---
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.

## 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 a WURCS column. The notebook examples use `wurcs` as the column name.

## 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 to WURCS conversion. For now, provide WURCS directly.

The final license and citation text should be set before public release.