# GeoTopoDiff: Learning Geometry--Topology Graph Priors through Boundary-Constrained Mixed Diffusion for Sparse-Slice 3D Porous Reconstruction

arXiv: https://arxiv.org/abs/2605.03764 · HTML: https://mlsanity.com/paper/2605.03764/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Placed in Flow matching, time series and science, one of 14 directions in Diffusion models.
- Builds on 13 of its 27 references that are in the map.
- First posted on arXiv 5 May 2026.

## Placed in

- Diffusion models / [Flow matching, time series and science](https://mlsanity.com/diffusion/flow-matching-time-series-and-science/)

## Builds on (most cited first, 13 of 13)

- [Denoising Diffusion Probabilistic Models](https://mlsanity.com/paper/2006.11239/) (2020)
- [Structured Denoising Diffusion Models in Discrete State-Spaces](https://mlsanity.com/paper/2107.03006/) (2021)
- [Diffusion Posterior Sampling for General Noisy Inverse Problems](https://mlsanity.com/paper/2209.14687/) (2022)
- [GeoDiff: a Geometric Diffusion Model for Molecular Conformation Generation](https://mlsanity.com/paper/2203.02923/) (2022)
- [Score-based Generative Modeling of Graphs via the System of Stochastic Differential Equations](https://mlsanity.com/paper/2202.02514/) (2022)
- [Solving 3D Inverse Problems using Pre-trained 2D Diffusion Models](https://mlsanity.com/paper/2211.10655/) (2022)
- [Decomposed Diffusion Sampler for Accelerating Large-Scale Inverse Problems](https://mlsanity.com/paper/2303.05754/) (2023)
- [Improving 3D Imaging with Pre-Trained Perpendicular 2D Diffusion Models](https://mlsanity.com/paper/2303.08440/) (2023)
- [Generating 3D structures from a 2D slice with GAN-based dimensionality expansion](https://mlsanity.com/paper/2102.07708/) (2021)
- [DiffusionBlend: Learning 3D Image Prior through Position-aware Diffusion Score Blending for 3D Computed Tomography Reconstruction](https://mlsanity.com/paper/2406.10211/) (2024)
- [Microstructure reconstruction of 2D/3D random materials via diffusion-based deep generative models](https://mlsanity.com/paper/2311.17319/) (2023)
- [Multi-plane denoising diffusion-based dimensionality expansion for 2D-to-3D reconstruction of microstructures with harmonized sampling](https://mlsanity.com/paper/2308.14035/) (2023)
- [MicroDiffusion: Implicit Representation-Guided Diffusion for 3D Reconstruction from Limited 2D Microscopy Projections](https://mlsanity.com/paper/2403.10815/) (2024)

## Abstract (arXiv)

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.