Coreference resolution in clinical discharge summaries, progress notes, surgical and pathology reports: a unified lexical approach

We developed a lexical rule-based system that uses a unified approach to resolving coreference across a wide variety of clinical records comprising discharge summaries, progress notes, pathology, radiology and surgical reports from two corpora (Ontology Development and Information Extraction (ODIE) and i2b2/VA) provided for the fifth i2b2/VA shared task. Taking the unweighted mean between 4 coreference metrics, validation of the system against the i2b2/VA corpus attained an overall F-score of 87.7% across all mention classes, with a maximum of 93.1% for coreference of persons, and a minimum of 77.2% for coreference of tests. For the ODIE corpus the overall F-score across all mention classes was 79.4%, with a maximum of 82.0% for coreference of persons and a minimum of 13.1% for coreference of diagnostic reagents. For the ODIE corpus our results are comparable to the mean reported inter-annotator agreement with the gold standard. We discuss the four categories of errors we identified, and how these might be addressed. The system uses a number of reusable modules and techniques that may be of benefit to the research community

Computerization of workflows, guidelines and care pathways: a review of implementation challenges for process-oriented health information systems

There is a need to integrate the various theoretical frameworks and formalisms for modeling clinical guidelines, workflows, and pathways, in order to move beyond providing support for individual clinical decisions and toward the provision of process-oriented, patient-centered, health information systems (HIS). In this review, we analyze the challenges in developing process-oriented HIS that formally model guidelines, workflows, and care pathways. A qualitative meta-synthesis was performed on studies published in English between 1995 and 2010 that addressed the modeling process and reported the exposition of a new methodology, model, system implementation, or system architecture. Thematic analysis, principal component analysis (PCA) and data visualisation techniques were used to identify and cluster the underlying implementation ‘challenge’ themes. One hundred and eight relevant studies were selected for review. Twenty-five underlying ‘challenge’ themes were identified. These were clustered into 10 distinct groups, from which a conceptual model of the implementation process was developed. We found that the development of systems supporting individual clinical decisions is evolving toward the implementation of adaptable care pathways on the semantic web, incorporating formal, clinical, and organizational ontologies, and the use of workflow management systems. These architectures now need to be implemented and evaluated on a wider scale within clinical settings

Automated recognition and post-coordination of complex clinical terms

One of the key tasks in integrating guideline-based decision support systems with the electronic patient record is the mapping of clinical terms contained in both guidelines and patient notes to a common, controlled terminology. However, a vocabulary of pre-coordinated terms cannot cover every possible variation - clinical terms are often highly compositional and complex. We present a rule-based approach for automated recognition and post-coordination of clinical terms using minimal, morpheme-based thesauri, neoclassical combining forms and part-of-speech analysis. The process integrates MetaMap with the open-source GATE framework

A tool for enhancing MetaMap performance when annotating clinical guideline documents with UMLS concepts

We developed a tool that integrates the National Library of Medicine's MetaMap software with GATE, an open-source text an- alytics framework. The tool allows non-ASCII encoded documents of numerous formats to be annotated with UMLS concepts. We created a GATE pipeline to chunk cardiovascular disease guideline text into default segments (blank-line delimited), XML element content, sentences and phrases, which were sequentially submitted to MetaMap for annotation. XML element, sentence and phrase chunking allowed term extraction and mapping to be completed in around 1/3 of the time taken with de- fault chunking, although with slight loss of accuracy (F1.0s=0.94-0.99). However, phrase chunking allows more complex input to be processed in real time, which is not possible with the other approaches. We discuss the results in relation to use of MetaMap's --term processing option for generating pre- and post-coordinated mappings from composite phrases

Shall Advocacy Vanish?

The subject of my remarks indicates that at some time in the past and as of now advocacy has been practiced. To me advocacy is the backbone and the real strength of justice in this great land of ours. The term advocate has been linked with the legal profession—and properly so—from the beginning of time. We are a profession that has always taken an objective point of view, as contrasted with the negative or defensive point of view, to the end that principles and ideals shall be maintained

3D Line textures and the visualization of confidence in Architecture

technical reportThis work introduces a technique for interactive walkthroughs of non-photorealistically rendered (NPR) scenes using 3D line primitives to define architectural features of the model, as well as indicate textural qualities. Line primitives are not typically used in this manner in favor of texture mapping techniques which can encapsulate a great deal of information in a single texture map, and take advantage of GPU optimizations for accelerated rendering. However, texture mapped images may not maintain the visual quality or aesthetic appeal that is possible when using 3D lines to simulate NPR scenes such as hand-drawn illustrations or architectural renderings. In addition, line textures can be modi ed interactively, for instance changing the sketchy quality of the lines, and can be exported as vectors to allow the automatic generation of illustrations and further modi cation in vector-based graphics programs. The technique introduced here extracts feature edges from a model, and using these edges, generates a reduced set of line textures which indicate material properties while maintaining interactive frame rates. A clipping algorithm is presented to enable 3D lines to reside only in the interior of the 3D model without exposing the underlying triangulated mesh. The resulting system produces interactive illustrations with high visual quality that are free from animation artifacts

Greenhouse gas reduction and other benefits of biogas upgrading

Biogas obtained from anaerobic digestion of livestock manure is a complex mixture containing ~60% methane (CH4) and other less valuable gases. Upgrading the biogas to reduce contaminants and increase the CH4 concentration is advantageous for several reasons