@inproceedings{chen-etal-2020-joint,
title = "Joint Learning with Pre-trained Transformer on Named Entity Recognition and Relation Extraction Tasks for Clinical Analytics",
author = "Chen, Miao and
Lan, Ganhui and
Du, Fang and
Lobanov, Victor",
editor = "Rumshisky, Anna and
Roberts, Kirk and
Bethard, Steven and
Naumann, Tristan",
booktitle = "Proceedings of the 3rd Clinical Natural Language Processing Workshop",
month = nov,
year = "2020",
address = "Online",
publisher = "Association for Computational Linguistics",
url = "https://aclanthology.org/2020.clinicalnlp-1.26",
doi = "10.18653/v1/2020.clinicalnlp-1.26",
pages = "234--242",
abstract = "In drug development, protocols define how clinical trials are conducted, and are therefore of paramount importance. They contain key patient-, investigator-, medication-, and study-related information, often elaborated in different sections in the protocol texts. Granular-level parsing on large quantity of existing protocols can accelerate clinical trial design and provide actionable insights into trial optimization. Here, we report our progresses in using deep learning NLP algorithms to enable automated protocol analytics. In particular, we combined a pre-trained BERT transformer model with joint-learning strategies to simultaneously identify clinically relevant entities (i.e. Named Entity Recognition) and extract the syntactic relations between these entities (i.e. Relation Extraction) from the eligibility criteria section in protocol texts. When comparing to standalone NER and RE models, our joint-learning strategy can effectively improve the performance of RE task while retaining similarly high NER performance, likely due to the synergy of optimizing toward both tasks{'} objectives via shared parameters. The derived NLP model provides an end-to-end solution to convert unstructured protocol texts into structured data source, which will be embedded into a comprehensive clinical analytics workflow for downstream trial design missions such like patient population extraction, patient enrollment rate estimation, and protocol amendment prediction.",
}
<?xml version="1.0" encoding="UTF-8"?>
<modsCollection xmlns="http://www.loc.gov/mods/v3">
<mods ID="chen-etal-2020-joint">
<titleInfo>
<title>Joint Learning with Pre-trained Transformer on Named Entity Recognition and Relation Extraction Tasks for Clinical Analytics</title>
</titleInfo>
<name type="personal">
<namePart type="given">Miao</namePart>
<namePart type="family">Chen</namePart>
<role>
<roleTerm authority="marcrelator" type="text">author</roleTerm>
</role>
</name>
<name type="personal">
<namePart type="given">Ganhui</namePart>
<namePart type="family">Lan</namePart>
<role>
<roleTerm authority="marcrelator" type="text">author</roleTerm>
</role>
</name>
<name type="personal">
<namePart type="given">Fang</namePart>
<namePart type="family">Du</namePart>
<role>
<roleTerm authority="marcrelator" type="text">author</roleTerm>
</role>
</name>
<name type="personal">
<namePart type="given">Victor</namePart>
<namePart type="family">Lobanov</namePart>
<role>
<roleTerm authority="marcrelator" type="text">author</roleTerm>
</role>
</name>
<originInfo>
<dateIssued>2020-11</dateIssued>
</originInfo>
<typeOfResource>text</typeOfResource>
<relatedItem type="host">
<titleInfo>
<title>Proceedings of the 3rd Clinical Natural Language Processing Workshop</title>
</titleInfo>
<name type="personal">
<namePart type="given">Anna</namePart>
<namePart type="family">Rumshisky</namePart>
<role>
<roleTerm authority="marcrelator" type="text">editor</roleTerm>
</role>
</name>
<name type="personal">
<namePart type="given">Kirk</namePart>
<namePart type="family">Roberts</namePart>
<role>
<roleTerm authority="marcrelator" type="text">editor</roleTerm>
</role>
</name>
<name type="personal">
<namePart type="given">Steven</namePart>
<namePart type="family">Bethard</namePart>
<role>
<roleTerm authority="marcrelator" type="text">editor</roleTerm>
</role>
</name>
<name type="personal">
<namePart type="given">Tristan</namePart>
<namePart type="family">Naumann</namePart>
<role>
<roleTerm authority="marcrelator" type="text">editor</roleTerm>
</role>
</name>
<originInfo>
<publisher>Association for Computational Linguistics</publisher>
<place>
