Variational Active Flow Matching for Discrete Online Black-Box Optimization

Many scientific design problems require identifying rare high-fitness objects in vast discrete spaces using costly black-box feedback. Variational active-generation methods, including variational search distributions (VSD) and conditioning by adaptive sampling (CbAS), address this by learning a distribution over high-fitness designs via inference on a level-set posterior. However, these methods rely on generators with explicit likelihoods, most commonly autoregressive models, creating a mismatch with modern non-autoregressive approaches, such as discrete diffusion and flow-based models, which refine designs in parallel and better capture multi-modal structure but have implicit marginal likelihoods. We introduce \textit{Active Flow Matching} (AFM), a variational active-generation framework that removes this likelihood bottleneck by reformulating level-set KL objectives over the conditional endpoint distributions of discrete flow models. AFM yields forward-, reverse-, and symmetric-KL objectives without requiring density evaluation. We show that forward-KL AFM is target-consistent, recovering the level-set posterior without access to marginal likelihoods. Empirically, across protein and small-molecule design tasks, AFM outperforms strong baselines, including autoregressive VSD and CbAS, inference-time guidance, KL-regularised fine-tuning, and Top-$K$ retraining.