2015 International Symposium on Intelligent Signal Processing and Communication Systems (ISPACS) November 9-12,2015
Performance Comparison of Denoising Methods for
Heart Sound Signal
Amy H. Salman*, Nur Ahmadit, Richard Mengko+, Armein Z. R. Langi, Tati L. R. Mengko'
Department of Electrical Engineering, School of Electrical Engineering and Infonnatics
Bandung Institute of Technology, 11. Ganesha No. 10 Bandung, 40132, Indonesia
Email: {*amy.tnurahmadi}@stei.itb.ac.id.+richard@mengko.com.{annein.z.r.langi tati}@stei.itb.ac.id
Abstract-This paper presents the performance analysis and
comparison of three denosing methods for heart sound signal
based on wavelet transform (WT), total variation (TV), and
empirical mode decomposition (EMD). Extensive simulations are
performed using normal and abnormal heart sound data and the
performance is evaluated in terms of signal-to-noise ratio (SNR),
root mean square error (RMSE), and percent root mean square
difference (PRD). The simulation results show that EMD based
denosing method outperforms two other methods.
Keywords-Heart Sound, Denoising, Wavelet Transform, Total
Variation, Empirical Mode Decomposition
1. INT RODUCT ION
Cardiovascular disease (CVD) has long been the lead
ing cause of death throughout the world. Accroding to the
American Heart Association, in 2010 alone, more than 2150
Americans die due to cardiac disease every single day, with
an average of 1 death every 40 seconds [1]. To reduce the
death rate, an early accurate diagnosis of CVD is of paramount
importance.
An intelligent computerized cardiac auscultation utiliz
ing advanced signal processing based on phonocardiography
(PCG) offers low-cost, non-invasive, and accurate diagnosis
and classification of heart diseases. PCG refers to the trac
ing technique of heart sounds and the recording of cardiac
acoustics vibration using microphone transducer [2], which
is nowadays already embedded in digital stethoscope. In this
scheme, signal denosing method plays an important role since,
in practice, heart sound signal is always contaminated with
noise and interference from various sources such as back
ground noise, power interference, breathing or lung sounds,
and skin movements in the surrounding environment. The
accuracy of results heavily depends on the performance of
signal denoising method. A poor signal denoising method will
lead to catastrophic result.
Several signal denoising methods exist in the literature
such as wavelet transfonn (WT) [3]-[5], total variation (TV)
[7]-[10], and empirical mode decomposition (EMD) [11]
[14]. Wavelet transfonn has been the most popular choice
for signal denoising method and proven to be able to pro
vide good denoising performance. However, wavelet denoising
requires predefined basis function selection (from too many
choices) suited to signal under consideration, which limits
the flexibility of the method. In addition, the decomposition
level and thresholding technique of wavelet denosing need
to be carefully considered as well. Total variation method,
978-1-4673-6499-7/15/$31.00 2015 IEEE
435
mainly used for image denoising, was proposed by [9] for
denoising heart sound signal. Empirical mode decomposition
(EMD), a relatively new non-linear and non-stationary signal
analysis method [11], offers interesting feature of adaptive and
data-driven decomposition capability. The application of EMD
denoising method to heart sound signal may lead to useful
results.
In this paper, the perfonnance of these methods for heart
sound signal denoising is evaluated and compared. The qual
itative evaluation is performed by visual inspection while
quantitative evaluation is carried out by using three standard
metrics: signal-to-noise ratio (SNR), root mean square error
(RMSE), and percent root mean square difference (PRD).
The simulation results show a superior performance of EMD
denoising method over others.
This paper is organized as follows. Section II describes
the theoritical background and mathematical notation used in
wavelet transfonn (WT), total variation (TV), and empirical
mode decomposition (EMD) denoising methods. Simulation
results and perfonnance evaluation both qualitative and quan
titative are given in Section m. Finally the conclusion is drawn
in Section IV.
II. DENOISING MET HODS
x(n), is expressed as
The noisy heart sound signal,
x(n) y(n) + O'e(n), n 0,1,2" " N 1 (1)
= = -
where y(n) denotes the clean signal and O'e(n) represents the
noise signal with Gaussian random variables e(n) and variance
0'2.
In this paper, three denoising methods based on wavelet
transform (WT), total variation (TV), and empirical mode
decomposition (EMD) are compared to find which method
offers the best perfonnance.
A. Wavelet Transform Denosing
The wavelet transform is a powerful signal analysis tool
with the ability to represent a signal simultaneously in the
time and frequency. It was firstly proposed by Alfred Haar
in his thesis (1909). However, the concept of wavelet became
solid and systematic only when scientists and engineers from
different backgrounds joined this field and began collaborating
in 1980's [2].
2015 International Symposium on Intelligent Signal Processing and Communication Systems (ISPACS) November 9-12,2015

