Advances in Physics: X

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Topological data analysis and machine learning

Daniel Leykam & Dimitris G. Angelakis

To cite this article: Daniel Leykam & Dimitris G. Angelakis (2023) Topological data analysis and
machine learning, Advances in Physics: X, 8:1, 2202331, DOI: 10.1080/23746149.2023.2202331
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ADVANCES IN PHYSICS: X
2023, VOL. 8, NO. 1, 2202331
https://doi.org/10.1080/23746149.2023.2202331

Topological data analysis and machine learning

Daniel Leykama and Dimitris G. Angelakisa,b,c
a
Centre for Quantum Technologies, National University of Singapore, Singapore; bSchool of Electrical
and Computer Engineering, Technical University of Crete, Greece; cAngelQ Quantum Computing,
Singapore

ABSTRACT ARTICLE HISTORY

Topological data analysis refers to approaches for system­ Received 30 June 2022
atically and reliably computing abstract ‘shapes’ of complex Accepted 8 April 2023
data sets. There are various applications of topological data Keywords
analysis in life and data sciences, with growing interest Machine learning; strongly
among physicists. We present a concise review of applica­ correlated quantum systems;
tions of topological data analysis to physics and machine persistent homology; phase
learning problems in physics including the unsupervised transition; quantum
detection of phase transitions. We finish with a preview of computing; condensed
anticipated directions for future research. matter physics; topological
phase

I. Introduction
Topological quantities are invariant under continuous deformations; an
often-cited example is that a doughnut can be continuously transformed
into a coffee mug – both are topologically equivalent to a torus. The
robustness of topological quantities to perturbations is inspiring physicists
in many fields, including condensed matter, photonics, acoustics, and

CONTACT Daniel Leykam [email protected] Centre for Quantum Technologies, 3 Science Drive
2, National University of Singapore, 117543, Singapore
© 2023 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.
org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is
properly cited. The terms on which this article has been published allow the posting of the Accepted Manuscript in a repository by
the author(s) or with their consent.
2 D. LEYKAM AND D. G. ANGELAKIS

mechanical systems [1–4]. In all these areas, topology has enabled the
prediction and explanation of surprisingly robust physical effects.
Most famously, the extremely precise quantisation of the Hall conductiv­
ity observed in two-dimensional electronic systems since the 1980s was
explained as a novel topological phase of matter, the quantum Hall phase
[5]. In this and many other examples from physics, we deal with smooth
deformations in some parameter space, such as the energy bands of solid
state electronic systems.
Physics is, however, an outlier among fields of science in that idealised
continuous models and functions can explain a wide variety of observed
phenomena. Other fields do not have the luxury of continuity and have to
make do out of sparse data and limited observations in high-dimensional
parameter spaces. Despite this very different setting, topological approaches
remain powerful.
A suite of computational topological techniques known as topological
data analysis (TDA) has been developed over the past 20 years to system­
atically define and study the ‘shape’ of complex discrete data in high-
dimensional spaces. TDA is attracting growing interest among physicists,
particularly those working on topological materials or the application of
machine learning techniques to physics [6–10].
At this time, we are aware of two existing reviews of TDA aimed at the
physics audience. The first by Carlsson, one of the founders of the field, gave
a broad survey of different techniques of TDA and their applications in
various areas of science [11]. The second review, by Murugan and
Robertson, provided a detailed pedagogical and physicist-friendly introduc­
tion to two important techniques, persistent homology and the Mapper
algorithm, applying them to the example of an astronomical dataset [12].
Since publication of these two reviews there has been growing interest in
applying TDA methods to physics, including the incorporation of TDA into
physics-targeted machine learning, with applications including the unsu­
pervised detection of phase transitions. Moreover, the field of TDA has
continued to evolve with new generalisations and techniques being actively
studied.
The aim of this article is to review cutting edge applications of TDA to
physics. We will provide a gentle introduction to the basic techniques,
survey how TDA shows promise for the detection of novel phases of matter,
and speculate on what we believe to be important directions for future
research, including opportunities offered by newer TDA methods such as
zigzag persistence.
The structure of this article is as follows: Section II provides a brief
introduction to TDA guided by the simple example of two-dimensional
point clouds. Section III discusses how TDA has been applied to identify
order parameters and phase transitions in various physical systems. Section
 ADVANCES IN PHYSICS: X 3

IV covers recent studies that employ TDA to compute features of physical

systems that are then incorporated into a larger machine learning pipeline.
Section V speculates on anticipated future directions and applications of
TDA to physics, and vice versa. We conclude with Section VI.

