ECG Motifs - Annotation Vectors

Annotation vectors are a series of numbers in the range [0, 1] which correspond to how significant a motif is at that index. For example, a 1 in the AV means that any motif starting at that index is heavily important and should be conserved whereas a 0 means that the motif can be discarded or ignored. As a result, annotation vectors allow you to ignore stop words or insigificant patterns in your data. This example shows you the basics of using annotation vectors on real-world data to select for specific motifs or patterns.

Data Overview

The data is a snippet from a large collection of ECG heartbeat data from the LTAF-71 database. The first half of this time series contains the calibration signal whereas the second half contains the actual ECG heartbeat.

import matrixprofile as mp
import numpy as np

from matplotlib import pyplot as plt
%matplotlib inline

ecg = mp.datasets.load('ecg-heartbeat-av')
ts = ecg['data']
window_size = 150

Motifs with Matrix Profile

Let’s compute the regular matrix profile and use that to find our top motif.

profile = mp.compute(ts, windows=window_size)
profile = mp.discover.motifs(profile, k=1)

figures = mp.visualize(profile)

As can be seen above, the top motif is the calibration signal. The reason why is because the calibration signal is more well-conserved than the heartbeat signal, which may have variance due to the slight irregularity of a heartbeat. However, since we have the domain-specific knowledge that the calibration signal should be ignored, we can use annotation vectors to help us discard the calibration signal motif.

# note the calibration signal starts to fade after the 1200th data point
threshold = 1200

# fill in first 1200 data points with 0s and rest with 1s to indicate
# that the calibration signal is not as important as heartbeat
av = np.append(np.zeros(threshold), np.ones(len(profile['mp']) - threshold))

Motifs with Corrected Matrix Profile

Now we can apply the AV that we created to our original matrix profile and get a “corrected” matrix profile, or CMP. We can then use this CMP to re-discover the top motif.

profile = mp.transform.apply_av(profile, "custom", av)
profile = mp.discover.motifs(profile, k=1, use_cmp=True)

figures = mp.visualize(profile)

Note how the top motif is now the heartbeat motif, which is the one we wanted to select. With domain-specific knowledge about the time series you are analyzing, annotation vectors can be an important tool in selecting for motifs that are important and ignoring motifs that are irrelevant.