@inproceedings{newman-griffis-zirikly-2018-embedding,
title = "Embedding Transfer for Low-Resource Medical Named Entity Recognition: A Case Study on Patient Mobility",
author = "Newman-Griffis, Denis and
Zirikly, Ayah",
editor = "Demner-Fushman, Dina and
Cohen, Kevin Bretonnel and
Ananiadou, Sophia and
Tsujii, Junichi",
booktitle = "Proceedings of the {B}io{NLP} 2018 workshop",
month = jul,
year = "2018",
address = "Melbourne, Australia",
publisher = "Association for Computational Linguistics",
url = "https://aclanthology.org/W18-2301",
doi = "10.18653/v1/W18-2301",
pages = "1--11",
abstract = "Functioning is gaining recognition as an important indicator of global health, but remains under-studied in medical natural language processing research. We present the first analysis of automatically extracting descriptions of patient mobility, using a recently-developed dataset of free text electronic health records. We frame the task as a named entity recognition (NER) problem, and investigate the applicability of NER techniques to mobility extraction. As text corpora focused on patient functioning are scarce, we explore domain adaptation of word embeddings for use in a recurrent neural network NER system. We find that embeddings trained on a small in-domain corpus perform nearly as well as those learned from large out-of-domain corpora, and that domain adaptation techniques yield additional improvements in both precision and recall. Our analysis identifies several significant challenges in extracting descriptions of patient mobility, including the length and complexity of annotated entities and high linguistic variability in mobility descriptions.",
}
<?xml version="1.0" encoding="UTF-8"?>
<modsCollection xmlns="http://www.loc.gov/mods/v3">
<mods ID="newman-griffis-zirikly-2018-embedding">
<titleInfo>
<title>Embedding Transfer for Low-Resource Medical Named Entity Recognition: A Case Study on Patient Mobility</title>
</titleInfo>
<name type="personal">
<namePart type="given">Denis</namePart>
<namePart type="family">Newman-Griffis</namePart>
<role>
<roleTerm authority="marcrelator" type="text">author</roleTerm>
</role>
</name>
<name type="personal">
<namePart type="given">Ayah</namePart>
<namePart type="family">Zirikly</namePart>
<role>
<roleTerm authority="marcrelator" type="text">author</roleTerm>
</role>
</name>
<originInfo>
<dateIssued>2018-07</dateIssued>
</originInfo>
<typeOfResource>text</typeOfResource>
<relatedItem type="host">
<titleInfo>
<title>Proceedings of the BioNLP 2018 workshop</title>
</titleInfo>
<name type="personal">
<namePart type="given">Dina</namePart>
<namePart type="family">Demner-Fushman</namePart>
<role>
<roleTerm authority="marcrelator" type="text">editor</roleTerm>
</role>
</name>
<name type="personal">
<namePart type="given">Kevin</namePart>
<namePart type="given">Bretonnel</namePart>
<namePart type="family">Cohen</namePart>
<role>
<roleTerm authority="marcrelator" type="text">editor</roleTerm>
</role>
</name>
<name type="personal">
<namePart type="given">Sophia</namePart>
<namePart type="family">Ananiadou</namePart>
<role>
<roleTerm authority="marcrelator" type="text">editor</roleTerm>
</role>
</name>
<name type="personal">
<namePart type="given">Junichi</namePart>
<namePart type="family">Tsujii</namePart>
<role>
<roleTerm authority="marcrelator" type="text">editor</roleTerm>
</role>
</name>
<originInfo>
<publisher>Association for Computational Linguistics</publisher>
<place>
<placeTerm type="text">Melbourne, Australia</placeTerm>
</place>
</originInfo>
<genre authority="marcgt">conference publication</genre>
</relatedItem>
<abstract>Functioning is gaining recognition as an important indicator of global health, but remains under-studied in medical natural language processing research. We present the first analysis of automatically extracting descriptions of patient mobility, using a recently-developed dataset of free text electronic health records. We frame the task as a named entity recognition (NER) problem, and investigate the applicability of NER techniques to mobility extraction. As text corpora focused on patient functioning are scarce, we explore domain adaptation of word embeddings for use in a recurrent neural network NER system. We find that embeddings trained on a small in-domain corpus perform nearly as well as those learned from large out-of-domain corpora, and that domain adaptation techniques yield additional improvements in both precision and recall. Our analysis identifies several significant challenges in extracting descriptions of patient mobility, including the length and complexity of annotated entities and high linguistic variability in mobility descriptions.</abstract>
<identifier type="citekey">newman-griffis-zirikly-2018-embedding</identifier>
<identifier type="doi">10.18653/v1/W18-2301</identifier>
<location>
<url>https://aclanthology.org/W18-2301</url>
</location>
<part>
<date>2018-07</date>
<extent unit="page">
<start>1</start>
<end>11</end>
</extent>
</part>
</mods>
</modsCollection>
%0 Conference Proceedings
%T Embedding Transfer for Low-Resource Medical Named Entity Recognition: A Case Study on Patient Mobility
%A Newman-Griffis, Denis
%A Zirikly, Ayah
%Y Demner-Fushman, Dina
%Y Cohen, Kevin Bretonnel
%Y Ananiadou, Sophia
%Y Tsujii, Junichi
%S Proceedings of the BioNLP 2018 workshop
%D 2018
%8 July
%I Association for Computational Linguistics
%C Melbourne, Australia
%F newman-griffis-zirikly-2018-embedding
%X Functioning is gaining recognition as an important indicator of global health, but remains under-studied in medical natural language processing research. We present the first analysis of automatically extracting descriptions of patient mobility, using a recently-developed dataset of free text electronic health records. We frame the task as a named entity recognition (NER) problem, and investigate the applicability of NER techniques to mobility extraction. As text corpora focused on patient functioning are scarce, we explore domain adaptation of word embeddings for use in a recurrent neural network NER system. We find that embeddings trained on a small in-domain corpus perform nearly as well as those learned from large out-of-domain corpora, and that domain adaptation techniques yield additional improvements in both precision and recall. Our analysis identifies several significant challenges in extracting descriptions of patient mobility, including the length and complexity of annotated entities and high linguistic variability in mobility descriptions.
%R 10.18653/v1/W18-2301
%U https://aclanthology.org/W18-2301
%U https://doi.org/10.18653/v1/W18-2301
%P 1-11
Markdown (Informal)
[Embedding Transfer for Low-Resource Medical Named Entity Recognition: A Case Study on Patient Mobility](https://aclanthology.org/W18-2301) (Newman-Griffis & Zirikly, BioNLP 2018)
ACL