 Apr; 108(4):594-601.
  25. Ananthakrishnan AN, Gainer VS, Perez RG, Cai T, Cheng SC, Savova G, Chen P, Szolovits P, Xia Z, De Jager PL, Shaw SY, Churchill S, Karlson EW, Kohane I, Perlis RH, Plenge RM, Murphy SN, Liao KP. Psychiatric co-morbidity is associated with increased risk of surgery in Crohn's disease. Aliment Pharmacol Ther. 2013 Feb; 37(4):445-54.
  26. Wu ST, Kaggal VC, Dligach D, Masanz JJ, Chen P, Becker L, Chapman WW, Savova GK, Liu H, Chute CG. A common type system for clinical natural language processing. J Biomed Semantics. 2013 Jan 03; 4(1):1.
  27. Deleger L, Molnar K, Savova G, Xia F, Lingren T, Li Q, Marsolo K, Jegga A, Kaiser M, Stoutenborough L, Solti I. Large-scale evaluation of automated clinical note de-identification and its impact on information extraction. J Am Med Inform Assoc. 2013 Jan 1; 20(1):84-94.
  28. Chapman WW, Savova GK, Zheng J, Tharp M, Crowley R. Anaphoric reference in clinical reports: characteristics of an annotated corpus. J Biomed Inform. 2012 Jun; 45(3):507-21.
  29. Rea S, Pathak J, Savova G, Oniki TA, Westberg L, Beebe CE, Tao C, Parker CG, Haug PJ, Huff SM, Chute CG. Building a robust, scalable and standards-driven infrastructure for secondary use of EHR data: the SHARPn project. J Biomed Inform. 2012 Aug; 45(4):763-71.
  30. Zheng J, Chapman WW, Miller TA, Lin C, Crowley RS, Savova GK. A system for coreference resolution for the clinical narrative. J Am Med Inform Assoc. 2012 Jul-Aug; 19(4):660-7.
  31. Savova GK, Olson JE, Murphy SP, Cafourek VL, Couch FJ, Goetz MP, Ingle JN, Suman VJ, Chute CG, Weinshilboum RM. Automated discovery of drug treatment patterns for endocrine therapy of breast cancer within an electronic medical record. J Am Med Inform Assoc. 2012 Jun; 19(e1):e83-9.
  32. Cairns BL, Nielsen RD, Masanz JJ, Martin JH, Palmer MS, Ward WH, Savova GK. The MiPACQ clinical question answering system. AMIA Annu Symp Proc. 2011; 2011:171-80.
  33. Chute CG, Pathak J, Savova GK, Bailey KR, Schor MI, Hart LA, Beebe CE, Huff SM. The SHARPn project on secondary use of Electronic Medical Record data: progress, plans, and possibilities. AMIA Annu Symp Proc. 2011; 2011:248-56.
  34. 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.
  35. Chapman WW, Nadkarni PM, Hirschman L, D'Avolio LW, Savova GK, Uzuner O. Overcoming barriers to NLP for clinical text: the role of shared tasks and the need for additional creative solutions. J Am Med Inform Assoc. 2011 Sep-Oct; 18(5):540-3.
  36. Zheng J, Chapman WW, Crowley RS, Savova GK. Coreference resolution: a review of general methodologies and applications in the clinical domain. J Biomed Inform. 2011 Dec; 44(6):1113-22.
  37. Savova GK, Chapman WW, Zheng J, Crowley RS. Anaphoric relations in the clinical narrative: corpus creation. J Am Med Inform Assoc. 2011 Jul-Aug; 18(4):459-65.
  38. Tao C, Wei WQ, Solbrig HR, Savova G, Chute CG. CNTRO: A Semantic Web Ontology for Temporal Relation Inferencing in Clinical Narratives. AMIA Annu Symp Proc. 2010 Nov 13; 2010:787-91.
  39. 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.
  40. Savova GK, Fan J, Ye Z, Murphy SP, Zheng J, Chute CG, Kullo IJ. Discovering peripheral arterial disease cases from radiology notes using natural language processing. AMIA Annu Symp Proc. 2010 Nov 13; 2010:722-6.
  41. Liu K, Chapman WW, Savova G, Chute CG, Sioutos N, Crowley RS. Effectiveness of lexico-syntactic pattern matching for ontology enrichment with clinical documents. Methods Inf Med. 2011; 50(5):397-407.
  42. Kullo IJ, Fan J, Pathak J, Savova GK, Ali Z, Chute CG. Leveraging informatics for genetic studies: use of the electronic medical record to enable a genome-wide association study of peripheral arterial disease. J Am Med Inform Assoc. 2010 Sep-Oct; 17(5):568-74.
  43. 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.
  44. Kremers HM, Myasoedova E, Crowson CS, Savova G, Gabriel SE, Matteson EL. The Rochester Epidemiology Project: exploiting the capabilities for population-based research in rheumatic diseases. Rheumatology (Oxford). 2011 Jan; 50(1):6-15.
  45. Sohn S, Savova GK. Mayo clinic smoking status classification system: extensions and improvements. AMIA Annu Symp Proc. 2009 Nov 14; 2009:619-23.
  46. Savova G, Bethard S, Styler W, Martin J, Palmer M, Masanz J, Ward W. Towards temporal relation discovery from the clinical narrative. AMIA Annu Symp Proc. 2009 Nov 14; 2009:568-72.
  47. Cheng LT, Zheng J, Savova GK, Erickson BJ. Discerning tumor status from unstructured MRI reports--completeness of information in existing reports and utility of automated natural language processing. J Digit Imaging. 2010 Apr; 23(2):119-32.
