2018 4th International Conference on Computer and Information Sciences (ICCOINS)
Optimization of Schizophrenia Diagnosis
Prediction using Machine Learning Techniques
Anant V Nimkar1 and Divesh R Kubal2
1,2 Department of Computer Engineering, Sardar Patel Institute of Technology,
Mumbai, India 400 058.
1anant nimkar@spit.ac.in, 2diveshkubal@spit.ac.in
Abstract— The objective of this paper is to automatically
diagnose the mental state disorder named schizophrenia by using
multimodal features which are extracted from Magnetic Reso-
nance Imaging (MRI) brain scans. The aim is to achieve highest
possible classification (binary) accuracy to achieve best possible
prediction of the schizophrenia diagnosis. The importance of
feature selection in combination with fine-tuning the parameters
of Machine Learning classifiers to solve this problem is explained.
Various supervised Machine Learning classifiers were employed
and compared with themselves and then with existing systems.
The proposed solution achieved AUC score of 0.9473 and an
accuracy of 0.9412 as opposed to till date best existing system’s
AUC score of 0.928.
Index Terms—MRI Scan, Support Vector Machine (SVM),
Boruta Feature Selection, Machine Learning Classifier,
Schizophrenia, Functional Network Connectivity (FNC), Source
Based Morphometry (SBM).
I. I NTRODUCTION
Schizophrenia is a chronic and severe mental state disorder
affecting thinking, feeling and also the behavior of a per-
son [1]. About 1% of the total population in the world suffers
from schizophrenia. The patients suffering from schizophrenia
may feel that they have completely lost touch with reality.
Schizophrenia is a rare mental disorder but if a patient is
diagnosed with such a disease, then the symptoms can be
very disabling. Mostly, the symptoms start at the age of
16 to 30. These symptoms fall in three categories namely
positive (hallucinations, delusions, thought disorder), negative
(no or reduced facial expressions, negligible pleasure feeling,
reduced speaking) and cognitive (problems in focusing and
memorizing) [2]. The causes of this mental disorder are
unknown, hence it is very difficult to treat schizophrenia.
Also, the mental disorders symptoms and the lack of standard
biologically-based clinical tests furthers increases the difficulty
to treat schizophrenia.
This article aims to propose a novel approach to accurately
classify between the patients having schizophrenia disease and
healthy persons. To make prediction accurate, both structural
connectivity as well as functional connectivity has to be con-
sidered as both these measures when combined provides much
more comprehensive description [1]. Structural connectivity
refers to how the neurons are physically connected with respect
to synaptic strength while functional connectivity is more of
a statistical concept as it captures deviations from statistical
978-1-5386-4744-8/18/$31.00 ©2018 IEEE ~ 1 ~
independence between distributed and neuronal units which
are often spatially remote, in various brain regions. It is
observed that in schizophrenia patients, the brain connectivity
is lower and also is different as compared to a healthy
brain connectivity. White matter is associated with structural
connectivity whereas grey matter is associated with functional
connectivity. In a typical schizophrenia patient, there is fewer
amounts of white matter and many complex alterations in
functional connectivity related to the grey matter. In the past
two decades, there have been considerable advancements in
neuroimaging techniques to study structural and functional
brain connectivity. This helped to get in-depth information
about various mental disorders like schizophrenia. There is
a vast amount of work done to solve this kind of problem.
The most popular approaches [3]–[5] with highest accuracy
till-date used Gaussian Process classifier, feature trimming
with random forest and training with Support Vector Machine
(Gaussian Kernel), and Distance Weighted Discrimination
methods respectively.
The highlight of this study is to tackle the high dimen-
sional data by using suitable feature selection technique. A
comparative analysis is also performed between the results
obtained without feature selection and with feature selection.
The paper kick starts with section II in which the survey
is conducted on the existing approaches and methods which
achieved considerable accuracy. Section III describes the pro-
posed methodology aimed to get a better performance in terms
of accuracy as compared with existing approaches. Finally,
the results obtained in this study are compared with existing
techniques in the section IV.
II. L ITERATURE S URVEY
There are various existing systems [6]–[9] that aimed to
solve the problem. A literature survey is conducted for the top
three approaches in order with respect to their performance.
The best performing model [3] to solve this problem used
Gaussian process (GP) classifier. This GP was implemented
along with prior distribution and scaled by probit transforma-
tion is given by the following equation,
 yi f (xi )
p(yi = 1|xi ) = Φ(yi f (xi )) = N (z|0, 1)dz (1)
−∞
 2018 4th International Conference on Computer and Information Sciences (ICCOINS)
Φ(.) is called as the Gaussian CDF (Cumulative Distribu-
tion Function). The observations are assumed to be drawn
from Bernoulli distribution with the probability of success as
p(yi = 1|xi ). The aim is to consider both the linear structure
as well as the linearities (short-scale) in latent space. Hence,
the covariance function is set such that it represents a linear
combination of three separate coveriance functions given by
the following equation,
   v=5/2
k(x, x ) = kconst. (x, x ) + klinear (x, x ) + kM atérn (x, x )
(2)
where, the individual covaiance functions are given as,

