GeoTopoDiff: Learning Geometry--Topology Graph Priors through Boundary-Constrained Mixed Diffusion for Sparse-Slice 3D Porous Reconstruction
Authors: Yue Shi, Peng Wang, Mingzhe Yu, Yunlong Zhao, Li Liu, Gareth D Hatton, Yan Lyu, Liangxiu Han
Organizations: Manchester Metropolitan University, Manchester M1 5GD, U.K. · University of Surrey, Surrey, GU2 7XH, U.K. · Johnson Matthey Billingham, TS23 1LB, U.K. · Imperial College London London SW7 2AZ, U.K.
Diffusion-based voxel prior modelling is challenging for the reconstruction of large-scale 3D porous microstructures. Due to the demanding requirements for simultaneously modelling both the continuous pore morphology and the discrete pore-throat topology, the diffusion models require fully observed CT scans to provide topology-faithful priors, which results in an inherent trade-off among throughput, topological fidelity, and field of view in practical industrial applications. We propose GeoTopoDiff, a graph diffusion-based framework for reconstructing 3D porous microstructures from sparse CT slices. GeoTopoDiff transfers the learning of diffusion priors from a voxel-based space to a mixed graph state space, which simultaneously encompasses continuous pore geometry and discrete pore-throat topology. A topology-aware partial graph prior from sparsely observed CT slices is introduced to constrain the reverse denoising process. Experiments on anisotropic PTFE and Fontainebleau sandstone show that GeoTopoDiff reduces morphology-related errors by 19.8% and topology-sensitive transport errors by 36.5% on average. Our findings suggest that the mixed graph state space promotes the diffusion denoising process to reduce posterior uncertainty under a sparse observations. All models and code have been made publicly available to facilitate the exploration of diffusion models in the field of 3D porous microstructures simulation.
State-of-the-art single-image 3D reconstruction methods often rely on complex hybrid architectures and loss functions, or compress geometry into latent spaces in order to leverage pre-trained latent diffusion models. In this work, we show that such architectural overhead and intricate loss formulations are unnecessary. We introduce a minimalist pixel-space Diffusion Transformer, built on a plain ViT, that operates directly on raw 3D point map patches and is conditioned on image tokens from a pre-trained DINOv3. Unlike existing latent diffusion approaches, we train our diffusion backbone entirely from scratch, eliminating the need for point map tokenizers. Despite its simplicity, our approach surpasses complex latent-based diffusion models while remaining significantly simpler than hybrid alternatives. Notably, it produces sharper geometric structure and is more robust in highly ambiguous regions, such as transparent objects.
Current topology aware diffusion models face an architectural mismatch by using Gaussian noise for corruption while recovering structural features through conditional side channels To fix this we introduce PFlow T a generative model that bases its forward process entirely on persistent homology In PFlow T time measures the destruction of H1 topological features like holes rather than Gaussian noise injection This forward process eliminates features based on their persistence The reverse network then directly inverts this structured corruption to predict the clean state in one step Tests on MNIST digits zero one and eight show PFlow T significantly outperforms a baseline model in generating requested Betti numbers and handling out of distribution tasks PFlow T is the first generative architecture using persistent homology for the forward process although we note it is currently limited to low resolution pixel space proxies
Generative models, particularly Diffusion Models (DM), have shown strong potential for Computed Tomography (CT) reconstruction serving as expressive priors for solving ill-posed inverse problems. However, diffusion-based reconstruction relies on Stochastic Differential Equations (SDEs) for forward diffusion and reverse denoising, where such stochasticity can interfere with repeated data consistency corrections in CT reconstruction. Since CT reconstruction is often time-critical in clinical and interventional scenarios, improving reconstruction efficiency is essential. In contrast, Flow Matching (FM) models sampling as a deterministic Ordinary Differential Equation (ODE), yielding smooth trajectories without stochastic noise injection. This deterministic formulation is naturally compatible with repeated data consistency operations. Furthermore, we observe that FM-predicted velocity fields exhibit strong correlations across adjacent steps. Motivated by this, we propose an FM-based CT reconstruction framework (FMCT) and an efficient variant (EFMCT) that reuses previously predicted velocity fields over consecutive steps to substantially reduce the number of Neural network Function Evaluations (NFEs), thereby improving inference efficiency. We provide theoretical analysis showing that the error introduced by velocity reuse is bounded when combined with data consistency operations. Extensive experiments demonstrate that FMCT/EFMCT achieve competitive reconstruction quality while significantly improving computational efficiency compared with diffusion-based methods. The codebase is open-sourced at https://github.com/EFMCT/EFMCT.