Feature Extraction Methods Applied to the Clustering of Electrocardiographic Signals.

A Comparative Study
David Cuesta-Frau, Juan C. Prez-Corts, Gabriela Andreu-Garca, Daniel Novk Department of Systems Informatics and Computers, Polytechnic University of Valencia Department of Cybernetics, Czech Technical University in Prague dcuesta@disca.upv.es Abstract
In this paper, a method to automatically extract the main information from a long-term electrocardiographic signal is presented. This method is based on techniques of pattern recognition applied to speech processing, like dynamic time warping, and trace segmentation. In order to fulfill this objective, a clustering process is applied to the set of beats present within the electrocardiographic signal. From each group obtained, one beat is taken as representative of all the beats in that cluster. Since the discrete sequences of beat features can have different length, the clustering process takes place in a pseudo-metric space, and the dissimilarity measure is calculated using dynamic programming. Due to the same reason, the clustering algorithm employed is the KMedians, including some optimizations to reduce the computational cost. An experimental comparative study, using four different feature extraction methods, linear, and non-linear temporal alignment of sequences, is performed using labeled registers from the MIT database. pattern recognition applications, which are very common in the medical field. Therefore, it would be convenient to add pattern recognition capabilities to biosignal processing tools, which is the general goal of the research presented in this paper. We have focused the biosignal processing possibilities on a particular, but very important, case: the processing of electrocardiographic signals. These signals are crucial in diagnosing many cardiac diseases. They are probably the most studied and used biological signals, and in some registers, like those known as Holter registers, their length is greater than 24 hours, which turns manual inspection into a very tedious task. Beats present in an electrocardiographic signal have some interesting features to take into account when implementing any automatic process. They form a semiperiodic signal, and, within the same register, variability is relatively small, namely, only a few different waveforms can be found. Finally, in the time scale, the component intervals and waves of each beat behave in a non-linear way. This means changes in beat duration do not affect equally the waves and intervals included in it [1], which is similar to what happens in speech processing, where changes in word duration do not affect vowels and consonant length the same way. For example, in figure 1, a standard beat, with the main component waves and intervals, is shown.
R

1. Introduction
Computer-aided medical applications is a field of enormous development in recent years. One of these applications consists of extracting significant information from raw data like ultrasonic and X-Ray images, biosignal registers (electrocardiogram, electroencephalogram, electronystagmogram, electrogastrogram, etc), echocardiograms, magnetic resonance imaging, tomography, etc . In all these applications, information is presented to doctors in a suitable way to provide an accurate diagnosis. In fact, there is a field of great importance, biosignal processing, where the use of computer as a medical tool is becoming more and more popular, thanks to its relatively low cost and the availability of many signal processing algorithms. Nevertheless, this algorithms are mainly focused on tasks such as noise reduction, domain transform, signal thresholding, etc. This could be appropriate in some cases, but not for those related to

P Q PR S

QRS

Interval Interval

Figure 1. Standard beat including main component waves: P,Q,R,S,T and U, and main intervals: PR and QRS. Making the most of these properties, we propose a method based on pattern recognition techniques, focused on long-term electrocardiographic registers, or Holter registers, to automatically extract significant beats from

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the whole initial set. In this manner, cardiologist will offer diagnosis more easily.

2. Method
The stages of the method are schematically shown in figure 2. The first one consists of acquiring the electrocardiographic signal. Given that in this research the goal is to reduce the quantity of beats, we assume the acquisition to be from any kind of long-term register. We also consider that standard signal processing methods like noise and baseline wandering reduction are included.
Data Acquisition

methods used in some pattern recognition problems which allows less computational cost and better performance than the raw amplitude values. Thus, in this research, three more feature extraction methods have been tested: trace segmentation, polygonal approximation, and Wavelet transform coefficients. Besides, in some cases, the output sequences will have the same length and therefore, we can work in an Euclidean space. Figure 3 shows relationship between the feature extraction methods.
Trace Segmentation

Amplitude Coefficients

Segmentation

Wavelet Coefficients

Normalization

Feature extraction

Clustering

Dissimilarity measure

Visual inspection (Diagnosis)

Figure 2. Process stages. It starts with signal acquisition by means of an electrocardiogram system and finishes with the diagnosis through examining a beat from each resultant cluster. Then, a segmentation process takes place to separate all the beats within the signal. To realize it, a QRS detection algorithm is applied in order to fix the beginning and ending of each beat as described in [2]. The set obtained will be referenced as P , and the number of beats as n . Therefore, the whole set expression is (eq.1):

pi [m ] p i' [m] Figure 3. Feature extraction methods utilized, using the amplitude coefficients as the input. It is remarkable the trace segmentation method, which allows us to work with sequences in an Euclidean space.