kconst. (x, x ) = α1
 
klinear (x, x ) = α2 xT x
√ (iv) Classification Model Training.
v=5/2  5r 5r
kM atérn (x, x ) = α3 (1 + + 2)
α4 3α4
 
 
where r stands for x − x . The covariance function is
represented as the linear combination of those three separate
covariance functions. α = α1 , α2 , α3 , α4 are the hyperpa-
rameters. To train the model, Laplace approximation scheme
was used until convergence. For latent sampling and for
hyperparameters, Elliptical Slice Sampling and Surrogate Slice
Sampler was used respectively. This approach achieved an
AUC score of 0.928 which is till-date best performing model.
The approach [4] based on feature-trimming proposed by A.
V. Lebedev consisted of two stages. The first stage comprised
of feature selection where the training data is appended by
both the noisy feature set and normally distributed values. This
merged feature set is then passed as an input to random forest
algorithm. The important features or the most discriminating
features were selected by choosing only those features which
scored the relevance above the noisy one based on Gini
coefficient. The features which were extracted from the feature
selection step were inputted to an SVM classifier based on
the Gaussian kernel. The entire process can be summarized as
follows:
(i) A random vector is introduced in the feature list.
(i) Then, the feature importance score for each feature is
calculated which is based on the mean decrease of
‘Gini index’ (outputted by Random Forest classifier
algorithm).
(iii) The attributes scoring higher importance score than
dummy variables are selected.
(iv) The final dataset obtained as an output of step (iii) is
then used to train the Support Vector Machine with the
Gaussian kernel.
This approach scored an AUC score of 0.923 which is second
best performing model.
The third approach [5] was based on a method from the
HDLSS (High-Dimensional Low Sample Size) class. HDLSS
class methods were optimized to deal with less amount of data
samples but having high dimensionality which is useful in this
problem statement as the data is of high dimensional. Distance
Weighted Discrimination (DWD) was adopted which is quite
similar to SVM. DWD has two important features namely,
• Explicitly accounting for distance between each sample
and the margin.
• Penalizing the samples which are clustered very close to
the solution margin. This assigned penalty prevents the
model from overfitting.

