# AFFINose Interaction Training

This folder is the public entrypoint for AFFINose training and data preparation.

The executable source files are currently preserved in the historical interaction-training directory:

```text
../bertint/
```

Use these files for the AFFINose workflow:

| Step | File |
|---|---|
| Build combined protein-glycan binding data | `../bertint/build_combined_dataset.py` |
| Generate glycan-disjoint splits | `../bertint/generate_glycan_splits.py` |
| Define the AFFINose model | `../bertint/bertint_v8.py` |
| Define the AFFINose dataset | `../bertint/dataset_v8.py` |
| Train AFFINose | `../bertint/training_v8.py` |
| Run AFFINose inference from a checkpoint | `../bertint/bertint_v8_inference.py` |
| Compare ablations | `../bertint/compare_ablation.py` |

The historical filenames are retained to keep the code traceable to the original training logs and manuscript provenance. In public-facing text, refer to this workflow as AFFINose.