II. Topological data analysis

Admittedly, TDA has a rather steep learning curve, since its foundation
differs from the topology of continuous spaces to which physicists are more
accustomed. However, after battling through the unfamiliar jargon and
notation one can develop a powerful intuition for the subject. Our aim
here is to give an equation-free sketch of the general approaches and
terminology, while referring the motivated reader to more comprehensive
and mathematically rigorous reviews [11–15].

A. From point clouds to persistence diagrams

As an instructive example, let us consider the two-dimensional point clouds
shown in Figure 1. Each point may correspond to a distinct measurement of
some object, e.g. the locations of photons arriving at a camera, or the
positions of particles in a system. With our eyes, we can clearly see that
each cloud has a different shape: The points in the ‘Circle’ and ‘Figure 8’
clouds are distributed around one and two loops, respectively. On the other
hand, the ‘Swiss Roll’ corresponds to a noisy one-dimensional point cloud
embedded into a higher (two-) dimensional space.
We would like to formalise these qualitative observations in a more
systematic way, such that we are not reliant on directly plotting the data,
which is an approach limited to two- or three-dimensional datasets. How
can we quantify the obviously different shapes of these point clouds?

Figure 1. Examples of noisy point clouds. Point clouds sampled from objects with differing
shapes and even differing dimensionality may be difficult to distinguish using standard
summary statistics such as the centre of mass and variance. In “Circle” and “Figure 8” the
noise randomly perturbs the points in the ambient two-dimensional space. In “Swiss Roll”
points are sampled from a one-dimensional interval before being embedded into the two-
dimensional space ðx; yÞ.
4 D. LEYKAM AND D. G. ANGELAKIS

Standard summary statistics such as the centre of mass or variance are

clearly inadequate, since they are not invariant under shape-preserving
translations or rescaling of the data.
Fortunately, graph theory provides rigorous ways of quantifying
intuitive shapes of discrete datasets including point clouds. The idea
is to construct a graph by connecting pairs of points (vertices) that are
sufficiently close together by edges and then to quantify its shape by
computing topological invariants of the graph, its Betti numbers Bk .
The kth Betti number is the number of k-dimensional holes, e.g. the
number of independent connected components (clusters B0 ) or non-
contractible loops (cycles B1 ). In practice, evaluating graph invariants
amounts to computing the ranks and null spaces of linear operators
(matrices) acting on the graph’s vertices and edges. In a nutshell, the
computation of the shape of point cloud data can be reduced to simple
linear algebra.
Higher-dimensional topological features can be similarly obtained by
constructing generalisations of graphs known as simplicial complexes,
which capture higher dimensional objects (faces, volumes, etc.) by triangu­
lation. A k-simplex is a combination of ðk þ 1Þ vertices; edges are 1-sim­
plices, triangular faces are 2-simplices, tetrahedral volumes are 3-simplices,
and so on. A k-simplicial complex is a collection of simplices with dimen­
sion of at most k.
Increasing k complicates matters. First, since k-simplices are combina­
torial objects, the number of possible simplices grows rapidly with k, limit­
ing practical calculations to low dimensional topological features. Second,
there is no unique way to construct a simplicial complex given only pairwise
distances between points and a cutoff scale; different methods may differ in
their computational costs, stability properties, and ability to faithfully repro­
duce the shapes of the underlying space from which the points are
sampled [16].
There is one big elephant in the room that we must address what do we
mean by ‘sufficiently close’ when connecting vertices to form a graph or
simplicial complex? How do we determine which pairs of vertices to link by
an edge and which pairs to leave disconnected? The number of cycles and
clusters will be sensitive to the choice of cutoff distance and even possibly
the addition or removal of a single edge, as illustrated in Figure 2. This
seems like a major problem making the approach lack robustness to noise
and other perturbations.
A neat solution to the scale-dependence of graph invariants obtained
from point clouds is to compute the shape of the graph over an entire
range of scales known as a filtration, i.e. study its topology as
a function of the cutoff length scale [17]. Topological features (e.g.
clusters and cycles) persisting over a wide range of scales are more
 ADVANCES IN PHYSICS: X 5

Figure 2. Simplicial complexes constructed from a point cloud using different cutoff distances
�i , where blue lines and orange shaded areas denote edges and faces, respectively. For small
cutoff distances all points are disconnected, forming a trivial simplicial complex with no edges
(�1 ). As the cutoff is increased nearby vertices start to become connected by edges (�2 ).
Increasing the cutoff further, triplets of points become connected, forming faces. In �3 and �4
the simplicial complex has a single connected component hosting a non-trivial cycle. For
sufficiently large cutoff distances the cycle is destroyed by the addition of faces covering the
entire interior of the point cloud (�5).

