Novel feature extraction technique based on ranks of Hankel matrices with application for ECG analysis
Ugnė Orinaitė^{1} , Mantas Landauskas^{2}
^{1, 2}Department of Mathematical Modelling, Faculty of Mathematics and Natural Sciences, Kaunas University of Technology, Kaunas, Lithuania
^{2}Corresponding author
Mathematical Models in Engineering, Vol. 7, Issue 2, 2021, p. 4049.
https://doi.org/10.21595/mme.2021.22138
Received 7 April 2021; received in revised form 14 June 2021; accepted 29 June 2021; published 30 June 2021
JVE Conferences
A novel feature extraction technique is presented in this paper. The term Hrankgram is coined here due to the similarity in concept with other feature extraction methods like spectrogram. The Hrankgram is twodimensional feature pattern which shows the change in algebraic complexity (measured using ranks of Hankel matrices) of a given signal at a different scale in time (estimated using phase space reconstruction with different time lags). In general feature extraction techniques could be classified into two broad types: time domain and frequency domain. The proposed technique fits into the first one. The proof of concept for the technique to detect changes in the signal was explained and an effect of additive noise was tested. Application of the technique was demonstrated to classify ECG signals for healthy and ill patients. The results shows that Myocardial infarction is detected most accurately although there is high imbalance in classification accuracy between the classes.
Keywords: Hankel matrix, ECG, feature extraction, CNN, ResNet.
1. Introduction
The application of Hankel matrices for electrocardiogram (ECG) analysis is not a new approach. The reliable and accurate feature measurement of ECG signals is used for the effective diagnosis of cardiovascular disease. An automated detection method for coronary artery disease based on a timefrequency representation (TFR) known as improved eigenvalue decomposition of Hankel matrix and Hilbert transform (IEVDHMHT) using ECG beats was proposed in [1]. A novel Adaptive Periodic Segment Matrix (APSM) based on Singular Value Decomposition (SVD) is proposed for extracting clean ECG signals from EMG artifacts [2].
Hankel matrices are also widely used not only in abnormality or illness detection from ECGs but also in denoising of the data using variable frequency complex demodulation (VFCDM) algorithm [3], ECG signal denoising algorithm based on the deep factor analysis [4]. Another methodology is based on the eigenvalue decomposition of the Hankel matrix. It has been observed that the endpoint eigenvalues of the Hankel matrix formed using noisy ECG signals are correlated with baseline wander and power line interference components, so the methodology removes BW and PLI noise by eliminating eigenvalues corresponding to noisy components [5]. As well as the positive and negative frequency components of complex signals are separately decomposed using recently developed eigenvalue decomposition of Hankel matrixbased method [6].
There are much more methods dedicated or applied to analyze ECG. One of the methods based on adaptive spectrotemporal filtering for ECG enhancement was used in order to accurately separate ECG and noise components suggesting that it is an ideal candidate for ECGbased fitness/athletic monitoring applications [7]. Also, the threshold value, threshold algorithm, and distribution function to evaluate the ECG signal denoising performance employing Dual tree complex wavelet transform (DTCWT) is published [8]. Ensemble Empirical Mode Decomposition (EEMD) based method in conjunction with the Block Least Mean Square (BLMS) adaptive algorithm (EEMDBLMS), and Discrete Wavelet Transform (DWT) combined with the Neural Network (NN), named the Wavelet NN (WNN) are also used for denoising the ECG signals [9].
There are some studies employing phase space reconstruction in ECG analysis. The combined method using Gaussian process and phase space reconstruction area following model selection for each subject yields EDR estimation system to obtain ECGderived respiratory signals [10]. Some new techniques have been proposed in recent years such as a singular spectrum analysis (SSA)based ECG denoising technique [11], [12], multilead modelbased ECG signal denoising method, in which a guided filter is inherently adapted to denoise ECG signal [13].
There are numerous research studies of 2D feature extraction from ECG. To achieve faster and accurate results in multichannel ECG signals, an artificial intelligence based automatic diagnosis system employing the texture features of twodimensional images, which are constructed by projecting the ECG signal vector as a row of the image, is proposed in the study [14], the main contribution is to expose that detection of cardiovascular defects can be done with the classical image texture methods by utilizing multichannel biomedical signals in a sufficiently shorttimeinterval. In addition to this, Onedimensional Local Difference Pattern (1DLDP) operator to extract the discriminating statistical features from ECG was used [15]. The authentication system using an efficient feature detection algorithm and a convolutional neural network (CNN) based on ECG was used for human authentication (a 12layer CNN allowed to achieve an average accuracy, sensitivity and positive predictivity of 97.92 %, 96.96 %, and 98.79 %) [16]. Also, an improved BioHashing and a matrix operation techniques can be quite helpful as cancelable biometric techniques for developing a human authentication system based on ECG signals [17], a new deep learning method for effectively classifying arrhythmia by using 2second segments of 2D recurrence plot images of ECG signals [18] and the algorithm that combines CNN with the ConstantQ NonStationary Gabor Transform (CQNSGT) [19] as well as a Hybrid CNNLSTM Network on imbalanced ECG datasets [20].
