FremyCompany
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README.md
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State-of-the-art methodologies operate by maximizing the similarity in representation of names referring to the same concept, and preventing collapse through contrastive learning. However, because biomedical names are not always self-explanatory, it sometimes results in non-semantic representations.
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BioLORD overcomes this issue by grounding its concept representations using definitions, as well as short descriptions derived from a multi-relational knowledge graph consisting of biomedical ontologies. Thanks to this grounding, our model produces more semantic concept representations that match more closely the hierarchical structure of ontologies. BioLORD-2023 establishes a new state of the art for text similarity on both clinical sentences (MedSTS) and biomedical concepts (
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This model is based on [sentence-transformers/all-mpnet-base-v2](https://huggingface.co/sentence-transformers/all-mpnet-base-v2) and was further finetuned on the [BioLORD-Dataset](https://huggingface.co/datasets/FremyCompany/BioLORD-Dataset) and LLM-generated definitions from the [Automatic Glossary of Clinical Terminology (AGCT)](https://huggingface.co/datasets/FremyCompany/AGCT-Dataset).
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State-of-the-art methodologies operate by maximizing the similarity in representation of names referring to the same concept, and preventing collapse through contrastive learning. However, because biomedical names are not always self-explanatory, it sometimes results in non-semantic representations.
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BioLORD overcomes this issue by grounding its concept representations using definitions, as well as short descriptions derived from a multi-relational knowledge graph consisting of biomedical ontologies. Thanks to this grounding, our model produces more semantic concept representations that match more closely the hierarchical structure of ontologies. BioLORD-2023 establishes a new state of the art for text similarity on both clinical sentences (MedSTS) and biomedical concepts (EHR-Rel-B).
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This model is based on [sentence-transformers/all-mpnet-base-v2](https://huggingface.co/sentence-transformers/all-mpnet-base-v2) and was further finetuned on the [BioLORD-Dataset](https://huggingface.co/datasets/FremyCompany/BioLORD-Dataset) and LLM-generated definitions from the [Automatic Glossary of Clinical Terminology (AGCT)](https://huggingface.co/datasets/FremyCompany/AGCT-Dataset).
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