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arXiv · 2606.19496

Calibrating Generative Models to Feature Distributions with MMD Finetuning

Nathaniel L. Diamant·Brian L. Trippe
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Abstract

Generative models can produce individually plausible samples while deviating substantially from a target set in the distribution of key features. For example, a model pretrained on broad drug-like chemical space may generate molecules whose molecular features differ from those of a therapeutic class of interest, such as known antibiotics. Correcting such distributional miscalibration is challenging: direct finetuning on the target set can overfit and does not control which features are matched. To fill this gap, we introduce kernel Calibrating Generative Models (kCGM). kCGM minimizes a maximum mean discrepancy (MMD) between generated and target feature distributions using an unbiased score-function estimator, with KL regularization to remain close to the pretrained model. On a target set of 174 antibiotics, direct finetuning sacrifices chemical validity for feature-distribution matching, whereas kCGM improves target feature matching while increasing validity. We further demonstrate kCGM in protein and DNA generation tasks, showing it can adapt autoregressive, continuous-space diffusion, and discrete diffusion models using only feature-level supervision. Code is available at https://github.com/smithhenryd/cgm.

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Nathaniel L. Diamant, Brian L. Trippe. 2026-06-17. Calibrating Generative Models to Feature Distributions with MMD Finetuning. https://arxiv.org/abs/2606.19496

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