@inproceedings{liu-etal-2024-named,
title = "Named Entity Recognition Under Domain Shift via Metric Learning for Life Sciences",
author = "Liu, Hongyi and
Wang, Qingyun and
Karisani, Payam and
Ji, Heng",
editor = "Duh, Kevin and
Gomez, Helena and
Bethard, Steven",
booktitle = "Proceedings of the 2024 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies (Volume 1: Long Papers)",
month = jun,
year = "2024",
address = "Mexico City, Mexico",
publisher = "Association for Computational Linguistics",
url = "https://aclanthology.org/2024.naacl-long.1",
pages = "1--21",
abstract = "Named entity recognition is a key component of Information Extraction (IE), particularly in scientific domains such as biomedicine and chemistry, where large language models (LLMs), e.g., ChatGPT, fall short. We investigate the applicability of transfer learning for enhancing a named entity recognition model trained in the biomedical domain (the source domain) to be used in the chemical domain (the target domain). A common practice for training such a model in a few-shot learning setting is to pretrain the model on the labeled source data, and then, to finetune it on a hand-full of labeled target examples. In our experiments, we observed that such a model is prone to mislabeling the source entities, which can often appear in the text, as the target entities. To alleviate this problem, we propose a model to transfer the knowledge from the source domain to the target domain, but, at the same time, to project the source entities and target entities into separate regions of the feature space. This diminishes the risk of mislabeling the source entities as the target entities. Our model consists of two stages: 1) entity grouping in the source domain, which incorporates knowledge from annotated events to establish relations between entities, and 2) entity discrimination in the target domain, which relies on pseudo labeling and contrastive learning to enhance discrimination between the entities in the two domains. We conduct our extensive experiments across three source and three target datasets, demonstrating that our method outperforms the baselines by up to 5{\%} absolute value. Code, data, and resources are publicly available for research purposes: https://github.com/Lhtie/Bio-Domain-Transfer .",
}
<?xml version="1.0" encoding="UTF-8"?>
<modsCollection xmlns="http://www.loc.gov/mods/v3">
<mods ID="liu-etal-2024-named">
<titleInfo>
<title>Named Entity Recognition Under Domain Shift via Metric Learning for Life Sciences</title>
</titleInfo>
<name type="personal">
<namePart type="given">Hongyi</namePart>
<namePart type="family">Liu</namePart>
<role>
<roleTerm authority="marcrelator" type="text">author</roleTerm>
</role>
</name>
<name type="personal">
<namePart type="given">Qingyun</namePart>
<namePart type="family">Wang</namePart>
<role>
<roleTerm authority="marcrelator" type="text">author</roleTerm>
</role>
</name>
<name type="personal">
<namePart type="given">Payam</namePart>
<namePart type="family">Karisani</namePart>
<role>
<roleTerm authority="marcrelator" type="text">author</roleTerm>
</role>
</name>
<name type="personal">
<namePart type="given">Heng</namePart>
<namePart type="family">Ji</namePart>
<role>
<roleTerm authority="marcrelator" type="text">author</roleTerm>
</role>
</name>
<originInfo>
<dateIssued>2024-06</dateIssued>
</originInfo>
<typeOfResource>text</typeOfResource>
<relatedItem type="host">
<titleInfo>
<title>Proceedings of the 2024 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies (Volume 1: Long Papers)</title>
</titleInfo>
<name type="personal">
<namePart type="given">Kevin</namePart>
<namePart type="family">Duh</namePart>
<role>
<roleTerm authority="marcrelator" type="text">editor</roleTerm>
</role>
</name>
<name type="personal">
<namePart type="given">Helena</namePart>
<namePart type="family">Gomez</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>
<originInfo>
<publisher>Association for Computational Linguistics</publisher>
<place>
<placeTerm type="text">Mexico City, Mexico</placeTerm>
</place>
</originInfo>
<genre authority="marcgt">conference publication</genre>
</relatedItem>
<abstract>Named entity recognition is a key component of Information Extraction (IE), particularly in scientific domains such as biomedicine and chemistry, where large language models (LLMs), e.g., ChatGPT, fall short. We investigate the applicability of transfer learning for enhancing a named entity recognition model trained in the biomedical domain (the source domain) to be used in the chemical domain (the target domain). A common practice for training such a model in a few-shot learning setting is to pretrain the model on the labeled source data, and then, to finetune it on a hand-full of labeled target examples. In our experiments, we observed that such a model is prone to mislabeling the source entities, which can often appear in the text, as the target entities. To alleviate this problem, we propose a model to transfer the knowledge from the source domain to the target domain, but, at the same time, to project the source entities and target entities into separate regions of the feature space. This diminishes the risk of mislabeling the source entities as the target entities. Our model consists of two stages: 1) entity grouping in the source domain, which incorporates knowledge from annotated events to establish relations between entities, and 2) entity discrimination in the target domain, which relies on pseudo labeling and contrastive learning to enhance discrimination between the entities in the two domains. We conduct our extensive experiments across three source and three target datasets, demonstrating that our method outperforms the baselines by up to 5% absolute value. Code, data, and resources are publicly available for research purposes: https://github.com/Lhtie/Bio-Domain-Transfer .</abstract>
<identifier type="citekey">liu-etal-2024-named</identifier>
<location>
<url>https://aclanthology.org/2024.naacl-long.1</url>
</location>
<part>
<date>2024-06</date>
<extent unit="page">
<start>1</start>
<end>21</end>
</extent>
</part>
</mods>
</modsCollection>
%0 Conference Proceedings
%T Named Entity Recognition Under Domain Shift via Metric Learning for Life Sciences
%A Liu, Hongyi
%A Wang, Qingyun
%A Karisani, Payam
%A Ji, Heng
%Y Duh, Kevin
%Y Gomez, Helena
%Y Bethard, Steven
%S Proceedings of the 2024 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies (Volume 1: Long Papers)
%D 2024
%8 June
%I Association for Computational Linguistics
%C Mexico City, Mexico
%F liu-etal-2024-named
%X Named entity recognition is a key component of Information Extraction (IE), particularly in scientific domains such as biomedicine and chemistry, where large language models (LLMs), e.g., ChatGPT, fall short. We investigate the applicability of transfer learning for enhancing a named entity recognition model trained in the biomedical domain (the source domain) to be used in the chemical domain (the target domain). A common practice for training such a model in a few-shot learning setting is to pretrain the model on the labeled source data, and then, to finetune it on a hand-full of labeled target examples. In our experiments, we observed that such a model is prone to mislabeling the source entities, which can often appear in the text, as the target entities. To alleviate this problem, we propose a model to transfer the knowledge from the source domain to the target domain, but, at the same time, to project the source entities and target entities into separate regions of the feature space. This diminishes the risk of mislabeling the source entities as the target entities. Our model consists of two stages: 1) entity grouping in the source domain, which incorporates knowledge from annotated events to establish relations between entities, and 2) entity discrimination in the target domain, which relies on pseudo labeling and contrastive learning to enhance discrimination between the entities in the two domains. We conduct our extensive experiments across three source and three target datasets, demonstrating that our method outperforms the baselines by up to 5% absolute value. Code, data, and resources are publicly available for research purposes: https://github.com/Lhtie/Bio-Domain-Transfer .
%U https://aclanthology.org/2024.naacl-long.1
%P 1-21
Markdown (Informal)
[Named Entity Recognition Under Domain Shift via Metric Learning for Life Sciences](https://aclanthology.org/2024.naacl-long.1) (Liu et al., NAACL 2024)
ACL