The paper is organized as follows. Our main results are provided in Section 2 and starts with required theoretical definitions followed by the problem formulation. The proposed algorithm is described in Section 3, experimental results are provided in Section 4, and the conclusions are drawn in Section 5.
2. Main results
2.1. Data description
ECG signals used in this analysis are from the open access PhysioNet database [21]. We use 521 records out of 549 records (the rest are not considered since they are not labeled) presented in this database from 268 subjects (209 men and 81 women, aged from 17 to 87). From one to five records are assigned to each subject and each record includes 15 simultaneously measured signals: the conventional 12 leads (i, ii, iii, avr, avl, avf, v1, v2, v3, v4, v5, v6) together with the 3 Frank lead ECGs (vx, vy, vz). In this paper we have chosen lead v2, since the corresponding electrode is places closer to the patient’s heart and in turn is related most to a general health of a patient. Each signal is digitized at 1000 samples per second and measured over a range of ± 16.384 mV as well as sampled up to 10 KHz. The diagnostic classes of the 268 subjects considered in this research are (numbers of the records in each of the class are shown in the brackets):
1. Dysrhythmia (16),
2. Cardiomyopathy/Heart failure (20),
3. Angina (3),
4. Valvular heart disease (6),
5. Myocarditis (4),
6. Myocardial infarction (368),
7. Bundle branch block (17),
8. Healthy control (80),
9. Hypertrophy (7).
Due to the high imbalance of the samples in the classes we have also performed numerical experiments with only two classes:
1. Myocardial infarction (368),
2. Healthy control (80).
2.2. Problem formulation
In this paper we formulate the problem as follows: by using twodimensional digital images as features of ECG segments detect whether those segments are of normal ECG or of ill person. In the case of multiple classes (more than 2), the ill person will be assigned into a different group of ill patients: those, who had experienced myocardial infarction, had ST/T change, experienced conduction disturbance, etc.
3. Algorithm
3.1. Preliminaries
The paper presents 2D feature extraction technique which is based on the rank of the sequence. Hankel matrix is employed for finding this rank so the rank itself is called the Hrank.
The rank of a sequence here is assumed to be the rank of a linear recurrence sequence as it was defined in [22] and is described using Hankel matrices as follows.
Consider a number sequence $S$:${\left\{{p}_{j}\right\}}_{j=0}^{+\infty}$; ${p}_{j}\in \mathbb{R}$. Corresponding sequence of Hankel matrices could be constructed:
The Hrank $m\in {\mathbb{Z}}_{0}$; $m<+\infty $; of the sequence $S$ is: $Hr\{{p}_{j}{\}}_{j=0}^{+\infty}=m$ if $det{H}_{m}\ne 0$ and $det{H}_{n}=0$, $n>m$. The rank of Hankel matrix describes algebraic relations of a sequence.
In theory a realworld series does not have a rank because it is practically impossible to find zero determinant for a matrix comprised of real numbers. Thus, it is a common property of all real phenomena. Nevertheless, it is still possible to approximate the data with algebraic series, i.e., by using the concept of pseudo rank of the number sequence.
By approximation with a linear recurrence sequence the ”0” is substituted by the machine epsilon (or error value):
3.2. The proposed technique for 2D feature extraction for ECG
We use pseudo ranks for evaluation of algebraic complexity for ECG segments obtained from state space reconstruction procedure which is described in detail below. This is the basis of 2D feature extraction. Later the features are entered into the CNN and ResNet with the aim to classify ECG segment as belonging to healthy or ill person depending on the data set used.
Let us explain the proposed feature extraction technique by starting at phase space reconstruction step. Consider uniformly sampled and denoised ECG time series of the second lead: $X=\left({x}_{1},{x}_{2},\dots ,{x}_{N}\right)$. Assume one has fixed the value of time lag $\tau $. By using this time lag we can reconstruct state space for the sequence $X$ in fixed width moving windows. The result is a list of uniformly sampled subsets of the original data:
is fixed to 50 which results in maximum possible Hrank equal to 25. ${n}_{stride}$ is the stride of moving window at which phase space is reconstructed and Hrank is computed.
For each subset ${X}_{i}^{\tau}$ we compute Hrank and do the same by taking different values of $\tau $ also ($\tau =\mathrm{1,2},\dots ,50$). Thus, each subset will have several Hranks showing the algebraic complexity of the phase space at different scale. The set of these Hranks comprise a vector of length 50 and could be noted as:
Fig. 1. Graphical representation of ECG phase space reconstruction leading to generation of Hrankgram
It could be noted that the use of ${n}_{stride}$ enables to obtain a number of vectors $\{{H}_{j}{\}}_{j=1}^{50}$ which are joined to the matrix $H$. The matrix $H$ essentially is a representation of the Hrank in different scales of the reconstructed signal being changed in time. The matrix $H$ is a twodimensional feature of the segment of ECG. It both evaluates the algebraic complexity of the signal and visualizes its change in time. This concept is very close to the spectrogram approach where the Fourier spectrum is visualized in columns and the rows represent time or vice versa. For this reason we coin our twodimentional feature as Hrankgram.
