| # Revised (shortcut-controlled) datasets | |
| Datasets for the revised *Emergence of Biological Structural Discovery in General-Purpose | |
| Language Models*. These remove the length and composition shortcuts present in naive constructions. | |
| - `protein_pairs_matched.csv` — standard homology, **length-matched** negatives | |
| (|len1-len2| ~2.6 for both classes). Columns: sentence1, sentence2, label, split. | |
| - `protein_pairs_remote_matched.csv` — remote homology (<25% identity, SCOP same-superfamily), | |
| length-matched; **no length/composition/k-mer shortcut** (a length+composition classifier scores | |
| 0.50, chance). Columns: sentence1, sentence2, label, split. | |
| `split` ∈ {train, val, test}. Validation is used only for polarity calibration; test is never used | |
| for model selection. Code: https://github.com/maris205/biopaws | |