Topology Meets Machine Learning: An Introduction Using the Euler Characteristic Transform
Bastian Rieck
Communicated by Notices Associate Editor Emilie Purvine
Machine learning is shaping up to be the transformative technology of our times: Many of us have interacted with models like ChatGPT, new breakthroughs in applications like healthcare are announced on an almost daily basis, and novel avenues for integrating these tools into scientific research are opening up, with some mathematicians already using large language models as proof assistants
Written for an audience of mathematicians with limited prior exposure to machine learning, this article aims to dispel some myths about the field, hoping to make it more welcoming and open. Indeed, from the outside, machine learning might look like a homogeneous entity, but in fact, the field is highly diverse, like mathematics itself. While the main thrust of the field arises from engineering advances, with bigger and better models, there is also plenty of space for mathematics and mathematicians. As a running example of how mathematics—beyond linear algebra and statistics, the classical drivers of machine learning—may enrich the field, this article focuses on topology, which recently started providing novel insights into the foundations of machine learning: Point-set topology, harnessing concepts like neighborhoods, can be used to extend existing algorithms from graphs to cell complexes
1. What is Machine Learning?
Before diving into concrete examples, let us first take a step back and introduce the field of machine learning. Machine learning is broadly construed as the art and science of employing algorithms to solve tasks, but with the added restriction that the algorithm should—in a certain sense that will become clear below—adapt itself to the data at hand. To substantiate this informal definition, we need to introduce some terms, beginning with the notion of a feature, which denotes a quantity derived from “raw” input data. For instance, given a set of chemical structures, the number of carbon atoms could be a feature. Adding other features—such as the number of oxygen atoms, ring structures, or aromatic bounds—then yields a high-dimensional representation of a chemical structure in the form of a feature vector, which, for convenience, we assume to live in some .
Machine-learning algorithms may thus, on a very high level, be seen as functions of the form , where indicates some domain of interest. When , we say that this is a regression task,Footnote1 whereas when is a set, we are dealing with a classification task. As a running example, suppose we are interested in classifying chemical structures. The domain could consist of the labels “toxic” and “harmless.” Since we have access to labels, our classification task is an example of supervised machine learning.Footnote2 Not every function is equally useful in this context, though. If would always predict “toxic,” it would not be a suitable function for our task (even though its prediction might be the safest bet). The allure of machine learning lies in the fact that it provides a framework to learn a suitable function by presenting the algorithm with numerous examples of different chemical structures, in the hope that with sufficient data, the underlying mechanism(s) driving toxicity can be derived. Thus, when we show this function a new example, its guess as to whether it is toxic or not is based on all previously seen examples. The field of machine learning has developed many suitable models for finding or approximating such functions. Chief among those is the concept of deep neural networks.Footnote3 Deep-learning models started a veritable revolution in some fields like computer vision, mostly because (i) they obviate the need for “hand-crafted” features, as used at the beginning of this section, and (ii) they consist of standalone building blocks, i.e., layers, that can be easily combined to build new models for solving domain-specific problems.
Initially, all layers of a deep neural network start with a random set of parameters or weights, which are then subsequently adjusted to minimize a loss function. A simple deep neural network—a fully connected neural network—produces an output based on an input via the recursion
where ranges over the layers, denotes a matrix of weights, is a bias term, and refers to a nonlinear activation function (like a sigmoid or ). Any original input is thus transformed in a nonlinear fashion,Footnote4 resulting in a final prediction , which is often normalized to using a softmax function, i.e.,
where denotes the th component of . In our running example, binary cross-entropy (BCE) would then be a suitable loss function. Mapping “harmless,” “toxic” to , the BCE loss for predictions is
where represents the true label of a sample and refers to the softmax-normalized prediction of the neural network, which we interpret as the probability of the sample being in class , i.e., being toxic. The parameters of the neural network are now subsequently adjusted using gradient descent or similar procedures, with the goal of minimizing Equation
A common myth concerning deep learning is that it “just” performs curve-fitting, arguably in a highly elaborate way. While this article cannot possibly counter all such claims, it should be pointed out that some neural networks can approximate functions in certain function spaces arbitrarily well. This property is also known as universal function approximation and implies that a certain class of neural networks is dense (usually with respect to the compact convergence topology) in the function space. For instance, feedforward neural networks are known to be able to approximate any Borel-measurable function between finite-dimensional spaces
The conceptual simplicity and modularity of deep neural networks is not without its downsides, though. To perform well, deep neural networks typically require enormous amounts of data as well as a humongous number of parameters. Unless specific provisions are taken, deep neural networks are not energy efficient, and their data requirements still pose serious obstacles in many domains. In addition, neural networks are still black box models with opaque outputs. Despite research in interpretable machine learning aiming to improve this state of affairs, there are still few models whose outputs can be checked easily by human operators, for instance. Even large language models (LLMs), arguably one of the most impressive feats of the field, suffer from shortcomings and are incapable of assessing their own outputs. Like other deep neural networks, they also remain vulnerable to adversarial attacks, i.e., inputs that are generated to provoke a bad response, often without the original user of the model being aware of it
2. Euler Characteristics Galore
The five platonic solids (tetrahedron, cube, octahedron, dodecahedron, and icosahedron) all have Euler characteristic .
