The power of Graph Neural Networks

Kåre von Geijer published on
15 min, 2944 words

There is something about graph algorithms - they are just always fun to think about! With that said, Graph Neural Netorks (GNN) are no exception. These are a form of neural network, but designed in a way to learn things about graphs. They have proven to be usefull for a plethora of graph learning problems in fields such as drug discovery, recommender systems, and protein folding. In this post, I will present the difficulty of directly applying neural networks (NN) to graphs, how message passing NN solves this, and end by looking at the expressive power of such GNN.

Background on Graphs

The mathematical notion of a graph is :

  • A Vertex set
    • These are the named vertices (nodes) in the graph.
  • An Edge set
    • Each edge connects two vertices.
  • Vertex labels
    • Each vertex has a set of labels, which contain some extra information about what the node represents. This could for example be geographical coordinates if the graph represents a map.

If you have not worked much with graphs, they might seem niche, but you later realize that they are everywhere. Here are a few examples of where graphs are used:

  • To model social networks,
  • Knowledge graphs are popular to build up a structured network of knowledge,
  • Geographical maps,
  • Modeling the 3D structure of proteins,
  • Solving fun programmaing puzzles,
  • And much more...

Goal of Graph Learning

There are three main embeddings we want to learn when to comes to graph learning:

  • Vertex embedding
    • Want to estimate some properties per node. For example the political party of a person on Facebook.
  • Edge embedding
    • Want to learn some relations between nodes. In a chemical graph, we could use this to predict the strength of the bonds (edges) between atoms (vertices).
  • Graph embedding
    • Here we want to learn a property about the whole graph in aggregate. When used in drug discovery, this could help predict the molecular properties of a drug (a graph).

Thes can be seen as the main embeddings we are usually interested in. However, as we will see later, in GNN we primarily care about vertex embeddings which we in turn aggregate to the other embedding types if wanted.

Applying Deep Learning to Graphs

Deep learning has recently proven to be extremely useful for a variety of machine learning tasks. Therefore, people have naturally been interesting in utilizing its power to learn things about large graphs.

Common Ideas of Deep Learning

Before we begin with GNN, we should look at what basic building blocks used in Deep Learning (DL). Classic DL network are constructed as several layers, each with the following characteristics:

  • First, we apply some form of linear transformation of the input (which can be modeled with a matrix multiplication). For example, this can be a fully connected layer in a NN, or a convolutional layer in a CNN.
  • Secondly, there is some non-linear activation function. This is the key which gives the network its elevated expressive power compared to a linear transformation. Examples of this can be versions of Rectified Linear Units (ReLU), which apply f(x) -> max(x, 0) to all inputs.

Naive Neural Networks

The easiest idea in DL is often to just throw simple neural networks (eg. multilayer perceptrons) at the problem, and one might want to simply throw a NN at a set of graphs to learn some hidden embedding for them (say we feed the adjacency matrix appended with node features as input). However, this quickly becomes problematic due to the complex nature of graphs. When learning things about text or images, we have a sequence or grid of inputs, which have very clear structures in comparison to the endless possibilities of graphs. Here are some concrete problematic points:

  • Variable size: Different graphs will have different sizes. This is also a problem for images, but there the naive solution of cropping/resizing and padding them work rather well. However, how would one rezise a graph? Where would we add padding or crop nodes?
  • Input invariance: As the topology in a graph is dynamically dependend on neighbors, there is no predefined order among the vertices. As most DL methods are dependent on the order of the input, the order you pass the nodes becomes paramount. We want a method where the order of the inputs have zero effect (the locaility will be based on edges instead of input position).

So, just throwing a neural network at a graph is not the way to go. Instead, we need a method which can handle variably sized graphs, as well as handle the complex topology and invarianve over node order which is so inherent to graphs.

Convolutional Neural Networks

We take inspiration from the idea of Convolutional Neural Networks (CNN), which are used extensively where the inputs are grids. The idea is that you convolve the input with some small kernel with learnable parameters (way less parameters than a fully connected layer). For 2D inputs, this can be seen as sliding this kernel (a small matrix) over the input grid, for each overlap pairwise multiplying overlapping values and then summing them together. This is done for all possible overlaps, and you get a transformed output. This is visualized below where we can see how a 3x3 kernel operates on a 3 by 3 area to find one output (then it slides to find the rest).


