bio2nl — data for Asymmetric Structural Transfer Between Natural Language and Biological Foundation Models

Datasets accompanying the bio2nl study of directional cross-domain structural transfer. Code: https://github.com/maris205/bio2nl

Contents

cpt_corpus/ — iso-token continued-pretraining corpora

Each file is exactly 50M GPT-2 tokens, differing only in sequence content (the iso-token ablation). Proteins are rendered as space-separated residues <protein> M K V ... </protein>.

file	content
cpt_protein.txt	real Swiss-Prot proteins (G2, main)
cpt_shuffled.txt	residue-shuffled proteins (G3; same AA freq/length, destroyed structure)
cpt_randomaa.txt	random amino acids from background frequency (G4)
cpt_text.txt	OpenWebText English (G1, control)
sprot.fasta	full Swiss-Prot source (575,503 proteins)
manifest.json	exact token counts per corpus

eval_nl/ — synthetic structural evaluation tasks

• dyck_L{40,60}_t3_*.jsonl — nested-bracket well-formedness (hard, non-saturating long-range structure)
• longrange_d{8,16,24}_*.jsonl — subject–verb agreement across distractors

Related

Protein-homology pairs use the existing dnagpt/biopaws release. PAWS-X, GLUE (CoLA/RTE), OpenWebText are downloaded from their standard sources.