robust and should provide a meaningful characterisation of the overall

shape of the data. On the other hand, features sensitive to small
changes in scale or the addition or removal of a few edges can be
attributed to noise and discarded if necessary. By studying the persis­
tence of topological features we will be able to distinguish robust
features from noise.
Persistence diagrams are one stable way to represent scale-dependent
topological features of a dataset [18]. Figure 3 shows persistence diagrams
computed for each of the point clouds in Figure 1. The most persistent
topological features not only allow us to infer the overall shape of the data
but also give information as to the geometry of the point cloud. For

Figure 3. Persistence diagrams of the two-dimensional point clouds shown in Figure 1 com­
puted using the Vietoris-Rips complex [16]. Each point represents a distinct topological feature.
Horizontal and vertical axes denote the length scales at which each feature is created (b; birth)
and destroyed (d; death) respectively. Points that are further from the diagonal dashed line
therefore persist over a larger range of scales and are said to have a longer “lifetime” l ¼ d b.
Since features must be created before they are destroyed, no points lie below the diagonal. At
sufficiently large spatial scales all points become connected to form a single connected graph,
corresponding to a single cluster with an infinite lifetime. Typically the infinite lifetime cluster is
either discarded or plotted at a finite d and distinguished using a horizontal dashed line.
6 D. LEYKAM AND D. G. ANGELAKIS

example, the birth scales of the long-lived cycles in the ‘Circle’ and
‘Figure 8’ clouds are related to a maximum separation between neighbour­
ing points comprising the cycle, while the death scale will be related to the
cycle’s diameter.
The attentive reader will notice that the persistence diagrams for
the ‘Circle’ and ‘Swiss Roll’ clouds share the same long-lived features,
despite their obviously differing shapes. Closer inspection will, how­
ever, reveal noticeable differences in their short-lived features. For
example, the cycles appearing in the ‘Swiss Roll’ dataset all have
similar birth scales, corresponding to the distance between the inner
and outer parts of the spiral and hinting at a one-dimensional embed­
ding. This suggests that the differing shapes of these two-point clouds
may indeed be captured by inspecting their short-lived features; thus,
persistent homology can also capture the local features (geometry) of
the data.

B. Comparing and computing persistence diagrams

While persistence diagrams provide a compact visual summary of the scale-

dependent topological features of a single dataset, it is not immediately clear
how we should go about comparing persistence diagrams computed for
different datasets; they will generally differ in their number of features and
level of noise, making it difficult to establish a common threshold between
genuine features and noise-induced features.
These issues motivated the development of stable distance and similarity
measures for persistence diagrams. Here, stability means that a small change
to one dataset results in, at most, a similarly small change in similarity to
other fixed persistence diagrams.
One example of a stable distance measure is the Wasserstein distance,
which is the smallest distance the points in a pair of persistence diagrams
must be moved in order to transform one diagram into the other. Unpaired
features (i.e. if one diagram has more features) are moved to the diagonal.
For example, Figure 4 shows the matching between the one-dimensional
cycles of the Circle, Figure 8, and Swiss Roll point clouds. Since all features
contribute to the Wasserstein distance, even the noise-induced ones close to
the diagonal, it can be less sensitive to changes in the most persistent
features. Another popular choice of distance measure is the bottleneck
distance, which is the largest deformation of a pair of features required to
convert one diagram to another (i.e. the Wasserstein distance under the p ¼
1 norm). The bottleneck distance is thus idependent of the short-lived
features near the diagonal.
Alternative approaches for characterising and comparing the informa­
tion contained in the persistence diagrams employ vectorisation: the
 ADVANCES IN PHYSICS: X 7

Figure 4. Matching (green lines) of the one-dimensional cycles of the Circle, Figure 8, and Swiss
Roll point clouds used to compute the Wasserstein distance, which corresponds to the total
length of the green lines.

