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Markovian Segmentation

of Brain Tumor MRI Images

Meryem Ameur

Laboratory of Information Processing and Decision Support


Faculty of Sciences and Technics
Sultan Moulay Slimane University
Beni Mellal city
Morocco

30 March 2017

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Outline

1 Introduction

2 Hidden Markov Chain With Independant Noise (HMC-IN)

3 Iterative Estimators

4 Experimental Results

5 Conclusion

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Introduction 1/3

Hidden Markov Model(HMM) is a stochastic process, it contains two


processes :
1 An observed process, noted Y.
2 A hidden process, noted X.
In Markovian segmentation we consider :
1 An observed process Y is an image to be segmented.
2 A hidden process X is an image result of segmentation .

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Example

Figure: Figure: Image


Observation Y Result X

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Introduction 2/3

To estimate the result image X = (Xn ) = {0 , ....., k } k K ,


where K is a number of membership class. It's initialized by the user. From
the observed image Y = (Yn ) R, n N , where N is a number of pixels
component the image. HMM(eld,chain,tree) used the Bayes theorem :
P(X ).P(Y |X )
P(X |Y ) = (1)
P(Y )

Where :
P(X |Y ) : is the probability of a posteriori law X knows Y .
P(X ) : is the probability of the a priori law .
P(Y |X ) : is the probability of the attached data law.
P(Y ) : is a constant of normalization P(Y ) = 1.

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Introduction 3/3

In this work, we propose a comparative study between EM algorithm and


ICE algorithm. We are used these estimators to estimate a parameters of
Hidden Markov Chain with Independant Noise model(HMC-IN) to
segment the brain tumor MRI images.

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Hidden Markov Chain With Independant Noise (HMC-IN)

It is a classical Markovian model, It's called Hidden Markov Chain with


Independent Noise (HMC-IN), because, it ignores the noise information
contained the image to be segmented Y .
Let the process Z = (X , Y ), where X = (Xn )Nn=1 and
Y = (Yn )N n=1 R.

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Hidden Markov Chain With Independant Noise (HMC-IN)

The process Z = (X , Y ) is a HMC-IN, if and only if :


1 The process X is a Markov Chain, it's homogeneous and stationary, its
law is as follows :
Y1
N
P(x) = P(X1 = x1 ). P(Xn+1 = xn+1 |Xn = xn ) (2)
n=1

2 The observations Y are conditionally independant of X .


3 Each observation yn , n N depends only on its hidden class xn .
P(Yn = yn |X ) = P(Yn = yn |Xn = xn ) (3)

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The laws of HMC-IN

The HMC-IN has two laws of probability :


1 The law of Markov chain X .
2 The law of attached data Y |X (observations).

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The parameters of HMC-IN

1 Markov chain parameter's x :


I The initial law PI (i) = p(x1 = i) i .
I The transition matrix A(i, j) = p(xn+1 = j|xn = i) i, j .
2 Attached data parameter's y |x (Gaussian law ) :
I The mean i i for each class k .
I The variance i2 i for each class k .
I The density f of the distribution Y condionally to X using :

1 (yn i )2
f =p exp[ ] (4)
2(i2 ) (i2 )

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Estimation phases

1 The initialization parameters phase.


2 The iterative estimation parameters phase.
3 The nal decision phase.

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Initialization phase

Conguration initial of X 0 by :
I K-means.
I FCM....
Initialization parameters of the X process x0 .
I PI (i)0 .
I A(i, j)0 .
Initialization parameters of the data attached law y0|x .
I (i)0 .
I ((i)2 )0 .

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Iterative Estimation phase

Estimation the parameters of HMC-IN = (x , y |x ) for a Q number of


iterations q Q .
1 EM : Expectation Maximization.
2 SEM :Stochastic Expectation Maximization.
3 ICE : Iterative Conditional Estimation.
These algorithms are based on Baum Welch algorithm to calculate
parameters.

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Baum Welch algorithm

Baum Welch algorithm proceeds as :


Calculated Forward probabilities n (i) = p(y1 , ....., yn , xn ).

Forward Algorithm
1 Initialization : (n = 1)

PI (i)fi (y1 )
1 (i) = P i (5)
j PI (i)fj (y1 )

2 Induction : (n > 1)
P
fi (yn+1 ) j n (j)A(i, j)
n (i) = P P i (6)
k fk (yn+1 ) j n (j)A(i, j)

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Baum Welch Algorithm

Calculated Backward probabilities n (i) = p(yn+1 , ....., yN |xn ).


Backward Algorithm
1 Initialization : (n = N)
N (i) = 1i, j (7)

2 Induction : (n < N)
P
j A(i, j)fj (yn+1 )n+1 (j)
n (i) = P P i, j (8)
k fk (yn+1 ) j n (j)A(i, j)

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Baum Welch Algorithm

Calculated a Marginal a posteriori probabilities n (i) = p(xn = i|yn ).


Marginal a posteriori Law n (i)
n (i) = n (i)n (i)i, j (9)
Calculated Joint a posteriori probabilities
n (i, j) = p(xn = i, xn+1 = j|yn ).