The core idea here is to utilize the spatial locality of adjacent cells to find some meaningfull embedding. We want to adapt this great idea to the much more complex topology to graphs!

From Images to Graphs

So, a 3x3 kernel for each node (disregarding edges) essentially adds a weighted sum of the neighbors of every cell. We can do this in graphs as well, where we in a similar fashion would create an intermediate embedding where each node collects some weighted sum of their neighbors embeddings (as can be seen below). Then, we can pass that through a non-linear activation function in similar vein to normal CNN.

Node Agg

Message Passing Neural Networks

Let's expand the idea from CNN which we showed before, to create a Message Passing Neural Network (MPNN). Given the following graph


we want to use the idea of neighbor aggregation to find intermediate embeddings. Furthermore, the algorithm should not just take the immediate neighbors into account, but also their neighbors, and their neighbors, and so on. This can be done by creating a custom computation network for each node. The following image depicts the computation graph for the green node above.

Green Computation Graph

This compuation graph defines the computation of the vertex embedding of the green node, and can be seen as some Deep Learning Network. How you select the aggregations (gray boxes) is what defines the GNN architecture (but you must make sure they are order invariant). The basic approach for the neighbor aggregation function is to first average all neighbor embeddings (linear), and then feed it through some neural network (nonlinear).

Furthermore, these computation graphs look different for each node, as they have different starting points. Here is the computation graph for the red node.

Red Computation Graph

So we can see that each node always collects the embeddings of the earlier layer of its neighbors. This can be seen as layers in a neural network, where the input to the first layer is the node labels, the input to the second layer is the embeddings from the first round of message passes, and so on. However, the aggregation and update functions (gray boxes) contain learnable parameters, and can vary in shape and functionality every layer (like the layers in a NN), and they (the boxes) are the same for all nodes in a certain layer. Thus, you need to define the number of layers beforehand, and their design. Formalizing one such layer, we get the following.

Here h is a vertex embedding and Upd and Agg are the update and aggregation functions (which contain learnable parameters). In the simplest case, Agg can be a linear transformation where we sum all u, multiply the sum with a square (learnable) weight matrix (W), and add a bias vector (b). The Upd can apply a similar transformation to the node itself, sum all of them together, and feed it through a non-linear activation function .

While this expresses the update function of a single vertex embedding, we can move it to matrix form to find the embeddings of all vertexes.

So becomes the final embeddings, after iterating for some predetermined n rounds.

Graph embedding

To get the graph embedding from the final vertex embeddings, we simply apply a final aggregation (eg. average) to all vertices, and then feed it through some NN (for example a multilayer perceptron).

A similar method can be used to transform these vertex embeddings to edge embeddings (or more generally p-vertex embeddings for p connected nodes).

Training the MPNN

We have now descibed how a Message Passing Graph Neural Network (MPNN) computes embeddings, given the learnable parameters/functions. But how do we actually train this network?

Well, it works basically the same as with a classical NN. In supervised learning (where we have labels on the training data) we define a loss function between the final embeddings and the given labels. This loss function could for example be the L2 norm (euclidean distance) if the labels are real nubmers, or the cross entropy if they are categorical. We then use methods such as Sthochastic Gradient Descent and back-progagation to uptade the learnable parameters after the loss function.

For unsupervised training we must work a bit extra as there are no training labels. Instead we strive for similar vertexes to have similar embeddings. Then we need some similarity metric, which could e.g. be calculated from a random walk experiment, a matric factorization, or graph proximity.

Expressive power

How that we have looked at modern GNNs, especially MPNN, we should take a step back and answer: What are these networks capable of? What are their expressive power? Furthermore, what is expressive power, and how do we measure it?

Notions of expressivity

To talk about expresssivity, we will define

  • H as the set of all possible learned networks,
  • G as the set of inspected graphs.

Then, for some embedding E, we say that

  • H can G-express E, if there exists a network in H such that that network gives the exact same embedding as E on all graphs in G.
  • H can G-approximate E if for any , there exists a network in H such that the difference between the networks encoding and E is smaller than for all graphs in G.

These defitions describe what embeddings we can possibly express with a certain GNN architecture. But then there is the distinguishing power of H, which concerns how many graphs the network can differentiate (with optimal values).

  • The distinguishing power of H is the sef of pairs from such that the embedding of both graphs are equal.