The trained model achieved an AUC score of 0.91282.
III. S CHIZOPHRENIA D IAGNOSIS P REDICTION
The proposed methodology for schizophrenia diagnosis
prediction consists of the following steps:
(i) Data Acquisition/Data Collection.
(ii) Data Pre-processing.
(iii) Feature Selection.
(v) Results Evaluation.
Each step plays an important role contributing towards the
final performance in terms of prediction accuracy.
A. Data Acquisition
Data collection or Data Acquisition can be considered as an
important step in neuroscience as a slight error in collecting
may cause inaccuracy in prediction after the predictive model
is built. The data collection procedure [10] was carried at
Mind Research Network which was funded by a Center
of Biomedical Research Excellence grant. The dataset that
is used in this study consists of two types of information
namely, Functional Network Connectivity (FNC, [11]) and
Source based Morphometry (SBM, [12]). The FNC data is
collected by Functional Magnetic Resonance Imaging (fMRI)
scans which can be considered as functional modality attribute
representing connecting patterns or synchronization between
a particular subject’s different cortical regions. On the other
hand, SBM data is collected with the help of structural MRI
scans representing the grey matter concentration in different
cortical regions of the subject’s brain.
The data consists of total 86 rows where each row represent-
ing a data extracted from a particular subject. The FNC data
is of 378 dimensional and SBM data is of 32 dimensional. So,
this study is dealing with pretty high dimensional data. For,
the prediction to be accurate, both the types of data have to be
considered. Hence, the final data is of 410-dimensional. The
n
data can be represented as, D = {(xi , yi )}i = 1 where, xi is
the total number of samples or instances and each instance is
of R410 dimensional. yi  {0, 1} is the target attribute. The data
is randomly split in 60% training data and remaining 40% test
data using stratified sampling.
B. Data Pre-processing
The data from both the sources (FNC and SBM) is com-
bined which resulted in the final data to be of 410 dimensional.
Due to the large variance and presence of outliers in the values
of many features of the combined dataset of FNC and SBM,
there is a need to normalize the data. Hence, the first step
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 2018 4th International Conference on Computer and Information Sciences (ICCOINS)
Fig. 1. Flowchart: Schizophrenia Diagnosis Prediction
before proceeding to build the final model, normalization is
performed. The normalization step will convert the data values
in the range between 0 and 1 thereby tackling the problem of
outliers and large variance. The final normalized combined
data (FNC and SBM) is then passed to feature selection step.
C. Feature Selection
Feature selection [13] is considered as one of the most
important steps to solve this problem. After implementing this
step, it is confirmed that the final model performed much
better. The objective is to minimize the total number of
predictors or to remove redundant predictors without losing
the information required to predict so that the model can train
fast, give more accuracy.
In this application, Boruta algorithm [14] is used, which
is an ensemble approach based on decision trees for feature
selection. The Boruta algorithm can be considered as a random
forest algorithm wrapper. An important characteristic is that
there is no need of fine-tuning the parameters and the algo-
rithm presents us with numerical estimates of features that
depicts their importance. The algorithm can be summarized
with the help of following steps:
(i) The number of features are extended by adding copies
of all the variables.
(ii) These added attributes are shuffled so that the correla-
tions among them can be removed.
(iii) A Random Forest algorithm is run on this so-called
extended system resulting in Z scores computation.
(iv) The maximum Z score among the shadow attributes
(MZSA) is found and then a hit is assigned to each
attribute which scored better than MZSA. MZSA plays
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an important role as it performs a two-sided equality test
for each attribute whose importance is undetermined.
(vi) The attributes scoring less MZSA score are considered
as ‘unimportant’ and are permanently removed from the
feature list.
(vii) Those attributes scoring slightly higher than MZSA are
considered as ‘important’ and are retained in feature list.
(viii) Finally all the shadow attributes are removed.
(ix) Repeat all the steps from (i) to (viii) until all the
variables get an importance score or the algorithm has
reached the specified threshold of random forest runs.
Boruta algorithm uses Z-score as the importance measure.
The computational runtime complexity in average and worst
case is O(NP) where N is the number of objects and P is
the number of attributes(in our case, P is 410) given as input
to Boruta algorithm. Hence, the algorithm took time in order
to converge to a result (depending upon the processing speed
and memory of machine/system). But it is worth waiting as the
results we get is of statistically significant selection of relevant
features. FSelector [15] and PCA(Principal Component Anal-
ysis) [16] feature selection methods were also used but that
proved to be ineffective for this dataset and Boruta emerged
victorious.
D. Classification Model Training
The features which were selected after performing feature
selection are used for building supervised Machine Learning
model. Various algorithms with different kernels were imple-
mented such as Support Vector Machine (SVM), Gaussian
Classifier, C5.0 Decision Tree, Logistic Regression, Naı̈ve
Bayes, Random Forest, Linear Discriminant Analysis (LDA).
1) Support Vector Machine: SVM can be simply thought
of as a surface that defines the boundary between various
data points plotted. The goal of SVM [17] is to construct
a maximum separating hyperplane which results in fairly
homogenous partitions of data on either side. The entire task
can be represented as a set of constraints of,
1
min →
− 2
2w
subject to,
yi ( →
−
w→−
xi − b) ≥ 1, ∀→
−
xi (3)
In this paper, linear, radial basis, polynomial and sigmoid
kernels are used. The AUC score obtained by radial basis,
polynomial, linear and sigmoid kernels are 0.9412, 0.8824,
0.8824 and 0.7059 respectively. Radial Basis kernel performed
well with accuracy of 94.73% while sigmoid SVM kernel
performed poorly with accuracy of 71.578%
2) C5.0 Decision Tree: C5.0 [18] is a very popular imple-
mentation of Decision Tree algorithm, which is an improve-
ment over C4.5. This algorithm is easy to deploy and easy to
interpret. C5.0 can be used on small as well as large datasets.
Only important attributes which are selected automatically are
used. Purity is measured with entropy. A sample is completely
homogeneous if the entropy value is 0. If the entropy value is
 2018 4th International Conference on Computer and Information Sciences (ICCOINS)
1, then it represents the maximum amount of disorder in the
sample. Entropy is given by the following equation,
c
Entropy(S) = pi log2 (pi ) (4)
i=1
Next, the algorithm has to decide which feature to split. The
algorithm then finds out the information gain, which is the
resulting homogeneity obtained when a feature is split which
is given by the following equation,
Inf oGain(F ) = Entropy(S1 ) − Entropy(S2 ) (5)
After the initial split, there are many partitions of data are
created, hence we need to find entropy across all the partitions,
which is given as,
n
Entropy(S) = wi Entropy(Pi ) (6)
i=1
C5.0 achieved its highest accuracy of 91.18% and AUC
score of 0.91 when adaboost is applied and ntrial (number of
trials) parameter is set to 90.
3) Random Forest: Random forests [19] are an ensemble
based machine learning algorithms. It is a combination of two
concepts, bagging, and random feature selection. The model
uses a vote to combine prediction of the tree after it creates
an ensemble. Random forests require only a small portion
out of full feature dataset which allows random forests to
perform nicely against huge datasets. Continuous as well as
discrete target values can be predicted by random forests. The
algorithm of the Random forest is as follows:
1) For b = 1, ..., B
a) A sampling with replacement is performed for all
n training samples called Xb , Yb
b) A regression tree or a decision tree is trained on
fb on Xb , Yb
2) After training the classifier model, predictions for un-

