PoreDiT: A Scalable Generative Model for Large-Scale Digital Rock Reconstruction
Authors: Yizhuo Huang, Baoquan Sun, Haibo Huang
Organizations: College of Intelligent Robotics and Advanced Manufacturing, FuDan University, Shanghai, China · State Key Laboratory of Shale Oil and Gas Enrichment Mechanisms and Efficient Development, Dongying, Shandong, China · Department of Modern Mechanics, University of Science and Technology of China, Hefei 230026, Hefei, Anhui, China
This manuscript presents PoreDiT, a novel generative model designed for high-efficiency digital rock reconstruction at gigavoxel scales. Addressing the significant challenges in digital rock physics (DRP), particularly the trade-off between resolution and field-of-view (FOV), and the computational bottlenecks associated with traditional deep learning architectures, PoreDiT leverages a three-dimensional (3D) Swin Transformer to break through these limitations. By directly predicting the binary probability field of pore spaces instead of grayscale intensities, the model preserves key topological features critical for pore-scale fluid flow and transport simulations. This approach enhances computational efficiency, enabling the generation of ultra-large-scale (10243 voxels) digital rock samples on consumer-grade hardware. Furthermore, PoreDiT achieves physical fidelity comparable to previous state-of-the-art methods, including accurate porosity, pore-scale permeability, and Euler characteristics. The model's ability to scale efficiently opens new avenues for large-domain hydrodynamic simulations and provides practical solutions for researchers in pore-scale fluid mechanics, reservoir characterization, and carbon sequestration.
Figures & tables
Figure 1: Overview of the PoreDiT framework and inference mechanism. The diagram illustrates the complete workflow from microscopic training to large-scale generation. (A) Probability Field Learning: The model predicts the conditional probability of pore phase existence, quantifying aleatoric uncertainty. (B) 3D Patch Embedding: Input volumes are partitioned into patch sequences to optimize memory efficiency while capturing global topology via Swin Transformers. (C) Large-scale Inference: A Gaussian-weighted overlap-tile strategy enables seamless gigavoxel reconstruction.
Figure 2: Schematic of the Forward Diffusion Process and Multi-modal Embedding Framework.
Figure 4: Schematic diagram of the reverse denoising inference process of the PoreDiT model.
Figure 5: Schematic diagram of the reverse denoising inference process of the PoreDiT model.
Figure 6: Visual comparison of microscopic structures. The left column displays 2D cross-sections ( 256×256 pixels) extracted from the ground truth volumes, and the right column shows the corresponding synthetic slices generated by our model. The rows correspond to samples with high (a, b), average (c, d), and low (e, f) porosity levels, respectively.
Figure 7: Comparison of 3D pore network structures. (a) Isosurface rendering of a real sandstone sub-volume ( 1283 voxels) randomly extracted from the training set. (b) A synthetic sub-volume ( 1283 voxels) generated by the PoreDiT model. Gray solid regions represent the pore space, illustrating the effective reconstruction of topological connectivity.
Figure 8: Comparison of the two-point correlation function S2(r) between the ground truth and generated samples.
Figure 9: Comparison of Minkowski Functionals (MFs) distributions between original training samples and synthetic samples. The panels display the statistical distributions of (a) Porosity ϕ (corresponding to M0 ), (b) Specific Surface Area SV (corresponding to M1 ), and (c) Euler Characteristic Density χV (corresponding to M2 ). The boxes represent the interquartile range (IQR), the central dashed lines indicate the median, whiskers extend to the full data range (excluding outliers), and ’+’ symbols denote outliers.
Figure 10: Permeability comparison via LBM simulations. The left panel shows the porosity-permeability relationship, indicating that the generated samples fall within the valid physical range of the ground truth. The right panel displays the probability density of permeability; despite a slight leftward shift in the peak ( ∼0.8 Darcy offset), the generated distribution (red) shows high structural similarity to the ground truth (black) and lies within its statistical support.
Figure 11: Generative Novelty Analysis. Histogram of the Distance to Nearest Neighbor ( Dmin ) for generated samples. The X-axis represents the pixel-wise distance ( ϵpixel ) to the nearest neighbor in the training set. The red dashed line ( x=0 ) indicates the theoretical position for ”exact data copying.” The solid teal line represents the Kernel Density Estimation (KDE) curve, and the dotted line indicates the mean distance of the samples.
