Deep learning-based methods have shown remarkable effectiveness in solving PDEs, largely due to their ability to enable fast simulations once trained. However, despite the availability of high-performance computing infrastructure, many critical applications remain constrained by the substantial computational costs associated with generating large-scale, high-quality datasets and training models. In this work, inspired by studies on the structure of Green's functions for elliptic PDEs, we introduce Neural-HSS, a parameter-efficient architecture built upon the Hierarchical Semi-Separable (HSS) matrix structure that is provably data-efficient for a broad class of PDEs. We theoretically analyze the proposed architecture, proving that it satisfies exactness properties even in very low-data regimes. We also investigate its connections with other architectural primitives, such as the Fourier neural operator layer and convolutional layers. We experimentally validate the data efficiency of Neural-HSS on the three-dimensional Poisson equation over a grid of two million points, demonstrating its superior ability to learn from data generated by elliptic PDEs in the low-data regime while outperforming baseline methods. Finally, we demonstrate its capability to learn from data arising from a broad class of PDEs in diverse domains, including electromagnetism, fluid dynamics, and biology.
Figures & tables
Figure 1: Model overview. The lifting and projection layers can be implemented either as HSS layers or as full-rank layers. We illustrate, as an example, the weight matrix structure with two different hierarchical levels.
Figure 2: Train size vs relative test error for different models. The models are trained on a 1D Poisson equation.
Figure 3: Left : Train size vs relative test error for different models. The models are trained on a 3D Poisson equation. Right : Timing of forward and backward for the different models.
Neural-HSS
FNO
ResNet
DeepONet
Green Learning
Equation
Params
Test Err
Params
Test Err
Params
Test Err
Params
Test Err
Params
Test Err
Heat Eq.
45 K
3×10−3
150 K
8×10−3
165 K
1×10−2
247 K
1×10−2
83 K
1×10−2
Poisson Neumann BC
37 K
2×10−4
102 K
3×10−3
165 K
4×10−1
247 K
9×10−3
83 K
3×10−3
Burgers’ Eq.
1.5 M
0.12
1.5 M
0.26
1.7 M
0.57
1.7 M
0.44
-
-
Table 1: Comparison between Neural-HSS and baseline models. We report the number of learnable parameters for each model and the test error Eq. 3 .
Neural-HSS
FNO
ResNet
DeepONet
Green Learning
FactFormer
Equation
Params
Test Err
Params
Test Err
Params
Test Err
Params
Test Err
Params
Test Err
Params
Test Err
Poisson Eq.
37K
7×10−8
132 K
7×10−6
165 K
3×10−4
280 K
2×10−2
83 K
5×10−5
3.9 M
6×10−3
Poisson Eq. (Mixed BC)
37 K
1×10−4
132 K
6×10−3
165 K
8×10−2
280 K
4×10−1
83 K
1×10−2
3.9 M
7×10−2
Poisson Eq. (L-shape domain)
37 K
2×10−2
132 K
2×10−1
165 K
7×10−1
280 K
8×10−1
83 K
5×10−1
3.9 M
2×10−1
Helmholtz equation
37 K
6×10−3
132 K
5×10−2
165 K
1×100
280 K
1×100
83 K
1×100
3.9 M
7×10−2
Gray–Scott Eq. (Forward)
329K
0.294
2.1M
0.331
1.99M
0.273
2.3M
0.315
-
-
3.9M
0.291
Table 2: Comparison between Neural-HSS and baseline models on 2D problems. We report the number of learnable parameters for each model and the test error Equation 2 . With NS Eq., we refer to the incompressible Navier-Stokes equation.
Appendix figures & tables13 assets
Supplementary material from the paper’s appendix.
Appendix
Figure 4: Train size vs relative test error for different models. The models are trained on a 3D Poisson equation
Figure 5: Ablation study on rank, outer rank, and levels for the Gray-Scott problem, where the color indicates the test error after training (rescaled from maximum to minimum observed, notice the scale in the colorbars).
Figure 6: Trajectory test loss varying β
Figure 7: Timing of one forward pass, calculated on different datasets.
