Organizations: College of Mechanical & Electrical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, China · School of Electronics, Electrical Engineering and Computer Science, Queen’s University Belfast, Belfast, United Kingdom · School of Mechanical and Aerospace Engineering, Queen’s University Belfast, Belfast, United Kingdom · School of Mechanical and Power Engineering, Nanjing Tech University, Nanjing, China · Department of Industrial and Systems Engineering, The Hong Kong Polytechnic University, Hong Kong, China · Department of Production Engineering, KTH Royal Institute of Technology, Stockholm, Sweden
Learning partial differential equation (PDE) dynamics across varying domains is central to predictive modelling and data-driven discovery of governing equations. However, geometric variation alters both field representation and the governing differential operators, confounding geometric effects with intrinsic physical properties in the observed dynamics. This work identifies geometry-physics confounding as a unified failure mechanism for PDE learning across varying domains. In forward operator learning, this confounding increases the burden of inferring geometry-dependent operator changes from finite data, reducing data efficiency and generalisation. In equation discovery, omitting geometry-induced operators misspecifies the candidate library, leading to biased parameters, missed governing terms and spurious terms. We propose a de-confounding framework that makes the known geometry-to-operator transformation explicit. Geometry-induced coefficient fields improve prediction and data efficiency across five operator-learning benchmarks, while geometry-complete candidate libraries recover the generating equations and reduce held-out PDE residuals by more than two orders of magnitude in both evolving-domain systems. By separating known geometric action from intrinsic physics, the proposed framework supports more reliable and data-efficient PDE learning across scientific and engineering problems with varying geometries.
Figures & tables
Figure 1: Geometry–physics confounding in PDE learning. a , Problem setup for PDE learning on varying geometries, illustrating sample observations pairing geometry with field data, operator learning of solution maps Fω , and equation discovery identifying governing differential laws. b , Geometry–physics confounding mechanism: a homogeneous isotropic diffusion process on a deformed domain and an equivalent fixed-domain model with geometry-induced capacity jg and transformed conductivity κg yield identical pulled-back dynamics. Fitting a misspecified reference model yields identical apparent diffusion coefficients ( κRef=0.010 ) across physically distinct systems (contour plot, right). c , De-confounding strategies: geometry-induced coefficient fields for operator learning (left) and geometry-complete candidate libraries for equation discovery (right). d , Learning failures and recovery: for operator rate prediction (left and centre), coordinate-based inputs yield high errors, while explicitly incorporating geometry-induced coefficient fields reduces error by over fivefold, and the geometry-induced PDE terms yield numerical-precision predictions ( <10−14 ). Prediction curves and shaded bands show means and ±1 s.d. across five optimisation runs. For equation discovery (right), the apparent reference coefficient exhibits a 19.3% geometric drift and an equation residual of 0.223 , whereas the geometry-complete candidate library recovers the generating coefficient with numerical-precision residual ( <10−16 ).
Figure 2Figure 3
Figure 4: Thermoelastic equation discovery and prediction on a held-out realization. a , Domain deformation ∣d∣ and metric distortion jd=detJd for a representative held-out realization. b , Generating and selected terms and the corresponding equations identified using the reference-coordinate (Ref) and geometry-complete (Geo) candidate libraries. Filled and open circles denote included and excluded terms, respectively, and the cross marks the generating term missed by Ref. In the equations, purple denotes the source term q and its fitted coefficient, blue denotes the mapped-diffusion term and its fitted coefficient, and black denotes the additional terms selected by Ref. c , Temperature prediction on a representative held-out trajectory at t=2.0 , comparing ground truth with predictions from the reference-coordinate and geometry-complete identified equations. Dashed outlines mark the true boundary. d , Coupled von Mises stress prediction computed from the predicted temperature and displacement fields. e , Relative errors in temperature and von Mises stress over time. f , Coefficient relative L2 error under 0–5% additive state-field noise. g , Full-trajectory relative L2 error across four held-out trajectories for temperature T , displacement d , and von Mises stress σv . The geometry closure is known.
