Symbolic Graph Networks for Robust PDE Discovery from Noisy Sparse Data
Authors: Xingyu Chen, Junxiu An, Jun Guo, Yuqian Zhou
Organizations: School of Software Engineering, Chengdu University of Information Technology, Chengdu, 610225, China · School of Statistics, Chengdu University of Information Technology, Chengdu, 610103, China · College of Applied Mathematics, Chengdu University of Information Technology, Chengdu, 610225, China · Key Laboratory of Mathematical Meteorology Chengdu University of Information Technology Chengdu, 610225, China
Data-driven discovery of partial differential equations (PDEs) offers a promising paradigm for uncovering governing physical laws from observational data. However, in practical scenarios, measurements are often contaminated by noise and limited by sparse sampling, which poses significant challenges to existing approaches based on numerical differentiation or integral formulations. In this work, we propose a Symbolic Graph Network (SGN) framework for PDE discovery under noisy and sparse conditions. Instead of relying on local differential approximations, SGN leverages graph message passing to model spatial interactions, providing a non-local representation that is less sensitive to high frequency noise. Based on this representation, the learned latent features are further processed by a symbolic regression module to extract interpretable mathematical expressions. We evaluate the proposed method on several benchmark systems, including the wave equation, convection-diffusion equation, and incompressible Navier-Stokes equations. Experimental results show that SGN can recover meaningful governing relations or solution forms under varying noise levels, and demonstrates improved robustness compared to baseline methods in sparse and noisy settings. These results suggest that combining graph-based representations with symbolic regression provides a viable direction for robust data-driven discovery of physical laws from imperfect observations. The code is available at https://github.com/CXY0112/SGN
Figures & tables
Figure 1: The overall framework of SGN. The architecture comprises two synergistic components: (1) the Graph Neural Simulator , which functions as a mesh-free discretization engine. It leverages graph message passing to extract robust non-local spatial operators from sparse and noisy observations, aided by auxiliary stabilization strategies; and (2) the Symbolic Inverse Analyzer , which distills these physics-aligned latent features into explicit, parsimonious governing equations.
Figure 2: Savitzky-Golay filtering. The dashed line exhibits the severe high-frequency jitter of raw noisy observations. In contrast, the solid curves demonstrate the smoothed physical trends recovered by increasing window sizes. This filtering effectively suppresses stochastic noise while preserving geometric structure, providing a stable, derivative-friendly initialization for the GNN simulator.
Table 1: Comparison of discovered formulas for the Wave Equation across different noise levels. (Note: Constants in the extracted formulas are rounded to appropriate significant figures, and expressions are moderately simplified for readability. The complete, unedited formulas and detailed variable nomenclature are provided in the Appendix.)
Figure 3: Visual comparison of predicted wave fields ( u(x,y,t) ) at time t=1.0 under different noise regimes. Top row: low noise (0.2%); Bottom row: severe noise (5.0%). Columns present Ground Truth, SGN (ours), and PDE-NET 2.0 (baseline). While all methods converge under low noise, SGN maintains structural stability and captures the physical wave front even at 5.0% noise, whereas PDE-NET 2.0 exhibits catastrophic numerical divergence (indicated by ‘Inf’ on a blank background).
Table 2: Comparison of discovered formulas for the Convection-Diffusion Equation across different noise levels. (Note: Constants in SGN’s extracted node formulas are moderately simplified for readability, with the global multiplier representing the learned time step Δt . The complete, unedited formulas and detailed variable nomenclature are provided in the Appendix.)
Figure 4: Visual comparison of predicted solutions for the Convection-Diffusion Equation with 0.5% noise. Spatial distributions are shown at two time steps: t=0.2 (top row) and t=2.0 (bottom row). Columns display Ground Truth, SGN, and PDE-NET 2.0. The figure illustrates the relative degradation of prediction coherent structures at longer simulation times for both learned models compared to Ground Truth.
Noise
MSE (on True)
Node Formula ( u,v update rules)
Message Formula ( e0,e1 spatial coupling)
0.0%
9.69×10−4
u≈cos(x)sin(y)⋅[−0.61sin(−0.13t)−0.98]
[Decoupled: Messages ignored by node formula]
v≈−cos(y)⋅(ux+uy−sin(x))⋅[0.94cos(…)]
0.1%
6.27×10−4
u≈u1⋅(0.9900558−0.0016⋅e0)
e0≈0.015(v1−u2)
v≈v1⋅(0.9902582−0.0007⋅e1)
e1≈0.159−0.026(t−u2)
0.5%
6.30×10−4
u≈0.9900131⋅u1−0.0046⋅e1
e0≈0.237−0.212cos(u1−v1−uy1)
v≈0.9900553⋅v1+0.0030⋅e1
e1≈−0.005(uy1+v1)
Table 3: Discovery results for the Navier-Stokes (Taylor-Green Vortex) system across different noise levels. The intermediate graph message functions are represented by e0 and e1 . Constants are moderately simplified for readability. The complete, unedited formulas and detailed variable nomenclature are provided in the Appendix.)
Figure 5: Snapshots of the Navier-Stokes flow dynamics under a severe 10% noise level. The figure illustrates the Ground Truth alongside the SGN predictions. Even when the underlying data is heavily obscured by high-frequency artifacts, the proposed SGN architecture flawlessly maintains the structural stability of the fluid flow, achieving highly consistent physical predictions without relying on dense spatial sampling.
Appendix figures & tables4 assets
Supplementary material from the paper’s appendix.