Figure 8: Timing of one forward+backward pass, calculated on two different datasets: Left : Heat equation. Right : Burgers’ equation. We refer to Appendix K for inference only timings.
Figure 9: Timing of one forward+backward pass, calculated on two different datasets: Left : 2D Poisson Equation Right : Gray-Scott and Navier-Stokes.We refer to Appendix K for inference only timings.
Configuration
Neural-HSS
FNO
ResNet
DeepONet
Green Learning
Depth
3
6
12
4 1 1 1 The depth is the same for the Trunk network and the Branch network
6
Embedding Dimension
256
32
48
192
128
Activation
Trainable LeakyReLU
GeLU
GeLU
GeLU
Rational activation 2 2 2 ( Boullé et al., 2020 )
Levels
3
-
-
-
-
Rank
2
-
-
-
-
Modes
-
12
-
-
-
Appendix
Table 3: Models and training configuration for the Heat Equation and Poisson Equation with Neumann boundary conditions.
Configuration
Neural-HSS
FNO
ResNet
DeepONet
Depth
4
6
12
4
Embedding Dimension
1024
64
150
512
Activation
Trainable LeakyReLU
GeLU
GeLU
GeLU
Levels
3
-
-
-
Rank
32
-
-
-
Modes
-
32
-
-
Appendix
Table 4: Models and training configuration for the Burgers’ Equation .
Configuration
Neural-HSS
FNO
ResNet
DeepONet
Green Learning
FactFormer
Depth
3
4
4
4 3 3 footnotemark: 3
6
1
Embedding Dimension
64
16
64
64
64
384
Activation
Trainable LeakyReLU
GeLU
GeLU
GeLU
Rational activation 4 4 footnotemark: 4
GeLU
Levels
2
-
-
-
-
-
Rank
2
-
-
-
-
-
outer rank
8
-
-
-
-
-
Appendix
Table 5: Models and training configuration for the 2D Poisson Equation and 2D Poisson Equation (L-shape domain) .
Configuration
Neural-HSS
FNO
ResNet
DeepONet
Green Learning
Depth
3
4
4
4 5 5 footnotemark: 5
6
1
Embedding Dimension
64
16
64
64
64
384
Activation
Trainable LeakyReLU
GeLU
GeLU
GeLU
Rational activation 6 6 footnotemark: 6
GeLU
Levels
2
-
-
-
-
-
Rank
2
-
-
-
-
-
outer rank
8
-
-
-
-
-
Appendix
Table 6: Models and training configuration for the Helmholtz equation .
Configuration
Neural-HSS
FNO
ResNet
DeepONet
FactFormer
Depth
3
4
4
4
1
Embedding Dimension
128×128
32
64
128
384
Activation
Trainable LeakyReLU
GeLU
GeLU
GeLU
GeLU
Levels
2
-
-
-
-
Rank
8
-
-
-
-
Outer Rank
8
-
-
-
-
Appendix
Table 7: Models and training configuration for the Incompressible Navier-Stokes and Gray-Scott .
Configuration
Neural-HSS
FNO
ResNet
DeepONet
Depth
1
2
2
4
Embedding Dimension
128×128×128
14
48
128
Activation
Trainable LeakyReLU
GeLU
GeLU
GeLU
Levels
2
-
-
-
Rank
4
-
-
-
Outer Rank
2
-
-
-
Appendix
Table 8: Models and training configuration for the data efficiency for 3D Poisson Equation . We report the training steps since for each training size we match the training steps at 16 k.
Configuration
Neural-HSS
FNO
ResNet
DeepONet
Green Learning
Depth
3
6
12
4 7 7 footnotemark: 7
6
Embedding Dimension
256
32
48
192
128
Activation
Trainable LeakyReLU
GeLU
GeLU
GeLU
Rational activation 8 8 footnotemark: 8
Levels
3
-
-
-
-
Rank
2
-
-
-
-
Modes
-
12
-
-
-
Appendix
Table 9: Models and training configuration for the data efficiency for 1D Poisson Equation .
