ASSESSMENT AND COMPARISON OF TIME REALIGNMENT
METHODS FOR SUPERVISED HEART BEAT CLASSIFICATION
G. de Lannoy
1
, M. Verleysen
1
and J. Delbeke
2
1
Machine Learning Group, Universit´e catholique de Louvain, pl. du Levant 3, 1348 Louvain-la-Neuve, Belgium
2
Departement of physiology and pharmacology, Universit´e catholique de Louvain
av. Hippocrate 54, 1200 Bruxelles, Belgium
Keywords:
Heart beat classification, Time realignment, Dynamic time warping, Trace segmentation, Wavelet transform,
Nearest neighbor classifier.
Abstract:
A reliable diagnosis of cardiac diseases can sometimes only be obtained by observing the heart of a patient
for a long time period where every single heart beat is of importance. Computer-aided classification of heart
beats is therefore of great help. The classification of the complete heart beat has many advantages compared
to a classification of the QRS complex only or feature extraction methods. Nevertheless, the task is challeng-
ing because of the time-varying property of the heart beats. In this work, four time-alignment methods are
evaluated and compared in the context of supervised heart beat classification. Among the four methods are
three time series resampling methods by linear interpolation, cubic splines interpolation and trace segmen-
tation. The fourth method is a realignment algorithm by dynamic time warping. The multiple sources of
artifacts are filtered by discrete wavelet transform. As it only relies on a dissimilarity measure, the k−nearest
neighbor classifier is a suitable choice for supervised classification of time series like ECG signals in multiple
classes. Two different experiments corresponding to inter-patient and intra-patient classification are conducted
on representative dataset built from the standard public MIT-BIH arrhythmia database.
1 INTRODUCTION
The importance of the electrocardiogram (ECG) sig-
nal for the diagnosis of cardiac diseases is widely
known (Clifford et al., 2006). However, a reliable di-
agnosis can sometimes only be obtained by observing
the ECG of a patient for a long-term period, compris-
ing hundreds to thousands of heart beats (Chudacek
et al., 2007; Cuesta-Frau et al., 2003; Jekova et al.,
2008). Just a very few number of these beats may ac-
tually reveal a pathology and the complete set of beats
must therefore be taken into account for the diagno-
sis.
Such long-term ECG signals are often recorded
using the very popular Holter recorders. These sys-
tems are ambulatory heart activity recordings, with a
signal storing time ranging from 24 to 48 hours. They
are used in the clinical diagnosis of some disease con-
ditions and by pharmaceutical groups for the evalua-
tion of new drugs during phase-one studies.
Due to the high number of beats to evaluate, anal-
ysis is performed off-line by cardiologists, keeping in
mind that the diagnosis may rely on just a few tran-
sient patterns. The duration of the process makes this
task very expensive. Reliable visual inspection is dif-
ficult and computer-aided detection of the pathologi-
cal beats is of major importance. However, this is a
difficult task in real situations.
First, several sources of noise typically pollute the
ECG signal. Among these, power line interferences,
muscular artifacts, poor electrode contacts and base-
line wandering due to respiration can sometimes be
identified. These artifacts can largely degrade the
quality of the signal and therefore complicate the beat
identification. Second, another hurdle is that the heart
rhythm can be quite unstable and variable in normal
conditions.
The classification of the complete heart beat is a
different problem than the classification of the QRS
complex only. In the latter case, beats are defined
by cutting a fixed-size window around the R spikes.
The size of the window is of similar length for all
beats, but the duration of QRS complexes varies with
time and pathologies. For this reason, a fixed win-
dow size may lead to incorrect extraction of the QRS
complex. Furthermore, some pathologies can only be
239
Lannoy G., Verleysen M. and Delbeke J. (2009).
ASSESSMENT AND COMPARISON OF TIME REALIGNMENT METHODS FOR SUPERVISED HEART BEAT CLASSIFICATION.