P = {p 0 , p1 ,..., p n 1 }

(1)

Trace segmentation is a technique used in isolated word recognition strategies to reduce the computational complexity and memory requirements, above all when the vocabulary is relatively great [3]. In this case we have adapted this method to unidimensional discrete amplitude sequences, in order to get a new discrete sequence with a fixed length. In fact, the process is similar to a nonuniform sampling procedure, where each sample corresponds to points of great variation in the original input sequence. The process starts processing every beat pi by calculating its associated accumulated derivative up to sample j , as shown in equation 2:

where

pi stands for the discrete sequence: pi [m] = {p i [0] , pi [1] ,..., p i [ni 1] }

representative of a beat. Following segmentation, all the beats are normalized in amplitude, since uniform changes in the amplitude do not represent differences in beat clinical meaning.

[ j ] = pi [k ] pi [k 1]
k =1

j +1

Pseudo-metric space

Polygonal Approximation

Euclidean Space

(2)

where

j + 1 ni 1 .

2.1. Feature extraction

The first two stages allow us to have a set of discrete sequences P , with signal amplitude values. These sequences, using some kind of temporal alignment to make them have the same length, and so calculate the dissimilarity between pairs, could be used in the clustering process. However, there are other feature extraction

As can be noticed, the output sequence is one sample shorter than the input sequence due to the need of q + 1 values to calculate q consecutive differences among them. It is of particular interest the accumulated derivative obtained with the complete input sequence, i.e., ni 2 , which is the reference taken to calculate the

sampling points. So, this value

[ni 2] is divided by

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the number of samples

' i

ni' desired for the final sequence

pi' [m ] =

{( j , p [ j ]),..., ( j
0 i 0

n i' 1

, p i jn ' 1
i

[ ])}

p , to get the interval length L . Next, taking the points where exceeds multiples of L , we indirectly obtain the points where pi must be sampled. Analytically, this
process is shown in equation 3.

pi' [m] = pi [r ] r = arg max j ([ j ] (m + 1) L ) (3)

0 m ni' 1

Finally, the third feature extraction method, based on Wavelet transform (WT), takes advantage of the possibility of this mathematical tool to extract, in a coefficient list form, the main features or approximation of a signal [5]. In this case, the WT is applied to each beat, in the discrete domain, and the coefficients obtained are included in the output sequence

pi' [m] .

In figure 4, the method of trace segmentation is depicted. Graphically the process can be explained as follows: each intersection of the curve with an y = C L line, where C , provides a value in the x axis corresponding to the sampling point.
[ j ] = pi [k ] pi [k 1]
k =1 j +1

2.2. Dissimilarity measure

As has been stated in the previous section, the set of sequences obtained from feature extraction methods, are not, in general, of the same length. Thus it is that a time normalization procedure is necessary prior to any distance measure calculation. In fact, we will refer to this measure as dissimilarity instead, due to this pseudo-metric nature. The elastic matching scheme used in dynamic programming has been used in this case. It provides an algorithm to find the dissimilarity between two discrete sequences, according to a distance measure between two values of such sequences. The cost at each node of the dynamic programming matrix is calculated in equation 4:

[ni 2]

...
4L 3L 2L

L
0 j0 j1 j2

...

Figure 4. Trace segmentation process. The curve corresponds to the union of values. Entering in the curve from multiples of L , the projection in x axis offers the sampling points. The second feature extraction method, polygonal approximation, is a method to calculate a list of vertices which match a planar curve according to certain conditions of error threshold. In this case the planar curve to approximate is the input discrete signal representing the beat, and the vertices list will form the output sequence. There are many methods to carry out this task. For its simplicity, we have chosen that proposed in [4], adapted to the unidimensional electrocardiographic signals. This method starts with a raw approximation consisting of a line from (0, pi 0 ) to (ni 1, p i ni 1 ) . Next,

G[i, j 1] + d [(i, j )(i, j 1)] G[i, j ] = min G[i 1, j ] + d [(i, j )(i 1, j )] G[i 1, j 1] + 2d [(i, j )(i 1, j 1)]

(4)

Further details of this algorithm can be found in [6].

