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arXiv · 2510.00352

AReUReDi: Annealed Rectified Updates for Refining Discrete Flows with Multi-Objective Guidance

Tong Chen·Yinuo Zhang·Pranam Chatterjee
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Abstract

Designing sequences that satisfy multiple, often conflicting, objectives is a central challenge in therapeutic and biomolecular engineering. Existing generative frameworks largely operate in continuous spaces with single-objective guidance, while discrete approaches lack guarantees for multi-objective Pareto optimality. We introduce AReUReDi (Annealed Rectified Updates for Refining Discrete Flows), a discrete optimization algorithm with theoretical guarantees of convergence to the Pareto front. Building on Rectified Discrete Flows (ReDi), AReUReDi combines Tchebycheff scalarization, locally balanced proposals, and annealed Metropolis-Hastings updates to bias sampling toward Pareto-optimal states while preserving distributional invariance. Applied to peptide and SMILES sequence design, AReUReDi simultaneously optimizes up to five therapeutic properties (including affinity, solubility, hemolysis, half-life, and non-fouling) and outperforms both evolutionary and diffusion-based baselines. These results establish AReUReDi as a powerful, sequence-based framework for multi-property biomolecule generation.

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Tong Chen, Yinuo Zhang, Pranam Chatterjee. 2025-09-30. AReUReDi: Annealed Rectified Updates for Refining Discrete Flows with Multi-Objective Guidance. https://arxiv.org/abs/2510.00352

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