In Proceedings of the International Conference on Bio-inspired Systems and Signal Processing, pages 239-244
DOI: 10.5220/0001434602390244
Copyright
c
 SciTePress

identified by using more information than this QRS
complex only. A complete heart beat is defined as the
activity between the start of a P wave and the start
of the next one. The time-varying property of such
data challenges the automatic computer-aided classi-
fication methods.
Indeed, standard classification algorithmswork on
data arrays of identical dimension. A pre-processing
step is therefore required to deal with time series of
different lengths. This pre-processing step can be the
extraction of the same number of typical ECG fea-
tures from each beat. However, the complete mor-
phology of the beat can hardly be summarized in a set
of features, and the discriminativeinformationmay be
missing in the chosen features. A more sophisticated
pre-processing step is to resample and/or to realign
the signal in order to have the same number of sam-
ples in each beat. The advantage is that the complete
heart beat can then be used as input to any classifier
without loss of information. Moreover, advanced re-
sampling methods can correct for time shifts and re-
align observations.
In this paper, four temporal realignment methods
are evaluated in the context of complete heart beat
classification. These methods have proven successful
in variousdisciplines such as speech processing, spec-
tral data analysis and signal filtering. The remaining
of this paper is structured as follows. After this intro-
duction, Section 2 gives a short review of the litera-
ture about the state of the art in ECG beat classifica-
tion. Section 3 sets the theoretical background for the
methods used in this work. Section 4 introduces the
methodology followed in this work. Finally, Section
5 shows the experiments on a real database and the
corresponding results.
2 STATE OF THE ART
A large body of literature about the ECG beat classifi-
cation has arisen in recent years. Computer-aided al-
gorithms for the automatic classification of the heart
beats can be separated in two groups: supervised or
unsupervised (Clifford et al., 2006). In the first case,
it is necessary to have a set of manually labeled heart
beats. In the second case, because manually labeled
reference beats are not available, automatic diagnosis
is impossible.
Clustering techniques are among the most used
unsupervised processing techniques (Clifford et al.,
2006). A comparison between clustering algorithms,
realignment algorithms and feature extraction meth-
ods for unsupervised beat classification has been con-
ducted in (Cuesta-Frau et al., 2003). More recently,
the results of the previous work have been improved
by introducing the J-means heuristic for heart beat
clustering (Rodriguez-Sotela et al., 2007). Self-
organizing maps (SOM) have also been investigated
with very promising results (Clifford et al., 2006).
The disadvantage of unsupervised methods, beside
the fact that an automatic diagnosis cannot be ob-
tained, is the empirical choice of the number of clus-
ters (or of SOM prototypes). In the case of heart beats,
this choice is hard to make a priori and it can signifi-
cantly affect the results.
The vast majority of supervised beat classification
algorithmsreportedin the literature work either on the
QRS complex only, either on features extracted from
the signal, or a combination of both (Clifford et al.,
2006). In the first case, only the QRS complex is ex-
tracted from the ECG signal by defining a fixed-size
window around the R spike. The beat time-varying
duration property is therefore avoided. In the second
case, common time-domain features include the time
interval between characteristic ECG patterns such as
R-R and Q-T intervals, the Hermite basis function ex-
pansion of the QRS complex and order statistics of
the QRS sequence. Frequency domain descriptors
such as Fourier or wavelet transform coefficients are
alternative interesting features. Classification meth-
ods such as artificial neural networks (ANNs), sup-
port vector machines (SVMs) and combined methods
have been applied with success for QRS classification
(Clifford et al., 2006). A recent comprehensive re-
view of supervised classification methods of the QRS
complex can be found in (Jekova et al., 2008).
These methods relying on the classification of the
QRS complex or of selected features may miss po-
tentially useful information for discrimination. Some
pathologies can indeed be more accurately identified
by using more information than the QRS complex
alone, such as Q-T intervals. Furthermore, using a
fixed-size window around the R spike may lead to
wrong QRS extraction because the duration of the
QRS complexes is not stationary. Also, the choice
of the features is of great importance. Summarizing
the complete morphology of the beats into a set of
features is a difficult and application dependent task
(Clifford et al., 2006; Jekova et al., 2008).