The algorithm of the proposed approach is depicted in Fig. 1. While estimating Hranks, in this paper we fix machine epsilon $\epsilon =$ 2.2×10^{16} and limit maximum rank by $H{r}_{max}=$ 30.
Some typical features extracted from the healthy and ill patient’s data are shown in Fig. 2. Note that the numerical values in each feature pattern is linearly transformed to the interval [0, 1]. In this way, patterns which are unusually bright or exceptionally dark are normalized. Thus the geometrical shapes in the feature pattern are preserved, but the numerical values become bounded and in turn more suitable for the input of neural networks.
3.3. On the proof of concept for the technique
The technique proposed is based on the rank of linear recurrence sequence (LRS). By investigating an ECG one assumes that it is LRS. But, of course, realworld sequences do not have a rank due to the presence of random noise. So the concept of pseudorank is introduced.
Suppose ECG as noisy LRS experiences a change in the dynamics. This in turn might and often will change the rank. Being a part of the Hrankgram the rank induces a visual change in the extracted 2D feature pattern. This euristic argument ensures that if algebraic complexity of the ECG is changing it will be noticeable in the feature pattern (if not visually then in the actual numerical values). This is the proof of the concept of the proposed algorithm.
Fig. 2. 2D feature patterns for healthy patients (parts (a)(c)), and ill patients (myocardial infarction, parts (d), (f)). White color corresponds to maximum Hranks while black depicts minimal Hranks in the observation window
a)
b)
c)
d)
e)
f)
Sometimes algorithms are tested on trivial data to show that they actually work. We use here a time series comprised of 3 concatenated sinusoids: ${x}_{1}=\mathrm{s}\mathrm{i}\mathrm{n}\frac{t}{10}$, ${x}_{2}=\mathrm{s}\mathrm{i}\mathrm{n}\frac{t}{2}$, and ${x}_{3}=\mathrm{s}\mathrm{i}\mathrm{n}\frac{t}{10}$ to demonstrate that Hrankgram reflects a change in the dynamics of the underlying data. This concatenated time series is also contaminated with additive Gaussian noise to demonstrate the robustness of the algorithm.
Fig. 3 clearly depicts that Hranks for moving windows gradually reacts to the inclusion of the second sinusoid which is of different frequency. The amount of additive noise even strengthens this effect. This could be explained by the fact that there are more possible values for Hranks for noisy sequences (they are usually higher in that case). But if the noise is high enough, the ranks will be also noticeably higher. And for completely random infinite sequence the rank is infinite.
Fig. 3. Sinusoids with different amount of additive Gaussian noise are depicted in parts (a)(c). part (a) corresponds to the case of no noise. Parameters for the noise intensity are $\mu =0$ and ${\sigma}_{1}=0$, ${\sigma}_{2}=0.01$, ${\sigma}_{3}=0.05$ correspondingly. Parts (d)(f) show Hrankgrams for each of the sinusoid
a)
b)
c)
d)
e)
f)
This simple numerical experiment supports the aforementioned euristic argument. Also, it shows that Hrankgram is robust to additive noise to a certain degree. Maximum tolerable amount of additive noise is another question and out of the scope of this paper.
3.4. Artificial neural network architectures used
As the main problem solved here is image classification we have used CNN and ResNet neural networks which are dedicated for solving exactly that type of problem. In general there is no particular method which could suggest the exact architecture of the network. Thus we performed a number of numerical experiments to determine the optimal number of layers as well as parameters for the filters. The experiments are summarized in the next section.
Usually 23 convolutional layers in CNN are sufficient for image classification task. So we have tested 2 to 4 layers. As for filter sizes, 2×2 to 5×5 were tested. The number of filters were also optimized by testing different variants. The best architectures are discussed in the next section. As for ResNet, same number of filters were tested, but only 2 and 3 residual blocks were considered. Note that ResNet is an improved version of CNN incorporating skip connections which acts as a dropout approach, but applied to the whole convolutional layer.
Software coding of artificial neural networks were done by using Python and Tensorflow with Keras.
Fig. 4. Architectures of CNN (part (a)) and ResNet (part (b)) used for classification of 2D features. Images generated by Netron software [23]
a)
b)
4. Experimental results
As described in Section 2.2 the problem solved here is to classify 2D feature patterns with respect of different ECG types. Of course, one can guess filter sizes and numbers by looking at the patterns of the images but usually we need to test a number of options and pick the best scenario. So it is almost a full sorting problem. A set of possible values for these parameters were mentioned in Section 3.4 and the top best results are summarized below. All the classification problems were repeated 64 times, each time randomly selecting 70 % of the images from each class for training and 30 % of the images for validation. This is in order to reduce the variance of the estimated accuracy. The random part also acts as cross validation of the modelling.
Table 1. Average classification accuracy for 9 classes of ECG feature patterns. The modelling was repeated 64 times. The bold values shows the best architecture of the neural network
CNN