2.3. Clustering algorithm

The clustering algorithm utilized is the K-Medians algorithm [7]. It is based on the well-known K-Means algorithm, but adapted to a non-Euclidean sample space. Being C = {C1 , C 2 ,..., C k } the partition resulting from the clustering process, using k clusters, the objective function becomes:

J (C ) =
where

i =1 pCi

d ( p, m )
i

(5)

[]

mi = pr , is the median of the cluster Ci , obtained

( ) r = arg min j d p , p j l p j C i p l C i
(6)

as described in equation #:

all the points between the extremes are examined in order to find the furthest from this line. If the threshold is exceeded at this point, it is taken as a new vertex and the algorithm proceeds iteratively with each resultant new line. The final iteration is reached when all the lines involved in the polygonal approximation fulfill the threshold restriction. Therefore, the new output sequence is:

of

In order to reduce the computational cost, only a subset Ci will be used to obtain the median beat. Finally,

such cluster median

mi , will be examined in order to

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provide a diagnosis, whereupon the quantity of beats to inspect has been reduced from n to k , with k << n .
Error(%)

100.00% 90.00% 80.00% 70.00%

3. Results
A set of experiments using more than 27000 labeled beats from the MIT Database [8] has been carried out. Results using different time normalization techniques (linear and non-linear), and feature extraction methods, as described in section 2.1, are shown in figures 5, 6, 7 and 8. The error value corresponds to the percentage of beats that do not belong to the majority class in the same cluster. The number of clusters is increased from 2 to 12. Polygonal approximation is only realized with non-linear temporal alignment.
70% 60% 50% Error(%) 40% 30% 20% 10% 0% 2 3 4 5 6 7 8 9 10 11 12 Clusters

60.00% 50.00% 40.00% 30.00% 20.00% 10.00% 0.00% 2 3 4 5 6 7 8 9 10 11 12

A

Clusters

Amplitude

Trace

WT

Polygon

Figure 8. Comparative results of the four feature extraction methods.

4. Discussion and Conclusion

In this paper a method to group electrocardiographic signals, in an unsupervised way, has been presented. The method is based on some techniques used in speech processing, and a comparative study of different feature extraction methods has been also carried out. From the results it can be clearly noticed that the best method is based on non-linear temporal alignment and trace segmentation as the feature extraction method. The major drawback is the computational cost, since the dynamic programming based dissimilarity and the KMedians algorithm need many calculations.

DTW

Linear

Figure 5. Clustering results using amplitude values.

70% 60% 50% Error(%) 40% 30% 20% 10% 0% 2 3 4 5 6 7 8 9 10 11 12 Clusters

5. References
[1] L. Srnmo et al., A Method for Evaluation of QRS Shape Features Using a Mathematical Model for the ECG, IEEE Transactions on Biomedical Engineering, 1981, Num. 10 . [2] G.M Friesen et al., A comparison of the Noise Sensitivity of Nine QRS Detection Algorithms, IEEE Transactions on Biomedical Engineering, 1990, Vol. 31, Num. 1, pp. 85-98. [3] R. Pieraccini, Pattern Compression in Isolated Word Recognition, Signal Processing, 7, 1984, pp. 1-15. [4] U.Ramer, An Iterative Procedure for the Polygonal Approximation of Plane Curves. Computer Graphics and Image Processing, 1972, Vol. 1, pp. 244-256. [5] I.Provaznik et al., Wavelet Transform in ECG signal Processing. Proceedings of the 15th Biennial Eurasip Conference BIOSIGNAL 2000. pp. 21-25. [6] D. Cuesta et al.,Dynamic Time Warping Applied to the Clustering of Electrocardiographic Signals, European Medical and Biological Engineering Conference, 1999, pp 504-505. [7] A. Juan, Optimization of non-supervised learning techniques and its application to pattern recognition (in Spanish), Thesis, Polytechnic University of Valencia 1999. [8] AL Goldberger et al. PhysioBank, PhysioToolkit, and Physionet: Components of a New Research Resource for Complex Physiologic Signals. Circulation. 2000, 101(23), pp. 215-220.

DTW

Linear

Figure 6. Clustering segmentation.

100% Error(%) 80% 60% 40% 20% 0% 2 3 4 5 6

results

using

trace

10

11

12

Clusters

DTW

Linear

Figure 7. coefficients.

Clustering

results

using

Wavelet

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