In order to circumvent these issues, realignment
methods have recently been applied with success
to unsupervised beat clustering (Cuesta-Frau et al.,
2003). The complete beat can then be considered by
the classification procedure. However, contrarily to
clustering, supervised classification algorithms rely
more easily on a set of features extracted from the
time series rather than on the raw time series them-
selves. For this reason, despite the advantages of
BIOSIGNALS 2009 - International Conference on Bio-inspired Systems and Signal Processing
240

these methods, very few studies have been reported on
supervised full beat classification after realignment.
The k−nearest neighbor (KNN) classifier is an excep-
tion to this. In a similar way to clustering methods, it
only relies on a dissimilarity metric between obser-
vations. Such dissimilarity metrics can naturally be
computed between time series of similar lengths. In
this work, four time series realignment methods are
evaluated in the context of complete heart beat classi-
fication by k-nearest neighbor classifier.
3 THEORETICAL BACKGROUND
This sections provides a brief account of the theo-
retical background for the signal processing methods
used in this work. The time-frequency filtering by
discrete wavelet transform is briefly described first.
Thereafter, the dynamic time warping realignment al-
gorithm is introduced. Finally, a brief summary to
the three resampling algorithms is provided. In the
remainder of this work, these methods are globally
referred to as the realignment methods.
3.1 The Discrete Wavelet Transform
The continuous wavelet transform (CWT) is a time-
frequency decomposition of a signal x(t) by the con-
volution of this signal with a so-called wavelet func-
tion ψ(t) (Mallat, 1999). From a wavelet function,
one can obtain a family of time-scale waveforms by
translation b and scaling a, with a, b ∈ R:
ψ
a,b
(t) =
1
√
a
ψ

t −b
a

. (1)
When a = 1 and b = 0, ψ(t) is called the mother
wavelet. The wavelet transform of a function x(t) ∈
L
2
(R) is a projection of this function on the wavelet
basis {ψ
a,b
} :
T(a, b) =
Z
+∞
−∞
x(t)ψ
a,b
(t)dt . (2)
The discrete wavelet transform (DWT) removes
the redundancy of the CWT by using dyadic scales
and discrete translations. The first DWT step pro-
duces two sets of coefficients: approximation coef-
ficients (low frequency components) and detail coef-
ficients (high frequency components), followed by a
dyadic decimation (downsampling). This process is
iterated log
2
(N) times at most, where N is the size of
the signal x(t) (Mallat, 1999).
3.2 Dynamic Time Warping
Dynamic time warping (DTW) is an algorithm that
finds an optimal alignment function between two
sequences of different lengths (Myers and Rabiner,
1981). It has for example been used with great suc-
cess in speech recognition and process control. The
sequences are warped non-linearly in the time dimen-
sion to determine a measure of their similarity inde-
pendent of certain non-linear variations in the time di-
mension.
Let x and y be two sequences of lengths n
x
and n
y
respectively. The objective is to find the best align-
ment between the two sequences, according to a cost
function. The alignment procedure allows us to com-
pare a value x(i) of x with a value y( j) of y. The
whole set of possible comparisons can be represented
as a matrix of size n
x
×n
y
, that can be seen as a multi-
stage graph. The objective is then to find a node path
(i
1
, j
1
), (i
2
, j
2
), ...,(i
f
, j
f
) of length f along the graph
such that the final cumulative cost D is minimal. The
latter is defined as
D =
f
∑
k=1
[d(i
k
, j
k
)|(i
k−1
, j
k−1
)] , (3)
where d(i, j) is a cost function that allows us to com-
pare a value x(i) of x with a value y( j) of y. A typi-
cal cost function is for example the squared Euclidean
distance:
d(i, j) = (x(i) −y( j))
2
. (4)
The optimization process is performed using dynamic
programming. The cumulative cost of the optimal
alignment path can then be used as a dissimilarity
measure.