known examples x can be done as follows,
B between performance measures of the algorithms implemented
1 ˆ 
fˆ = f (x )
B
b=1
Two important parameters have been considered while im-
plementing random forests, the number of the tree (ntree) and
the number of features the algorithm selects during each itera-
tion. Random Forests perform better when the ntree parameter
is increased up to a certain limit. The Random Forest achieved
considerable accuracy and AUC score of 0.91.18% and 0.921
respectively.
4) K-Nearest Neighbour (K-NN): Modeling complex re-
lationships between predictors and target is made easy with
KNN. No assumptions are made about underlying data dis-
tribution in KNN. KNN used a simple Euclidean distance
formula. Finding the value of k (number of clusters) is the
main challenge. We can reduce the impact of variance by
reducing the value of k but this increases the bias considerably.
Hence we have to take a suitable value for k between two
extremes. K-NN achieved an accuracy of 79.41% and an AUC
score of 0.81578.
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5) Linear Discriminant Analysis: LDA [20] is primarily
used as a dimensional reduction technique and it shares some
similar properties with PCA (Principal Component Analysis).
The major difference between PCA and LDA is that LDA
models the difference between the classes of the data whereas
PCA does not. LDA performed quite poor on this application
by scoring an accuracy of 79.41% and AUC score of 0.7947.
6) Gaussian Process Classifier: Gaussian Processes
(GPs) [21] aims to extend multivariate Gaussian distributions
to infinite dimensionality. In formal terms, a GP tend to
generate the data which is located over the entire same domain
in such a way that a multivariate. It is a non-parametric
approach where it finds a distribution over the possible
functions f (x) that are consistent with the observed data. GP
classifier was the best classifier in the existing system. In this
paper, five kernels of GP classifier is implemented namely,
laplacedot, vanilladot, polydot, rbfdot which achieved AUC
of 0.924, 0.8807018, 0.8807, 0.8421 respectively. Laplacedot
kernel performed well with an accuracy of 92% while rbfdot
kernel performed comparatively poor with an accuracy of
82.35%.
7) Naı̈ve Bayes: Naı̈ve Bayes [22] performs well against
categorical target attributes. It makes the assumption that all
predictors are independent and equally important, which is
not applicable in most real-world scenarios. The algorithm
performs well when these assumptions are violated and holds
true even in extreme circumstances where strong dependencies
are found among features. Naı̈ve Bayes achieved an accuracy
and AUC score of 85.29% and 0.8543 respectively.
IV. R ESULTS AND D ISCUSSION
In this paper, 7 popular state-of-the-art machine learning
algorithms along with different kernels have been implemented
and the results with respect to different evaluation metrics is
depicted. Table I and table II depicts the comparative analysis
before and after feature selection respectively. With the help
of these two tables and figure 4 it can be deduced that feature
selection does play a vital role to achieve high performance in
terms of accuracy. After feature selection, to be precise, SVM
with RBF (Radial Basis Function) kernel machine learning
algorithm topped the chart with 94.12% accuracy and AUC
of 0.9473 which is followed by Gaussian Classifier with a
laplacedot kernel having 92% accuracy and AUC of 0.924.
Just behind the Gaussian Classifier with the laplacedot kernel,
came Random Forest algorithm having an accuracy of 91.18%
and AUC of 0.924 when the number of trees is set to 150
(ntree=150). Support Vector Machine with sigmoid kernel
achieved lowest accuracy and AUC of 70.59% and 0.7157
respectively. Figure 2 represents the comparative analysis of all
the algorithms implemented with respect to various evaluation
parameters. Table III compares the AUC score of this paper
and existing systems. It clearly shows that the approach of
this paper outperforms the existing systems by quite a good
margin.
 2018 4th International Conference on Computer and Information Sciences (ICCOINS)

