Topology of time series

This notebook explores how giotto-tda can be used to gain insights from time-varying data by using ideas from from dynamical systems and persistent homology.

If you are looking at a static version of this notebook and would like to run its contents, head over to GitHub and download the source.

Useful references

See also

License: AGPLv3

From time series to time delay embeddings

The first step in analysing the topology of time series is to construct a time delay embedding or Takens embedding, named after Floris Takens who pioneered its use in the study of dynamical systems. A time delay embedding can be thought of as sliding a “window” of fixed size over a signal, with each window represented as a point in a (possibly) higher-dimensional space. A simple example is shown in the animation below, where pairs of points in a 1-dimensional signal are mapped to coordinates in a 2-dimensional embedding space.

A 2-dimensional time delay embedding

A 2-dimensional time delay embedding

More formally, given a time series \(f(t)\), one can extract a sequence of vectors of the form \(f_i = [f(t_i), f(t_i + 2 \tau), \ldots, f(t_i + (d-1) \tau)] \in \mathbb{R}^{d}\), where \(d\) is the embedding dimension and \(\tau\) is the time delay. The quantity \((d-1)\tau\) is known as the “window size” and the difference between \(t_{i+1}\) and \(t_i\) is called the stride. In other words, the time delay embedding of \(f\) with parameters \((d,\tau)\) is the function

\[\begin{split}TD_{d,\tau} f : \mathbb{R} \to \mathbb{R}^{d}\,, \qquad t \to \begin{bmatrix} f(t) \\ f(t + \tau) \\ f(t + 2\tau) \\ \vdots \\ f(t + (d-1)\tau) \end{bmatrix}\end{split}\]

and the main idea we will explore in this notebook is that if \(f\) has a non-trivial recurrent structure, then the image of \(TD_{d,\tau}f\) will have non-trivial topology for appropriate choices of \((d, \tau)\).

A periodic example

As a warm-up, recall that a function is periodic with period \(T > 0\) if \(f(t + T) = f(t)\) for all \(t \in \mathbb{R}\). For example, consider the function \(f(t) = \cos(5 t)\) which can be visualised as follows:

import numpy as np
import plotly.graph_objects as go

x_periodic = np.linspace(0, 10, 1000)
y_periodic = np.cos(5 * x_periodic)

fig = go.Figure(data=go.Scatter(x=x_periodic, y=y_periodic))
fig.update_layout(xaxis_title="Timestamp", yaxis_title="Amplitude")
fig.show()