GNN Survey


GNN Survey


In my opinion, graph neural networks is worth exploring within research field, not engineering field, especially large scale application. Anyway, this survey is a naive summarization of my recent reading. Writing in English is just a practice of my poor writing ability.

Without whistles and bells, there are some equivalent concepts or notions in graph terminology. First of all, graph signal is general representation, which stands for collection of node embeddings or node signals whatever domain we talk about. Graph Fourier Transformation (GFT) is just discrete version Fourier Transformation (FT). Fourier Transformation (FT) converts temporal signals to frequency signal with the help of operator $e^{-iwt}$ (sine, cosine base function), and vice versa. In a similar way, GFT converts spatial domain to spectral domain with the help of $\phi^T$ (eigen base vector).

Note spatial domain is also known as vertex domain , graph domain or data space domain. In the contrast, Spectral domain is also denoted as feature space domain.

More straightforwardly, GFT converts node function(signal) to an eigen function(signal). Here node function represents a node-wise function, which means every node has a value (scalar or multi-dimensional feature (tensor)), shaped $n_1 \times d$ . eigen function denotes a eigen-wise function, which means every eigen value (or vectors) has a value (scalar or multi-dimensional feature (tensor)), shaped $n_2 \times d$ . Note we assume that $n_1 == n_2 == #eigen \, vectors == #eigen \, values$, because the initial kernel graph construction is based on data matrix, which is usually full-rank due to dataset variance.

It is easy to find that we obtain a new node representation (embedding) by aforementioned GFT. However that transformation utilizes graph global structure (because of Laplacian or Adjacency matrix) to embed own nodes. Using this determinism-will idea, we can adjust embeddings by manual setting or learnable manner, which is also named as spectral-based method and the best practice is Graph Convolutional Networks (GCN). In this article, I call it global view embedding, details in section 2.

Apparently, global view embeddings is limited to undirected graph (due to decomposition of real symmetric matrix) and strongly corelated to node ordering. So operating embeddings on vertex domain directly is desirable. This kind of method is named spatial-based method and the best practice is Message Passing Protocol (MPP) or Recurrent Graph Neural Networks (RecGNN). In this article, I call it local view embedding, details in section 3.

So far, we have solved node embedding problems in both global and local view. We can also conduct graph embedding and time-dependent graph data, details in section 4 and section 5.

Some notations or denotations are as follows:

Notations Descriptions
$G$ a graph
$V$ the set of nodes in a graph
$v$ a node $v \in V$
$N(v)$ set of neighbor nodes of $v$
$E$ the set of edges in a graph
$e_{ij}$ an edge $e_{ij} \in E$
$A$ or $W$ the graph adjacent matrix
$X \in R^{n \times d}$ node feature matrix
$x^{v} \in R^{d}$ feature of node $v$
$X^e \in R^{n \times c}$ edge feature matrix
$x^{e}_{(v,u)} \in R^{c}$ feature of edge $e$ between $v$ and its neighbor $u$
$n$ $n = |V|$ the number of nodes
$m$ $m = |E|$ the number of edges
$d$ the dimension of node feature
$h$ the hidden dimension of node feature
$c$ the dimension of edge feature
$L$ Laplacian eigen map
$\mu_i, \lambda_i$ $i$-th eigen vector and eigen value of Laplacian matrix
$\phi$ $\phi = [ \mu_1, \cdots, \mu_n]$ Graph Fourier Inverse Transformation Operator

Global View

Laplacian Eigen Map and Total Variation

Let’s begin the extraordinary adventure with global view embedding. Please keep it in your mind that global view is globality of original data (spatial domain), which means spectral domain is not dependent or orthogonal to spatial domain, but different views of the same data.

Given a undirected graph $G$, we firstly obtain Laplacian Eigen Map $L = D - A$, where $D$ is degree diagonal matrix. Specifically, $D = {d_{ij}}$ and $d_{ii} = \sum_{k = 1}^{n}A_{ik} = \sum_{k=1}^{n}A_{ki}$, $d_{ij} = 0$ when $i \ne j$, $A$ is adjacency matrix with $A_{ii} = 0$. Although there are modified Laplacian Eigen Map (such as normalized Laplacian, random walk Laplacian), we simply use the vanilla version.

