Now showing items 1-12 of 12

    • Automatic Prediction of Rheumatoid Arthritis Disease Activity from the Electronic Medical Records 

      Lin, Chen; Karlson, Elizabeth W.; Canhao, Helena; Miller, Timothy A.; Dligach, Dmitriy; Chen, Pei Jun; Perez, Raul Natanael Guzman; Shen, Yuanyan; Weinblatt, Michael E.; Shadick, Nancy A.; Plenge, Robert M.; Savova, Guergana K. (Public Library of Science, 2013)
      Objective: We aimed to mine the data in the Electronic Medical Record to automatically discover patients' Rheumatoid Arthritis disease activity at discrete rheumatology clinic visits. We cast the problem as a document ...
    • A common type system for clinical natural language processing 

      Wu, Stephen T; Kaggal, Vinod C; Dligach, Dmitriy; Masanz, James J; Chen, Pei; Becker, Lee; Chapman, Wendy W; Savova, Guergana Kirilova; Liu, Hongfang; Chute, Christopher G (BioMed Central, 2013)
      Background: One challenge in reusing clinical data stored in electronic medical records is that these data are heterogenous. Clinical Natural Language Processing (NLP) plays an important role in transforming information ...
    • Discovering body site and severity modifiers in clinical texts 

      Dligach, Dmitriy; Bethard, Steven; Becker, Lee; Miller, Timothy; Savova, Guergana K (BMJ Publishing Group, 2014)
      Objective: To research computational methods for discovering body site and severity modifiers in clinical texts. Methods: We cast the task of discovering body site and severity modifiers as a relation extraction problem ...
    • Electronic Health Record Based Algorithm to Identify Patients with Autism Spectrum Disorder 

      Lingren, Todd; Chen, Pei; Bochenek, Joseph; Doshi-Velez, Finale; Manning-Courtney, Patty; Bickel, Julie; Wildenger Welchons, Leah; Reinhold, Judy; Bing, Nicole; Ni, Yizhao; Barbaresi, William; Mentch, Frank; Basford, Melissa; Denny, Joshua; Vazquez, Lyam; Perry, Cassandra; Namjou, Bahram; Qiu, Haijun; Connolly, John; Abrams, Debra; Holm, Ingrid A.; Cobb, Beth A.; Lingren, Nataline; Solti, Imre; Hakonarson, Hakon; Kohane, Isaac S.; Harley, John; Savova, Guergana (Public Library of Science, 2016)
      Objective: Cohort selection is challenging for large-scale electronic health record (EHR) analyses, as International Classification of Diseases 9th edition (ICD-9) diagnostic codes are notoriously unreliable disease ...
    • Evaluating the state of the art in disorder recognition and normalization of the clinical narrative 

      Pradhan, Sameer; Elhadad, Noémie; South, Brett R; Martinez, David; Christensen, Lee; Vogel, Amy; Suominen, Hanna; Chapman, Wendy W; Savova, Guergana (Oxford University Press, 2014)
      Objective: The ShARe/CLEF eHealth 2013 Evaluation Lab Task 1 was organized to evaluate the state of the art on the clinical text in (i) disorder mention identification/recognition based on Unified Medical Language System ...
    • An information model for computable cancer phenotypes 

      Hochheiser, Harry; Castine, Melissa; Harris, David; Savova, Guergana; Jacobson, Rebecca S. (BioMed Central, 2016)
      Background: Standards, methods, and tools supporting the integration of clinical data and genomic information are an area of significant need and rapid growth in biomedical informatics. Integration of cancer clinical data ...
    • Large-scale evaluation of automated clinical note de-identification and its impact on information extraction 

      Deleger, Louise; Molnar, Katalin; Savova, Guergana; Xia, Fei; Lingren, Todd; Li, Qi; Marsolo, Keith; Jegga, Anil; Kaiser, Megan; Stoutenborough, Laura; Solti, Imre (BMJ Group, 2012)
      Objective: (1) To evaluate a state-of-the-art natural language processing (NLP)-based approach to automatically de-identify a large set of diverse clinical notes. (2) To measure the impact of de-identification on the ...
    • Methods to Develop an Electronic Medical Record Phenotype Algorithm to Compare the Risk of Coronary Artery Disease across 3 Chronic Disease Cohorts 

