Distant Supervision with Transductive Learning for Adverse Drug Reaction Identification from Electronic Medical Records
Information extraction and knowledge discovery regarding adverse drug reaction (ADR) from large-scale clinical texts are very useful and needy processes. Two major difficulties of this task are the lack of domain experts for labeling examples and intractable processing of unstructured clinical texts...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Hindawi
2017
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5635478/ https://www.ncbi.nlm.nih.gov/pubmed/29090077 http://dx.doi.org/10.1155/2017/7575280 |
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author | Taewijit, Siriwon Theeramunkong, Thanaruk Ikeda, Mitsuru |
author_facet | Taewijit, Siriwon Theeramunkong, Thanaruk Ikeda, Mitsuru |
author_sort | Taewijit, Siriwon |
collection | PubMed |
description | Information extraction and knowledge discovery regarding adverse drug reaction (ADR) from large-scale clinical texts are very useful and needy processes. Two major difficulties of this task are the lack of domain experts for labeling examples and intractable processing of unstructured clinical texts. Even though most previous works have been conducted on these issues by applying semisupervised learning for the former and a word-based approach for the latter, they face with complexity in an acquisition of initial labeled data and ignorance of structured sequence of natural language. In this study, we propose automatic data labeling by distant supervision where knowledge bases are exploited to assign an entity-level relation label for each drug-event pair in texts, and then, we use patterns for characterizing ADR relation. The multiple-instance learning with expectation-maximization method is employed to estimate model parameters. The method applies transductive learning to iteratively reassign a probability of unknown drug-event pair at the training time. By investigating experiments with 50,998 discharge summaries, we evaluate our method by varying large number of parameters, that is, pattern types, pattern-weighting models, and initial and iterative weightings of relations for unlabeled data. Based on evaluations, our proposed method outperforms the word-based feature for NB-EM (iEM), MILR, and TSVM with F1 score of 11.3%, 9.3%, and 6.5% improvement, respectively. |
format | Online Article Text |
id | pubmed-5635478 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | Hindawi |
record_format | MEDLINE/PubMed |
spelling | pubmed-56354782017-10-31 Distant Supervision with Transductive Learning for Adverse Drug Reaction Identification from Electronic Medical Records Taewijit, Siriwon Theeramunkong, Thanaruk Ikeda, Mitsuru J Healthc Eng Research Article Information extraction and knowledge discovery regarding adverse drug reaction (ADR) from large-scale clinical texts are very useful and needy processes. Two major difficulties of this task are the lack of domain experts for labeling examples and intractable processing of unstructured clinical texts. Even though most previous works have been conducted on these issues by applying semisupervised learning for the former and a word-based approach for the latter, they face with complexity in an acquisition of initial labeled data and ignorance of structured sequence of natural language. In this study, we propose automatic data labeling by distant supervision where knowledge bases are exploited to assign an entity-level relation label for each drug-event pair in texts, and then, we use patterns for characterizing ADR relation. The multiple-instance learning with expectation-maximization method is employed to estimate model parameters. The method applies transductive learning to iteratively reassign a probability of unknown drug-event pair at the training time. By investigating experiments with 50,998 discharge summaries, we evaluate our method by varying large number of parameters, that is, pattern types, pattern-weighting models, and initial and iterative weightings of relations for unlabeled data. Based on evaluations, our proposed method outperforms the word-based feature for NB-EM (iEM), MILR, and TSVM with F1 score of 11.3%, 9.3%, and 6.5% improvement, respectively. Hindawi 2017 2017-09-26 /pmc/articles/PMC5635478/ /pubmed/29090077 http://dx.doi.org/10.1155/2017/7575280 Text en Copyright © 2017 Siriwon Taewijit et al. https://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Article Taewijit, Siriwon Theeramunkong, Thanaruk Ikeda, Mitsuru Distant Supervision with Transductive Learning for Adverse Drug Reaction Identification from Electronic Medical Records |
title | Distant Supervision with Transductive Learning for Adverse Drug Reaction Identification from Electronic Medical Records |
title_full | Distant Supervision with Transductive Learning for Adverse Drug Reaction Identification from Electronic Medical Records |
title_fullStr | Distant Supervision with Transductive Learning for Adverse Drug Reaction Identification from Electronic Medical Records |
title_full_unstemmed | Distant Supervision with Transductive Learning for Adverse Drug Reaction Identification from Electronic Medical Records |
title_short | Distant Supervision with Transductive Learning for Adverse Drug Reaction Identification from Electronic Medical Records |
title_sort | distant supervision with transductive learning for adverse drug reaction identification from electronic medical records |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5635478/ https://www.ncbi.nlm.nih.gov/pubmed/29090077 http://dx.doi.org/10.1155/2017/7575280 |
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