Decomposing $L$ and we can obtain eigen vectors $\mu_i$ and associated eigen values $\lambda_i$, suppose that $\lambda_1 < \lambda_2 < \cdots < \lambda_n$:

\[\phi^{-1}L\phi = \Lambda \\ where \, \phi = [ \mu_1, \cdots, \mu_n], \, \Lambda = \left[\begin{matrix} \lambda_1 & 0 & \cdots & 0 \\ 0 & \lambda_2 & \cdots & 0 \\ \vdots & \vdots & \ddots & \vdots \\ 0 & 0 & \cdots & \lambda_n \end{matrix}\right] \\ and \, \phi^{-1} = \phi^T, \, orthogomal \, matrix\]

Now, let’s find some interesting properties of $L$. we simply suppose that the dimension of node feature is 1. Note when it is more than 1, we can conduct the following procedure in a predictor-wise manner to get the same perspective, thus $X = \left[\begin{matrix} x_1 & x_2 & \cdots & x_n\end{matrix}\right]^T \in R^n$ and $x_i$ is a scalar feature of node $i$.

\[\begin{align} LX &= (D-A)X \\ &= \left[\begin{matrix} x_1d_{11} \\ x_2d_{22} \\ \vdots \\ x_nd_{nn} \end{matrix}\right] - \left[\begin{matrix} x_{1i}a_{1i} + x_{1j}a_{1j} + \cdots \\ x_{2i}a_{2i} + x_{2j}a_{2j} + \cdots \\ \vdots \\ x_{ni}a_{ni} + x_{nj}a_{nj} + \cdots\\ \end{matrix}\right] \\ &where \, e_{1i} \, e_{1j} \, e_{2i} \, e_{2j} \, e_{ni} \, e_{nj} \cdots \in E \\ &= \left[\begin{matrix} \sum_{j \in N(1)}a_{1j}(x_1 - x_j) \\ \sum_{j \in N(2)}a_{2j}(x_2 - x_j) \\ \vdots \\ \sum_{j \in N(n)}a_{nj}(x_n - x_j) \end{matrix}\right] \end{align}\]

It is obvious

  • that Laplacian Operator (Laplacian Eigen Map) represents the difference (or variation) between every node and its neighbors.
  • that decomposition of Laplacian Eigen Map $L\mu = \lambda\mu$ has trivial solutions when $\lambda = 0$ (I will show $\lambda \ge 0$ next paragraph) and the number of trivial solutions (the multiplicity of the smallest eigen value $0$ ) is just the number of connected components (Note there is one trivial solution at least , that is with the same value for all nodes), because we can assign a fixed value for every connected components and make every node in this component with this value. Same or not same value(s) for different connected components is dependent on the specific situation.
  • that spectral clustering is a method for clustering ( dimensionality reduction and clustering), which just partitions the low-frequency base signals (regarding eigen vectors corresponding to the second least eigen value as reduced results).

Let’s take one more step in a $n$-element quadratic form or standard form:

\[\begin{align} X^TLX &= \left[\begin{matrix} x_1 & x_2 & \cdots & x_n \end{matrix}\right] \left[\begin{matrix} \sum_{j \in N(1)}a_{1j}(x_1 - x_j) \\ \sum_{j \in N(2)}a_{2j}(x_2 - x_j) \\ \vdots \\ \sum_{j \in N(n)}a_{nj}(x_n - x_j) \end{matrix}\right] \\ &= \sum_{e_{ij} \in E}{a_{ij}(x_i - x_j)^2} \end{align}\]

It is apparent

  • that $L$ is a semi-positive definite matrix, and least eigen value $\lambda_1 = 0$ and I have proofed its trivial solutions ahead of time.

  • that both $LX$ and $X^TLX$ represent the difference or variation between every node and its neighbors. we call the latter as Total Variation (denoted as $TV(X)$).