variable length information encoded in the ðb; dÞ pairs of the persistence

diagrams is mapped to a vector or vectors in a fixed-dimensional space;
different persistence diagrams can then be studied using familiar tools
such as vector inner products. For example, one might compute a set of
summary statistics such the entropy or moments of the feature lifetimes
l ¼ jd bj [19–21], assuming they are relevant to the task at hand. Often
the relevant features are unknown a priori and it is preferable to compute
a high-dimensional vectorisation to minimise the loss of relevant infor­
mation. One example is the persistence landscape, a stable and invertible
(i.e. information-preserving) persistence diagram vectorisation [22,23].
Using a distance measure or vectorisation allows one to combine per­
sistent homology with powerful machine learning techniques such as
artificial neural networks or clustering algorithms to compare topological
features of different datasets and perform tasks including shape-based
identification and classification of different point clouds, which will be
explained further in Sec. IV. However, one important consideration in
applying vectorisation or distance measures is that they can introduce
additional hyper-parameters that may affect the sensitivity to different
topological features of the data.
There are a variety of software libraries for computing persistence dia­
grams, their vectorisation, and distance measures [24–27], surveyed in Ref.
[28]. Crucial for applications, persistence diagrams can be efficiently com­
puted given a filtration by building up a simplicial complex one element at
a time and detecting any changes to the topological features at each step.
This yields not only the feature birth and death scales but also their
representations, e.g. edges comprising a cycle. Nevertheless, due to the
combinatorial nature of simplicial complexes, the computational require­
ments grow rapidly with the feature dimension k, with most practical
applications limited to k � 2.
8 D. LEYKAM AND D. G. ANGELAKIS

To compute a persistence diagram, the end-user must provide at

a minimum either the data points or a distance matrix encoding pairwise
distances between points. One can also consider custom filtrations. For
example, when dealing with image data one can use the greyscale pixel
values as a filtration parameter, constructing a simplicial complex out of
pixels less than (or exceeding) a given threshold [29,30]. The resulting
sublevel (superlevel) set filtration summarises the critical points of an
image, i.e. its local minima, maxima, and saddle points, as well as their
higher-dimensional generalisations.

C. Other approaches and recent developments

The above discussion of persistent homology has been limited to the
simplest case of simplicial complexes constructed from two-dimensional
point clouds. There are a variety of related techniques for studying complex
datasets by reducing them to families of graphs or simplicial complexes,
which we only mention briefly here due to space constraints.
The Mapper algorithm reduces point clouds to simpler low-
dimensional graphs by performing clustering on overlapping subsets of
the data [31,32]. Local anomalies such as intersections and cusps can be
similarly detected by comparing the persistent homology of different
subsets of the data [33].
Standard persistent homology constructs filtrations as a sequence of
nested simplicial complexes; as the filtration parameter (e.g. cutoff distance)
is increased, edges and higher-dimensional simplices are added to the
complex and never removed. In certain situations, e.g. when studying
temporal network dynamics, simplices can be both added and removed as
the control parameter is varied. Zigzag persistence is a technique that
enables the identification of significant topological features in this case [34].
Another important problem is to compute persistent topological features
as the multiple control parameters are varied, which is termed multidimen­
sional persistence [35]. This problem is a lot more complicated than the
single parameter case, due to the absence of simple persistence diagram
representations.
We considered examples where point clouds are used to construct undir­
ected graphs and simplicial complex, encoded by matrices with binary
elements f0; 1g, denoting whether a simplex is present or absent.
Persistent homology can also be calculated with respect to other fields,
such as integers modulo 3, describing e.g. directed graphs or simplices,
which can be useful for analysing data, with twists including points sampled
from the surface of Möbius strips [25].
 ADVANCES IN PHYSICS: X 9

Figure 5. (A) Noisy sampling of the chaotic trajectory of the Lorenz attractor and (b) topology-
based filtered data, adapted from Ref. [36]. (c) Snapshots of a chaotic two-dimensional fluid and
(d) estimates of finite-size effects using image eigendecompositions (SVG) and a TDA-based
disorder estimator (TDA) showing the two methods give similar results, adapted from Ref [40].

III. Applications of topological data analysis to physics

A. Early examples
Early applications of TDA appearing in physics journals in the 2000s
considered examples where the underlying data already has a well-
defined shape or graph structure, making the construction of graphs
more straightforward. Examples include dynamical systems [36], ran­
dom clouds of spheres [37], random networks [38], and binary image
data [39,40].
In the case of over-sampled time-series measurements of dynamical
systems, the sampled points will form a single continuous curve in the
absence of noise. This fact can be used for topological filtering of
certain types of noise, e.g. when a small fraction of the measured points
are perturbed, as shown in Figure 5(a). By computing the scale-
dependent distribution of zeroth Betti numbers B0 one can separate
points belonging to the dynamical trajectory (forming a single large
cluster) from noise-perturbed points (each forming a separate cluster),
filtering out the latter in Figure 5(b) and improving the accuracy of
estimated Lyapunov exponents [36].
A second early application was the analysis of convection in two-
dimensional fluids under heating [39,40]. There, the fluid separates
into distinct hot and cold regions, as illustrated in Figure 5(c). In this
case, the zeroth and first Betti numbers B0;1 were used to characterise
the shape of the hot and cold regions. The scaling of the number of
distinct microstates (shapes) with the area of the fluid yields an
effective dimension of the dynamics that could be computed more
efficiently than the conventional approach based on the singular value
decomposition of the images’ two-point correlation functions. One
10 D. LEYKAM AND D. G. ANGELAKIS

