Steering an ESM2-3B hydrophobicity SAE direction shifts predicted solvent accessibility

Parsan et al. scale Matryoshka SAEs to ESM2-3B and identify a single decoder feature in a layer-36 SAE that correlates strongly with residue hydrophobicity [parsan-yang-yang-2025-protein-sae-steering] Adding the unit-norm decoder vector (alpha=-0.275) to the hidden state raises ESMFold's predicted myoglobin solvent-accessible surface area 31.5% with modest structural disruption (RMSD 2.76 Angstrom) [parsan-yang-yang-2025-protein-sae-steering] The effect persists even when the correct input sequence is provided, so it acts on the structure module itself rather than via an altered predicted sequence [parsan-yang-yang-2025-protein-sae-steering] Random-direction steering gives minimal response and a strength sweep shows a monotonic dose-response (GRAVY -0.36 to +1.53) [parsan-yang-yang-2025-protein-sae-steering]