5,014 research outputs found
Development and validation of a pragmatic natural language processing approach to identifying falls in older adults in the emergency department
BACKGROUND:
Falls among older adults are both a common reason for presentation to the emergency department, and a major source of morbidity and mortality. It is critical to identify fall patients quickly and reliably during, and immediately after, emergency department encounters in order to deliver appropriate care and referrals. Unfortunately, falls are difficult to identify without manual chart review, a time intensive process infeasible for many applications including surveillance and quality reporting. Here we describe a pragmatic NLP approach to automating fall identification.
METHODS:
In this single center retrospective review, 500 emergency department provider notes from older adult patients (age 65 and older) were randomly selected for analysis. A simple, rules-based NLP algorithm for fall identification was developed and evaluated on a development set of 1084 notes, then compared with identification by consensus of trained abstractors blinded to NLP results.
RESULTS:
The NLP pipeline demonstrated a recall (sensitivity) of 95.8%, specificity of 97.4%, precision of 92.0%, and F1 score of 0.939 for identifying fall events within emergency physician visit notes, as compared to gold standard manual abstraction by human coders.
CONCLUSIONS:
Our pragmatic NLP algorithm was able to identify falls in ED notes with excellent precision and recall, comparable to that of more labor-intensive manual abstraction. This finding offers promise not just for improving research methods, but as a potential for identifying patients for targeted interventions, quality measure development and epidemiologic surveillance
Shingle 2.0: generalising self-consistent and automated domain discretisation for multi-scale geophysical models
The approaches taken to describe and develop spatial discretisations of the
domains required for geophysical simulation models are commonly ad hoc, model
or application specific and under-documented. This is particularly acute for
simulation models that are flexible in their use of multi-scale, anisotropic,
fully unstructured meshes where a relatively large number of heterogeneous
parameters are required to constrain their full description. As a consequence,
it can be difficult to reproduce simulations, ensure a provenance in model data
handling and initialisation, and a challenge to conduct model intercomparisons
rigorously. This paper takes a novel approach to spatial discretisation,
considering it much like a numerical simulation model problem of its own. It
introduces a generalised, extensible, self-documenting approach to carefully
describe, and necessarily fully, the constraints over the heterogeneous
parameter space that determine how a domain is spatially discretised. This
additionally provides a method to accurately record these constraints, using
high-level natural language based abstractions, that enables full accounts of
provenance, sharing and distribution. Together with this description, a
generalised consistent approach to unstructured mesh generation for geophysical
models is developed, that is automated, robust and repeatable, quick-to-draft,
rigorously verified and consistent to the source data throughout. This
interprets the description above to execute a self-consistent spatial
discretisation process, which is automatically validated to expected discrete
characteristics and metrics.Comment: 18 pages, 10 figures, 1 table. Submitted for publication and under
revie
An Analysis of Scripting Languages for Research in Applied Computing
There are several scripting languages that exist
today. However, some are used more frequently and popular
than others. This is due to certain characteristics and features
that they possess. Particularly in applied computing fields like
software engineering, bioinformatics and computational biology,
scripting languages are gaining popularity. This paper presents a
comparative study of ten popular scripting languages that are
used in the above mentioned fields/area. For making comparison,
we have identified the factors against which these languages are
evaluated. Accordingly, based on selected criteria we determine
their suitability in the fields of software engineering,
bioinformatics and computational biology research. This will
serve as a guide to researchers to choose the appropriate
scripting language in the various fields
BRAHMS: Novel middleware for integrated systems computation
Biological computational modellers are becoming increasingly interested in building large, eclectic models, including components on many different computational substrates, both biological and non-biological. At the same time, the rise of the philosophy of embodied modelling is generating a need to deploy biological models as controllers for robots in real-world environments. Finally, robotics engineers are beginning to find value in seconding biomimetic control strategies for use on practical robots. Together with the ubiquitous desire to make good on past software development effort, these trends are throwing up new challenges of intellectual and technological integration (for example across scales, across disciplines, and even across time) - challenges that are unmet by existing software frameworks. Here, we outline these challenges in detail, and go on to describe a newly developed software framework, BRAHMS. that meets them. BRAHMS is a tool for integrating computational process modules into a viable, computable system: its generality and flexibility facilitate integration across barriers, such as those described above, in a coherent and effective way. We go on to describe several cases where BRAHMS has been successfully deployed in practical situations. We also show excellent performance in comparison with a monolithic development approach. Additional benefits of developing in the framework include source code self-documentation, automatic coarse-grained parallelisation, cross-language integration, data logging, performance monitoring, and will include dynamic load-balancing and 'pause and continue' execution. BRAHMS is built on the nascent, and similarly general purpose, model markup language, SystemML. This will, in future, also facilitate repeatability and accountability (same answers ten years from now), transparent automatic software distribution, and interfacing with other SystemML tools. (C) 2009 Elsevier Ltd. All rights reserved
Open Science in Software Engineering
Open science describes the movement of making any research artefact available
to the public and includes, but is not limited to, open access, open data, and
open source. While open science is becoming generally accepted as a norm in
other scientific disciplines, in software engineering, we are still struggling
in adapting open science to the particularities of our discipline, rendering
progress in our scientific community cumbersome. In this chapter, we reflect
upon the essentials in open science for software engineering including what
open science is, why we should engage in it, and how we should do it. We
particularly draw from our experiences made as conference chairs implementing
open science initiatives and as researchers actively engaging in open science
to critically discuss challenges and pitfalls, and to address more advanced
topics such as how and under which conditions to share preprints, what
infrastructure and licence model to cover, or how do it within the limitations
of different reviewing models, such as double-blind reviewing. Our hope is to
help establishing a common ground and to contribute to make open science a norm
also in software engineering.Comment: Camera-Ready Version of a Chapter published in the book on
Contemporary Empirical Methods in Software Engineering; fixed layout issue
with side-note
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