3.3 Trace Segmentation
Trace segmentation (TS) is a non-uniform sampling
method used in speech recognition to normalize the
duration of utterances. Standard vector-space norms
can then be used to compare them. The objective is to
retain only the samples of the signal where the main
changes take place (Cuesta-Frau et al., 2003).
Given a sequence x of length n, let us define the
partial accumulated derivate ∆
j
of x:
∆
j
=
j+1
∑
i=2
|x(i) −x(i−1)| . (5)
The accumulated derivative at the end of the sequence
is
∆ =
n
∑
i=2
|x(i) −x(i−1)| . (6)
ASSESSMENT AND COMPARISON OF TIME REALIGNMENT METHODS FOR SUPERVISED HEART BEAT
CLASSIFICATION
241

If h is the desired number of samples after trace seg-
mentation, the average interval amplitude value of ∆
is given by
L =
∆
h
. (7)
Let us now define the output sequence x
tr
of length
h obtained by trace segmentation of x. Each sample
x
tr
(l) is taken from the sample x( j) corresponding to
the time when the accumulated derivate exceeds an
integer multiple of L:
x
tr
(l) = x( j)|j = argmin
1<i<n−1
(l ×L < ∆
i
) , (8)
with x
tr
(1) = x(1) and x
tr
(h) = x(n). The sequence
x
tr
thereby includes the values of x where only the
main changes take place.
3.4 Interpolation
Given a sequence x of length n, obtained by sampling
or experiment, regression analysis tries to estimate a
function which closely fits those data points. Inter-
polation is a specific case of curve fitting, in which
the function must go exactly through the data points.
One of the simplest interpolation methods is linear in-
terpolation. In this case, a linear function is fit at each
interval x
k
, x
k+1
.
Spline interpolation uses low-degree polynomials
in each of the intervals, and chooses the polynomial
pieces such that they fit smoothly together. The re-
sulting function is called a spline (De Boor, 1978).
Spline interpolation incurs a smaller error than linear
interpolation, and the interpolant is smoother. How-
ever, the interpolant is easier to evaluate than the high-
degree polynomials used in polynomial interpolation.
In both cases, the estimated function then allows
us to resample (or stretch) the sequence by generating
new data points within the range of the discrete set of
known data points.
4 METHODOLOGY
In this work, supervised classification of complete
heart beats is considered. Let us assume that a refer-
ence database has been obtained and annotated, with
all pathologies of interest being represented. Given
a new ECG signal, for example recorded using an
Holter system, one wants to use the information con-
tained in the reference database in order to predict the
pathologies present in the new signal.
First, all the beats within the signal must be sepa-
rated. Several computer-aided annotation algorithms
have been reported in the literature in order to auto-
matically detect the ECG characteristic points for beat
extraction (Clifford et al., 2006).
Thereafter, a realignment of the beats must be
achieved. Four sequence alignment methods are eval-
uated in this work. The first two are interpolation
methods: linear interpolation (LI) and cubic splines
interpolation (CSI). The third method is the trace seg-
mentation method (TS) and the fourth is the dynamic
time warping (DTW) realignment algorithm.
Next, noise and artifacts are filtered by time-
frequency filtering using the the discrete wavelet
transform (DWT) of the heart beats. Moreover,the di-
mensionality of the observations is strongly reduced
by the downsampling of the approximation coeffi-
cients at each step of the DWT. This reduces the com-
putational cost of the classification algorithm.
Finally, the realigned and filtered heart beats are
reduced to zero mean and unit variance. The beats are
then given as input to a classifier. A natural choice
for supervised classification of time series in multi-
ple classes is the k-nearest neighbor (KNN) classifier.
The k-nearest neighbor (KNN) algorithm is a super-
vised classifier where an observation (corresponding
to one heart beat) is assigned to the class most com-
mon amongst its k nearest neighbors in the reference
set. The algorithm is supervised, because the neigh-
bors are taken from a reference set of observations for
which the correct classification is known. This can be
thought of as the training set for the algorithm, though
no explicit training step is required.
