Revisit the implementation

Oct 13, 2025 by wbrum.org 44 views

Incorrect Implementation of the Main KuramotoGNN Computation (eq10)

The KuramotoGNN model is a novel approach to graph neural networks that combines the principles of the Kuramoto model with graph neural networks. The main computation of KuramotoGNN is given by equation 10 in the paper, which reads:

\dot x_i = \omega_i + K\sum_ja_{ij}\sin(x_j-x_i).

However, upon closer inspection of the code in src/function_laplacian_diffusion.py, it appears that the equation is implemented differently. Specifically, lines 60-66 implement the equation as:

\dot X = \omega_i + KR\sin(AX-X)

where $A$ is a matrix of the averaged attention weights, and $AX$ refers to the variable $phi$ in line 62, obtained from the spmm operation.

At first glance, it may seem that the two equations are equivalent. However, upon closer inspection, it becomes clear that the attention matrix $A$ is applied outside the sine function in the first equation, but inside the sine function in the second equation. This subtle difference can have significant implications for the behavior of the KuramotoGNN model.

In the first equation, the attention weights are applied directly to the sine function, which means that the attention weights are being used to modulate the strength of the interactions between nodes. In contrast, in the second equation, the attention weights are applied outside the sine function, which means that the attention weights are being used to scale the entire interaction term.

One of the most puzzling aspects of the implementation in src/function_laplacian_diffusion.py is the introduction of the variable $R$ . This variable is not mentioned in the paper, nor is it explicitly commented in the code. As a result, it is unclear what role $R$ plays in the implementation.

However, based on the context in which $R$ is used, it appears that $R$ is being used to scale the interaction term. Specifically, the line of code that introduces $R$ reads:

KR = K * R

This suggests that $R$ is being used to scale the constant $K$ by a factor of $R$ . However, without further information, it is difficult to say exactly what role $R$ plays in the implementation.

In conclusion, the implementation of the main KuramotoGNN computation in src/function_laplacian_diffusion.py appears to be incorrect. Specifically, the attention matrix $A$ is being applied outside the sine function, rather than inside the sine function as in the original equation. Additionally, the variable $R$ is being used to scale the interaction term, but its role is unclear.

To resolve this issue, it is necessary to revisit the implementation and ensure that it accurately reflects the original equation. This may involve modifying the code to apply the attention matrix $A$ inside the sine function, and removing the variable $R$ or clarifying its role in the implementation.

Based on the analysis above, we recommend the following:

Revisit the implementation: Carefully review the implementation in src/function_laplacian_diffusion.py and ensure that it accurately reflects the original equation.
Apply attention matrix A inside sine function: Modify the code to apply the attention matrix $A$ inside the sine function, rather than outside the sine function.
Remove or clarify R: Remove the variable $R$ or clarify its role in the implementation to ensure that it is consistent with the original equation.

By following these recommendations, we can ensure that the KuramotoGNN model is implemented correctly and accurately reflects the original equation.
Q&A: Incorrect Implementation of the Main KuramotoGNN Computation (eq10)

In our previous article, we discussed the incorrect implementation of the main KuramotoGNN computation in src/function_laplacian_diffusion.py. We highlighted the differences between the original equation and the implemented code, and provided recommendations for resolving the issue. In this article, we will answer some of the most frequently asked questions (FAQs) related to this topic.

A: The main KuramotoGNN computation is given by equation 10 in the paper, which reads:

\dot x_i = \omega_i + K\sum_ja_{ij}\sin(x_j-x_i).

This equation describes the dynamics of the KuramotoGNN model, where $\dot x_i$ is the derivative of the state variable $x_i$ with respect to time, $\omega_i$ is the natural frequency of node $i$ , $K$ is a coupling constant, $a_{ij}$ is the attention weight between nodes $i$ and $j$ , and $x_j$ is the state variable of node $j$ .

A: The main difference between the original equation and the implemented code is the application of the attention matrix $A$ . In the original equation, the attention weights are applied directly to the sine function, whereas in the implemented code, the attention weights are applied outside the sine function.

A: The attention matrix $A$ is applied outside the sine function in the implemented code because of a misunderstanding of the original equation. The correct implementation should apply the attention weights directly to the sine function, as in the original equation.

A: The variable $R$ is used to scale the interaction term in the implemented code. However, its role is unclear, and it is not mentioned in the paper. To resolve this issue, it is necessary to revisit the implementation and clarify the role of $R$ .

A: To resolve the issue with the implemented code, you can follow these steps:

Revisit the implementation: Carefully review the implementation in src/function_laplacian_diffusion.py and ensure that it accurately reflects the original equation.
Apply attention matrix A inside sine function: Modify the code to apply the attention matrix $A$ inside the sine function, rather than outside the sine function.
Remove or clarify R: Remove the variable $R$ or clarify its role in the implementation to ensure that it is consistent with the original equation.

A: Using the incorrect implementation can lead to incorrect results and potentially affect the performance of the KuramotoGNN model. To avoid these consequences, it is essential to resolve the issue with the implemented code.

A: You can find more information about the KuramotoGNN model in the original paper, which is available online. Additionally, you can consult the documentation and code repositories for the KuramotoGNN model to learn more about its implementation and usage.

In this article, we answered some of the most frequently asked questions related to the incorrect implementation of the main KuramotoGNN computation in src/function_laplacian_diffusion.py. We provided recommendations for resolving the issue and emphasized the importance of accurate implementation to ensure the correct behavior of the KuramotoGNN model.