On November 12, 2026, researchers Paarth Batra and Aryan Keluskar from The Biodesign Institute released a preprint on arXiv (2611.16881v1) demonstrating that leading protein language models fail contact map prediction when subjected to invariant amino-acid alphabet relabeling. The diagnostic evaluation reveals that neural architectures rely heavily on canonical residue identities rather than learning invariant coevolutionary…