Figure 5: Tumour-growth equation discovery and prediction on a held-out realization. a , Free-boundary motion and nutrient evolution on a shared colour scale. The domains are uniformly rescaled within each snapshot to make growth visible. Arrows indicate the initial direction of boundary motion and labels report physical domain area A . b , Generating mapped-diffusion ( 0.012DR[c] ) and ALE-transport ( AR[c] ) PDE contributions at t=1.2 . c , Generating and selected terms and the corresponding identified equations. Filled and open circles denote included and excluded terms, respectively, and crosses mark the generating terms missed by Ref. In the equations, purple denotes the source and consumption terms and their fitted coefficients, blue denotes the mapped-diffusion and ALE-transport terms and their fitted coefficients, and black denotes the additional terms selected by Ref. d , Closed-loop relative errors over time for nutrient Ec , boundary radius ER , and domain area EA . e , Coefficient relative L2 error under 0–5% state-field noise. f , Full-trajectory relative L2 error across four held-out trajectories for nutrient c , boundary R , and area A . The moving-boundary closure is known.
Term
Physical-domain form
Geometry-induced form
Short notation
Gradient
∇xu
Jg−T∇ξu
Gg[u]
Advection
b⋅∇xu
(Jg−1b)⋅∇ξu
Cg[u]
Diffusion
Δxu
jg−1Divξ(Kg∇ξu)
Dg[u]
Time derivative
∂tu∣x
∂tu∣ξ−Ag[u]
—
Reaction/source
r(u)+s
r(u)+s∘Φg
—
Table 1: Common PDE terms and their geometry-induced forms.
Component
DIMON
DIMON-Geo
Geometry branch
[20,100,100,100]
Three [121,32,32,100] branches
Boundary branch
[68,150,150,150,100]
[68,150,150,150,100]
Tensor-branch fusion
Not used
Elementwise product
Coordinate trunk
[2,100,100,100]
[2,100,100,100]
Table S1: Laplace network configurations. Each tensor component in DIMON-Geo has a separate branch with the listed dimensions.
Table S4: Airfoil-flow network configurations. Both models use the structured-mesh backbone specified in S4.
Component
Transolver
Transolver-Geo
Input channels
2 physical coordinates
2 reference coordinates and 6 geometry channels
Input MLP
[2,256,128]
[8,256,128]
Attention blocks
8
8
Hidden width / heads
128 / 8
128 / 8
Slice tokens / MLP ratio
64 / 1
64 / 1
Output channels
1
1
Table S5: Elasticity network configurations. Both models use irregular-mesh physics attention.
Extended Data Fig. 1: Candidate-library availability and selection. Term-by-term comparison of candidate construction and sparse selection. The geometry-complete library for each system contains the same four-term template: mapped diffusion, state-modulated mapped diffusion, ALE transport and state-modulated ALE transport. For each system, the first column marks the generating support. Ref and Geo denote the reference-coordinate and geometry-complete libraries, each shown through library-membership and selected-support columns. Open squares mark available candidates and grey dashes mark terms absent from a library. Purple and blue circles mark terms selected by Ref and Geo, respectively. Purple triangles mark additional Ref selections, and red crosses mark missed generating terms.
Extended Data Fig. 2: Training and held-out evolving-domain realizations. Final-state gallery for the four training and four held-out trajectories in each system. The held-out set changes source placement and geometric response beyond the combinations used for sparse identification.
Extended Data Fig. 3: Thermoelastic transfer across all held-out realizations. Final-state temperature truth, reference-coordinate prediction and absolute error, and geometry-complete prediction and absolute error for all four held-out trajectories. Prediction rows share a physical-value colour scale and error rows share an absolute-error scale. Labels report final-state relative L2 error. The known elastic closure is used in both integrations.
Extended Data Fig. 4: Tumour transfer across all held-out realizations. Final-state nutrient truth, reference-coordinate prediction and absolute error, and geometry-complete prediction and absolute error for all four held-out trajectories. Prediction rows share a physical-value colour scale and error rows share an absolute-error scale. Labels report final-state relative L2 error. The known moving-boundary closure is used in both integrations.
