Model reference · open weights
biobert-nli is an open-weight embedding model from gsarti. AxForge deploys and operates it for you on dedicated EU-owned hardware — with the licence handled where one is required.
Available as managed deployment — configured and operated for you on dedicated EU hardware, quoted per deployment.
What it is
| Released by | gsarti |
|---|---|
| Type | Embedding models |
| Task | Embeddings |
| Context | 512 tokens |
| Runs with | transformers |
| Released | 2022-03-02 |
| Popularity | 1k downloads / month |
| Licence | Unknown |
About
This is the model BioBERT [1] fine-tuned on the SNLI and the MultiNLI datasets using the sentence-transformers library to produce universal sentence embeddings [2].
The model uses the original BERT wordpiece vocabulary and was trained using the average pooling strategy and a softmax loss.
Base model: monologg/biobert_v1.1_pubmed from HuggingFace's AutoModel.
Training time: ~6 hours on the NVIDIA Tesla P100 GPU provided in Kaggle Notebooks.
Parameters:
| Parameter | Value |
|---|---|
| Batch size | 64 |
| Training steps | 30000 |
| Warmup steps | 1450 |
| Lowercasing | False |
| Max. Seq. Length | 128 |
Performances: The performance was evaluated on the test portion of the STS dataset using Spearman rank correlation and compared to the performances of a general BERT base model obtained with the same procedure to verify their similarity.
| Model | Score |
|---|---|
biobert-nli (this) | 73.40 |
gsarti/scibert-nli | 74.50 |
bert-base-nli-mean-tokens[3] | 77.12 |
An example usage for similarity-based scientific paper retrieval is provided in the Covid Papers Browser repository.
References:
[1] J. Lee et al, BioBERT: a pre-trained biomedical language representation model for biomedical text mining
[2] A. Conneau et al., Supervised Learning of Universal Sentence Representations from Natural Language Inference Data
[3] N. Reimers et I. Gurevych, Sentence-BERT: Sentence Embeddings using Siamese BERT-Networks
From the published model card. Full card on the HuggingFace links in the sidebar.
Using it via the API
Once AxForge deploys biobert-nli for you, it answers on the OpenAI-compatible API — the same base URL and keys as every other model. (biobert-nli 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":"biobert-nli","input":"text to embed"}'
Create an account — your API key is available in the console. 3M free tokens every 30 days with every new account.