      Liao, Katherine P.; Ananthakrishnan, Ashwin N.; Kumar, Vishesh; Xia, Zongqi; Cagan, Andrew; Gainer, Vivian S.; Goryachev, Sergey; Chen, Pei; Savova, Guergana K.; Agniel, Denis; Churchill, Susanne; Lee, Jaeyoung; Murphy, Shawn N.; Plenge, Robert M.; Szolovits, Peter; Kohane, Isaac; Shaw, Stanley Y.; Karlson, Elizabeth W.; Cai, Tianxi (Public Library of Science, 2015)
      Background: Typically, algorithms to classify phenotypes using electronic medical record (EMR) data were developed to perform well in a specific patient population. There is increasing interest in analyses which can allow ...
    • Modeling Disease Severity in Multiple Sclerosis Using Electronic Health Records 

      Xia, Zongqi; Secor, Elizabeth; Chibnik, Lori B.; Bove, Riley M.; Cheng, Suchun; Chitnis, Tanuja; Cagan, Andrew; Gainer, Vivian S.; Chen, Pei J.; Liao, Katherine P.; Shaw, Stanley Y.; Ananthakrishnan, Ashwin N.; Szolovits, Peter; Weiner, Howard L.; Karlson, Elizabeth W.; Murphy, Shawn N.; Savova, Guergana K.; Cai, Tianxi; Churchill, Susanne E.; Plenge, Robert M.; Kohane, Isaac S.; De Jager, Philip L. (Public Library of Science, 2013)
      Objective: To optimally leverage the scalability and unique features of the electronic health records (EHR) for research that would ultimately improve patient care, we need to accurately identify patients and extract ...
    • Normalizing acronyms and abbreviations to aid patient understanding of clinical texts: ShARe/CLEF eHealth Challenge 2013, Task 2 

      Mowery, Danielle L.; South, Brett R.; Christensen, Lee; Leng, Jianwei; Peltonen, Laura-Maria; Salanterä, Sanna; Suominen, Hanna; Martinez, David; Velupillai, Sumithra; Elhadad, Noémie; Savova, Guergana; Pradhan, Sameer; Chapman, Wendy W. (BioMed Central, 2016)
      Background: The ShARe/CLEF eHealth challenge lab aims to stimulate development of natural language processing and information retrieval technologies to aid patients in understanding their clinical reports. In clinical text, ...
    • Suboptimal Clinical Documentation in Young Children with Severe Obesity at Tertiary Care Centers 

      Brady, Cassandra C.; Thaker, Vidhu V.; Lingren, Todd; Woo, Jessica G.; Kennebeck, Stephanie S.; Namjou-Khales, Bahram; Roach, Ashton; Bickel, Jonathan P.; Patibandla, Nandan; Savova, Guergana K.; Solti, Imre; Holm, Ingrid A.; Harley, John B.; Kohane, Isaac S.; Crimmins, Nancy A. (Hindawi Publishing Corporation, 2016)
      Background and Objectives. The prevalence of severe obesity in children has doubled in the past decade. The objective of this study is to identify the clinical documentation of obesity in young children with a BMI ≥ 99th ...
    • Towards comprehensive syntactic and semantic annotations of the clinical narrative 

      Albright, Daniel; Lanfranchi, Arrick; Fredriksen, Anwen; Styler, William F; Warner, Colin; Hwang, Jena D; Choi, Jinho D; Dligach, Dmitriy; Nielsen, Rodney D; Martin, James; Ward, Wayne; Palmer, Martha; Savova, Guergana K (BMJ Publishing Group, 2013)
      Objective: To create annotated clinical narratives with layers of syntactic and semantic labels to facilitate advances in clinical natural language processing (NLP). To develop NLP algorithms and open source components. ...