(IJCSIS) International Journal of Computer Science and Information Security,Vol. 9, No.6, 2011
Improving the Performance of Translation WaveletTransform using BMICA
Janett Walters-Williams
School of Computing & Information TechnologyUniversity of Technology, JamaicaKingston 6, Jamaica W.I. jwalters@utech.edu.jm
Yan Li
Department of Mathematics & Computing,Centre for Systems Biology, University of SouthernQueensland, Toowoomba, Australialiyan@usq.edu.au
Abstract
—Research has shown Wavelet Transform to be one of the best methods for denoising biosignals. Translation-Invariantform of this method has been found to be the best performance.In this paper however we utilize this method and merger with ournewly created Independent Component Analysis method –BMICA. Different EEG signals are used to verify the methodwithin the MATLAB environment. Results are then comparedwith those of the actual Translation-Invariant algorithm andevaluated using the performance measures Mean Square Error(MSE), Peak Signal to Noise Ratio (PSNR), Signal to DistortionRatio (SDR), and Signal to Interference Ratio (SIR).Experiments revealed that the BMICA Translation-InvariantWavelet Transform out performed in all four measures. Thisindicates that it performed superior to the basic Translation-Invariant Wavelet Transform algorithm producing cleaner EEGsignals which can influence diagnosis as well as clinical studies of the brain.
Keywords-B-Spline; Independent Component Analysis; Mutual Information; Translation-Invariant Wavelet Transform
I.
I
NTRODUCTION
The nervous system sends commands and communicates bytrains of electric impulses. When the neurons of the humanbrain process information they do so by changing the flow of electrical current across their membranes. These changingcurrents (potentials) generate electric fields that can berecorded from the scalp. Studies are interested in theseelectrical potentials but they can only be received by directmeasurement. This requires a patient to under-go surgery forelectrodes to be placed inside the head. This is not acceptablebecause of the risk to the patient [25]. Researchers thereforecollect recordings from the scalp receiving the globaldescriptions of the brain activity. Because the same potential isrecorded from more than one electrode, signals from theelectrodes are supposed to be highly correlated. Figure 1shows how the potentials are collected from the scalp. Theseare collected by the use of an electroencephalograph andcalled electroencephalogram (EEG) signals.
Figure 1: Collecting EEG signals
EEG is widely used by physicians and scientists tostudybrainfunction and to diagnose neurological disorders.Any misinterpretations can lead to misdiagnosis.These signalsmust therefore present a true and clear picture about brainactivities as seen in Figure 2. EEG signals are however highlyattenuated and mixed with non-cerebral impulses called
artifacts
or
noise [
15
].
The presence of these noisesintroduces spikes which can be confused with neurologicalrhythms. They also mimic EEG signals, overlaying thesesignals resulting in signal distortion (Figure3). Correctanalysis is therefore impossible; a true diagnosis can only beseen when all these noises are eliminated or attenuated. EEGrecordings are really therefore a combination of noise and thepure EEG signal defined mathematically below (using
S
as thepure EEG signal,
N
the noise and
E
representing the recordedsignal):
( ) ( ) ( )
E t S t N t
= +
(1)
48http://sites.google.com/site/ijcsis/ISSN 1947-5500
(IJCSIS) International Journal of Computer Science and Information Security,Vol. 9, No.6, 2011
Figure 2: Clean pure EEG SignalFigure 3: EEG Signal corrupted with EKG and line signals
Numerous methods have been proposed by researchers toremove artifacts in EEG and are reviewed in [6, 13, 20, 22,24]. The goal of these methods is to decompose the EEGsignals into spatial and temporal distinguishable components.After identification of components constituting noise, the EEGis reconstructed without them. Methods include PrincipalComponents Analysis (PCA), the use of a dipole model andmore recently Independent Component Analysis (ICA) andWavelet Transform (WT). Which method is considered thebest is not the topic of this research. Here we focus onimproving WT using a new ICA method called – B-SplineMutual Information Independent Component Analysis(BMICA).The paper is organized as follows: after this introduction of EEG signals and the need to denoise Section 2 presents thedenoising methods utilized in the paper. We then review thereasons for merger in Section 3 and describe the experimentsconducted in Section 4. In Section 5 we present the results,comparison of these results and a summary. Finally in Section6 we present the conclusion.II.