  • Let’s take one more step, supposing that $Y = \phi^TX = \left[\begin{matrix} y_1 & y_2 & \cdots & y_n \end{matrix}\right]^T$ is the embedding of vertex signal/function with the eigen vectors as the bases. $Y$ is also known as eigen signal/function.

    \[\begin{align} TV(X) &= X^TLX = X^T\phi \Lambda \phi^T X \\ &= Y^T \Lambda Y \; (normalized \; form) \\ &= \sum_{i = 1}^{n}{\lambda_iy_i^2} \end{align}\]

Now we have drawn a clear conclusion that $TV(X)$ is the squared sum of signal residuals between every node and its neighbors in spatial domain and is the squared sum of eigen-value-weighted eigen function/signal (coordinate representations or embeddings) in spectral domain.

Based on aforementioned analysis and given a topology structure of a graph, we can optimize the graph signals by $argmin \;TV(X)$ easily. Obviously, $TV(X)$ has the smallest value $0$ when vertex signal has the same direction with the eigen vector associated the least eigen value $\lambda_1 = 0$. More importantly, we have obtained this kind of eigen vectors by trivial solutions. In a word, $TV(X)$ has the smallest value $0$ if the vertex signal is made up of a fixed constant for all vertices of the whole graph or all vertices of current connected component. It is also intuitive to make this conclusion from definition of Laplacian Operator (difference or variation). On the contrary, $argmax \;TV(X)$ is a difficult optimization.

In addition, we can also observe the relations between variation and spectral domain. i.e., different eigen values have different contributions to the variation/difference. Specifically speaking, large eigen values contribute more than small eigen values. Therefore, if the embedding specific to the eigen vectors associated to large eigen values is large, the graph signal tends to be unsmooth, jittering and high-variance. On the contrary, the graph signal is smooth, mean and uniformly identical. Please keep this observation in mind, I will formulate Graph Convolutional Networks from it.

So far, I have summarized the properties of $L$, different views and optimization of $TV(X)$ and obtained a intuitive but amazingly powerful inference that smoothness of graph signals is strongly related (or equivalent to) magnitude of embeddings of different eigen vectors. There is no doubt that optimization of $TV(X)$ is meaningless in the practical scenario, because It reassigns graph signals and ignores the original graph signals completely. Naturally, we need a kind of operation that changes the smoothness of a given graph (i.e., low-pass, high-pass or band-pass), which is also known as filtering in digital signal processing (DSP) field.

Graph Filtering

In concept , graph filtering is a 2-step procedure that consists of graph-spectrum transformation (graph Fourier transformation) and modified reconstruction respectively. In equation, it is represented as following:

  • obtain embeddings using graph-spectrum transformation (map from spatial domain to spectral domain):

    \[Y = \phi^TX = \left[\begin{matrix} y_1 \\ y_2 \\ \vdots \\ y_n \end{matrix}\right]\]
  • modify embeddings explicitly to smooth or unsmoooth the graph signals:

\[\begin{align} \hat{Y} = h(\Lambda)Y = \left[\begin{matrix} h(\lambda_1) & 0 & \cdots & 0 \\ 0 & h(\lambda_2) & \cdots & 0 \\ \vdots & \vdots & \ddots & \vdots \\ 0 & 0 & \cdots & h(\lambda_n) \end{matrix}\right] \left[\begin{matrix} y_1 \\ y_2 \\ \vdots \\ y_n \end{matrix}\right] = \left[\begin{matrix} h(\lambda_1)y_1 \\ h(\lambda_2)y_2 \\ \vdots \\ h(\lambda_n)y_n \end{matrix}\right] \end{align}\]
  • reconstruct the spatial graph signal (vertex function/signal) using modified embeddings (map from spectral to spatial):

    \[\hat{X} = \phi \hat{Y} = h(\lambda_1)y_1 \mu_1 + h(\lambda_2)y_2 \mu2 + \cdots + h(\lambda_n)y_n \mu_n\]

Aforementioned procedure is intuitive because smoothness is equivalent to embeddings of eigen vectors corresponding to large or small eigen values. Changing embeddings is just to adapt smoothness of graph signals. We can also regard this in a different view:

\[\begin{align} \hat{X} &= H X \\ & where \; H = \phi h(\Lambda) \phi^T \end{align}\]

In convolution theory, we conventionally call $H$ filter matrix and $h(\Lambda), h$ represent response matrix and response function respectively. Note filter matrix $H$ is also known as Graph Shift Operator (GSO).