| Polyhedron | Vertices | Edges | Faces | |
| Tetrahedron | 2 | 4 | 6 | 4 |
| Cube | 2 | 8 | 12 | 6 |
| Octahedron | 2 | 6 | 12 | 8 |
| Dodecahedron | 2 | 20 | 30 | 12 |
| Icosahedron | 2 | 12 | 30 | 20 |
An illustration of the Euler Characteristic Curve calculation procedure. Starting from a 3D model, specified as a mesh with vertices, edges, and faces, we perform a single filtration in the direction of the -axis. The filtration values are shown in the cross-section of the shaded model, with warmer colors corresponding to larger filtration values. Finally, the Euler Characteristic Curve is plotted for all thresholds. (The mesh depicts the “Enterprise NCC-1701-D,” from Star Trek: The Next Generation. It was originally created by Moreno Stefanuto and made available under a “Free Standard” license. This paper depicts a modified version by the author.)
We focus our discussion on the Euler Characteristic Transform (ECT). Being an invariant that bridges geometry and topology, it is perfectly suited for such an overview article because it provides connection points for the largest number of researchers. The ECT is based on the concept of the Euler characteristic. This integer-based quantity serves as a summary statistic of the “shape” of a graph or simplicial complex. We define an (abstract) simplicial complex as a family of sets that is closed under taking subsets (also known as faces). A simplicial complex generalizes a graph by permitting more than mere dyadic relations. We refer to the elements (sets) of a simplicial complex as its simplices and, given a simplex , we say that its dimension is . A -dimensional simplicial complex thus consists of simplices of dimension up to and including . For example, graphs can be considered -dimensional simplicial complexes, consisting of edges (dimension ) and vertices (dimension ). Given a -dimensional simplicial complex , we write to refer to its simplices of dimension . The Euler characteristic of is then defined as an alternating sum of simplex counts, i.e.,
The Euler characteristic affords several equivalent definitions (for instance, in terms of the Betti numbers of ), generalizes to different objects (graphs, simplicial complexes, polyhedra, …), and is a topological invariant, meaning that if two spaces (objects) are homotopy equivalent, their Euler characteristic is the same. This is depicted in Figure 1 by means of the classical example of the five platonic solids. Since all these spaces are homotopy-equivalent to the -sphere, they all share Euler characteristic .
While a single number is insufficient to fully characterize a shape, it is possible to lift it to a multiscale summary known as the Euler Characteristic Transform (ECT), introduced by Turner et al.
where denotes the standard Euclidean inner product. In the parlance of computational topology, this function can be used to obtain a filtration of in terms of its subcomplexes: Given a threshold , we define . Evaluating the Euler characteristic of each then yields the Euler Characteristic Curve (ECC) associated to the direction . Referring to the set of all finite geometric simplicial complexes as , the ECC is an integer-valued function of the form
The ECC thus maps a simplicial complex , together with a direction and a threshold , to the Euler characteristic of its corresponding subcomplex. Figure 2 depicts the ECC calculation procedure for a mesh, i.e., a geometric simplicial complex in , consisting of vertices, edges, and faces (triangles). We consider a single filtration along the -axis of the mesh, i.e., , sweeping the spaceship from bottom to top via , where as a consequence of the range of the vertex coordinates of the mesh. For each , we calculate the Euler characteristic , leading to the ECC associated to the direction .
While more “expressive” than a single Euler characteristic, the ECC still depends on the choice of direction. By using multiple directions, we may hope to obtain a better representation of . This leads to the Euler Characteristic Transform, which is defined as the function that assigns each direction to its corresponding ECC, i.e.,
where denotes the set of functions from to . Turner et al.
We briefly recapitulate the proof idea underlying Ghrist et al.
Ghrist et al.