L
ITEATURE
R
EVIEWE
A.
Wavelet Transform
Wavelet Transform (WT) is a form of time-frequency analysisbeen used successfully in denoising biomedical signals bydecomposing signals in the time-scale space instead of time-frequency space. It is so because it uses a method calledwavelet shrinkage proposed by Donoho and Johnstone [7].Each decomposed signal is called a wavelet. Figure 4 showsthe difference between a wave/signal and a wavelet.There are two basic types of WT. One type is designed to beeasily reversible (invertible); that means the original signal canbe easily recovered after it has been transformed. This kind of WT is used for image compression and cleaning (noise andblur reduction). Typically, the WT of the image is firstcomputed, the wavelet representation is then modifiedappropriately, and then the WT is reversed (inverted) to obtaina new image.
Figure 4. Demonstration of (a) a signal and (b) a wavelet
The second type is designed for signal analysis for study of EEG or other biomedical signals. In these cases, a modifiedform of the original signal is not needed and the WT need notbe inverted (it can be done in principle, but requires a lot of computation time in comparison with the first type of WT).WT decomposes a signal into a set of coefficients called thediscrete wavelet transform (DWT) according to:
, ,
( ) ( )
j k j k t Z
C E t g t
∈
=
∑
(2)where
C
j,k
is the wavelet coefficient and
g
j,k
is the scalingfunction defined in [23] as:
2
2 (2 )
j j
g t k
−−
−
(3)The wavelet and scaling functions depend on the chosenwavelet family, such as Haar, Daubechies and Coiflet.Compressed versions of the wavelet function match the high-frequency components, while stretched versions match thelow-frequency components. By correlating the original signalwith wavelet functions of different sizes, the details of thesignal can be obtained at several scales or moments. Thesecorrelations with the different wavelet functions can bearranged in a hierarchical scheme called multi-resolutiondecomposition. The multi-resolution decomposition algorithmseparates the signal into “details” at different moments andwavelet coefficients [19-20]. As the moments increase theamplitude of the discrete details become smaller, however thecoefficients of the useful signals increase [27-28].Considering Eq. (1) the wavelet transform of
E(t)
produceswavelet coefficients of the noiseless signal
S(t)
and thecoefficients of the noise
N(t).
Researchers found that waveletdenoising is performed by taking the wavelet transform of thenoise-corrupted
E(t)
and passing the detail coefficients, of thewavelet transform, through a threshold filter where the details,if small enough, might be omitted without substantiallyaffecting the main signals. There are two main threshold filters– soft and hard. Research as shown that soft-thresholding hasbetter mathematical characteristics [27-29] and providessmoother results [10]. Once discarded these coefficients arereplaced with zeroes during reconstruction using an inverse
49http://sites.google.com/site/ijcsis/ISSN 1947-5500
(IJCSIS) International Journal of Computer Science and Information Security,Vol. 9, No.6, 2011
wavelet transform to yield an estimate for the true signal,defined as:
( ) ( )
( )
( )
^1
( ) ( )] ( )
th
S t D E t W W E t
−
= = Λ
(4)where
th
Λ
is the diagonal thresholding operator that zeroesout wavelet coefficients less than the threshold,
th.
