PQMass: Probabilistic Assessment of the Quality of Generative Models using Probability Mass Estimation

Conditional generators provide a natural tool for controllable generation, including settings where the desired condition is a new composition of observed attributes or experimental factors. In many applications, especially in scientific domains, such models are attractive to explore conditions for which real samples are rare, expensive, or not yet observed. However, this creates a circularity for evaluation: standard conditional quality metrics require a reference target distribution, but in the extrapolative regime that distribution is unavailable by definition. We address this problem with a post-hoc, per-sample trust score for assessing conditional samples using only the training distribution. The score combines two estimable quantities: global realism, measuring compatibility with the real data manifold, and attribute-wise faithfulness, measuring whether a sample is closer to the requested attributes than to plausible alternatives. We show that the score can recover meaningful comparisons across extrapolated generations, under a mild coverage condition on the observed attributes. These comparisons enable effective filtering, ranking, and abstention of generations and can be used directly on off-the-shelf pretrained models. In biological imaging, selected samples preserve real morphological structure better and improve downstream predictive performance, while similar gains are observed on controlled vision benchmarks. Finally, we show how the score can be applied during generation, enabling abstention before full decoding. Code is available at https://github.com/berkerdemirel/faithful-cond-gen.

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.

We propose the Monge Inception Distance (MIND), a metric for evaluating generative models that addresses key limitations of the widely adopted Fréchet Inception Distance (FID). The MIND metric leverages the sliced Wasserstein distance to compare distributions by averaging one-dimensional optimal transport distances, efficiently computed via sorting. This approach circumvents the estimation of high-dimensional means and covariance matrices, which underlie FID's poor sample complexity and vulnerability to adversarial attacks. We empirically demonstrate three primary advantages: (i) it is more sample-efficient by one order of magnitude, (ii) it is faster to compute by two orders of magnitude, (iii) it is more robust to adversarial attacks such as moment-matching. We show that MIND with 5k samples can replace the evaluation performance of FID with 50k samples, providing high correlation with this standard benchmark and superior discriminative performance. We further demonstrate that even smaller sample sizes (e.g., 1k or 2k) remain highly informative for rapid model iteration.