3. Using the Euler Characteristic Transform in a Machine-Learning Model
Given the invertibility results and the fact that the ECT is highly efficient to implement, its integration into machine-learning models is only logical. Before we discuss how to use the ECT with a deep-learning model, let us first ponder some of its practical uses with classicalFootnote7 machine-learning methods like support vector machines. Central to such algorithms is their use of handcrafted features; while often eschewed in deep learning,Footnote8 the power of such features should not be underestimated—in particular when combined with methods like the ECT.
The results by Curry et al.
Regardless of the discretization strategy, the resulting matrix can be viewed as an image, although care must be taken to understand that the ordering of directions, i.e., the columns of the matrix/image, is entirely arbitrary. Figure 3 depicts this visualization for randomly selected directions. When using the “raw” values of to index the rows, we observe substantially more zeros. This is because we chose thresholds based on the global minimum and maximum across all filtrations, meaning that any individual ECT, whose range is typically much smaller than the global one, rises to its respective maximum very quickly. The column-normalized version, by contrast, exhibits more variability, with different columns appearing to have a smaller width—this is a perceptual illusion, though, arising from the fact that each column now gradually increases in intensity. Unlike the “raw” version, care must be taken when considering differences between individual columns.
Visualizing the ECT of the model in Figure 2 as a discretized image using either the raw -values (left), or a rescaled version (right) where each column is normalized individually to . Each -axis shows randomly selected directions, while each -axis corresponds to the filtration values , with the lowest value starting at the top of the image. Every column in the image corresponds to an individual ECT, with the pixel color indicating the value for a specific filtration threshold .
Raw

Column-normalized

Setting aside the dissimilarities between the two variants, it is possible to compare shapes by calculating an appropriate distance between their respective ECT images. Such approaches work best when shapes are aligned to a shared coordinate system
How can we move beyond such handcrafted features and use deep learning to find task-specific ECTs? The answer lies in picking a different representation, which enables us to learn an appropriate set of directions as opposed to sampling it. One obstacle to overcome here involves the fact that the ECT is a discrete quantity based on step functions. Such functions are at odds with deep-learning models, which prefer their inputs to be smooth and differentiable. While different variants of the ECT exist, for instance a smooth one obtained by mean-centering and integration
To approximate the ECT, we first notice that any ECC can be written as a sum of indicator functions, i.e., we rewrite Equation
where denotes all -simplices of , and refers to the filtration from Equation
where denotes a scaling parameter that controls the tightness of the approximation. Figure 4 depicts this approximation for various values; we can see that is indeed a suitable (smooth) replacement for an indicator function. This minor modification has major advantages: Each of the summands in Equation
Lest we get lost in implementation details, it is better to assume a more elevated position and take stock of what we already have: Using the approximation above, we have turned the ECT from a discrete function into a function that continuously depends on its input parameters. In machine-learning terminology, we may thus treat this calculation as a layer. Assuming that all coordinates have at most unit norm so that , our ECT layer has two hyperparameters, namely (i) the number of thresholds to discretize , and (ii) the number of directions. The input to our layer is a geometric simplicial complex , and the output is an matrix (equivalently, we may apply such a construction to all types of spaces that afford an Euler characteristic, including cell complexes, for instance). Notice that when learning an ECT for a data set of different objects, one matrix (i.e., the discretized image of an ECT) for each sample in the input batch is returned, resulting in a multidimensional array output, which is also referred to as a tensor.Footnote10 Given the continuous dependence on its input parameters, we refer to the construction above as the Differentiable Euler Characteristic Transform
An indicator function (dashed) and its approximation using differently scaled sigmoid functions, with .
4. Two Applications of Differentiable Euler Characteristic Transforms
(a) We can learn the directions required to match the ECT of a simple data set. (b) Starting with a set of random directions, our initial “guess” of the ECT looks nothing like the original. (c) After several optimization steps, which minimize the dissimilarity between “our” ECT and the original one, we obtain a good approximation. We have thus learned a set of suitable directions for calculating the ECT.
Original
Untrained
Trained
The ECT layer we defined above gives rise to a fixed-size vectorial representation, which may either be integrated into a larger neural network—thus effectively handing off the ECT results for deeper processing—or which can be used directly on its own. As an example of the latter case, we can for instance compare two outputs of an ECT layer using a loss function. Treating the outputs as high-dimensional vectors and , we can use the squared -norm of their difference, normalized by the dimension, as a criterion of how well they are aligned. This loss function is also known as the mean squared error (MSE). It is commonly used to solve problems in representation learning, so it is perfectly suited for a small experiment: Suppose we have a simple data set in whose (discretized) ECT we know. Starting from a randomly initialized set of directions, can we learn the “best” set of directions to align the two ECTs? It turns out that the approximation scheme defined in Equation
We can also learn the coordinates of a point cloud based on the ECT. (a) We sample points from a double annulus. (b) The initial configuration of our coordinates is a random sample from a noisy circle. (c) After minimizing the coordinates based on measuring the dissimilarity between the “desired” ECT and the current one, we are able to approximate the input point cloud closely (red points show the learned coordinates, black points the original ones).