application of the effective dimension is the detection of boundary

effects, as shown in Figure 5(d). The strong contrast between hot and
cold regions of the images in this case meant that persistent homology
was not required; analysis of the graph formed at a single cutoff scale
was sufficient.

B. Persistent homology of point clouds and images

In many applications, the construction of well-defined shape from the data

is less straightforward, or one may be interested in identifying structures
present at different spatial scales. For example, in the case of point cloud
data, it may be difficult to assign a size or radius to the individual points. In
other cases, one may want to apply intuition obtained from simple analy­
tically solvable limits to more realistic systems [41,42]. In situations such as
these, persistent homology becomes a powerful tool for extracting mean­
ingful shape information from the raw data.
For example, suppose we wish to study the microscopic structure of
materials. The raw data naturally takes into account the positions of the
constituent atoms and their sizes. Persistent homology enables studying
the multi-scale structure of materials using just the positions of atoms
in three-dimensional space (obtained from imaging or simulations)
together with the standard Euclidean distance. The authors of Refs.
[43,44] and used persistence diagrams computed from molecular
dynamics simulations of various materials exhibiting glassy phases to
characterise their structure.
Figure 6 shows examples of persistence diagrams obtained for liquid,
glass, and crystalline phases of silica. In the crystalline phase, the clustering
of feature births and deaths reveals scales corresponding to the bond lengths
of the material, i.e. separations between the constituent atoms. Moreover,

Figure 6. Persistence diagrams obtained from molecular dynamics simulations of liquid (a),
amorphous (b), and crystalline (c) phases of silica. Point colours indicate the multiplicity (on
a logarithmic scale) of one-dimensional features. Insets in (b) illustrate representative cycles
corresponding to short- and medium-range order in the amorphous phase. Adapted from Ref.
[44].
 ADVANCES IN PHYSICS: X 11

inspection of the cycles corresponding to persistent features also reveals the

nature of the short-range order appearing in the glass phase.
Subsequent works applied similar techniques to amorphous ices [45],
granular media [46,47], spin configurations in lattice spin models and gauge
theories [48,49], and two-dimensional materials, where the measures
obtained using persistent homology can be directly compared with more
standard metrics [50].
Another application of the point cloud formalism concerns the analysis of
time-series signals, including the detection of chaotic dynamics. Already in
the 1990s, there was interest in applying computational topology to study
the shape of the dynamics in phase space, including quantifying the shape of
chaotic attractors [51]. Here, the key ingredient is Takens’ embedding
theorem, which states that a sequence of observations ϕt taken at regular
time intervals τ can be used to reconstruct the shape of the dynamics by
constructing a point cloud of n-dimensional vectors
vt ¼ ðϕt ; ϕt τ ; ϕt 2τ ; . . .Þ, provided the embedding dimension n is suffi­
ciently large.
Persistent homology enables the systematic study of dynamics via the
shape of the point clouds in the high-dimensional embedding space [52–
54]. For example, period-doubling transitions can be detected via the
emergence of new persistent clusters. Successive period-doubling transi­
tions as a system approaches the chaotic regime results in the creation of
many clusters, which merge into a single line or volume.
Applying persistent homology to image data enables the study of the
shapes of images in which there may not be a clear distinction between
‘bright’ and ‘dark’ regions, or in images where structural information at
multiple intensity scales is important. Large point cloud datasets for which
a direct persistent homology calculation may be quite time-consuming can
alternatively be studied using image filtrations by converting the cloud to
a density image [55].
Early works on persistent homology of images used Betti numbers to
characterise solar magnetic field distributions [56] and force networks in
different kinds of compressed granular media, studying the number and
connectivity of regions at different scales [57,58]. More recently, persis­
tence diagrams obtained from images have been used to study non-
Gaussian temperature fluctuations in the cosmic microwave background
[59], the shape of iso-frequency contours in photonic crystals [60], many-
body dynamics, and solitons in Bose-Einstein condensates [61,62], phase
transitions in spin models [63,64], and order–disorder transitions in
nematic liquid crystals [65] and optical waveguide lattices [66]. Recent
work aims to better understand how to relate the shape information
captured by TDA to physical properties, including the permeability of
fractured materials [67].
12 D. LEYKAM AND D. G. ANGELAKIS