Thus, a high distinguishing power (counting number in set) is bad and means that the network cannot differentiate different graphs.

So far, the focus in the ML community has been on characterizing the distinguishing power of GNN, to hopefully shed some light on what graph properties a learning method can detect and use.

Color Refinement

Before moving on to the juicy parts, we have to take a detour to the classical algorithm of color refinement, which has some interesting connections to MPNN. This is an algorithms to color a graph, and is often used as a good heuristic for if two graphs are non-isomorphic (not identical).

Here is an overview of how the algorithm works:

  • At the start of the algorithm, all nodes are identically colored.
  • Repeatedly, identically colored vertices are separated into different colors based on color histograms of neighbors.
  • Two graphs are not isomorphic if they have different color histograms.

This is simplest to show visually. Here are two graphs, which together goes through the iterations of the algorithm. After the second iteration, they contain different colors, so we can conclude they are not isomorphic!


However, if we apply the same algorithm to the following non-isomorphic graphs, the algorithm cannot guarantee that they are not isomorphic.


This means that the coloring cannot distinguish these last two graphs, meaning the pair is within the algorithms distinguishing power. For example it

  • cannot distinguish d-regular graphs,
  • cannot count cycles,
  • can only capture tree information.

Expressive power of MPNN

So what does this color refinement have to do with the expressive power of MPNN? Well, Xu et al. 2019 and Morris et al. 2019 both proved that

If colour refinement cannot tell two graphs apart then neither can any MPNN!

Furthermore, Morris et al. 2019 proved that the distinguishing powers are equal:

There exists a GNN 101 which can embed G and H differently when colour refinement assigns them different colours.

This is bleak news for MPNN as extensive earlier research on color refinement has shown its severe limitations in expressive power. For example, as we said above, it can only capture information about tree-like dependencies, and cannot really capture cycles.

Increasing the Expressive power of MPNN

There are different ways to approach the problem of limited expressive power of GNNs, and most of it seems like early DL (or alchemy), where you just try things and have faith.

Idea: Feature engineering

One proposed improvement is the old school feature engineering, which Deep learning was supposed to eliminate. By adding features such as

  • number of edges,
  • number of cycles of a specific length,
  • matches with certain patterns,
  • other centrality measures, our MPNN can boost their distinguishing power as they gain some information outside trees. However, this is a cheap trick, and only solves the problem for the certain patterns overlapping with your features. You can always combine such patterns in a way that the network cannot distinguish.

Idea: Random vertex identifiers

One can note that two nodes with the same features (color in graph refinement) will be treated equally by MPNN. What if we add vertex identifiers to distinguish different nodes?

This is useful for cycle detection, and is equivalent to color refinement where every node starts with a unique color. A common way to choose these identifiers is at random, where we get the theorem

rMPNNs(+) approximate any invariant graph/vertex embedding with high probability.

However, this feels very ugly, as we completely destroy one of the key features of GNN: invariance. However, as the labels are assigned randomly, and mainly matter to differentiate nodes, there are some averaging schemes which make this work rather well (some tradeoff between invariance, expressiveness, and complexity).

Idea: Global information

This feels a bit like advanced feature engineering, and you can boost the expressiveness by extracting global graph information to use as positional encodings of vertices. For example, including the spectral information of the graph can give a large boost, and has been used in several papers from 2023.


The idea of Graph Neural Networks feel very natural in todays world, where both graphs and Deep learning are so prevalent. Even though MPNN are shown to have inherent limitation in their expressiveness, they seems to work relatively well in practice, especially when you enhance them with some extra information.

I have only scrached the surface, and think it would be fun to learn more about different GNN. The simple MPNN with averaging and a perceptron layer was cool, but I wonder what new architectures are having success. Is is similar to the development history of normal NN?

Further Reading

I learned about this topic from professor Floris Geerts, at the ACM Europe Summer School on Data Science 2023, where he mainly focused on the expressive power part (cut short in this post). This is where I took most of the information regarding the expressive power here. If you want to learn more about the expressive power of GNN, I suggest you go and look at his website to find some of his talks and publications.

If you don't care much for the expressive power, and just want to learn more about the design of GNN, such as different MPNN architectures, and their uses, I recommend the course CS224W from Stanford. All the lectures are available for free on youtube here. It seems to be an excellent course covering the foundations of GNN.