Feature Extraction
Transformers
PyTorch
TensorFlow
JAX
Safetensors
English
bert
biomedical
lexical semantics
bionlp
biology
science
embedding
entity linking
Instructions to use cambridgeltl/SapBERT-from-PubMedBERT-fulltext with libraries, inference providers, notebooks, and local apps. Follow these links to get started.
- Libraries
- Transformers
How to use cambridgeltl/SapBERT-from-PubMedBERT-fulltext with Transformers:
# Use a pipeline as a high-level helper from transformers import pipeline pipe = pipeline("feature-extraction", model="cambridgeltl/SapBERT-from-PubMedBERT-fulltext")# Load model directly from transformers import AutoTokenizer, AutoModel tokenizer = AutoTokenizer.from_pretrained("cambridgeltl/SapBERT-from-PubMedBERT-fulltext") model = AutoModel.from_pretrained("cambridgeltl/SapBERT-from-PubMedBERT-fulltext", device_map="auto") - Inference
- Notebooks
- Google Colab
- Kaggle
Update README.md
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README.md
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**[news]** A cross-lingual extension of SapBERT will appear in the main onference of **ACL 2021**! <br>
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**[news]** SapBERT will appear in the conference proceedings of **NAACL 2021**!
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### Expected input and output
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The input should be a string of biomedical entity names, e.g., "covid infection" or "Hydroxychloroquine". The [CLS] embedding of the last layer is regarded as the output.
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For more details about training and eval, see SapBERT [github repo](https://github.com/cambridgeltl/sapbert).
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### SapBERT-PubMedBERT
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SapBERT by [Liu et al. (2020)](https://arxiv.org/pdf/2010.11784.pdf). Trained with [UMLS](https://www.nlm.nih.gov/research/umls/licensedcontent/umlsknowledgesources.html) 2020AA (English only), using [microsoft/BiomedNLP-PubMedBERT-base-uncased-abstract-fulltext](https://huggingface.co/microsoft/BiomedNLP-PubMedBERT-base-uncased-abstract-fulltext) as the base model.
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### Citation
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```bibtex
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**[news]** A cross-lingual extension of SapBERT will appear in the main onference of **ACL 2021**! <br>
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**[news]** SapBERT will appear in the conference proceedings of **NAACL 2021**!
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### SapBERT-PubMedBERT
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SapBERT by [Liu et al. (2020)](https://arxiv.org/pdf/2010.11784.pdf). Trained with [UMLS](https://www.nlm.nih.gov/research/umls/licensedcontent/umlsknowledgesources.html) 2020AA (English only), using [microsoft/BiomedNLP-PubMedBERT-base-uncased-abstract-fulltext](https://huggingface.co/microsoft/BiomedNLP-PubMedBERT-base-uncased-abstract-fulltext) as the base model.
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### Expected input and output
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The input should be a string of biomedical entity names, e.g., "covid infection" or "Hydroxychloroquine". The [CLS] embedding of the last layer is regarded as the output.
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For more details about training and eval, see SapBERT [github repo](https://github.com/cambridgeltl/sapbert).
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### Citation
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```bibtex
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