Spatiotemporal partial differential equations (PDEs) underpin a wide range of scientific and engineering applications. Neural PDE solvers offer a promising alternative to classical numerical methods. However, existing approaches typically require large numbers of training trajectories, while high-fidelity PDE data are expensive to generate. Under limited data, their performance degrades substantially, highlighting their low data efficiency. A key reason is that PDE dynamics embody strong structural inductive biases that are not explicitly encoded in neural architectures, forcing models to learn fundamental physical structure from data. A particularly salient manifestation of this inefficiency is poor generalization to unseen source terms. In this work, we revisit Green's function theory-a cornerstone of PDE theory-as a principled source of structural inductive bias for PDE learning. Based on this insight, we propose DGNet, a discrete Green network for data-efficient learning of spatiotemporal PDEs. The key idea is to transform the Green's function into a graph-based discrete formulation, and embed the superposition principle into the hybrid physics-neural architecture, which reduces the burden of learning physical priors from data, thereby improving sample efficiency. Across diverse spatiotemporal PDE scenarios, DGNet consistently achieves state-of-the-art accuracy using only tens of training trajectories. Moreover, it exhibits robust zero-shot generalization to unseen source terms, serving as a stress test that highlights its data-efficient structural design.
Yingjie Tan, Quanming Yao, Yaqing Wang
Qiuzhen College, Tsinghua University · Department of Electronic Engineering, Tsinghua University · Beijing Institute of Mathematical Sciences and Applications
Solving high-frequency partial differential equations (PDEs) with neural networks is notoriously difficult due to the spectral bias of conventional architectures. We propose the Multi-Scale Separable Fourier Neural Network (MS-SFNN), a framework designed to overcome this limitation by explicitly encoding multi-scale Fourier features within a separable representation. The network factorizes the solution into d single-coordinate subnetworks with fixed, randomly initialized weights; these subnetworks are combined via element-wise products to form a rich set of basis functions. This separable construction scales linearly with the problem dimension, thus inherently alleviating the curse of dimensionality. Crucially, each subnetwork is equipped with trainable scaling factors coupled with cosine activations, providing an adaptive mechanism for multi-scale frequency selection that endows the model with strong spectral approximation capability. The PDE solution is expressed as a linear combination of these learned basis functions, and the combination coefficients are determined by solving a large-scale least-squares system. To resolve the memory bottleneck in high-frequency or three-dimensional settings, we replace automatic differentiation (AD) with analytical derivatives of the basis functions and use a memory-efficient batched QR decomposition for solving the least-squares systems efficiently. Extensive numerical experiments demonstrate that MS-SFNN achieves superior accuracy and substantially outperforms state-of-the-art methods, including Physics-Informed Neural Network (PINN) and the Separated-Variable Spectral Neural Network (SV-SNN).
Qihong Yang, Qiaolin He
School of Mathematics, Sichuan University, city=Chengdu, postcode=610065, country=China
The matrices arising from large scale N-body problems can be efficiently represented using hierarchical matrices, whose key idea is that the admissible off-diagonal sub-matrices can be well approximated by low-rank matrices across a hierarchy of matrix partitions. HODLR (Hierarchical Off-Diagonal Low-Rank) matrices are a subclass of hierarchical matrices in which all off-diagonal submatrices at every level of a recursive binary partition are low-rank. In this article, we present a neural network that learns the inverse operation of HODLR matrices based on the fast direct solver for HODLR matrices developed by Ambikasaran and Darve (2013). We further extend the architecture to learn nonlinear solution operators associated with PDEs by replacing some of the linear layers with deep sub-networks. We demonstrate the performance of the proposed architecture by performing a comprehensive set of experiments that include (i) solving a linear problem such as the Fredholm integral equation of the second kind, (ii) solving PDEs such as the nonlinear Schrödinger equation, Burgers' equation, and the steady-state Darcy's flow equation, (iii) generalization study across varying parameter values, (iv) comparing the inference time of the proposed network with the run time of a classical numerical solver, and (v) comparing the proposed network with some of the existing neural operator learning networks.
Jashwanth Reddy Kadaru, Vaishnavi Gujjula
Department of Computer Science & Engineering, International Institute of Information Technology Bangalore (IIIT-B), India · Department of Data Science and Artificial Intelligence, International Institute of Information Technology Bangalore (IIIT-B), India