43,348 research outputs found
Towards a New Science of a Clinical Data Intelligence
In this paper we define Clinical Data Intelligence as the analysis of data
generated in the clinical routine with the goal of improving patient care. We
define a science of a Clinical Data Intelligence as a data analysis that
permits the derivation of scientific, i.e., generalizable and reliable results.
We argue that a science of a Clinical Data Intelligence is sensible in the
context of a Big Data analysis, i.e., with data from many patients and with
complete patient information. We discuss that Clinical Data Intelligence
requires the joint efforts of knowledge engineering, information extraction
(from textual and other unstructured data), and statistics and statistical
machine learning. We describe some of our main results as conjectures and
relate them to a recently funded research project involving two major German
university hospitals.Comment: NIPS 2013 Workshop: Machine Learning for Clinical Data Analysis and
Healthcare, 201
Effective Feature Representation for Clinical Text Concept Extraction
Crucial information about the practice of healthcare is recorded only in
free-form text, which creates an enormous opportunity for high-impact NLP.
However, annotated healthcare datasets tend to be small and expensive to
obtain, which raises the question of how to make maximally efficient uses of
the available data. To this end, we develop an LSTM-CRF model for combining
unsupervised word representations and hand-built feature representations
derived from publicly available healthcare ontologies. We show that this
combined model yields superior performance on five datasets of diverse kinds of
healthcare text (clinical, social, scientific, commercial). Each involves the
labeling of complex, multi-word spans that pick out different healthcare
concepts. We also introduce a new labeled dataset for identifying the treatment
relations between drugs and diseases
Building a semantically annotated corpus of clinical texts
In this paper, we describe the construction of a semantically annotated corpus of clinical texts for use in the development and evaluation of systems for automatically extracting clinically significant information from the textual component of patient records. The paper details the sampling of textual material from a collection of 20,000 cancer patient records, the development of a semantic annotation scheme, the annotation methodology, the distribution of annotations in the final corpus, and the use of the corpus for development of an adaptive information extraction system. The resulting corpus is the most richly semantically annotated resource for clinical text processing built to date, whose value has been demonstrated through its use in developing an effective information extraction system. The detailed presentation of our corpus construction and annotation methodology will be of value to others seeking to build high-quality semantically annotated corpora in biomedical domains
Joining up health and bioinformatics: e-science meets e-health
CLEF (Co-operative Clinical e-Science Framework) is an MRC sponsored project in the e-Science programme that aims to establish methodologies and a technical infrastructure forthe next generation of integrated clinical and bioscience research. It is developing methodsfor managing and using pseudonymised repositories of the long-term patient histories whichcan be linked to genetic, genomic information or used to support patient care. CLEF concentrateson removing key barriers to managing such repositories ? ethical issues, informationcapture, integration of disparate sources into coherent ?chronicles? of events, userorientedmechanisms for querying and displaying the information, and compiling the requiredknowledge resources. This paper describes the overall information flow and technicalapproach designed to meet these aims within a Grid framework
Named Entity Recognition in Electronic Health Records Using Transfer Learning Bootstrapped Neural Networks
Neural networks (NNs) have become the state of the art in many machine
learning applications, especially in image and sound processing [1]. The same,
although to a lesser extent [2,3], could be said in natural language processing
(NLP) tasks, such as named entity recognition. However, the success of NNs
remains dependent on the availability of large labelled datasets, which is a
significant hurdle in many important applications. One such case are electronic
health records (EHRs), which are arguably the largest source of medical data,
most of which lies hidden in natural text [4,5]. Data access is difficult due
to data privacy concerns, and therefore annotated datasets are scarce. With
scarce data, NNs will likely not be able to extract this hidden information
with practical accuracy. In our study, we develop an approach that solves these
problems for named entity recognition, obtaining 94.6 F1 score in I2B2 2009
Medical Extraction Challenge [6], 4.3 above the architecture that won the
competition. Beyond the official I2B2 challenge, we further achieve 82.4 F1 on
extracting relationships between medical terms. To reach this state-of-the-art
accuracy, our approach applies transfer learning to leverage on datasets
annotated for other I2B2 tasks, and designs and trains embeddings that
specially benefit from such transfer.Comment: 11 pages, 4 figures, 8 table
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