TABLE l. INPUT PARAMETERS SETTING

The wavelet transfonn can be classified into two groups:
continuous wavelet transfonn (CWT) and discrete wavelet Parameter Description Chosen Setting

transfonn (DWT). CWT of a signal x(t) is defined as original signal x(n)

tptr tlueshold selection rule rigsure
sorh h
X(a, b) = I: x(t)1j;,b(t)dt (2) seal
n
thresholding technique
tlueshold's rescaling method
decomposition level
mln

way dblO
denotes a complex conjugate and 1j;a b(t) serves as
(mother) wavelet function
where *

,
the basis functions which are obtained by scaling (dilation)
and shifting (translation) a wavelet function 1j;(t) (also called
as mother wavelet) with scaJe a and time b, respectively, as of signal x(n) with threshold T is expressed as follows
shown below
(3)
_ _ {
x (n) - 0x(n),, Ix(n)1 T
Ix(n)1 < T (5)

CWT performs continuous shifting over a continuously scal
able function of a signal and caJculates the correlation between
them. This continuous process will result in highly redundant
wavelet coefficients and large computation time. To remove
this redundancy and enable faster computation, DWT is used
instead by modifying the wavelet representation as follows
(4)
where ao (fixed, > 1) and bo (> 0) represent the fundamental
scaJe factor and time shift, respectively, and m and n are
integers multiple of those two parameters.
Wavelet transform has been widely used for denoising
the corrupted heart sounds signaJ. Wavelet denoising method
comprises three steps: decomposition, thresholding, and re
construction. The noisy signaJ is firstly decomposed using
appropriate (mother) wavelet function 1j;(t) and selected de
composition level N. The obtained wavelet coefficients are
thresholded so that the irrelevant components (noise) are
removed and the relevant components (infonnation) are kept.
MATLAB has built-in function wden for wavelet denoising
as described in [6]. Several input parameters and their setting
for this function are explained in Table I where rigsure
represents the selection using the principle of Steins Unbiased
Risk Estimate (SURE), h means hard thresholding, and mIn
denotes threshold rescaling using a level-dependent estimation
of the level noise.
B. Tot al Variation Denoising
Total Variation (TV), invented by Rudin, Osher, and Fatemi
[7], is a powerful denoising method which has great benefit
of preserving and enhancing important features such as edge
in images. Despite being commonly used for image denoising,
it can also be used for I-D signal denoising as proposed by
[8]. Varghees and Ramachandran [9] employed TV method for
removing noise embedded in heart sound signals.
TV denoising approximates the signaJ y( n) from the noisy
signal x(n) by solving the optimization problem:
fj argmax Ilx - YII + AII(Y)lll' (6)
y
=

Signal reconstruction is then perfonned using inverse wavelet

transfonn to obtain the approximated clean signal.
To obtain an optimal result, selection of appropriate pa
rameters of wavelet function, decomposition level, and thresh
olding technique is crucial. There are numerous wavelet fam
ilies with different properties. The one more resembling the
original signal will yield better denoising result. In this paper,
Daubechies dblO wavelet function, as shown in Figure 1,
where the scaJar A is the regularization parameter which
controls the degree of smoothing and (y) represents the
first order difference of signal y. The increase in A value will
give more weight to the second term, total variation solution,
a measure of how much signaJ changes. In generaJ, larger
noise requires bigger A value. The h -nonn of a vector y is
defined as Ilylll L:n Iv(n)l, while the 12-nonn is defined as
=