TABLE I
P ERFORMANCE OF M ACHINE L EARNING A LGORITHMS BEFORE F EATURE S ELECTION (H IGHEST TO L OWEST )

Algorithms Accuracy AUC kappa Sensitivity Specificity p-value

SVM - Linear 0.8529 0.8473 0.6996 0.8 0.8947 0.0002725
Logistic Regression 0.8529 0.8403 0.6953 0.7333 0.9474 2.73E-04
SVM - Sigmoid 0.8235 0.828 0.6471 0.8667 0.7895 0.01104
K-Nearest Neighbor 0.8235 0.8210526 0.6421 0.8 0.8421 1
Gaussian Classifier - polydot 0.8235 0.814 0.637 0.7333 0.8947 1.10E-03
Gaussian Classifier - rbfdot 0.7941 0.8017 0.5911 0.8667 0.7368 0.003731
Naive Bayes 0.8529 0.8 0.6996 0.8 0.8947 0.0002725
SVM - Radial Basis 0.7941 0.7947 0.5854 0.8 0.7895 0.003731
Gaussian Classifier - vanilladot 0.7941 0.7907 0.5735 0.6667 0.8947 3.73E-03
SVM - Polynomial 0.7059 0.73684 0.4426 1 0.4737 0.004427
Linear Discriminant Analysis 0.7353 0.728 0.4594 0.667 0.7895 0.02669
Random Forest (ntree = 150) 0.7353 0.728 0.4594 0.6667 0.7895 2.67E-02
C5.0 (Number of Trials = 90) 0.6471 0.6421 0.2842 0.6 0.6842 1.95E-01
Gaussian Classifier - laplacedot 0.4412 0.5 0 1 0 3.64E-05