C. Finding meaning using abstract distance measures

So far we have considered examples where we have some intuitive notion
of the shape of the underlying data, and the role of TDA has been to study
these shapes more systematically. One exciting emerging application of
TDA is in studying and discovering structure in complex systems for
which simple visualisations (such as images or phase space trajectories)
do not exist, including families of high-energy physics models [68–70].
This typically requires the identification of a suitable distance measure for
the data.
For example, in the case of quantum many-body systems measures of
entanglement between pairs of subsystems, such as the concurrence or
entanglement entropy, can be used to study the abstract shapes of quantum
states and group them into different classes [71–73]. Understanding this
entanglement structure may be helpful for judging when approximation
techniques, such as tensor networks, may be used to efficiently simulate the
system of interest.
Another important application of abstract distance measures is in the
study of condensed matter systems at finite temperatures, where one
would like to quantify the ‘shape’ of an ensemble of system configurations
sampled at a given temperature to detect phase transitions and critical
points [48,63,64,74]. There are various notions of distance that can be
applied in this context, including the geodesic distance between different
spin configurations [75] and the quantum distance based on the overlap
between eigenfunctions [60,76]. Tests of the Anderson, Hubbard, and
Potts models suggest that TDA may be useful for precisely detecting
critical points without requiring a computationally expensive finite size
scaling analysis [77,78].

IV. Machine learning for physics using topological data analysis

A. Applications of machine learning to physics

Machine learning offers a powerful data-driven approach for modelling,

characterising, and designing complex physical systems [6–8,10], including
topological materials [79–85]. Two classes of machine learning approaches
attracting interest among physicists are supervised and unsupervised learn­
ing algorithms. Supervised learning aims to correctly classify new observa­
tions after being trained on a set of labelled examples. Unsupervised
learning aims to detect novel features in unlabelled datasets, e.g. by grouping
similar observations into clusters or identifying outliers.
Dealing with the deluge of data generated by high energy physics
experiments was an early application of large-scale machine learning
techniques to physics [6,86]. Anomaly-detection techniques are used to
 ADVANCES IN PHYSICS: X 13

identify the small fraction of interesting events to be recorded and

processed further. Supervised learning techniques based on human-
labelled or computer-generated examples can be used to convert the
high-dimensional raw detector data (e.g. particle trajectories and depos­
ited energies) into a signal of interest (e.g. the type of particles gener­
ated). Similar techniques are now being adopted in other fields
involving high repetition rate experiments, including reconstructing
ultrashort optical pulses [87], identifying solitons in Bose-Einstein con­
densates [88], and optimizing the fidelity of quantum gates [89]. In all
these examples, machine learning can be used to perform tasks faster
and at a larger scale than conventional approaches.
The performance of machine learning algorithms is closely tied to the
quality and quantity of the input data; the machine learning model needs
a sufficiently large set of relevant observations to make accurate predictions.
On the one hand, the computational costs of machine learning algorithms
can be enormous when they are applied to real-world problems involving
large-scale datasets. On the other hand, in many physics problems the
amount of available data may be highly constrained (e.g. due to high costs
of fabrication, characterization, or computational resources), making
approaches compatible with sparse datasets essential.

B. Combining TDA with machine learning

TDA methods are promising as a means of enhancing the performance of
machine learning methods [15]. Instead of feeding all observables of the
system of interest (e.g. entire images or full many-body quantum wavefunc­
tions) into the machine learning algorithm, TDA can identify a smaller set
of relevant topological features, which can be used as input into a simpler
and faster machine learning model. Especially, TDA methods seem natu­
rally suited to studying phenomena such as topological phase transitions,
which may be difficult to capture using conventional techniques.
As noted in Sec.tion II B, a key challenge in combining TDA with
machine learning is the question of how best to convert the information
encoded into persistence diagrams into a format usable by machine
learning algorithms. The two main approaches are distance measure-
based and vectorisation.
The authors in Refs. [48,76–78,90] have used distance measures of
persistence diagrams to compute the distance matrices used as inputs
for kernel-based machine learning algorithms for supervised and
unsupervised detection of phase transitions in several lattice models
including the Ising, XY, and Heisenberg spin models [64,77] and
classification of biological time series [54,91,92]. There are many
possible metrics to use. In practice, the Wasserstein and bottleneck
14 D. LEYKAM AND D. G. ANGELAKIS