is used since it highly resembles the heart sound signaJ. In

addition, dblO wavelet has orthogonal property which enables
perfect reconstruction of signal and have been reported to
produce best result among others [3] [4]. The decomposition
level, N 5, is chosen as recommended in [5]. Hard
=
thresholding technique is selected as it provides better result
compared to soft thresholding technique. The hard thresholding
db10 Wavelet
IIyl12 = (L:n Iv(n)12)1/2 .
In this work, a Majorization-Minimzation (MM) aJgorithm
[10] is used to solve a sequence of optimization problems.
The parameter A is set to 0.3 based on the experiment and
characteristic of heart sound signaJs. The aJgorithm is run for
50 iterations to find more accurate result.
C. Empirical Mode Decomposit ion Denoising
Empirical mode decomposition (EMD), since firstly pro

: !f . 1
posed by Huang in 1998 [11], has gained popularity as data
anaJysis method especiaJly for non-stationary and non-linear
signaJs such as biomedicaJ (including heart sounds) signaJs.
EMD, in contrast to other methods such wavelets and fourier
which require predefined basis function, is fully data-driven
o 5 10 15 20 method that does not require any a priori known basis. EMD
adaptively decomposes a signaJ into a series of simple oscilla
Fig. l. Daubechies db to wavelet function tory AM-FM components caJled as intrinsic mode functions

436
2015 International Symposium on Intelligent Signal Processing and Communication Systems (ISPACS) November 9-12,2015

(IMFs) through iterative procedure (known as sifting). An
IMF is defined as a function that satisfies two conditions: the
number of extrema (maxima and minima) and zero crossing
must be equal or differ by at most 1; and the average value
of the envelopes derived from local maxima and minima is
(approximately) zero.
Even though EMD still lacks a solid mathematical founda
tion which could be used for theoritical analysis and perfor
mance evaluation, it is oftenly proven to provide interesting
and useful results. The sifting procedure of EMD for decom
posing the signal x (n) into IMFs is systematically described
as follows:
1) Specify all the local extrema (maxima and minima)
of x (n)
oscillation modes (low frequency). Figure 2 shows signal x (n)
decomposition into 10 IMFs and final residue signal.
One of main applications which utilizes the characteristics
of EMD technique is signal denoising. EMD, whose decom
position is based on elementary substractions, enables perfect
reconstruction of a signal. The EMD denoising method starts
by identifying which IMFs carry dominantly noise and which
IMFs contain primarily useful information. This is done by
comparing the actual energy density with the estimated energy
density (to form noise-only model [12]) of IMFs. The actual
energy density of IMFs is calculated as follows
1 N .
Ei= L h' (n), i=1,2,3,L (8)
Nn
l =

2) Interpolate between local maxima using cubic spline

Iine to form upper envelope emax (n) and local min
ima to form lower envelope emin (n)
3) Calculate the local mean based on formed upper and
lower envelopes, m ( n) = ( emax ( n) + emin (n))/ 2
4) Substract this mean from the original signal to extract
the detail d(n) = x ( n) - m (n) . If d( n) does not sat
isfy IMF conditions (stopping criteria), the procedure
1) to 4) are iterated with new input signal d(n)
5) If d(n) satisfies the criteria of an IMF, it is stored
as an IMF, hi (n) = d( n) where i refers to ith IMF.
Residue signal is obtained by substracting the IMF
from the original signal, r(n) = x ( n) - hi ( n)
6) Perform the same step from 1) with the new signal
r( n) until the final residue signal is constant or
monotonic function.
After the completion of EMD process, the original signal
can be written in terms of its IMF and residue signal as follows:
-
L 1
( )
x n = L hi (n) + rL (n) (7)
i l =
where L refers to decomposition level and i denotes IMF
order. Lower-order of IMFs contains fast oscillation modes
(high frequency) while higher-order of IMFs represent slow
with i corresponds to IMF order. The estimated energy density
(variance) of IMFs can be approximated using the formula [13]
below
V1 =
(
median(l hl - median( h1 )1)
2
(9)
)
0.6745
(10)
where (3 and p equal to 0.719 and 2.01, respectively [12].
The IMFs whose actual energy density exceed the value of
their estimated energy density defined by noise-only model
are categorized as information-dominated signal and should
be included in signal reconstruction step; otlIerwise those
IMFs will be excluded. For instance, as shown in Figure
3, only information-dominated IMFs (number 3,4,7,8,9,10)
will be processed for final reconstruction, which leads to a
term "partial reconstruction" of a signal.
Due to the fact that the noise embedded in IMFs is colored
(not Gaussian distributed), even the information-dominated
IMFs still may contain noise having different energy density.
To remove those colored noise, IMF-dependent threshold value
is required. Considering that IMFs have zero mean and in
any interval of zero crossing [ zj zj+1 l the absolute ampliLude
of ith IMF is very small, the thresholding scheme will be
based on the single extrema hi ( rj), where rj corresponds to
the extrema's time instance on this interval. The tresholding