It is obvious

  • that graph filtering is just a linear transformation with filter matrix $H$.
  • that different filter matrix $H$ will generate different transformed graph signals, such as
    • if $h$ is an identical mapping, $H = L$, $\hat{X} = LX$ is smoother than $X$ naturally (due to residuals). Furthermore, $L^kX$ will smoother than $L^{k-1}X$ (due to residuals of residuals), note $L^0X = X$. This kind of filter matrices is names Chebyshev Base Filter Matrix and I will discuss it later.
    • if $h$ is an one mapping, $H = I_n$, $\hat{X} = X$ do nothing meaningful.
    • if $h$ is a zero mapping, $H = 0, \hat{X} = 0$ do nothing meaningful.
    • furthermore, although we have no explicit formations of response function $h$, we still claim that bot adjacence matrix $A$ and degree diagonal matrix D are GSOs. I will regard $A$ as a GSO in later discussion of GCN.
  • that properties of filter matrices / graph shift operators (GSOs) can be summarized as following:
    • linear transformation: $H(\alpha X + \beta Y) = \alpha HX + \beta HY$
    • commutative law (swappable): $H_1(H_2X) = (H_1H_2)X$
    • condition of inversible filtering: response function $h$ is inversible (we can replace original values with inversed values in the response matrix $h(\Lambda)$)

Because there are a great number of response functions $h$, we can choose different $h$ to construct different response matrices $h(\Lambda)$. However, please keep it in mind that the easy but power $h$ and $h(\Lambda)$ is identical mapping and laplacian eigen map $L$ respectively on account of the variation/difference of $L$. Approximately, we can conduct Taylor Expansion w.r.t. $L$ ( or $\lambda_i$) to fit any filter matrix (GSO) $H$ ( or $h$ function), which is computed as:

\[\begin{align} h(\lambda_i) &= \sum_{k=0}^{K}{h_k \lambda_i^k} \\ h(\Lambda) &= \sum_{k=0}^{K}{h_k \Lambda^k} \\ H &= \phi h(\Lambda) \phi^T \\ &= \phi (\sum_{k=0}^{K}{h_k \Lambda^k}) \phi^T \\ &= \sum_{k=0}^{K}{h_k L^k} = \left[\begin{matrix} \sum_{k=0}^{K}{h_k \lambda_1^k} & 0 & \cdots & 0 \\ 0 & \sum_{k=0}^{K}{h_k \lambda_2^k} & \cdots & 0 \\ \vdots & \vdots & \ddots & \vdots \\ 0 & 0 & \cdots & \sum_{k=0}^{K}{h_k \lambda_n^k} \end{matrix}\right]\\ \end{align}\]

This equation is trivial due to both algebra view ($\phi \Lambda^k \phi^T = L^k $) and chain-based filtering transformation view ($L^{k+1}(X) = L(L^k(X))$). The aforementioned kind of filter matrix also known as Chebyshev Network. We can remember it by 3 ways ( i.e., Taylor Expansion of response function $h(\lambda_i)$, response matrix $h(\Lambda)$ and filter matrix (GSO)) $H = \sum_{k=0}^{K}{h_k L^k} $.

Let’s simplify this equation and explore the explicit relation between response function and filter matrix (note this relation is usually complicated and agnostic but here is a simple but generally power Chebyshev Network):

\[\begin{align} H &= \left[\begin{matrix} \sum_{k=0}^{K}{h_k \lambda_1^k} & 0 & \cdots & 0 \\ 0 & \sum_{k=0}^{K}{h_k \lambda_2^k} & \cdots & 0 \\ \vdots & \vdots & \ddots & \vdots \\ 0 & 0 & \cdots & \sum_{k=0}^{K}{h_k \lambda_n^k} \end{matrix}\right] \\ &= diag(\left[\begin{matrix} \sum_{k=0}^{K}{h_k \lambda_1^k} & \sum_{k=0}^{K}{h_k \lambda_2^k} & \cdots & \sum_{k=0}^{K}{h_k \lambda_n^k} \end{matrix}\right]^T) \\ &= diag(\left[\begin{matrix} 1 & \lambda_1 & \lambda_1^2 & \cdots & \lambda_1^K \\ 1 & \lambda_2 & \lambda_2^2 & \cdots & \lambda_2^K \\ \vdots & \vdots & \vdots & \ddots & \vdots \\ 1 & \lambda_n & \lambda_n^2 & \cdots & \lambda_n^K \\ \end{matrix}\right] \left[\begin{matrix} h_0 \\ h_1 \\ \vdots \\ h_K \end{matrix}\right]) \\ &= diag(\Psi \pmb{h}) \end{align}\]