Filter sizes

Convolutional layers

Number of filters

Average accuracy


Training

Validation


2

3

[8 16 32]

0.7127

0.6931

3

3

[8 16 32]

0.7137

0.6924

2

3

[11 22 33]

0.7128

0.6934

2

3

[9 11 18]

0.7117

0.6936

ResNet


Filter sizes

Residual blocks

Number of filters

Average accuracy


Training

Validation


2

2

[16 32 64]

0.8255

0.6938

2

3

[16 32 64 128]

0.9980

0.6938

3

3

[16 32 64 128]

0.9991

0.6938

4

2

[16 32 64]

0.9363

0.6938

Table 2. Average sensitivity and specificity for the investigation of 9 classes of ECG feature patterns using optimal CNN and ResNet networks. The modelling was repeated 64 times
ANN

No. classes

Sensitivity

Specificity

CNN

9

[0 0 0 0 0 0.9994 0 0.0013 0]${\mathrm{}}^{T}$

[1 1 1 1 1 0.0022 1 0.9990 1]${\mathrm{}}^{T}$

ResNet

9

[0 0 0 1 0 0 0 0 0]${\mathrm{}}^{T}$

[1 1 1 0 1 1 1 1 1]${\mathrm{}}^{T}$

Table 1 shows that on average ResNet gives better accuracy while working with 9 classes of feature patterns (0.6938 versus 0.6936). One can observe that accuracy in the validation set is very similar between different neural network architectures. This is mainly the result of some classes containing just a few items.
In this paper we have used one against all approach to estimate sensitivity and specificity for multiclass classification problem. Sensitivity estimates of the classification problem for CNN and ResNet approaches (Table 2) are not evenly distributed between the classes. As for CNN, the feature patterns are always assigned to class 6 (Myocardial infarction) or 8 (Healthy control), but for ResNet the patterns are assigned to class 4 (Valvular heart disease). This suggests that smallest peculiarities of the feature patterns does not need to be considered for classification. CNN, being of lower capabilities to memorize smaller objects compared to ResNet, outperformed the latter.
Fig. 5. Training dynamics for CNN (parts (a)(d)) and ResNet (parts (e)(h)) neural networks with 9 classes of ECG feature patterns. CNN was comprised of 3 convolutional layers with 9, 11 and 18 2×2 filters. ResNet was comprised of 2 residual blocks with 16 and 32 as well as 32 and 64 2×2 filters
a)
b)
c)
d)
e)
f)
g)
h)
Considering the training dynamics (Fig. 5) with 9 classes of ECG feature patterns, supremacy of the CNN architecture is more emphasized. One can observe that the training process stabilizes in both training and testing samples as early as at epoch 3. On the contrary, ResNet overfits (accuracy in the training set keeps increasing but it is stable at the testing set) right after the first epoch. Furthermore, the loss function (categorical or binary cross entropy depending on the number of classes considered) keeps to decrease at epoch 8. The modelling was repeated 64 times and we can note that each time training dynamics was similar – this shows a high stability of the results.
As we can see in the Table 3, average classification accuracy in the training set as well as in the validation set using only 2 classes is greater compared to the average classification accuracy having 9 classes. Comparing two artificial neural networks, ResNet is more accurate than CNN in the validation set (0.8222 versus 0.8219). Thus, the best classification experiments, either choosing 2 or 9 classes, are both the same with respect of their filter sizes (2), residual blocks (2), convolutional layers (3) and the number of filters (9, 11 and 18 for the CNN and 16, 32 and 64 for the ResNet). It could be mentioned that the results obtained do not strongly depend on the type of artificial neural network. It also suggests that lower complexity neural networks could be employed for the classification task of feature patterns extracted.
Table 3. Average classification accuracy having 2 classes of ECG feature patterns. The modelling was repeated 64 times. The bold values show the best architecture of the neural network
CNN


