@inproceedings{sakhovskiy-etal-2024-biomedical,
title = "Biomedical Entity Representation with Graph-Augmented Multi-Objective Transformer",
author = "Sakhovskiy, Andrey and
Semenova, Natalia and
Kadurin, Artur and
Tutubalina, Elena",
editor = "Duh, Kevin and
Gomez, Helena and
Bethard, Steven",
booktitle = "Findings of the Association for Computational Linguistics: NAACL 2024",
month = jun,
year = "2024",
address = "Mexico City, Mexico",
publisher = "Association for Computational Linguistics",
url = "https://aclanthology.org/2024.findings-naacl.288",
pages = "4626--4643",
abstract = "Modern biomedical concept representations are mostly trained on synonymous concept names from a biomedical knowledge base, ignoring the inter-concept interactions and a concept{'}s local neighborhood in a knowledge base graph. In this paper, we introduce Biomedical Entity Representation with a Graph-Augmented Multi-Objective Transformer (BERGAMOT), which adopts the power of pre-trained language models (LMs) and graph neural networks to capture both inter-concept and intra-concept interactions from the multilingual UMLS graph. To obtain fine-grained graph representations, we introduce two additional graph-based objectives: (i) a node-level contrastive objective and (ii) the Deep Graph Infomax (DGI) loss, which maximizes the mutual information between a local subgraph and a high-level graph summary. We apply contrastive loss on textual and graph representations to make them less sensitive to surface forms and enable intermodal knowledge exchange. BERGAMOT achieves state-of-the-art results in zero-shot entity linking without task-specific supervision on 4 of 5 languages of the Mantra corpus and on 8 of 10 languages of the XL-BEL benchmark.",
}
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<abstract>Modern biomedical concept representations are mostly trained on synonymous concept names from a biomedical knowledge base, ignoring the inter-concept interactions and a concept’s local neighborhood in a knowledge base graph. In this paper, we introduce Biomedical Entity Representation with a Graph-Augmented Multi-Objective Transformer (BERGAMOT), which adopts the power of pre-trained language models (LMs) and graph neural networks to capture both inter-concept and intra-concept interactions from the multilingual UMLS graph. To obtain fine-grained graph representations, we introduce two additional graph-based objectives: (i) a node-level contrastive objective and (ii) the Deep Graph Infomax (DGI) loss, which maximizes the mutual information between a local subgraph and a high-level graph summary. We apply contrastive loss on textual and graph representations to make them less sensitive to surface forms and enable intermodal knowledge exchange. BERGAMOT achieves state-of-the-art results in zero-shot entity linking without task-specific supervision on 4 of 5 languages of the Mantra corpus and on 8 of 10 languages of the XL-BEL benchmark.</abstract>
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%0 Conference Proceedings
%T Biomedical Entity Representation with Graph-Augmented Multi-Objective Transformer
%A Sakhovskiy, Andrey
%A Semenova, Natalia
%A Kadurin, Artur
%A Tutubalina, Elena
%Y Duh, Kevin
%Y Gomez, Helena
%Y Bethard, Steven
%S Findings of the Association for Computational Linguistics: NAACL 2024
%D 2024
%8 June
%I Association for Computational Linguistics
%C Mexico City, Mexico
%F sakhovskiy-etal-2024-biomedical
%X Modern biomedical concept representations are mostly trained on synonymous concept names from a biomedical knowledge base, ignoring the inter-concept interactions and a concept’s local neighborhood in a knowledge base graph. In this paper, we introduce Biomedical Entity Representation with a Graph-Augmented Multi-Objective Transformer (BERGAMOT), which adopts the power of pre-trained language models (LMs) and graph neural networks to capture both inter-concept and intra-concept interactions from the multilingual UMLS graph. To obtain fine-grained graph representations, we introduce two additional graph-based objectives: (i) a node-level contrastive objective and (ii) the Deep Graph Infomax (DGI) loss, which maximizes the mutual information between a local subgraph and a high-level graph summary. We apply contrastive loss on textual and graph representations to make them less sensitive to surface forms and enable intermodal knowledge exchange. BERGAMOT achieves state-of-the-art results in zero-shot entity linking without task-specific supervision on 4 of 5 languages of the Mantra corpus and on 8 of 10 languages of the XL-BEL benchmark.
%U https://aclanthology.org/2024.findings-naacl.288
%P 4626-4643
Markdown (Informal)
[Biomedical Entity Representation with Graph-Augmented Multi-Objective Transformer](https://aclanthology.org/2024.findings-naacl.288) (Sakhovskiy et al., Findings 2024)
ACL