-6
I \ - e - Real Energy
I

-8
,, I
\
\
\
----+-- Estimated Energy

'es

-9

-10

i
!!! -11
N

-12

-13

-14

-15

-16
1 10
IMF

Fig. 2. Signal decomposition using EMD Fig. 3. Semilog diagram of real vs estimated energy density of [MFs

437
2015 International Symposium on Intelligent Signal Processing and Communication Systems (ISPACS) November 9-12,2015

Input Signal Input Signal Input Signal

3ot=H:5t', =====,,::
: ===
:: ==1ft *
'= : ====J :.w. ,vlf--
: 1
t:"': _FF--3
== J!"====3 ", ==='Wo:
II--=J1
0.5
Noisy Signal
1.5
Noisy Signal
1 1.5 o 0.5
Noisy Signal
1 1.5

-'6b\ , 'v-
, 1
0--0.5=-- --- ---C' ---'.5
-
. 1 Wavelet Denoising w Wavelet Denoising w Wavelet Denoising
1
oH 1 30v.- -- 11.5 f-'
'0

"E -1
J
0 0.5 1.5 0.5 1 0 0.5 1 1.5
TV Denoising TV Denoising TV Denoising

jH ' 1 -1 -'
o 0.5
EMD Denoising
1 1.5 0'----
-- --0.-5
c: ----
EMD Denoising
----,.5 0 ---0.5=-- ---' ----'.5
EMD Denoising

-168 ,*:==:J
o 3f=:::"===I
0.5 1.5
-16''1=FE=
0 0.5
"
=If--
l 1.5 -16
oE
=
0.5

E
W3f---
1
=:J1--- 1.5
Time Time Time

Ca) Normal SI S2 with SNR 0 dB (b) S3 Gallop with SNR 5 dB (c) S4 Gallop with SNR LO dB

Fig. 4. Visual performance comparison of heart sound signal denoising methods

scheme which follows the hard thresholding is expressed as
follows
Ihi(rj)1 > Ti
Ihi(rj)1 :::; Ti
where hi([zj zj+lD represents the samples from time instant
zj to Zj+l of tth IMF. The threshold value used in this scheme
is expressed below
Ti = C ylV;2 InN, i = 1, 2, 3,
where C is 0.1 found by empirical simulations and V; is esti
mated energy density (variance) of ith IMF. This thresholding
scheme which is inspired and adapted from wavelet [14] will
set to zero all the samples from time instant [zj zj+ll if the
single extrema amplitude below the theshold value meaning
that there is no useful information (only noise) in the specified
time instant. Otherwise, all the samples will be retained.
The final signal reconstruction can be obtained by summing
up all the included IMFs (whose actual energy density ex
ceeding its estimated estimated energy as described previously)
using the following formula
q
y= L h(n)
i=p
where p and q indicates the lowest and highest index of
included IMF.
The qualitative performance evaluation of three denoising
methods were performed by visual inspection and comparison.
Figure 4 presents the input clean signal, noisy signal, and
(11) denoised (reconstructed) signal using wavelet, TV, and EMD
denoising methods. Only three simulation cases (different input
signal and SNR value) are shown. Based on Figure 4, it is
shown that EMD denosing method performs better among
others with the fact that its denoised signal is the most similar
(resembling) the original signal. If we look closely and zoom in
L (12) this figure, we will know that the amplitude of denoised signal
by TV method are slightly reduced. Although denoised signal
by wavelet method keeps the amplitude of its main components
almost the same as original one, the amplitude outside the main
components interval is changed.
The quantitative performance are evaluated based on three
metrics namely signal-to-noise ratio (SNR), root mean square
error (RMSE), and percent root mean square difference (PRD),
which are calculated as follows:
SNR = 10 log 10 2:=:=1 [y(n)]2 (14)
2:=:=1 [y(n) - y (n)J2
RMSE =
2:=:=1 [y(n) - y (n)J2 (15)
(13) N
PRD = (16)

