arXiv:2606. 01595v1 Announce Type: new Abstract: Bayesian inference provides a principled framework for modeling epistemic uncertainty in neural networks by treating predictions as distributions rather than deterministic values.
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.
Transport-Coupled Bayesian Flows for Molecular Graph Generation (TopBF) addresses a key mismatch in existing diffusion models for molecular graph generation by eliminating the need for hard discretization during sampling. The framework generates graphs directly in continuous parameter distributions, learns graph topology via a Quasi-Wasserstein optimal‑transport coupling with geodesic costs, and enables property‑conditioned generation without retraining. Experiments on QM9 and ZINC250k show that TopBF achieves higher structural fidelity and more efficient generation compared to prior methods.
arXiv:2607. 09277v1 Announce Type: new Abstract: Three-dimensional (3D) molecule generation has been dominated by diffusion models, which achieve strong generation quality but typically require the molecular size to be specified a priori.
arXiv:2606. 13955v1 Announce Type: new Abstract: Latent diffusion is a promising framework for scalable 3D molecular generation, but it requires a latent space that remains smooth, valid, and navigable beyond posterior samples.
arXiv:2603. 23398v3 Announce Type: replace-cross Abstract: Generative modeling of discrete data, such as graphs, underpins many scientific and industrial applications, including molecular discovery and materials design.
arXiv:2607. 07330v1 Announce Type: cross Abstract: Hypergraph neural networks have shown powerful capability in modeling higher-order relations, yet their predictive uncertainty remains underexplored.
arXiv:2604. 13354v2 Announce Type: replace-cross Abstract: The discovery of inorganic crystal structures with targeted properties is a significant challenge in materials science.
arXiv:2606. 01220v1 Announce Type: cross Abstract: Generating molecules that simultaneously satisfy drug-like properties and conform to the 3D structure of a target protein is a core challenge in structure-based drug design (SBDD).
arXiv:2606. 07239v1 Announce Type: new Abstract: The success of generative molecular design hinges on a model's steerability toward high-reward samples.
Diffusion models represent a leading paradigm for graph generation, with notable impact in domains such as molecular design. Yet, scaling these models to large graphs remains an open problem.
arXiv:2607. 07232v1 Announce Type: cross Abstract: Diffusion models represent a leading paradigm for graph generation, with notable impact in domains such as molecular design.
arXiv:2604. 17838v2 Announce Type: replace Abstract: Generative modeling within constrained sets is essential for scientific and engineering applications involving physical, geometric, or safety requirements (e.