Joint a posteriori Law n (i, j)


n (i)A(i, j)fj (yn+1 )n+1 (j)
n (i, j) = P P i, j (10)
k fk (yn+1 ) l n (l)A(l, k)

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A.EM Algorithm

EM Algorithm
For a number of iteration q Q :
Step(E ) :
I Calculate n (i), n (i), n (i, j) and n (i), using Baum Welch.
Step(M ) :
[q]
I Estimate parameters of the Markov chain x using the deterministic
strategy.

PI (i)[q] = 1 (i)i (11)


PN
1 n (i, j)
[q]
A(i, j) = Pn= N
i, j (12)
n=1 n (i)

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EM Algorithm

Estimate parameters of law attached data y[q]|x for each class i also by
the deterministic strategy.
PN
1 yn n (i)
[q]
i = Pn=
N
i (13)
n=1 n (i)
PN [q] 2
2 [q] n=1 (yn i ) n (i)
(i ) = PN i (14)
n=1 n (i)

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B.ICE Algorithm

ICE Algorithm
For each iteration q Q :
Calculate n (i), n (i), n (i, j) and n (i), using Baum Welch.
Simulate a sample of X q for one random simulation using the
parameters of the iteration q

Estimate the parameters of Markov chain x[q] using deterministic


strategy.
PI (i)[q] = 1 (i)i (15)

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ICE Algorithm

PN
1 n (i, j)
A(i, j) [q]
= Pn=
N
i, j (16)
n=1 n (i)

Estimate data attached parameters y[q]|x for each class i using


stochastic strategy :
yn 1[xn = i]
PN
1
[q]
i = Pn= i (17)
n=1 1[xn
N
= i]

n=1 (yn i ) 1[xn


PN [q] 2
2 [q] = i]
(i ) = i (18)
n=1 1[xn = i]
PN

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Complexity of ICE and EM (Comparaison)

Task ICE EM
Calculate O(K 2 N) O(K 2 N)
Calculate O(K 2 N) O(K 2 N)
Calculate O(K 2 N) O(K 2 N)
Calculate O(KN) O(KN)
Calculate PI O(K ) O(K )
Calculate A O(K 2 N) O(K 2 N)
Calculate O(KN) O(KN)
Calculate 2 O(KN) O(KN)
Simulate X O(KN) not executable
Table: Complexity of EM and ICE algorithms

From this table, we notice that the complexity of ICE is superior than the
complexity of EM. Because, ICE simulates the hidden process X one time
in each iteration q Q . This task makes ICE more complex than EM.
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Final Decision phase

Final Bayesian estimator consists to estimate X the nal conguration of


result image X .
MPM : Maximum Posteriori Mode.
MPM Estimator
The solution in image segmentation by Hidden Markov Chain according
MPM is : maximize the marginal a posteriori probability n (i) :
xnmpm = argmaxi (n (i)n (i)) = argmaxi ((n (i))) (19)
The complexity of this estimator is O(KN).

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Experiments
We use K-means algorithm to initialize the conguration of X0 where
K = 3.
Concerning the initial law PI 0 we have :
PI0 =
0.33

0.33
0.33
Concerning the matrix of transition A0 (i, j), we have :
A0 =
0.5 0.25 0.25

0.25 0.5 0.25
0.25 0.25 0.5
The mean 0 and the variance ( 2 )0 from the conguration of X0 .
We have a number of iterations Q = 30.
We have used this type of initialization parameters in all experiments
presented in this work.
We have used the thresholding technic to extract the interset region.
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Experiment 1

Figure: Experiment 1

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Experiment 2

Figure: Experiment 2

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Experiment 3

Figure: Experiment 3

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Results 1/2 :PSNR index SSIM index and error rate
We have compared these estimators in term of the PSNR index, the SSIM
index, the error rate and the convergence.
Experiments PSNR ICE SSIM ICE PSNR EM SSIM EM
Experiment 1 24,0672 0.5710 24,0672 0.5697
Experiment 2 18.4713 0.4773 18.4713 0.4784
Experiment 3 21,8050 0.5157 21,8058 0.5150
Table: PSNR index and SSIM index

Experiments Error rate ICE Error rate EM


Experiment 1 8,1357 8,1357
Experiment 2 9.6075 9.6075
Experiment 3 10,0450 10,0450
Table: error rate

In term of the quality of segmentation the dierence is not important.


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Results 2/2 : Convergence

Experiments ICE EM
Experiment 1 5 iterations 7 iterations
Experiment 2 6 iterations 8 iterations
Experiment 3 7 iterations 8 iterations
Table: The convergence of ICE and EM algorithms

In term of the convergence ICE converge faster than EM.

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Conclusion

A Comparative study between two iterative estimators such as :


I EM.
I ICE.

To estimate a parameters of HMC-IN model.


Under the nal Bayesian criteria.
I MPM.
In Segmentation of.
I Brain tumor MRI images.
To extract brain tumor position
I Thresholding technic.

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Conclusion

Under ve criteria of comparaison.


1 The complexity.
2 The PSNR index.
3 The SSIM index.
4 The error rate.
5 The convergence.

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Conclusion

From the results we notice that :


1 In term of the Complexity ICE is more complex than EM.
2 In term of the quality of segmentation the dierence is not important.
3 In term of the convergence ICE converge faster than EM.

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Perspectives

Perspectives
Using these estimator algorithms to :
1 Segment color textured images using a pairewise Markov chain model.
2 Segment the MRI images using the triplet Markov chain, considering
that X is non stationary.

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