Figure 12: Visual inspection of the most similar pair (Data-Copying Check). (Left) The generated sample with the minimum distance metric. (Middle) The nearest neighbor sample identified from the training set. (Right) The pixel-wise difference map between the two. High-intensity red regions indicate significant pixel residuals ( Dmin≈0.33 ), confirming structural distinctness.
Figure 13: Ablation Study: Impact of physical guidance on morphological consistency ( S2(r) ). The green dotted line represents the Unconditional Baseline, the red solid points with error bars represent the Porosity-Guided model (Ours), and the black dashed line represents the Ground Truth (GT).
Figure 14: Ablation Study: Controllability Analysis of Physical Properties. (a) Probability Density Function (PDF) of absolute permeability K . The grey shaded area, red curve, and black dashed line represent the Unconditional Baseline, Porosity-Guided model, and Ground Truth, respectively. (b) Joint distribution of porosity ϕ and permeability K . Grey triangles, red crosses, and blue circles correspond to the Unconditional, Porosity-Guided, and Ground Truth samples, respectively.
Sample Name
Dimensions (Voxels)
Porosity ( ϕ )
Connectivity (Largest Cluster %)
Ground Truth
10003
0.2672
99.43%
Gen_512
5123
0.2701
99.15%
Gen_1024
10243
0.2725
99.49%
Table 1: Comparison of physical properties across different reconstruction scales. Note that permeability is analyzed separately in Figure 18 via sub-volume partitioning.
Figure 15: Three-dimensional visualization of the pore network structure within the generated large-scale sample ( 5123 voxels, since 10243 is difficult to visualize).The grey isosurface represents the pore space, illustrating global connectivity without visible stitching artifacts.
Figure 16: A representative orthogonal cross-section (Slice No. 0257) extracted from the 10243 generated volume. Black regions denote pore space, and white regions denote the solid matrix. The image demonstrates seamless texture transition and long-range structural coherence.
Figure 17: Statistical comparison between the Ground Truth (black dashed line) and the generated large-scale sample (red solid line). (a) The overlapping S2∗(r) curves indicate high statistical isomorphism in skeletal structure. (b) The parallel descent of the L(r) curves suggests a consistent pore size distribution, despite a slight porosity offset.
Figure 18: Porosity-Permeability Relationship Analysis of Large-scale Generation. The gray circles and dashed line represent the ground truth experimental data and its exponential fit trend. The red diamonds and blue triangles represent the sub-volumes sliced from the generated 5123 (8 sub-volumes) and 10243 (64 sub-volumes) samples, respectively. The tight clustering around the GT trend line confirms physical consistency and stationarity across scales.
Figure 19: Generalization verification on Ketton Limestone. (a) Comparison of the Two-point Correlation Function S2(r) . The generated samples (red) exhibit high morphological consistency with the ground truth (black), accurately reproducing the characteristic correlation length ( lc ) and specific surface area. (b) Joint porosity-permeability distribution. The generated samples (red crosses) tightly cluster around the trend of the ground truth data (black circles), demonstrating that the model preserves the physical transport properties of the carbonate rock.
Part I: Methodology and Physical Fidelity
Method
Paradigm
S 2 Mismatch
Permeability ( K )
Connectivity
Stochastic (SA)
Optimization (SA)
Very Low
—
Poor ( S2 only) / Good (Hybrid)
DCGAN
Adversarial Training
Good Agreement
Good Match
Good (Euler Characteristic)
WGAN-GP
Deep Learning
Good Agreement
—
Qualitatively Good (No Metric)
PG-GAN
Deep Learning
—
—
Good (Pore Network Matched)
RockGPT
DL (Autoregressive)
Good Agreement
Good (Dist. Match)
Good (Euler Characteristic)
Table 2: Comparative analysis of PoreDiT against established reconstruction paradigms. The comparison is divided into two parts for clarity. Part I focuses on methodology and physical fidelity metrics ( S2 , K , Connectivity), while Part II details scalability and computational efficiency metrics. Values for PoreDiT are experimentally derived from the Bentheimer sandstone dataset ( 10243 ).