  48. Coden A, Savova G, Sominsky I, Tanenblatt M, Masanz J, Schuler K, Cooper J, Guan W, de Groen PC. Automatically extracting cancer disease characteristics from pathology reports into a Disease Knowledge Representation Model. J Biomed Inform. 2009 Oct; 42(5):937-49.
  49. Savova GK, Coden AR, Sominsky IL, Johnson R, Ogren PV, de Groen PC, Chute CG. Word sense disambiguation across two domains: biomedical literature and clinical notes. J Biomed Inform. 2008 Dec; 41(6):1088-100.
  50. Meystre SM, Savova GK, Kipper-Schuler KC, Hurdle JF. Extracting information from textual documents in the electronic health record: a review of recent research. Yearb Med Inform. 2008; 128-44.
  51. Savova GK, Ogren PV, Duffy PH, Buntrock JD, Chute CG. Mayo clinic NLP system for patient smoking status identification. J Am Med Inform Assoc. 2008 Jan-Feb; 15(1):25-8.
  52. Jiang G, Harris MR, Savova GK, Chute CG. Formalizing the International Classification of Functioning, Disability, and Health (ICF) using Formal Concept Analysis (FCA). AMIA Annu Symp Proc. 2007 Oct 11; 994.
  53. Kim H, Harris MR, Savova GK, Speedie SM, Chute CG. Toward near real-time acuity estimation: a feasibility study. Nurs Res. 2007 Jul-Aug; 56(4):288-94.
  54. Ogren PV, Savova G, Buntrock JD, Chute CG. Building and evaluating annotated corpora for medical NLP systems. AMIA Annu Symp Proc. 2006; 1050.
  55. Kim H, Harris MR, Savova G, Chute CG. Content coverage of SNOMED-CT toward the ICU nursing flowsheets and the acuity indicators. Stud Health Technol Inform. 2006; 122:722-6.
  56. Savova G, Harris M, Pakhomov S, Chute CG. Frame semantics and the domain of functioning, disability and health. AMIA Annu Symp Proc. 2005; 1106.
  57. Harris MR, Savova GK, Johnson TM, Chute CG. A term extraction tool for expanding content in the domain of functioning, disability, and health: proof of concept. J Biomed Inform. 2003 Aug-Oct; 36(4-5):250-9.
  58. Harris M, Kim H, Rhudy L, Savova G, Chute C. Testing the generalizability of the ISO model for nursing diagnoses. AMIA Annu Symp Proc. 2003; 274-8.
  59. Savova GK, Harris M, Johnson T, Pakhomov SV, Chute CG. A data-driven approach for extracting "the most specific term" for ontology development. AMIA Annu Symp Proc. 2003; 579-83.
  60. Wilke RA, Xu H, Denny JC, Roden DM, Krauss RM, McCarty CA, Davis RL, Skaar T, Lamba J, Savova G. The emerging role of electronic medical records in pharmacogenomics. Clin Pharmacol Ther. 2011 Mar; 89(3):379-86.
  61. Kim H, Harris MR, Savova GK, Chute CG. The first step toward data reuse: disambiguating concept representation of the locally developed ICU nursing flowsheets. Comput Inform Nurs. 2008 Sep-Oct; 26(5):282-9.
  62. Lin C, Karlson EW, Dligach D, Ramirez MP, Miller TA, Mo H, Braggs NS, Cagan A, Gainer V, Denny JC, Savova GK. Automatic identification of methotrexate-induced liver toxicity in patients with rheumatoid arthritis from the electronic medical record. J Am Med Inform Assoc. 2015 Apr; 22(e1):e151-61.
  63. Castro V, Shen Y, Yu S, Finan S, Pau CT, Gainer V, Keefe CC, Savova G, Murphy SN, Cai T, Welt CK. Identification of subjects with polycystic ovary syndrome using electronic health records. Reprod Biol Endocrinol. 2015 Oct 29; 13:116.
  64. Ananthakrishnan AN, Cagan A, Cai T, Gainer VS, Shaw SY, Savova G, Churchill S, Karlson EW, Murphy SN, Liao KP, Kohane I. Identification of Nonresponse to Treatment Using Narrative Data in an Electronic Health Record Inflammatory Bowel Disease Cohort. Inflamm Bowel Dis. 2016 Jan; 22(1):151-8.
  65. Lin C, Dligach D, Miller TA, Bethard S, Savova GK. Multilayered temporal modeling for the clinical domain. J Am Med Inform Assoc. 2016 Mar; 23(2):387-95.
  66. Kirby JC, Speltz P, Rasmussen LV, Basford M, Gottesman O, Peissig PL, Pacheco JA, Tromp G, Pathak J, Carrell DS, Ellis SB, Lingren T, Thompson WK, Savova G, Haines J, Roden DM, Harris PA, Denny JC. PheKB: a catalog and workflow for creating electronic phenotype algorithms for transportability. J Am Med Inform Assoc. 2016 Nov; 23(6):1046-1052.
  67. Brady CC, Thaker VV, Lingren T, Woo JG, Kennebeck SS, Namjou-Khales B, Roach A, Bickel JP, Patibandla N, Savova GK, Solti I, Holm IA, Harley JB, Kohane IS, Crimmins NA. Suboptimal Clinical Documentation in Young Children with Severe Obesity at Tertiary Care Centers. Int J Pediatr. 2016; 2016:4068582.
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Related Laboratory

Natural Language Processing Laboratory

Our mission is to develop and implement Natural Language Processing (NLP) technologies to apply to the electronic medical record.  These technologies include core NLP tasks such as relation extraction, coreference resolution, and parsing, and make use of statistical machine learning methods.

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