III. RESULTS AND AN ALY SIS where y(n) denotes the clean original signal, y (n) refers to the
denoised (reconstructed) signal, and N represents the length
To evaluate the qualitative and quantitative performance
of the signal.
of these three denoising methods, we performed a number
of simulations using a simulated heart sound data obtained SNR is defined as the ratio of the power of a signal
from University of Michigan's Heart Sound & Murmur Library (useful information) and the power of noise (irrelevant signal).
[15]. In this simulations, we used three types of heart sound RMSE is used to measure the accuracy of denoising method
signals encoded in 44100 Hz sample rate and 16 bits/sample.
The detailed information including the environmental setting
TABLE II. HEART SOUND SIGNALS USED FOR SIMULATION
when the heart sounds were recorded and their corresponding
diagnosis results is shown in Table II. White Gaussian noise
Name Recording Setting Diagnosis
with SNR 0,5,10,15, and 20 were added to the clean input
signal y(n) to form noisy signal x ( n). The simulations were
Normal Sl S2 Apex, Supine, Bell Normal
S3 Gallop Apex, Left Ducubitus, Bell Both Normal and Cardiomyopathy
carried out using MATLAB which runs on dual-core CPU S4 Gallop Apex, Left Ducubitus, Bell Left Ventricular Hypertrophy
@2.2 GHz environment.

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2015 International Symposium on Intelligent Signal Processing and Communication Systems (ISPACS) November 9-12,2015

TABLE Ill. PERFORMANCE COMPARISON OF DENOISING METHODS

Heart Jnput SNR (dB) RMSE PRD (%)

Sound SNR (dB) WT TV EMD WT TV EMD WT TV EMD

0 9.825 7.9689 10.0415 0.038535 0.047716 0.037586 32.2665 39.9537 31.4716

13.6502 13.416J 14.4448 0.024808 0.025486 0.022639 20.7726 21.3399 J8.9566
Normal SJ S2 10 17.7381 15.6839 18.17 0.015495 0.019629 0.014744 12.9746 16.4364 12.3453
J5 21.502J 15.6268 2J.6JJ3 0.010046 0.OJ9759 0.0099206 8.4IJ9 J6.5446 8.3068
20 24.8797 16.1052 25.4756 0.0068095 0.0187 0.006358 5.7018 15.6581 5.3238

0 9.825 7.9689 10.0415 0.038535 0.047716 0.037586 32.2665 39.9537 31.4716

13.6502 13.416J 14.4448 0.024808 0.025486 0.022639 20.7726 21.3399 J8.9566
S3 Gallop 10 17.7381 15.6839 18.17 0.015495 0.019629 0.014744 12.9746 16.4364 12.3453
J5 21.502J 15.6268 2J.6JJ3 0.010046 0.OJ9759 0.0099206 8.4IJ9 J6.5446 8.3068
20 24.8797 16.1052 25.4756 0.0068095 0.0187 0.006358 5.7018 15.6581 5.3238

