5,361 research outputs found
Implementing a Portable Clinical NLP System with a Common Data Model - a Lisp Perspective
This paper presents a Lisp architecture for a portable NLP system, termed
LAPNLP, for processing clinical notes. LAPNLP integrates multiple standard,
customized and in-house developed NLP tools. Our system facilitates portability
across different institutions and data systems by incorporating an enriched
Common Data Model (CDM) to standardize necessary data elements. It utilizes
UMLS to perform domain adaptation when integrating generic domain NLP tools. It
also features stand-off annotations that are specified by positional reference
to the original document. We built an interval tree based search engine to
efficiently query and retrieve the stand-off annotations by specifying
positional requirements. We also developed a utility to convert an inline
annotation format to stand-off annotations to enable the reuse of clinical text
datasets with inline annotations. We experimented with our system on several
NLP facilitated tasks including computational phenotyping for lymphoma patients
and semantic relation extraction for clinical notes. These experiments
showcased the broader applicability and utility of LAPNLP.Comment: 6 pages, accepted by IEEE BIBM 2018 as regular pape
Predicting the Effectiveness of Self-Training: Application to Sentiment Classification
The goal of this paper is to investigate the connection between the
performance gain that can be obtained by selftraining and the similarity
between the corpora used in this approach. Self-training is a semi-supervised
technique designed to increase the performance of machine learning algorithms
by automatically classifying instances of a task and adding these as additional
training material to the same classifier. In the context of language processing
tasks, this training material is mostly an (annotated) corpus. Unfortunately
self-training does not always lead to a performance increase and whether it
will is largely unpredictable. We show that the similarity between corpora can
be used to identify those setups for which self-training can be beneficial. We
consider this research as a step in the process of developing a classifier that
is able to adapt itself to each new test corpus that it is presented with
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
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