Messenger RNA Design via Expected Partition Function and Continuous Optimization

TL;DR

This paper introduces a continuous optimization framework for RNA design using an expected partition function, enabling more effective ensemble free energy optimization compared to traditional methods like LinearDesign.

Contribution

The authors develop a novel continuous optimization approach for RNA design based on the expected partition function, improving ensemble free energy optimization.

Findings

Outperforms LinearDesign in ensemble free energy minimization.

Provides larger improvements on longer RNA sequences.

Enables gradient descent optimization for discrete RNA design problems.

Abstract

The tasks of designing RNAs are discrete optimization problems, and several versions of these problems are NP-hard. As an alternative to commonly used local search methods, we formulate these problems as continuous optimization and develop a general framework for this optimization based on a generalization of classical partition function which we call "expected partition function". The basic idea is to start with a distribution over all possible candidate sequences, and extend the objective function from a sequence to a distribution. We then use gradient descent-based optimization methods to improve the extended objective function, and the distribution will gradually shrink towards a one-hot sequence (i.e., a single sequence). As a case study, we consider the important problem of mRNA design with wide applications in vaccines and therapeutics. While the recent work of LinearDesign can efficiently optimize mRNAs for minimum free energy (MFE), optimizing for ensemble free energy is much harder and likely intractable. Our approach can consistently improve over the LinearDesign solution in terms of ensemble free energy, with bigger improvements on longer sequences.