MINA: linear probes reveal coding-sequence family signal in frozen DNA encoders (opens in new tab)

Frozen DNA encoders are often used as genomic feature extractors, but downstream fine-tuning does not show what information is already linearly accessible in their unchanged embeddings. We introduce MINA (Model Interrogation of Nucleotide Architectures), a lightweight probing benchmark for testing whether frozen DNA embeddings can recover (i) a 5-way protein-family label for each gene and (ii) the 1,536-dimensional GenePT embedding of each gene's natural-language summary. We compare recoverab...