Digital reconstruction of porous materials has become increasingly critical for applications ranging from geological reservoir characterization to tissue engineering and electrochemical device design. While traditional methods such as micro-computed tomography and statistical reconstruction approaches have established foundations in this field, the emergence of deep learning techniques, particularly Generative Adversarial Networks (GANs), has revolutionized porous media reconstruction capabilities. This review systematically analyzes 96 peer-reviewed articles published from 2017 to early 2026, examining the evolution and applications of GAN-based approaches for porous material image reconstruction. We categorize GAN architectures into six distinct classes, namely Vanilla GANs, Multi-Scale GANs, Conditional GANs, Attention-Enhanced GANs, Style-based GANs, and Hybrid Architecture GANs. Our analysis reveals substantial progress including improvements in porosity accuracy (within 1% of original samples), permeability prediction (up to 79% reduction in mean relative errors), and achievable reconstruction volumes (from initial 643 to current 2,2003 voxels). Despite these advances, persistent challenges remain in computational efficiency, memory constraints for large-scale reconstruction, and maintaining structural continuity in 2D-to-3D transformations. This systematic analysis provides a comprehensive framework for selecting appropriate GAN architectures based on specific application requirements.
Ali Sadeghkhani, Brandon Bennett, Masoud Babaei +1
School of Computer Science, University of Leeds, Leeds, UK. · School of Chemical Engineering, The University of Manchester, Manchester, UK.
Carbonate reservoirs offer significant capacity for subsurface carbon storage, oil production, and underground hydrogen storage. X-ray computed tomography (X-ray CT) coupled with numerical simulations is commonly used to investigate the multiphase flow behaviors in carbonate rocks. Carbonates exhibit pore size distribution across scales, hindering the comprehensive investigation with conventional X-ray CT images. Imaging samples at both macro and micro-scales (multi-scale imaging) proved to be a viable option in this context. However, multi-scale imaging faces two key limitations: the trade-off between field of view and voxel size necessitates resource-intensive imaging, while multi-scale multi-physics numerical simulations on resulting digital models incur prohibitive computational costs. To address these challenges, we propose a machine learning-enhanced data assimilation framework that leverages experimental drainage relative permeability measurements to achieve efficient characterization of micro-scale structures, delivering a data-driven solution toward a high-fidelity multiscale digital rock modeling. We train a dense neural network (DNN) as a proxy to a multi-scale pore network simulator and couple it with an ensemble smoother with multiple data assimilation (ESMDA) algorithm. DNN-ESMDA framework simultaneously infers the CO2-brine drainage relative permeability of microporosity phases with associated uncertainty estimation, revealing the relative importance of each rock phase and guiding future characterization. Our DNN-ESMDA framework achieves a computational speedup, reducing inference time from thousands of hours to seconds compared with the usage of conventional multiscale numerical simulation. Given this computational efficiency and applicability, the machine learning-enhanced ESMDA framework presents a generalizable approach for characterizing multiscale carbonate rocks.
Zhenkai Bo, Ahmed H. Elsheikh, Hannah P. Menke +5
Institute of GeoEnergy Engineering, Heriot-Watt University, Edinburgh, EH14 4AS, United Kingdom · Department of Geoscience & Engineering, Technical University of Delft, Delft, The Netherlands · PETRONAS Research Sdn Bhd, Bangi, Selangor, Malaysia
Obtaining truly representative pore-scale images that match bulk formation properties remains a fundamental challenge in subsurface characterization, as natural spatial heterogeneity causes extracted sub-images to deviate significantly from core-measured values. This challenge is compounded by data scarcity, where physical samples are only available at sparse well locations. This study presents a multi-conditional Generative Adversarial Network (cGAN) framework that generates representative pore-scale images with precisely controlled properties. The framework was trained on thin section samples from four depths (1879.50-1943.50 m) of a carbonate formation, simultaneously conditioning on porosity and depth within a single model. It processes RGB thin section images that preserve critical mineralogical information (anhydrite-dolomite differentiation, grain boundaries, porosity distinctions) lost in conventional grayscale representations, capturing characteristics from grainstone fabrics to crystalline textures with anhydrite inclusions. The model achieved strong porosity control (R^2 = 0.95) across all formations with mean absolute errors of 0.0099-0.0197. Morphological validation confirmed preservation of average pore radius, specific surface area, and tortuosity within acceptable tolerances. Two-point correlation (S2) analysis confirmed that generated images preserve the spatial continuity and characteristic length scales of natural pore networks, with results consistent across the imaging resolutions tested (1.8-3.0 micron/pixel). Validated against core sample properties, generated images showed higher property fidelity with dual-constraint errors of 1.9-12.4% compared to 37.5-713.6% for randomly extracted real sub-images. This capability provides practical tools for subsurface characterization, particularly valuable for carbon storage, geothermal energy, and groundwater management.
Ali Sadeghkhani, Brandon Bennett, Masoud Babaei +1
School of Computer Science, University of Leeds, Leeds, LS2 9JT, UK. · Department of Chemical Engineering, The University of Manchester,2026 Manchester, M13 9PL, UK.