Appendix
Variable
Physical and Architectural Description
t
The temporal evolution step t of the dynamical system.
x , y
The spatial coordinates of the grid nodes.
u_prev
For scalar fields (Wave, Convection-Diffusion), the field value u of the central node at the previous time step.
x_prev , y_prev
For vector fields (Navier-Stokes), the two state components of the central node at the previous time step, corresponding to horizontal ( u ) and vertical ( v ) velocities.
*_prev1
In message functions, the historical state variable of the neighbor node (source node, j ).
*_prev2
In message functions, the historical state variable of the central node (target node, i ).
Appendix
Table 1: Nomenclature and physical interpretations of the symbolic variables discovered by SGN.
Discovering governing Partial Differential Equations (PDEs) from sparse and noisy data is a challenging issue in data-driven scientific computing. Conventional sparse regression methods often suffer from two major limitations: (i) the instability of numerical differentiation under sparse and noisy data, and (ii) the restricted flexibility of a pre-defined candidate library. We propose Weak-PDE-Net, an end-to-end differentiable framework that can robustly identify open-form PDEs. Weak-PDE-Net consists of two interconnected modules: a forward response learner and a weak-form PDE generator. The learner embeds learnable Gaussian kernels within a lightweight MLP, serving as a surrogate model that adaptively captures system dynamics from sparse observations. Meanwhile, the generator integrates a symbolic network with an integral module to construct weak-form PDEs, avoiding explicit numerical differentiation and improving robustness to noise. To relax the constraints of the pre-defined library, we leverage Differentiable Neural Architecture Search strategy during training to explore the functional space, which enables the efficient discovery of open-form PDEs. The capability of Weak-PDE-Net in multivariable systems discovery is further enhanced by incorporating Galilean Invariance constraints and symmetry equivariance hypotheses to ensure physical consistency. Experiments on several challenging PDE benchmarks demonstrate that Weak-PDE-Net accurately recovers governing equations, even under highly sparse and noisy observations.
Xinxin Li, Xingyu Cui, Jin Qi +3
School of Mathematical Sciences, East China Normal University, Shang Hai, 200241, China · Institute of Applied Physics and Computational Mathematics, 100094, Beijing, China · Shanghai Zhangjiang Institute of Mathematics, 201203, Shanghai, China +2
Discovering governing partial differential equations (PDEs) from noisy observational data is a fundamental challenge in scientific machine learning. Traditional symbolic regression (SR) methods often struggle to identify accurate equations within vast combinatorial search spaces, largely due to their inability to incorporate essential domain-specific prior knowledge. Furthermore, reliance on pointwise evaluations and discrete finite differences inherently amplifies high-frequency noise, creating deceptive fitness landscapes that derail the optimization process. To resolve these bottlenecks, we propose LLM-PDESR, a framework that integrates the structural hypothesis generation of Large Language Models (LLMs) with a mathematically rigorous evaluation environment. By employing C^4-continuous quintic splines for robust differentiation and subdomain weighted residuals as natural low-pass filters, our approach effectively mitigates the fitness landscape distortion that plagues existing methods. A Pareto-driven feedback loop then enables the LLM to iteratively refine candidate equations, balancing predictive accuracy with structural parsimony. We evaluate LLM-PDESR on 23 canonical PDEs and five structurally novel equations (including a multivariate system) specifically designed to preclude dataset memorization and test true discovery capabilities. Demonstrating real-world applicability, the framework successfully extracts a consistent structural skeleton for an interpretable 1D dynamical surrogate (1D-CACE) directly from noisy ERA5 reanalysis data. Extensive experiments and out-of-distribution testing confirm that LLM-PDESR significantly outperforms state-of-the-art methodologies in structural recovery, noise resilience, and the avoidance of spurious complexity and equation bloat.
Jinyang Du, Hao Ma, Xiaohu Shi +4
College of Computer Science and Technology, Jilin University, Changchun, China · School of Big Data and Artificial Intelligence, Guangdong University of Finance and Economics, Guangzhou, China · Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, China +2
Models based on partial differential equations (PDEs) are powerful for describing a wide range of complex phenomena in the natural sciences. Accurately identifying the PDE model, which represents the underlying physical law, is essential for a proper understanding of the problem. This reconstruction typically relies on indirect and noisy measurements of the system's state and, without specifically tailored methods, rarely yields symbolic expressions, thereby limiting interpretability. In this work, we address this limitation by considering neural network architectures based on rational functions for the symbolic representation of physical laws. These networks combine the approximation power of rational functions with the flexibility to represent arithmetic operations, and generalize ParFam and EQL-type architectures used in symbolic regression for physical law learning. We further establish regularity results for these symbolic networks. Our main contribution is a reconstruction result showing that, if there exists an admissible physical law that is expressible within the symbolic network architecture, then in the limit of noiseless and complete measurements, symbolic networks recover a physical law within the PDE model that is representable by the architecture. Moreover, the recovered law corresponds to a regularization-minimizing parameterization, promoting interpretability and sparsity in case of L1-regularization. Under an additional identifiability condition, the unique true physical law is recovered. These reconstruction and regularity results are derived at the continuous level prior to discretization due to a formulation in function space. Empirical results using the ParFam architecture are consistent with the theoretical findings and suggest the feasibility of reconstructing interpretable physical laws in practice.
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IDea Lab - The Interdisciplinary Digital Lab at the University of Graz, Austria. · Aleph Alpha Research, Germany.