mRNA Design and Optimization with Deep Knowledge-Infused Approach

Abstract

The mRNA optimization is essential for mRNA vaccines, therapies, and industrial protein production. Based on current explorations, an ideal optimization approach should simultaneously (i) prevent unintended amino-acid changes, (ii) optimize multiple, biologically relevant objectives, and (iii) retain computational efficiency. However, existing methods are forced to trade off between these perspectives, forming an "impossible triangle." We present RNop, a knowledge-infused Transformer that integrates mechanism-aligned losses to address this problem. By encoding biological prior knowledge in losses, RNop makes knowledge infusion explicit and controllable across optimization focus. Trained on over 6 million sequences, in silico analyses show RNop resolves the "impossible triangle" of mRNA optimization with absolute sequence fidelity, significantly improved biological metrics, and high throughput. In in vitro validation, it can deliver up to 2.28-fold expression gain. Ablation studies reveal how each prior contributes to targeted improvements, yielding mechanism-level interpretability. RNop represents a shift in mRNA optimization methodology: by infusing explicit and interpretable knowledge, the "black-box" mRNA design can be transformed into a predictable, explainable engineering problem. RNop is designed as an extensible platform: additional biological priors can be incorporated as modular, mechanism-aligned loss functions, enabling future development and adaptation to related sequence design problems.