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:
1from huggingface_hub import hf_hub_download
2
3checkpoint = hf_hub_download(
4 repo_id="supanthadey1/bertose-glycan-encoder",
5 filename="checkpoints/bertose_glycan_encoder.pt",
6)
7vocab = hf_hub_download(
8 repo_id="supanthadey1/bertose-glycan-encoder",
9 filename="vocab/bpe_vocabulary.json",
10)
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.
License
This repository is released under the Apache License 2.0. See LICENSE.
This repository does not perform IUPAC-condensed/name-to-WURCS conversion. For now, provide WURCS directly.
