@inproceedings{shlyk-etal-2024-real,
title = "{REAL}: A Retrieval-Augmented Entity Linking Approach for Biomedical Concept Recognition",
author = "Shlyk, Darya and
Groza, Tudor and
Mesiti, Marco and
Montanelli, Stefano and
Cavalleri, Emanuele",
editor = "Demner-Fushman, Dina and
Ananiadou, Sophia and
Miwa, Makoto and
Roberts, Kirk and
Tsujii, Junichi",
booktitle = "Proceedings of the 23rd Workshop on Biomedical Natural Language Processing",
month = aug,
year = "2024",
address = "Bangkok, Thailand",
publisher = "Association for Computational Linguistics",
url = "https://aclanthology.org/2024.bionlp-1.29",
doi = "10.18653/v1/2024.bionlp-1.29",
pages = "380--389",
abstract = "Large Language Models (LLMs) offer an appealing alternative to training dedicated models for many Natural Language Processing (NLP) tasks. However, outdated knowledge and hallucination issues can be major obstacles in their application in knowledge-intensive biomedical scenarios. In this study, we consider the task of biomedical concept recognition (CR) from unstructured scientific literature and explore the use of Retrieval Augmented Generation (RAG) to improve accuracy and reliability of the LLM-based biomedical CR. Our approach, named REAL (Retrieval Augmented Entity Linking), combines the generative capabilities of LLMs with curated knowledge bases to automatically annotate natural language texts with concepts from bio-ontologies. By applying REAL to benchmark corpora on phenotype concept recognition, we show its effectiveness in improving LLM-based CR performance. This research highlights the potential of combining LLMs with external knowledge sources to advance biomedical text processing.",
}
<?xml version="1.0" encoding="UTF-8"?>
<modsCollection xmlns="http://www.loc.gov/mods/v3">
<mods ID="shlyk-etal-2024-real">
<titleInfo>
<title>REAL: A Retrieval-Augmented Entity Linking Approach for Biomedical Concept Recognition</title>
</titleInfo>
<name type="personal">
<namePart type="given">Darya</namePart>
<namePart type="family">Shlyk</namePart>
<role>
<roleTerm authority="marcrelator" type="text">author</roleTerm>
</role>
</name>
<name type="personal">
<namePart type="given">Tudor</namePart>
<namePart type="family">Groza</namePart>
<role>
<roleTerm authority="marcrelator" type="text">author</roleTerm>
</role>
</name>
<name type="personal">
<namePart type="given">Marco</namePart>
<namePart type="family">Mesiti</namePart>
<role>
<roleTerm authority="marcrelator" type="text">author</roleTerm>
</role>
</name>
<name type="personal">
<namePart type="given">Stefano</namePart>
<namePart type="family">Montanelli</namePart>
<role>
<roleTerm authority="marcrelator" type="text">author</roleTerm>
</role>
</name>
<name type="personal">
<namePart type="given">Emanuele</namePart>
<namePart type="family">Cavalleri</namePart>
<role>
<roleTerm authority="marcrelator" type="text">author</roleTerm>
</role>
</name>
<originInfo>
<dateIssued>2024-08</dateIssued>
</originInfo>
<typeOfResource>text</typeOfResource>
<relatedItem type="host">
<titleInfo>
<title>Proceedings of the 23rd Workshop on Biomedical Natural Language Processing</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">Sophia</namePart>
<namePart type="family">Ananiadou</namePart>
<role>
<roleTerm authority="marcrelator" type="text">editor</roleTerm>
</role>
</name>
<name type="personal">
<namePart type="given">Makoto</namePart>
<namePart type="family">Miwa</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">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">Bangkok, Thailand</placeTerm>
</place>
</originInfo>
<genre authority="marcgt">conference publication</genre>
</relatedItem>
<abstract>Large Language Models (LLMs) offer an appealing alternative to training dedicated models for many Natural Language Processing (NLP) tasks. However, outdated knowledge and hallucination issues can be major obstacles in their application in knowledge-intensive biomedical scenarios. In this study, we consider the task of biomedical concept recognition (CR) from unstructured scientific literature and explore the use of Retrieval Augmented Generation (RAG) to improve accuracy and reliability of the LLM-based biomedical CR. Our approach, named REAL (Retrieval Augmented Entity Linking), combines the generative capabilities of LLMs with curated knowledge bases to automatically annotate natural language texts with concepts from bio-ontologies. By applying REAL to benchmark corpora on phenotype concept recognition, we show its effectiveness in improving LLM-based CR performance. This research highlights the potential of combining LLMs with external knowledge sources to advance biomedical text processing.</abstract>
<identifier type="citekey">shlyk-etal-2024-real</identifier>
<identifier type="doi">10.18653/v1/2024.bionlp-1.29</identifier>
<location>
<url>https://aclanthology.org/2024.bionlp-1.29</url>
</location>
<part>
<date>2024-08</date>
<extent unit="page">
<start>380</start>
<end>389</end>
</extent>
</part>
</mods>
</modsCollection>
%0 Conference Proceedings
%T REAL: A Retrieval-Augmented Entity Linking Approach for Biomedical Concept Recognition
%A Shlyk, Darya
%A Groza, Tudor
%A Mesiti, Marco
%A Montanelli, Stefano
%A Cavalleri, Emanuele
%Y Demner-Fushman, Dina
%Y Ananiadou, Sophia
%Y Miwa, Makoto
%Y Roberts, Kirk
%Y Tsujii, Junichi
%S Proceedings of the 23rd Workshop on Biomedical Natural Language Processing
%D 2024
%8 August
%I Association for Computational Linguistics
%C Bangkok, Thailand
%F shlyk-etal-2024-real
%X Large Language Models (LLMs) offer an appealing alternative to training dedicated models for many Natural Language Processing (NLP) tasks. However, outdated knowledge and hallucination issues can be major obstacles in their application in knowledge-intensive biomedical scenarios. In this study, we consider the task of biomedical concept recognition (CR) from unstructured scientific literature and explore the use of Retrieval Augmented Generation (RAG) to improve accuracy and reliability of the LLM-based biomedical CR. Our approach, named REAL (Retrieval Augmented Entity Linking), combines the generative capabilities of LLMs with curated knowledge bases to automatically annotate natural language texts with concepts from bio-ontologies. By applying REAL to benchmark corpora on phenotype concept recognition, we show its effectiveness in improving LLM-based CR performance. This research highlights the potential of combining LLMs with external knowledge sources to advance biomedical text processing.
%R 10.18653/v1/2024.bionlp-1.29
%U https://aclanthology.org/2024.bionlp-1.29
%U https://doi.org/10.18653/v1/2024.bionlp-1.29
%P 380-389
Markdown (Informal)
[REAL: A Retrieval-Augmented Entity Linking Approach for Biomedical Concept Recognition](https://aclanthology.org/2024.bionlp-1.29) (Shlyk et al., BioNLP-WS 2024)
ACL