Optimization of patient throughput and wait time in emergency departments (ED) is an important task for hospital systems. For that reason, Emergency Severity Index (ESI) system for patient triage was introduced to help guide manual estimation of acuity levels, which is used by nurses to rank the patients and organize hospital resources. However, despite improvements that it brought to managing medical resources, such triage system greatly depends on nurse's subjective judgment and is thus prone to human errors. Here, we propose a novel deep model based on the word attention mechanism designed for predicting a number of resources an ED patient would need. Our approach incorporates routinely available continuous and nominal (structured) data with medical text (unstructured) data, including patient's chief complaint, past medical history, medication list, and nurse assessment collected for 338,500 ED visits over three years in a large urban hospital. Using both structured and unstructured data, the proposed approach achieves the AUC of @math for the task of identifying resource intensive patients (binary classification), and the accuracy of @math for predicting exact category of number of resources (multi-class classification task), giving an estimated lift over nurses' performance by 16 in accuracy. Furthermore, the attention mechanism of the proposed model provides interpretability by assigning attention scores for nurses' notes which is crucial for decision making and implementation of such approaches in the real systems working on human health.
We introduce an extensible and modifiable knowledge representation model to represent cancer disease characteristics in a comparable and consistent fashion. We describe a system, MedTAS P which automatically instantiates the knowledge representation model from free-text pathology reports. MedTAS P is based on an open-source framework and its components use natural language processing principles, machine learning and rules to discover and populate elements of the model. To validate the model and measure the accuracy of MedTAS P, we developed a gold-standard corpus of manually annotated colon cancer pathology reports. MedTAS P achieves F1-scores of 0.97-1.0 for instantiating classes in the knowledge representation model such as histologies or anatomical sites, and F1-scores of 0.82-0.93 for primary tumors or lymph nodes, which require the extractions of relations. An F1-score of 0.65 is reported for metastatic tumors, a lower score predominantly due to a very small number of instances in the training and test sets. This issue of JAMIA focuses on natural language processing (NLP) techniques for clinical-text information extraction. Several articles are offshoots of the yearly ‘Informatics for Integrating Biology and the Bedside’ (i2b2) (http: www.i2b2.org) NLP shared-task challenge, introduced by ( see page 552 )1 and co-sponsored by the Veteran's Administration for the last 2 years. This shared task follows long-running challenge evaluations in other fields, such as the Message Understanding Conference (MUC) for information extraction,2 TREC3 for text information retrieval, and CASP4 for protein structure prediction. Shared tasks in the clinical domain are recent and include annual i2b2 Challenges that began in 2006, a challenge for multi-label classification of radiology reports sponsored by Cincinnati Children's Hospital in 2007,5 a 2011 Cincinnati Children's Hospital challenge on suicide notes,6 and the 2011 TREC information retrieval shared task involving retrieval of clinical cases from narrative records.7 @PARASPLIT Although NLP research in the clinical domain has been active since the 1960s, progress in the development of NLP applications for clinical text has been slow and lags behind progress in the general NLP domain. There are several barriers to NLP development in the clinical domain, and shared tasks like the i2b2 VA Challenge address some of these barriers. Nevertheless, many barriers remain and unless the community takes a more active role in developing novel approaches for addressing the barriers, advancement and innovation will continue to be slow. @PARASPLIT Historically, there have been substantial barriers to NLP development in the clinical domain. These barriers are not unique to the clinical domain: they also occur in the fields of software engineering and general NLP. @PARASPLIT ### Lack of access to shared data @PARASPLIT Because of concerns regarding patient privacy and worry about revealing unfavorable institutional practices, hospitals and clinics have been extremely reluctant to allow access to clinical data for researchers from outside … @PARASPLIT Correspondence to Dr Wendy W Chapman, Department of Biomedical Informatics, University of California San Diego, 9500 Gilman Dr, Bldg 2 #0728, La Jolla, California, USA; wwchapman at ucsd.edu 