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Multi-ontology embeddings approach on human-aligned multi-ontologies representation for gene-disease associations prediction()

OBJECTIVES: Knowledge graphs and ontologies in the biomedical domain provide rich contextual knowledge for a variety of challenges. Employing that for knowledge-driven NLP tasks such as gene-disease association prediction represents a promising way to increase the predictive power of a model. METHOD...

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Autores principales: Wang, Yihao, Wegner, Philipp, Domingo-Fernández, Daniel, Tom Kodamullil, Alpha
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10651438/
https://www.ncbi.nlm.nih.gov/pubmed/38027969
http://dx.doi.org/10.1016/j.heliyon.2023.e21502
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author Wang, Yihao
Wegner, Philipp
Domingo-Fernández, Daniel
Tom Kodamullil, Alpha
author_facet Wang, Yihao
Wegner, Philipp
Domingo-Fernández, Daniel
Tom Kodamullil, Alpha
author_sort Wang, Yihao
collection PubMed
description OBJECTIVES: Knowledge graphs and ontologies in the biomedical domain provide rich contextual knowledge for a variety of challenges. Employing that for knowledge-driven NLP tasks such as gene-disease association prediction represents a promising way to increase the predictive power of a model. METHODS: We investigated the power of infusing the embedding of two aligned ontologies as prior knowledge to the NLP models. We evaluated the performance of different models on some large-scale gene-disease association datasets and compared it with a model without incorporating contextualized knowledge (BERT). RESULTS: The experiments demonstrated that the knowledge-infused model slightly outperforms BERT by creating a small number of bridges. Thus, indicating that incorporating cross-references across ontologies can enhance the performance of base models without the need for more complex and costly training. However, further research is needed to explore the generalizability of the model. We expected that adding more bridges would bring further improvement based on the trend we observed in the experiments. In addition, the use of state-of-the-art knowledge graph embedding methods on a joint graph from connecting OGG and DOID with bridges also yielded promising results. CONCLUSION: Our work shows that allowing language models to leverage structured knowledge from ontologies does come with clear advantages in the performance. Besides, the annotation stage brought out in this paper is constrained in reasonable complexity.
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spelling pubmed-106514382023-10-30 Multi-ontology embeddings approach on human-aligned multi-ontologies representation for gene-disease associations prediction() Wang, Yihao Wegner, Philipp Domingo-Fernández, Daniel Tom Kodamullil, Alpha Heliyon Research Article OBJECTIVES: Knowledge graphs and ontologies in the biomedical domain provide rich contextual knowledge for a variety of challenges. Employing that for knowledge-driven NLP tasks such as gene-disease association prediction represents a promising way to increase the predictive power of a model. METHODS: We investigated the power of infusing the embedding of two aligned ontologies as prior knowledge to the NLP models. We evaluated the performance of different models on some large-scale gene-disease association datasets and compared it with a model without incorporating contextualized knowledge (BERT). RESULTS: The experiments demonstrated that the knowledge-infused model slightly outperforms BERT by creating a small number of bridges. Thus, indicating that incorporating cross-references across ontologies can enhance the performance of base models without the need for more complex and costly training. However, further research is needed to explore the generalizability of the model. We expected that adding more bridges would bring further improvement based on the trend we observed in the experiments. In addition, the use of state-of-the-art knowledge graph embedding methods on a joint graph from connecting OGG and DOID with bridges also yielded promising results. CONCLUSION: Our work shows that allowing language models to leverage structured knowledge from ontologies does come with clear advantages in the performance. Besides, the annotation stage brought out in this paper is constrained in reasonable complexity. Elsevier 2023-10-30 /pmc/articles/PMC10651438/ /pubmed/38027969 http://dx.doi.org/10.1016/j.heliyon.2023.e21502 Text en © 2023 The Authors https://creativecommons.org/licenses/by/4.0/This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Research Article
Wang, Yihao
Wegner, Philipp
Domingo-Fernández, Daniel
Tom Kodamullil, Alpha
Multi-ontology embeddings approach on human-aligned multi-ontologies representation for gene-disease associations prediction()
title Multi-ontology embeddings approach on human-aligned multi-ontologies representation for gene-disease associations prediction()
title_full Multi-ontology embeddings approach on human-aligned multi-ontologies representation for gene-disease associations prediction()
title_fullStr Multi-ontology embeddings approach on human-aligned multi-ontologies representation for gene-disease associations prediction()
title_full_unstemmed Multi-ontology embeddings approach on human-aligned multi-ontologies representation for gene-disease associations prediction()
title_short Multi-ontology embeddings approach on human-aligned multi-ontologies representation for gene-disease associations prediction()
title_sort multi-ontology embeddings approach on human-aligned multi-ontologies representation for gene-disease associations prediction()
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10651438/
https://www.ncbi.nlm.nih.gov/pubmed/38027969
http://dx.doi.org/10.1016/j.heliyon.2023.e21502
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