Original
Untrained
Trained
However, learning the directions could be considered somewhat solipsistic in that we derived a new representation (the ECT) and then showed that we can learn its parameters. Indeed, this experiment is more of a “smoke test,” since learning the parameters of a representation is the very basis of machine learning! To build a stronger experiment showcasing the power of the ECT, let us consider learning coordinates instead. Recall that our approximation from Figure 4 permits us to also affect the coordinates themselves: Any loss function that we evaluate will depend on the directions and the coordinates; thus, if we make the coordinates a parameter of our layer, we can modify them similarly to the example shown above. Using an MSE loss, this time we search for input coordinates that minimize the differences of our ECT to a target ECT (machine-learning researchers also like to use the term ground truth). Figure 6 depicts an example, using directions and . We again manage to learn suitable coordinates that align our two point clouds. This can be very helpful when working with coarser representations of data, i.e., we may use this procedure to find the best approximation of a downsampled point cloud to its original version, leading to an ECT-based compression algorithm.
These tasks provide a glimpse of the versatility of the ECT. While learning directions or coordinates is not necessarily a machine-learning task sui generis, a computational layer based on the ECT permits more flexible applications. In conjunction with a loss term, we can employ the ECT in a variety of tasks. For instance, we can use it to classify geometric graphs, i.e., low-dimensional simplicial complexes whose vertices and edges are embedded in some . This task is typically dominated by graph neural networks, which employ a mechanism called message passing that amounts to locally transporting information via the edges of a graph.Footnote11 The ECT offers a new and surprisingly competitive method for classifying such graphs
5. The Future of Topology in Machine Learning
The ECT served as the leitmotif of this article, demonstrating how to connect concepts from applied topology and modern machine-learning methods with relatively few hitches. The reader is strongly recommended to check out an excellent overview article by Munch
- 1.
Learning functions on topological spaces such as simplicial complexes or cell complexes.
- 2.
Building hybrid models that imbue neural networks with knowledge about topological structures in the data.
- 3.
Analyzing qualitative properties of neural networks.
In the first area, topology can be used to generalize existing machine-learning paradigms to a larger variety of input data sets; this is appealing because not every data set “lives” in a nice Euclidean space or a graph, and the inclusion of higher-order neighborhoods would provide a shift in perspective, aiding knowledge discovery. Researchers in topological data analysis (TDA) might feel particularly comfortable in the second area since it is one of the declared aims of TDA to understand topological features in data. Nevertheless, hybrid models do not necessarily have to draw upon concepts from TDA; new and daring methods could for instance focus on computational aspects of Riemannian geometry like curvature or make use of new invariants like metric-space magnitude. Finally, the third area shifts the perspective and lets topology return to its roots in that it can serve as a lens through which to study, for instance, the training behavior of neural networks. Understanding these training dynamics could lead to smaller, more efficient models, but also shed some light on the soft underbelly of deep-learning models, namely their susceptibility to unstable training regimens, “adversarial” input data, or their propensity for hallucinations.
Each of the three areas for new research has something enticing to offer, not only for machine learning but also for (applied) topology. There is vast potential for new topology-aware models to serve as proof assistants or even try to search for new conjectures and counterexamples. It is said that only those with their feet on rock can build castles in the air. Topology can provide this rock upon which robust machine-learning research can be built. Thinking beyond topology, the author hopes that this article may also stir up the curiosity of mathematicians coming from other domains. Machine-learning research will only benefit from more inquisitive minds and there are countless things waiting to be discovered. To get a taste of potential directions, readers are invited to peruse an excellent expository article on deep learning
Acknowledgments
The author is indebted to Ernst Röell, Emily Simons, and the anonymous referees for their helpful comments, which served to substantially improve this article.
This work has received funding from the Swiss State Secretariat for Education, Research, and Innovation (SERI).
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Bastian Rieck is a professor of computer science at University of Fribourg. His email address is bastian.grossenbacher@unifr.ch.
Article DOI: 10.1090/noti3193
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All figures are courtesy of Bastian Rieck.
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