It has beenshown that this algorithm offers the advantages of smoothnessand adaptation. It has been shown that this algorithm offers theadvantages of smoothness and adaptation however it may alsoresult in a blur of the signal energy over several transformdetails of smaller amplitude which may be masked in thenoise. This results in the detail been subsequently truncatedwhen it falls below the threshold. These truncations can resultin overshooting and undershooting around discontinuitiessimilar to the Gibbs phenomena in the reconstructed denoisedsignal. Coifman and Donoho [4] proposed a solution bydesigning a cycle spinning denoising algorithm which(i)
shifts the signal by collection of shifts, within range of cycle spinning(ii)
denoise each shifted signal using a threshold (hard orsoft)(iii)
inverse-shift the denoised signal to get a signal in thesame phase as the noisy signal(iv)
Averaging the estimates.The Gibbs artifacts of different shifts partially cancel eachother, and the final estimate exhibits significantly weakerartifacts [4]. This method is called a translation-invariant (TI)denoising scheme. Experimental results in [1] confirm thatsingle TI wavelet denoising performs better than thetraditional single wavelet denoising. Research has also shownthat TI produces smaller approximation error whenapproximating a smooth function as well as mitigating Gibbsartifacts when approximating a discontinuous function.
B.
Independent Component Analysis Independent Component Analysis (
ICA) is an approach for thesolution of the BSS problem [5]. It can be representedmathematically according to Hyvarinen, Karhunen & Oja [12]as:
X As n
= +
(5)where
X
is the observed signal,
n
is the noise,
A
is the mixingmatrix and
s
the independent components (ICs) or sources. (Itcan be seen that mathematically it is similar to Eq. 1). Theproblem is to determine
A
and recover
s
knowing only themeasured signal
X
(equivalent to
E(t)
in Eq. (1)). This leads tofinding the linear transformation
W
of
X,
i.e
.
the inverse of themixing matrix
A
, to determine the independent outputs as:
u WX WAs
= =
(6)where
u
is the estimated ICs. For this solution to work theassumption is made that the components are statisticallyindependent, while the mixture is not. This is plausible sincebiological areas are spatially distinct and generate a specificactivation; they however correlate in their flow of information[11].ICA algorithms are suitable for denoising EEG signalsbecause(i)
the signals recorded are the combination of temporalICs arising from spatially fixed sources(ii)
the signals tend to be transient (localized in time),restricted to certain ranges of temporal and spatialfrequencies (localized in scale) and prominent overcertain scalp regions (localized in space) [20].
B-Spline Mutual Information Independent Component Analysis (BMICA)
There have been many Mutual Information (MI) estimatorsin ICA literature which are very powerful yet difficult toestimate resulting in unreliable, noisy and even biasestimation. Most algorithms have their estimators based oncumulant expansions because of ease of use
[
16]. B-Splineestimators according to our previous research [26] however,have been shown to be one of the best nonparametricapproaches, second to only wavelet density estimators. Innumerical estimation of MI from continuous microarray data,a generalized indicator function based on B-Spline has beenproposed to get more accurate estimation of probabilities;hence we have designed a B-Spline defined MI contrastfunction. Our MI function is expressed in terms of entropy as:
( )
( , ) ( ) ( , )
I X Y H X H Y H X Y
= + −
(7)
where
,
( ) ( )log ( )( , ) ( , )log ( , )
i iii j i ji j
H X p x p x H X Y p x y p x y
= −= −
∑∑
(8)Eq. (6) contains the term
−
H
(
X, Y
), which means thatmaximizing MI is related to minimizing joint entropy. MI isbetter than joint entropy however because it includes themarginal entropies
H
(X) and
H(Y)
[13]. Entropy in our designis based on probability distribution functions (pdfs) and ourdesign defines a pdf using a B-Spline calculation resulting in
~,1
1( ) ( )
N i k i uu
p x B x N
=
=
∑
(9)where
11
( ) ( )
nk i i k i
B x DB x
+−=
=
∑
(10)
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Improving the Performance of Translation Wavelet Transform using BMICA
Research has shown Wavelet Transform to be one of the best methods for denoising biosignals. Translation-Invariant form of this method has been found to be the best performance. In this paper however we utilize this method…
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