0 9.825 7.9689 10.0415 0.038535 0.047716 0.037586 32.2665 39.9537 31.4716

5 13.6502 13.416J 14.4448 0.024808 0.025486 0.022639 20.7726 21.3399 J8.9566
S4 Gallop 10 17.7381 15.6839 18.17 0.015495 0.019629 0.014744 12.9746 16.4364 12.3453
J5 21.502J 15.6268 2J.6JJ3 0.010046 0.OJ9759 0.0099206 8.4IJ9 J6.5446 8.3068
20 24.8797 16.1052 25.4756 0.0068095 0.0187 0.006358 5.7018 15.6581 5.3238

26 0.045 45
..
24 40

0.040
22 /" 35
"

.
0.035

.
20
to 0.030 30
_

Z
18

if) 16
/*.
../.-
..
0.025 25
0
'5
r:: 0.020
:.---- . -- . '"
"- 20
.

% 14
0
12 0.015 15 ...-- .-

10 /' 0.010 : 10
!
O.OOS
:

10 15 20 10 15 20 10 15 20
Input SNR Level (dB) Input SNR Level (dB) Input SNR Level (dB)

(a) Normal Sl S2 (b) S3 Gallop (e) S4 Gallop

Fig. 5. Perfomlance comparison of denoising methods over (a) Nomlal Sl S2 (b) S3 Gallop and (c) S4 Gallop heart sounds signal

in preserving the quality of information in the denoised signal
by calculating the sample standard deviation of the differences
between denoised signal and original signal. PRO is frequently
used as a method of quantifying the distortion or the difference
between the original and the reconstructed signal. The PRO
indicates reconstruction fidelity by point wise comparison with
the original data. A denoising method is said to perfom better
if at a particular input SNR, the value of output SNR is larger
while the value of RMSE and PRO are smaller.
Comparative simulation results of three denoising methods
(WT, TV, and EMO) on the basis of SNR, RMSE, and PRO
are shown in Table III. It is shown that for all three tapes
of heart sound with the addition of white Gaussian noise (0
dB, 5 dB, 10 dB, 15 dB, and 20 dB), EMO denoising method
consistently yields larger SNR value, and smaller RMSE and
PRO values. For example Normal S1 S2 heart sound signal,
EMO method shows SNR value 10.0415 dB, RMSE 0.037586
and PRO 31.4716 % where as WT (TV) method shows 9.825
(7.9689) SNR, 0.038535 (0.047716) RMSE, and 32.2665 %
(39.9537 %) PRO for 0 dB input SNR level. The performance
of EMO method for S3 gallop and S4 gallop over input SNR
level range (0 dB - 20 dB) is superior as well compared to
WT and TV methods.
Graphical visualization of comparative simulation results is
depicted in Figure 5. Figure 5a shows the comparative output
SNR value of three denoising methods for Normal SI S2 heart
sound signal with respect to different input SNR levels. It is
shown that EMO method (green line) is always above WT
(black line) and TV (red line) methods indicating that EMO
methods consistently produces largest output SNR value. The
comparative RMSE value vs input SNR level for S3 gallop
heart sound signal is shown in Figure 5b. It is shown that EMO
method (green line) is always below WT (black line) and TV
(red line) methods indicating that EMO methods consistently
produces smallest RMSE value. The comparative PRO value
over different input SNR levels for S4 gallop heart sound signal
is plotted in Figure 5c, which clearly shows EMO method's
superiority over WT and TV methods.
IV. CONCLUSION
Analysis and comparison of heart sound signal denoising
methods based on wavelet transform (WT), total variation
(TV), and empirical mode decomposition (EMO) is presented
in this paper. White Gaussian noises with input SNR level 0
dB, 5 dB, 10 dB, 15 dB, and 20 dB are artificially added
to clean original normal and abnormal heart sound signals
obtained from the University of Michigan Health System.
Based on extensive simulations, EMO based denoising method
consistently yields best performance in terms of three standard
metrics: signal-to-noise ratio (SNR), root mean square error
(RMSE), and percent root mean square difference (PRO).

439
2015 International Symposium on Intelligent Signal Processing and Communication Systems (ISPACS) November 9-12,2015

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