In order to identify the closest neighbors, a dissim-
ilarity metric must be defined. When using the three
first realignment methods the KNN distance measure
is the Euclidean distance between observations, com-
puted on the aligned beats. In the case of the DTW
warping algorithm, the DTW dissimilarity measure
can directly be used in the KNN method, without ef-
fectively computing the realigned time series.
5 EXPERIMENTS AND RESULTS
The performances of the four realignment methods
are evaluated on the public standard MIT-BIH ar-
rhythmia database (Goldberger et al., 2000). It con-
tains 48 half-hour recordings of annotated ECG with
a sampling rate of 360Hz and 11-bit resolution over
a 10-mV range. Except recordings 201 and 202,
each recording comes from a different patient, so the
database contains a total of 47 subjects. The orig-
inal annotations are used. The method defined in
(Rodriguez-Sotela et al., 2007) for extracting com-
plete beats from the R spike annotations is used.
The five main types of heart beats represented in the
database are used in this study: (1) normal beats (N)
- 74820 cases, (2) left bundle branch block beats (L) -
BIOSIGNALS 2009 - International Conference on Bio-inspired Systems and Signal Processing
242

8050 cases, (3) right bundle branch block beats (R) -
7220 cases, (4) prematureventricularcontractions(V)
- 6970 cases, and (5) paced beats (P) - 7000 cases.
From each of the 47 recordings, three beats of
each type available in the recording are randomly se-
lected. Each patient is thus fairly represented in the
dataset. Nevertheless, only a small subset of record-
ings contains L, R and P types, while almost every
recording contains the N class. Therefore, in order
to obtain the same number of representatives for each
class, other beats are then randomly selected amongst
the recordings and added to the experimental set un-
til equally balanced classes are obtained. The final
experimental dataset contains a total number of 600
heart beats, including an equal number of 120 beats
per class where the 47 patients are fairly represented.
The level 3 approximation coefficients of the
DWT with a biorthogonal mother wavelet are used
as features. The classification performances are eval-
uated using a KNN classifier with k = 3 neighbors.
Two different experiments are conducted. The first
one is an intra-patient classification where the com-
plete training set is used for the classification of each
heart beat. A typical leave-one-out methodology is
used for the evaluation of the performances. The sec-
ond experiment is an inter-patient classification. A
leave-one-out method is also used. However, when
classifying a heart beat of a given patient, all beats
coming from this patient are removed from the train-
ing set. The classification is therefore based only
on the annotated beats of other patients, which is a
much harder generalization task. Table 1 shows the
intra-patient classification results and Table 2 holds
the inter-patient classification results. The values are
average rates computed over ten different random se-
lections during the construction of the experimental
dataset.
When considering the intra-patient experiment,
very similar results are obtained by the two interpo-
lation methods with an average of 90% correct clas-
sifications. Surprisingly, the dynamic time warping
algorithm provides slightly worst results with an av-
erage of 88%. Amongst the four methods, trace seg-
mentation obtains the worst results with an average of
only 70%. The computational time of the two inter-
polation methods and the trace segmentation method
are very similar, allowing real-time analysis. On the
other hand, the running time of the DTW algorithm
makes this method only suitable for off-line analysis.
The results obtained with the inter-patient experi-
ment in Table 2 are unsatisfactory, especially for the
L, R and N types. However, the low results for these
classes are preliminary, since the MIT-BIH database
only contains four patients with left bundle branch
block and five patients with right bundle branch block,
which is quite insufficient for generalization. These
results regarding generalization between patients of
the MIT database are confirmed in other recent works
(Jekova et al., 2008). Furthermore, the three L, R and
N classes are often considered to be of the same clin-
ical relevance. Indeed, the Association for the Ad-
vancement of Medical Instrumentation (AAMI) rec-
ommends to group these three classes together (Maier
et al., 1999). Table 3 holds the results when the three
L, R and N types are merged together. The results are
comparable to intra-patient performances, and show
that the generalization between patients is possible.
