• Use ESM-2-650M embeddings from an unmasked sequence to predict masked one-at-a-time probability vectors (by MLP), reducing the need for multiple forward passes
• Combine OFS pseudo-perplexity technique within an iterative refinement workflow (MCMC) to explore and optimize protein sequences for enhanced functional properties
• Evaluate OFS method on ProteinGym DMS assays and the fitness of reconstructed ancestral sequences. OFS pseudo-perplexity can detect the reported elevated stability in reconstructed ancestral sequences