| --- |
| library_name: pytorch |
| license: other |
| tags: |
| - glycans |
| - wurcs |
| - bertose |
| - embeddings |
| - pytorch |
| --- |
| |
| # BERTose Glycan Encoder |
|
|
| This repository contains the BERTose checkpoint for WURCS glycan embedding inference. It is the release-facing glycan representation model used by the companion notebook. |
|
|
| ## Quick Start |
|
|
| The recommended user path is the companion notebook: |
|
|
| ```python |
| from huggingface_hub import hf_hub_download |
| |
| checkpoint = hf_hub_download( |
| repo_id="supanthadey1/bertose-glycan-encoder", |
| filename="checkpoints/bertose_glycan_encoder.pt", |
| ) |
| vocab = hf_hub_download( |
| repo_id="supanthadey1/bertose-glycan-encoder", |
| filename="vocab/bpe_vocabulary.json", |
| ) |
| ``` |
|
|
| No Hugging Face token is required for this BERTose checkpoint now that the repository is public. |
|
|
| ## Files |
|
|
| - `checkpoints/bertose_glycan_encoder.pt` - BERTose glycan encoder checkpoint. |
| - `vocab/bpe_vocabulary.json` - WURCS BPE vocabulary. |
| - `src/bertose_model.py` - BERTose model definition. |
| - `src/bertose_layers.py` - Transformer layers used by BERTose. |
| - `src/wurcs_bpe_tokenizer.py` - WURCS BPE tokenizer. |
|
|
| ## Input |
|
|
| Provide one WURCS glycan string or a CSV batch with `sample_id,wurcs`. |
|
|
| Free-text glycan names, common names, SNFG drawings, and IUPAC-condensed strings are not parsed directly by this checkpoint. Convert those inputs to WURCS first, then run BERTose embedding inference. |
|
|
| ## Output |
|
|
| Dense glycan embeddings. The companion notebook defaults to `[CLS]` pooling and also supports mean pooling over valid glycan tokens. |
|
|
| ## Notes |
|
|
| This repository does not perform IUPAC-condensed/name-to-WURCS conversion. For now, provide WURCS directly. |
|
|
| License metadata is currently `other`; update it when the final release license and citation text are chosen. |
|
|