TABLE II
P ERFORMANCE OF M ACHINE L EARNING A LGORITHMS AFTER F EATURE S ELECTION (H IGHEST TO L OWEST )

Algorithms Accuracy AUC kappa Sensitivity Specificity p-value

SVM - Radial Basis 0.9412 0.9473 0.8824 1 0.8947 0.4795
Gaussian Classifier - laplacedot 0.92 0.924 0.85 1 0.864 0.4795
Random Forest (ntree = 150) 0.9118 0.921 0.8247 1 0.8421 8.49E-06
Logistic Regression 0.9118 0.914 0.8223 0.9333 0.8947 8.49E-06
C5.0 (Number of Trials = 90) 0.9118 0.91 0.8247 1 0.8421 8.49E-06
SVM - Polynomial 0.8824 0.8947 0.7679 1 0.7895 0.1336
SVM - Linear 0.8824 0.8877 0.7647 0.9333 0.8421 0.6171
Gaussian Classifier - vanilladot 0.8824 0.8807018 0.7614 0.8667 0.8947 5.45E-05
Gaussian Classifier - polydot 0.8824 0.8807 0.7614 0.8667 0.8947 5.45E-05
Naive Bayes 0.8529 0.8543 0.7038 0.8667 0.8421 0.000272
Gaussian Classifier - rbfdot 0.8235 0.8421 0.6566 1 0.6842 0.04122
K-Nearest Neighbor 0.7941 0.8157895 0.602 1 0.6316 0.003731
Linear Discriminant Analysis 0.7941 0.7947 0.5854 0.8 0.7895 0.003731
SVM - Sigmoid 0.7059 0.7157895 0.4198 0.8 0.6316 0.3428

TABLE III
C OMPARATIVE A NALYSIS OF AUC SCORE WITH EXISTING SYSTEMS

Algorithm AUC
SVM - Radial Basis 0.9473
Solin, Arno et. al 0.928
Lebedev and Alexander V 0.923
Koncevičius and Karolis 0.91282

Implementation is characterized by 2 phases, namely with

feature selection and without feature selection. Using feature
selection machine learning algorithms resulted in achieving
significantly better accuracy. The paper is focused on feature
selection and parameter fine-tuning of each algorithm which in
turn helped to increase accuracy. Figure 3 depicts best three
performing algorithms with the highest accuracy and AUC
score in order.
The comparison between other existing approaches is also
depicted in the table III. The approach presented in this paper
outperforms all the top existing systems. To compare this pa-
per’s approach with existing systems, AUC performance met-
Fig. 2. Statistics after Feature Selection
ric is considered. AUC (true positive/false negative) measure
is considered in this paper for making a comparative analysis
because AUC efficiently deals with situations there exists a
very skewed sample distribution, and to avoid overfitting to
a single class. Accuracy is straightforward and it deals with
zeros and ones. But there are many classifiers which output a
probability value than 0 and 1. In such cases, it’s intuitive to

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 2018 4th International Conference on Computer and Information Sciences (ICCOINS)
Fig. 3. Machine Learning algorithms with highest accuracy and AUC
consider 0.5 as the threshold, but it’s not the right way when
a particular classifier outputs 0.6 for negative samples and 0.9
for positive samples. In such cases, AUC plays an important
role by considering all the thresholds.
Fig. 4. AUC score before and after Feature Selection
V. C ONCLUSION
The paper is focused on trying to increase accuracy and
efficiency of machine learning algorithms. Only applying algo-
rithms to datasets without analyzing and extracting important
features does not give the best accuracy. This paper shows
different steps involved such as data cleaning, data prepro-
cessing, training model, testing model and using model. For
getting best out of the algorithm, this paper gives us techniques
about how to extract features, reducing the dimensionality of
the original dataset, fine-tuning the parameters, etc. Finally,
after comparing the accuracies of the blind application of
algorithm against the well-followed process given in this paper,
we can see all the steps involved in methodology are important,
especially feature selection in this problem statement, and
they all contribute to getting the best out of the algorithms.
This entire system flow resulted in more accurate diagnosis
prediction of Schizophrenia.
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