Filter sizes

Convolutional layers

Number of filters

Average accuracy


Training

Validation


2

3

[8 16 32]

0.8212

0.8218

3

3

[8 16 32]

0.8215

0.8219

2

3

[11 22 33]

0.8211

0.8215

2

3

[9 11 18]

0.8209

0.8219

ResNet


Filter sizes

Residual blocks

Number of layers

Average accuracy


Training

Validation


2

2

[16 32 64]

0.9500

0.8222

2

3

[16 32 64 128]

0.9920

0.8222

3

3

[16 32 64 128]

0.9883

0.8222

4

2

[16 32 64]

0.9799

0.8222

Table 4. Average sensitivity and specificity for the investigation of 2 classes of ECG feature patterns using optimal CNN and ResNet networks. The modelling was repeated 64 times
ANN

No. classes

Sensitivity

Specificity

CNN

2

[0.9994 0.0007]${\mathrm{}}^{T}$

[0.0007 0.9994]${\mathrm{}}^{T}$

ResNet

2

[0 1]${\mathrm{}}^{T}$

[1 0]${\mathrm{}}^{T}$

Table 4 shows that in the case of only 2 classes again CNN was able to distinguish the feature patterns better between the classes. Same as in the previous case with 9 classes, features patterns corresponding to Myocardial infarction are detected with greater accuracy compared to other types of patterns. In the practical applications this would not necessary be an unwanted feature. It might be safer to raise a red flag than to ignore an important illness.
Fig. 6. Training dynamics for CNN (parts (a)(d)) and ResNet (parts (e)(h)) neural networks with 2 classes of ECG feature patterns. CNN was comprised of 3 convolutional layers with 9, 11 and 18 2×2 filters. ResNet was comprised of 2 residual blocks with 16 and 32 as well as 32 and 64 2×2 filters
a)
b)
c)
d)
e)
f)
g)
h)
Classification of feature patterns with 2 classes results in a very similar average training dynamics as with 9 classes also (Fig. 6). The only difference here is a slightly bigger spread of the accuracy and loss functions about their corresponding average values. Despite this result the overall classification accuracy is higher with 2 classes of feature patterns. This could be naturally expected as the classification complexity is smaller for lower number of classes.
5. Conclusions
Hrankgram as feature extraction method resulted in detecting Myocardial infarction more accurately compared to other classes of ECG. But important notice here is that the accuracy is low for feature patterns representing other types of ECG. In general, ECG might not be the best data to analyze with Hrankgrams. Note that often professionals look at ECG as a set of intervals between particular positions in the signal. The Hrankgram focuses on changes in algebraic complexity of the signal analyzed. Changes in values of those intervals might not necessary go along with the changes in algebraic complexity.
It was demonstrated that Hrankgram is robust to additive noise. This is an important property, since realworld signals such as ECG are susceptible to natural and systematic noise.
More advanced neural networks like ResNet typically have large number of parameters to be trained. CNN in this regard is generally much smaller network. The data set used contained only 521 records which is a very small number considering the dimension of the parameter space of the target function of the neural networks used. This is a natural limitation of this research with respect of the classification accuracy. Accuracy of 0.6938 with 9 classes and of 0.8222 with 2 classes still looks reasonable in this context.
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