Transformer-based protein generation with regularized latent space optimization

Egbert Castro, Abhinav Godavarthi, Julian Rubinfien, Kevin B. Givechian, Dhananjay Bhaskar, Smita Krishnaswamy

Abstract: The space of possible proteins is vast, and optimizing proteins for specific target properties computationally is an ongoing challenge, even with large amounts of data. Castro and colleagues combine a transformer-based model with regularized prediction heads to form a smooth and pseudoconvex latent space that allows for easier navigation and more efficient optimization of proteins.