Model reference · open weights
SapBERT-from-PubMedBERT-fulltext is an open-weight embedding model from cambridgeltl, listed in the AxForge catalogue. AxForge can bring it up on EU-owned hardware for you on request — with the licence handled where one is required.
About
datasets: - UMLS [news] A cross-lingual extension of SapBERT will appear in the main onference of ACL 2021! <br [news] SapBERT will appear in the conference proceedings of NAACL 2021! SapBERT-PubMedBERT SapBERT by Liu et al. (2020). Trained with UMLS 2020AA (English only), using microsoft/BiomedNLP-PubMedBERT-base-uncased-abstract-fulltext as the base model. Expected input and output 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. Extracting embeddings from SapBERT The following script converts a list of strings (entity names) into embeddings. For more details about training and eval, see SapBERT github repo. Citation
Summarised from the published model card. Read the full card on the HuggingFace links below.
Specifications
| Maker | cambridgeltl |
|---|---|
| Type | Embedding models |
| Parameters (lead) | 109M |
| Context | 512 tokens |
| Variants | 1 |
| Runs with | transformers |
| Released | 2022-03-02 |
| Popularity | 1.4M downloads / month |
| Likes | 78 |
| Licence | Open weights |
How it works
Variants
Open weights ship in several sizes and precisions. One page, all the variants — pick the one that fits your GPU. VRAM figures are estimates from model size.
| Variant | Params | Precision | VRAM | Fits 16 GB | Weights |
|---|---|---|---|---|---|
| SapBERT-from-PubMedBERT-fulltext | 109M | BF16 | ~0.3 GB | ✓ | Weights ↗ |
Using it via the API
Once AxForge deploys sapbert-from-pubmedbert-fulltext for you, it answers on the OpenAI-compatible API — the same base URL and keys as every other model. (sapbert-from-pubmedbert-fulltext below is illustrative; you get the exact model name on deployment.)
$ curl -sS https://api.axforge.ai/v1/embeddings \
-H "Authorization: Bearer $AXFORGE_API_KEY" \
-H "Content-Type: application/json" \
-d '{"model":"sapbert-from-pubmedbert-fulltext","input":"text to embed"}'
Licence
Open weights under apache-2.0 — commercial use is permitted. Deploy it on AxForge EU hardware on request. Read the licence ↗
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