distances [76,77] can be time-consuming to compute. There are faster

alternatives, including the sliced Wasserstein distance [48] and Fisher
kernel [90]; however, they introduce additional hyper-parameters,
which need to be optimised.
Vectorisation-based approaches can reduce the persistence diagrams into
a simpler format that is more easily interpretable, at the expense of losing
some of the contained information. For example, the authors in Refs.
[62,66,74] employed simple summary statistics of the feature lifetimes
including their Shannon entropy and norms to verify that persistent homol­
ogy does indeed detect relevant features that can be used to train machine
learning models. Alternatively, the authors in Refs. [63,64] and employed
persistence images [93], which form a discretised representation of persis­
tence diagrams. One word of caution in the use of the persistence images is
that their construction involves hyper-parameters that should be optimised
to obtain good performance [15].
Once the persistence diagrams have been converted into a format
usable by machine learning algorithms, the final step is to choose
a specific machine learning model. Several studies have considered
supervised classification using logistic regression and support vector
machines, which find an optimal separating hyperplane between dif­
ferent data classes [62–64]. More recent studies comparing various
machine learning models suggest that classification and clustering
based on topological features can still be a highly nonlinear problem,
making nonlinear machine learning methods, such as multidimen­
sional scaling, neural networks, or k-nearest neighbours a better
choice [48,64,74].

C. Learning phase transitions using TDA

The prospect of discovering novel phases of matter motivates studies of
machine learning-based approaches for detecting phase transitions.
Supervised learning methods can make use of labelled data drawn from
known phases or exactly solvable limits to draw inferences about the
location of phase boundaries [94,95]. On the other hand, unsupervised
methods such as manifold learning use an appropriately chosen-
similarity measure to compare different samples and group them into
different classes, without requiring precise knowledge of the number of
distinct phases [79–85].
The reliable detection of phase transitions using machine learning
requires the use of an appropriate cost function or similarity measure
that is sensitive to the transition of interest. For example, topological
phase transitions require the bulk band gap of the system to close and
re-open, motivating the use of non-local similarity measures invariant
 ADVANCES IN PHYSICS: X 15

Figure 7. TDA-based machine learning of phase transitions in the two-dimensional XY

model. (a) Persistence diagram computed using a filtration based on correlations between
neighbouring spins. (b) the persistence diagram is vectorised into a persistence landscape.
(c,d) Examples of average persistence images obtained from spin configurations sampled
from ordered (c) and disordered (d) phases. (e) Coefficients of a trained logistic model;
blue and red regions denote parts of the persistence images assigned as indicators to the
ordered and disordered phases, respectively. (f) Finite size scaling of the logistic regression
prediction used to estimate the phase transition point. Blue and red regions denote
ranges used for the model training data. Vertical blue line denotes the expected transition
point. Adapted from Ref. [64].

under gap-preserving deformations [81] or sensitive to points at which

the gap closes [82,85]. These measures typically involve hyper-
parameters, such as the kernel resolution, which must be chosen care­
fully to ensure good accuracy.
By directly capturing shape information of the system of interest,
persistent homology-based methods are able to capture phase transi­
tions using simpler models with fewer hyper-parameters. Figure 7
shows an example of a persistent homology-based machine learning
pipeline for studying phase transitions in the two-dimensional XY
model [64]. Persistence diagrams are computed for a given spin con­
figuration based on the relative angle between neighbouring spins. The
persistence diagram is then vectorised into a persistence landscape
encoding the probability of obtaining features with a given birth scale
and lifetime, which can be averaged over spin configurations sampled at
a given temperature. The averaged persistence landscapes obtained for
various temperatures are then used to train a machine learning model,
such as logistic regression, which estimates the location of the phase
transition using the training data.
16 D. LEYKAM AND D. G. ANGELAKIS

V. Future directions
A. New techniques for topological data analysis
An area of active research among physicists is the application of TDA tools
to analyse the structure of more complex systems including flow networks
involving directed links [96] and time-evolving networks [92]. One
approach used in recent studies that is compatible with standard persistent
homology tools is to convert the directed network into a regular point cloud
using a diffusion map, which constructs edges between a pair of vertices
ði; jÞ by computing the probability of diffusion between i and j. It will be
interesting to explore alternate approaches that can work directly with
unidirectional or time-evolving systems without requiring diffusion maps,
such as zigzag persistence [97].
The metrics used for quantifying differences between persistence dia­
grams have applications beyond persistent homology. For example, Skinner
et al. [98] used the Wasserstein distance to compare different local neigh­
bourhood structures of disordered media, based on the intuition that it
encodes the energy cost required to transform one configuration into
another. The advantage of such a topological metric compared to more
conventional measures including the Kullback–Leibler divergence is that
the former is better at distinguishing weakly-overlapping distributions. Are
there other examples where such metrics can be linked to physical
observables?

