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ObjectiveTo 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.MethodsManual annotation of a clinical narrative corpus of 127 606 tokens following the Treebank schema for syntactic information, PropBank schema for predicate-argument structures, and the Unified Medical Language System (UMLS) schema for semantic information. NLP components were developed.ResultsThe final corpus consists of 13 091 sentences containing 1772 distinct predicate lemmas. Of the 766 newly created PropBank frames, 74 are verbs. There are 28 539 named entity (NE) annotations spread over 15 UMLS semantic groups, one UMLS semantic type, and the Person semantic category. The most frequent annotations belong to the UMLS semantic groups of Procedures (15.71%), Disorders (14.74%), Concepts and Ideas (15.10%), Anatomy (12.80%), Chemicals and Drugs (7.49%), and the UMLS semantic type of Sign or Symptom (12.46%). Inter-annotator agreement results: Treebank (0.926), PropBank (0.891-0.931), NE (0.697-0.750). The part-of-speech tagger, constituency parser, dependency parser, and semantic role labeler are built from the corpus and released open source. A significant limitation uncovered by this project is the need for the NLP community to develop a widely agreed-upon schema for the annotation of clinical concepts and their relations.ConclusionsThis project takes a foundational step towards bringing the field of clinical NLP up to par with NLP in the general domain. The corpus creation and NLP components provide a resource for research and application development that would have been previously impossible.

Mobile eye-tracking and motion-capture techniques yield rich, precisely quantifiable data that can inform our understanding of the relationship between visual and motor processes during task performance. However, these systems are rarely used in combination, in part because of the significant time and human resources required for post-processing and analysis. Recent advances in computer vision have opened the door for more efficient processing and analysis solutions. We developed a post-processing pipeline to integrate mobile eye-tracking and full-body motion-capture data. These systems were used simultaneously to measure visuomotor integration in an immersive virtual environment. Our approach enables calculation of a 3D gaze vector that can be mapped to the participant's body position and objects in the virtual environment using a uniform coordinate system. This approach is generalizable to other configurations, and enables more efficient analysis of eye, head, and body movements together during visuomotor tasks administered in controlled, repeatable environments.

Get-Up-and-Go Test is commonly used for assessing the physical mobility of the elderly by physicians. This paper presents a method for automatic analysis and classification of human gait in the Get-Up-and-Go Test using a Microsoft Kinect sensor. Two types of features are automatically extracted from the human skeleton data provided by the Kinect sensor. The first type of feature is related to the human gait (e.g., number of steps, step duration, and turning duration); whereas the other one describes the anatomical configuration (e.g., knee angles, leg angle, and distance between elbows). These features characterize the degree of human physical mobility. State-of-the-art machine learning algorithms (i.e. Bag of Words and Support Vector Machines) are used to classify the severity of gaits in 12 subjects with ages ranging between 65 and 90 enrolled in a pilot study. Our experimental results show that these features can discriminate between patients who have a high risk for falling and patients with a lower fall risk.

The Multi-source Integrated Platform for Answering Clinical Questions (MiPACQ) is a QA pipeline that integrates a variety of information retrieval and natural language processing systems into an extensible question answering system. We present the system's architecture and an evaluation of MiPACQ on a human-annotated evaluation dataset based on the Medpedia health and medical encyclopedia. Compared with our baseline information retrieval system, the MiPACQ rule-based system demonstrates 84% improvement in Precision at One and the MiPACQ machine-learning-based system demonstrates 134% improvement. Other performance metrics including mean reciprocal rank and area under the precision/recall curves also showed significant improvement, validating the effectiveness of the MiPACQ design and implementation.