Although numerous studies dealing with heart
beat classification have been reported in the literature,
a comparison is difficult to make. Indeed, few stud-
ies address multi-class problems including more than
the N and V heart beat classes. Also, only a subset
including 5 to 10 recordings of the MIT database is
usually used in these studies. Moreover, the training
dataset is constructed in quite different ways, and por-
tions of the recordings including noise are sometimes
rejected during the extraction of beats. For exam-
ple, (Ham and Han, 1996) obtained very different re-
sults with 44 recordings in comparison with (Moraes
et al., 2002) using only 6 recordings to discriminate
between V and N beat types.
In this work, the experimental dataset is created
in such way that the number of heart beats is equally
balanced between each class and that all 47 patients
of the database are fairly represented. The noisy por-
tions of the recordings are also included in the data.
Furthermore, the inter-patient and intra-patient heart
beat classifications are two very different objectives
and are therefore separated in this study.
Table 1: Intra-patient correct classification rate.
N L R V P
LI 91.1 84.5 89.7 92.4 95.8
CSI 91.3 84.4 89.8 92.4 95.8
DTW 90.3 82.1 85.8 91.2 95.0
TS 60.1 64.0 75.0 79.7 73.7
Table 2: Inter-patient correct classification rate.
N L R V P
LI 32.0 15.9 38.2 71.1 85.0
CSI 32.1 15.9 38.4 71.1 85.2
DTW 43.3 4.6 46.2 51.2 75.1
TS 27.9 11.7 8.5 53.7 56.8
ASSESSMENT AND COMPARISON OF TIME REALIGNMENT METHODS FOR SUPERVISED HEART BEAT
CLASSIFICATION
243

Table 3: Inter-patient correct classification rate, when merg-
ing the L R and N types.
N+L+R V P
LI 81.1 80.7 92.6
CSI 81.3 80.7 92.7
DTW 74.4 79.2 90.0
TS 60.0 72.6 72.6
6 CONCLUSIONS
In this work, four time-alignment methods are evalu-
ated and compared in the context of supervised heart
beat classification. Amongst these methods are three
time series resampling algorithms by linear interpo-
lation, cubic splines interpolation and trace segmen-
tation. The fourth method is a realignment algorithm
by dynamic time warping. The multiple sources of
noise and artifacts are filtered by means of a time-
frequency decomposition by discrete wavelet trans-
form. The downsampling induced by DWT approx-
imation coefficients also reduces the dimension of the
observations. Since it only relies on a dissimilarity
measure between observations, the KNN classifier is
a natural choice for supervised classification of time
series in multiple classes.
Experiments are conducted on a representative
dataset built from the standard public MIT-BIH ar-
rhythmia database. The five main types of heart beats
are considered. The experimental dataset is created
so as to include an equal number of beats per class
with all patients being fairly represented. For intra-
patient classification, very similar results are obtained
by the two interpolation methods with an average cor-
rect classification rate of 90%. Surprisingly, the dy-
namic time warping algorithm provides slightly lower
results with an average of 88%. Amongst the four
methods, the trace segmentation obtains the worst re-
sults with an average of only 70%. On the other hand,
the results obtained for inter-patient classification are
unsatisfactory, especially for the L and R types. How-
ever, the low yield obtained for these classes are
preliminary, since the number of patients with these
pathologies in the MIT-BIH database is insufficient
for generalization. When merging these three classes
together as recommended by the AAMI, the results
achieved are then comparable to intra-patient classifi-
cation.
Very few other studies work on a reliable dataset
with multi-class, inter and intra patient classification
and comparisons to other works are difficult to ob-
tain. Further works will include a comparison with
the results of other QRS classification and feature ex-
traction methods using the same dataset.
ACKNOWLEDGEMENTS
G. de Lannoy is funded by a Belgian F.R.I.A. grant.
This work was partly supported by the Belgian
“R´egion Wallonne” ADVENS 4994 project.
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