<placeTerm type="text">Online</placeTerm>
</place>
</originInfo>
<genre authority="marcgt">conference publication</genre>
</relatedItem>
<abstract>In drug development, protocols define how clinical trials are conducted, and are therefore of paramount importance. They contain key patient-, investigator-, medication-, and study-related information, often elaborated in different sections in the protocol texts. Granular-level parsing on large quantity of existing protocols can accelerate clinical trial design and provide actionable insights into trial optimization. Here, we report our progresses in using deep learning NLP algorithms to enable automated protocol analytics. In particular, we combined a pre-trained BERT transformer model with joint-learning strategies to simultaneously identify clinically relevant entities (i.e. Named Entity Recognition) and extract the syntactic relations between these entities (i.e. Relation Extraction) from the eligibility criteria section in protocol texts. When comparing to standalone NER and RE models, our joint-learning strategy can effectively improve the performance of RE task while retaining similarly high NER performance, likely due to the synergy of optimizing toward both tasks’ objectives via shared parameters. The derived NLP model provides an end-to-end solution to convert unstructured protocol texts into structured data source, which will be embedded into a comprehensive clinical analytics workflow for downstream trial design missions such like patient population extraction, patient enrollment rate estimation, and protocol amendment prediction.</abstract>
<identifier type="citekey">chen-etal-2020-joint</identifier>
<identifier type="doi">10.18653/v1/2020.clinicalnlp-1.26</identifier>
<location>
<url>https://aclanthology.org/2020.clinicalnlp-1.26</url>
</location>
<part>
<date>2020-11</date>
<extent unit="page">
<start>234</start>
<end>242</end>
</extent>
</part>
</mods>
</modsCollection>
%0 Conference Proceedings
%T Joint Learning with Pre-trained Transformer on Named Entity Recognition and Relation Extraction Tasks for Clinical Analytics
%A Chen, Miao
%A Lan, Ganhui
%A Du, Fang
%A Lobanov, Victor
%Y Rumshisky, Anna
%Y Roberts, Kirk
%Y Bethard, Steven
%Y Naumann, Tristan
%S Proceedings of the 3rd Clinical Natural Language Processing Workshop
%D 2020
%8 November
%I Association for Computational Linguistics
%C Online
%F chen-etal-2020-joint
%X In drug development, protocols define how clinical trials are conducted, and are therefore of paramount importance. They contain key patient-, investigator-, medication-, and study-related information, often elaborated in different sections in the protocol texts. Granular-level parsing on large quantity of existing protocols can accelerate clinical trial design and provide actionable insights into trial optimization. Here, we report our progresses in using deep learning NLP algorithms to enable automated protocol analytics. In particular, we combined a pre-trained BERT transformer model with joint-learning strategies to simultaneously identify clinically relevant entities (i.e. Named Entity Recognition) and extract the syntactic relations between these entities (i.e. Relation Extraction) from the eligibility criteria section in protocol texts. When comparing to standalone NER and RE models, our joint-learning strategy can effectively improve the performance of RE task while retaining similarly high NER performance, likely due to the synergy of optimizing toward both tasks’ objectives via shared parameters. The derived NLP model provides an end-to-end solution to convert unstructured protocol texts into structured data source, which will be embedded into a comprehensive clinical analytics workflow for downstream trial design missions such like patient population extraction, patient enrollment rate estimation, and protocol amendment prediction.
%R 10.18653/v1/2020.clinicalnlp-1.26
%U https://aclanthology.org/2020.clinicalnlp-1.26
%U https://doi.org/10.18653/v1/2020.clinicalnlp-1.26
%P 234-242
Markdown (Informal)
[Joint Learning with Pre-trained Transformer on Named Entity Recognition and Relation Extraction Tasks for Clinical Analytics](https://aclanthology.org/2020.clinicalnlp-1.26) (Chen et al., ClinicalNLP 2020)
ACL