University of Washington - Biomedical Language Processing Group
Improving acesss to information hidden in biomedical text.
 

Assertion classifier [ download ]

This software implements the methodologies for determining the assertion category of a medical concept mentioned in clinical text as described in the following paper:
     Cosmin Adrian Bejan, Lucy Vanderwende, Fei Xia, and Meliha Yetisgen-Yildiz.
     Assertion modeling and its role in clinical phenotype identification.
     Journal of Biomedical Informatics (JBI), 2012.
     http://www.ncbi.nlm.nih.gov/pubmed/23000479
The development of this software was funded by Microsoft Research Connections.


Statistical feature selection [ download ]

This software is part of the statistical feature selection approach used for better identifying patients with a specific phenotype as described in the following paper:
     Cosmin Adrian Bejan, Fei Xia, Lucy Vanderwende, Mark M Wurfel, and Meliha Yetisgen-Yildiz.
     Pneumonia identification using statistical feature selection.
     Journal of the American Medical Informatics Association (JAMIA), 2012.
     http://www.ncbi.nlm.nih.gov/pubmed/22539080
The development of this software was funded by Microsoft Research Connections.


Statistical section chunker [ download page ]

The University of Washington - Biomedical Language Processing Group Clinical Record Section Chunker is a Java-based application for identifying section boundaries and labeling section headings for clinical records. It integrates the Mallet Machine Learning toolkit to train a Maximum Entropy model over files annotated with a section heading schema. Details can be found at the following paper:
     M. Tepper, D. Capurro, F. Xia, L. Vanderwende, M. Yetisgen-Yildiz. Statistical Section Segmentation in Free-Text Clinical Records. 
    Proceedings of the International Conference on Language Resources and Evaluation (LREC), Istanbul, May, 2012. 
     
The development of this software was funded by AHRQ.

University of Washington
Biomedical and Health Informatics
Department of Linguistics
(c) 2011 UW-BioNLP