B. Quantum topological data analysis

All of the examples considered in the physics literature relate to the study of
low-dimensional topological features using TDA, largely because higher
dimensional features are both harder to interpret and become extremely
time-consuming to compute for large datasets, due to exponential scaling.
The advent of more efficient quantum algorithms for TDA, including the
computation of Betti numbers and persistence diagrams, is anticipated to
enable the study of higher-dimensional topological features in complex
datasets.
The first quantum algorithm for TDA was proposed by Lloyd et al. in
2016 [99]. Their algorithm exhibited an exponential speedup for calcu­
lating Betti numbers by using quantum phase estimation to efficiently
construct combinatorial Laplacians of simplicial complexes and identify
cycles by computing their zero modes. This proposal was followed in
2018 by a small-scale, few-qubit proof-of-concept quantum optics
experiment [100].
Subsequent studies have started to address the limitations of the first
quantum TDA algorithm [101] by proposing more efficient variants
 ADVANCES IN PHYSICS: X 17

[102–104] as well as quantum algorithms for computing persistent Betti

numbers [105,106] and the Wasserstein distance [107]. While most of
these algorithms are designed for future fault-tolerant quantum com­
puters, there is also the potential for near-term quantum speedups using
shallow quantum circuits with depth linear in the number of input data
points, exploiting the efficient implementation of the boundary operator
using entangled quantum states [108–111]. While the prospect of an
exponential speed-up compared to the best classical TDA algorithms is
entrancing, whether and when such a large speed for practical problems
will be achieved is under debate [102,103,111–113], especially with new
and improved classical algorithms still being developed [114].

C. Learning physics versus machine learning physics

One challenge encountered by existing literature applying TDA to physics
problems is that the techniques are unfamiliar to the physics audience.
Many of the original TDA articles in which techniques were first introduced
are highly theoretical and mathematically rigorous, thus articles in physics
journals require long introductions explaining the approaches used to this
non-specialist audience. This can lead to a focus on the technical calculation
details while perhaps obscuring the bigger picture.
For instance, many articles include examples of persistence dia­
grams computed from the system of interest in order to illustrate
qualitative differences between different phases and states. However,
the persistence diagram is itself not easily interpretable, requiring
knowledge of the form of the input data and filtration used. For this
reason, many studies then apply machine learning techniques to
extract quantitative predictions from the information contained in
the persistence diagrams.
On the other hand, as physicists we would prefer to make sense of
the system ourselves, rather than delegate understanding to a machine
learning algorithm. What is of interest to us are which topological
features are meaningful and what they look like. The approach used
in Ref. [44], where representative cycles of the persistent features are
included as insets in the persistence diagrams [reproduced here in
Figure 6(b)], is one way their meaning can be made more explicit.
Still, selecting appropriate features can be challenging when there is
no clear boundary between the signal and the noise. It will be interest­
ing to explore other TDA-based techniques for dimensionality reduc­
tion and compactly conveying the significant features of high-
dimensional physical systems to non-specialists in TDA.
18 D. LEYKAM AND D. G. ANGELAKIS

VI. Conclusion
In summary, we have attempted to give an overview of emerging physics
applications of topological data analysis methods, focusing on persistent
homology. The take-home message is that TDA can compress complex
datasets into their essential (topological) features, enabling the training of
simpler machine learning models compared to widely used and computa­
tionally expensive general-purpose artificial neural networks. Nevertheless,
as topological data analysis is relatively new it is still largely employed on an
ad-hoc basis and further work is needed to establish a standard set of
methods that non-specialists can trust [15].
Topological data analysis has already been fruitfully applied to other areas
of research including image analysis and medical science, enabling the
extraction of useful insights from complicated hard-to-visualise datasets.
We hope that the techniques discussed here and in other recent reviews
aimed at the physics audience [11,12] will not merely provide a transient
fashionable alternative to more standard methods of data analysis used by
physicists but will form a new set of long-lasting tools enabling a better
understanding of complex physical systems from classical to quantum.

Disclosure statement
No potential conflict of interest was reported by the author(s).

Funding
This research is supported by the National Research Foundation, Singapore, and A*STAR
under its CQT Bridging Grant and Quantum Engineering Programme NRF2021-QEP2-02-
P02, A*STAR (#21709) and by EU HORIZON—Project 101080085 — QCFD.

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