Extended Data Fig. 5: Sensitivity to state-field noise. Support F1 , coefficient relative L2 error and clean held-out PDE residual after identification from state fields with 0–5% additive noise relative to the field standard deviation. Large symbols show medians across five noise realizations and pale points show individual realizations. Geometry variables remain noise-free.
Extended Data Fig. 6: Training-set size and subset stability. Support F1 , coefficient relative L2 error and held-out PDE residual versus the number of clean training realizations for the geometry-complete candidate library. All subsets of one to four trajectories are enumerated. Large symbols show the subset median and pale points show individual subsets.
Neural operators have emerged as powerful data-driven solvers for PDEs, offering substantial acceleration over classical numerical methods. However, existing transformer-based operators still face critical challenges when modeling PDEs on complex geometries: directly processing over massive mesh points is computationally expensive, while operating in raw discretization coordinates may obscure the intrinsic geometry where physical interactions are more naturally expressed. To address these limitations, we introduce the Charted Axial Transformer Operator (CATO), a geometry-adaptive and derivative-aware neural operator for PDEs on general geometries. Instead of applying attention directly in the physical coordinate system, CATO learns a continuous latent chart that maps mesh coordinates into a learned chart space, where chart-conditioned axial attention efficiently captures long-range dependencies with reduced computational cost. In addition, CATO introduces a derivative-aware physics loss for steady-state PDEs that jointly supervises solution values, mesh-consistent gradients, and an auxiliary flux-like field, improving physical fidelity and reducing oversmoothing. We further provide a theoretical approximation result showing that, under a favorable chart, charted axial attention can represent low-rank axial solution operators with controlled error, and that small chart perturbations induce bounded approximation degradation. CATO achieves the best performance across all evaluated datasets, yielding an average improvement of approximately 26.76% over the strongest competing baselines while reducing the number of parameters by 81.98%. These results highlight the effectiveness of learning geometry-adaptive charts and derivative-aware physical supervision for accurate and efficient PDE operator learning.
Learning PDE operators on complex domains requires capturing interactions among fields on vertices, edges, and faces, alongside global responses shaped by topology. Existing neural operators accommodate irregular geometries but often overlook these distinct field supports or their condition-dependent coupling. We introduce the Dynamic Kuramoto--Hodge Operator (DKHO), which combines topology-constrained interactions with learned coordination. DKHO encodes conditions on their native cochain supports, evolves Kuramoto-inspired relation states through the boundary and coboundary operators that compose the Dirac operator, and decodes non-harmonic and harmonic responses in orthogonal Hodge subspaces. Topology thus determines where information can flow, while learned dynamics adapts how it is exchanged to each PDE instance. Across porous-medium Darcy flow, torus transport--diffusion, and cavity magnetostatics, DKHO-large reduces prediction error by approximately 61% on average over leading baselines, while DKHO-small remains competitive using only 11.5--24.3% as many parameters. These results suggest that coupling topological structure with adaptive dynamics provides an effective inductive bias for accurate and parameter-efficient PDE operator learning on complex geometries and topologies.
Xiang Li, Yue Song
Tsinghua University · Beijing University of Chemical Technology
Learning solution operators for partial differential equations (PDEs) on irregular and geometry-dependent domains remains a central challenge in scientific machine learning. While spectral methods provide strong inductive biases for modeling global interactions, they are typically limited to regular domains, and existing neural approaches often require domain warping, interpolation, or costly geometric embeddings. We introduce the \textbf{Graph Spectral Neural Operator (GSNO)}, a neural operator that combines spatial graph spectral decompositions with temporal Fourier transforms through a unified space--time spectral kernel. This formulation enables globally coherent operator learning on non-Cartesian discretizations without domain warping or autoregressive rollouts. By replacing learned geometric embeddings with a graph Laplacian spectral basis, GSNO provides geometry-aware spectral learning with low parameter complexity. Across steady and unsteady PDE benchmarks on irregular and geometry-dependent domains, GSNO achieves strong accuracy with reduced runtime and parameter counts, while demonstrating robust zero-shot generalization across mesh resolutions and geometry families.
Abdolmehdi Behroozi, Chaopeng Shen
Department of Civil and Environmental Engineering, Penn State University, University Park, PA 16802, USA