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Uncertainty Estimation for Molecular Diffusion Models

arXiv:2606.13451v1 Announce Type: new Abstract: Diffusion models have seen wide adoption for 3D molecular generation, yet they offer no principled signal of when a generated molecule is likely to be of low quality. We propose a post-hoc method for estimating per-sample uncertainty in pretrained molecular diffusion models. Building on a Laplace approximation of the denoising network, we measure the variability of the noise prediction across the generation trajectory. Empirically, we show that the resulting uncertainty score is informative of sample quality, exhibiting a negative correlation with established sample-level quality metrics. We further study how the proposed uncertainty score can be used to filter generated samples, improving model performance via test-time scaling.

Variational Test-time Optimization for Diffusion Synchronization

Collaborative generation, which coordinates multiple diffusion trajectories to extend the capabilities of pretrained priors, has emerged as a powerful paradigm for extending the applicability of diffusion models. Among existing approaches, diffusion synchronization provides a scenario-agnostic solution by introducing general guidance mechanisms. However, current synchronization approaches rely heavily on heuristics and still require task-specific tailoring, which limits their generalizability and performance. In this work, we mathematically derive a synchronization framework based on optimal control, providing a principled explanation of diffusion synchronization. During sampling, we optimize control variables to guide multiple trajectories toward coherent solutions while remaining close to the underlying diffusion prior. Our method operates entirely at test-time without additional training, thereby enabling broad applicability across diverse generation scenarios when combined with strong pretrained priors. We demonstrate consistent improvements over baselines on three representative collaborative generation tasks, covering a wide range of modalities and applications. Beyond performance gains, our work establishes a novel foundation for collaborative generation, opening a principled path toward extending pretrained generative models to new collaborative generation settings.