where $\Psi \in R^{n \times K} $ is Vandermonde Matrix (not $n$-order Vandermonde Determinant), $ \pmb{h} $ is a coefficient vector, which represents response function $h$ naturally.

when $n==K$, $ \pmb{h} = \Psi^{-1}diag^{-1}(H) $, but $K « n$ is a common case.

So far I have obtained a relatively useful conclusion on graph filtering and Chebyshev Network best practice. However specifying response function $h$ or $\pmb{h}$ is not a wise idea, we wanna optimize it by a differentiable and end-to-end manner.

Graph Convolutional Networks

Let’s review the convolution theory of digital signal processing (DSP) field. Convolution is a binary operation to transform the signals for the convenience of down-stream processing. Specifically, given signals $f$ and $g$, $1$-d convolution on them is computed as

\[(g \star f) (x)= \int f(x-t) g(t) dt\]

It is obvious that we transform from $t$ domain to $x$ domain. Taking this convolution to Fourier Transformation in continuous space, we find that it just a special case with $g(t) = e^{-iwt}$:

\[\mathcal{F} f(x) = \int f(x-t) e^{-iwt}dt\]

Fourier Transformation has an amazing property (also known as theorem of convolution) that Fourier Transformation of convoluted signals is just convolution of transformed signals:

\[\mathcal{F} (g \star f) = \mathcal{F} g \star \mathcal{F}f\]

Now we can also adapt this property directly to discrete space (Graph Convolution).

The motivation of graph convolution is that conducting convolution of original space (spatial domain) is difficult, while this is trivial (simply multiply) in transformed space (spectral domain) due to the strip of correlation using eigen decomposition. Indeed, it also encompasses unnecessary global view under some circumstance. Anyway we can rewrite it using notations of graph theory:


\[\begin{align} g \star f &= \mathcal{F}^{-1}(\mathcal{F} g \star \mathcal{F} f) \\ &= \phi(\phi^T g \odot \phi^T f) \\ &= \phi \left(diag(\phi^T g) \phi^T f \right) \\ &= \left( \phi \; diag(\phi^T g) \phi^T \right) f \\ \end{align}\]

where $\odot$ represents element-wise multiplication (Hadamard Product) and $\phi$ is eigenvectors of graph corresponding to signal $g$ (not $f$). Now we can find that graph convolution takes one more step than graph fourier transformation (graph filtering), That is graph fourier transformation is to change the smoothness of its own signals according to its own structure (eigen base), while graph convolution is to change the smoothness of others according to its. In other words, there is no notion or concept of response function (explicit or implicit) in graph convolution. Response matrix is not $h(\Lambda)$ any longer but $diag(\phi^Tg)$, which is just $\hat{g}$ (embeddings or transformed signals of $g$ using its own structure), note that this is just a standard graph filtering process.

Now let’s parameterize the graph convolution. There are 3 kinds of scheme:

  • parameterize the filter matrix $H_{\theta} = \phi \; diag(\phi^T g) \phi^T \in R^{n \times n}$.
  • parameterize the response matrix (also known as fourier embeddings of other signals) $R_{\theta} = diag(\phi^T g) \in R^{n \times n}$, but $n$ parameters.
  • constrain the response matrix and make it similar to the counterpart of graph filtering, that is, $R_{\theta} = h(\Lambda) = \sum_{k=0}^{K}{h_k \Lambda^k} $, but $K$ parameters. note $K « n$ in general.

Local View

Embedding View

Spatial-Temporal View