metadata
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.