external_data/EXTERNAL_DATA.md

External data disclosure

Extra training rows were used from CatPred-DB (https://huggingface.co/datasets/RosettaCommons/CatPred-DB; Boorla and Maranas, Nature Communications 2025, doi:10.1038/s41467-025-57215-9; license CC BY 4.0). Source files used (train files for training; val/test files only to exclude their enzymes): kcat/kcat_train.csv, kcat/kcat_test.csv (only to EXCLUDE its enzymes), kcat/kcat_val.csv (only to EXCLUDE its enzymes), km/km_train.csv, km/km_test.csv (only to EXCLUDE its enzymes), km/km_val.csv (only to EXCLUDE its enzymes).

Filtering applied before training (to avoid leakage):

1. SMILES canonicalised with RDKit and mapped to the competition's SMILES strings where identical.
2. Removed (SMILES, sequence) pairs already in the competition training set.
3. Removed every enzyme sequence that appears in the public validation inputs, and every near-copy (3-mer cosine >= 0.8).
4. Only the CatPred-DB *_train.csv files are used; every enzyme that appears in its *_val.csv or *_test.csv files is removed.

The competition test set is private, so we cannot check it directly; if any test items are present in this external data, the organisers may remove them from the evaluation, as announced. The exact rows used are in external_data/catpred_filtered_rows.parquet. Protein embeddings use the pretrained ESM2 model facebook/esm2_t12_35M_UR50D (MIT license).