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International Journal of Computer Engineering and Applications, Volume XI, Issue VIII, August 17, www.ijcea.com ISSN 2321-3469 RATNA NITIN PATIL AND Dr. SHARVARI CHANDRASHEKHAR TAMANE 76 A NOVEL SCHEME FOR PREDICTING TYPE 2 DIABETES IN WOMEN: USING KMEANS WITH PCA AS DIMENSIONALITY REDUCTION RATNA NITIN PATIL 1 , Dr. SHARVARI CHANDRASHEKHAR TAMANE 2 1 Department of Computer Engineering, Reasearch Scholor, Babasaheb Ambedkar Marathwada University, Aurangabad, India. 2 Department of Computer Engineering JNEC, Babasaheb Ambedkar Marathwada University, Aurangabad, India. ABSTRACT: Disease diagnosis is one of the applications where machine learning algorithms are giving successful results. Different classifiers can be used to explore patients’ data and extract a predictive model. Machine learning algorithms can provide reliable performance in determining diabetes mellitus. PIMA Indian Dataset consists of women’s records. The risk of developing diabetes in Women is quite high. Hence, the idea is to Detect and Predict this Disorder with the help of Machine Learning techniques. In this study firstly PCA is used as dimensionality reduction and then KMeans is used to cluster the data set. The prime objective of this research work is to provide a better classification of diabetes. The experimental results show the performance of this work on PIDD. Keywords: Diabetes mellitus; early diagnosis; PCA; machine learning; clustering; KMeans. [1] INTRODUCTION Diabetes mellitus (DM) is a group of metabolic disorders in which there are high blood sugar levels over a prolonged period. The chronic hyperglycemia of diabetes is associated with long-term damage, dysfunction, and failure of different organs, especially the eyes, kidneys, nerves, heart, and blood vessels. Diabetes Mellitus is a metabolic disease where the person will have high blood sugar due to the pancreas unable to produce sufficient insulin or

A NOVEL SCHEME FOR PREDICTING TYPE 2 DIABETES … · A NOVEL SCHEME FOR PREDICTING TYPE 2 DIABETES IN WOMEN: USING KMEANS WITH PCA AS DIMENSIONALITY REDUCTION Ratna Nitin Patil and

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International Journal of Computer Engineering and Applications, Volume XI, Issue VIII, August 17, www.ijcea.com ISSN 2321-3469

RATNA NITIN PATIL AND Dr. SHARVARI CHANDRASHEKHAR TAMANE 76

A NOVEL SCHEME FOR PREDICTING TYPE 2 DIABETES IN

WOMEN: USING KMEANS WITH PCA AS DIMENSIONALITY

REDUCTION

RATNA NITIN PATIL 1, Dr. SHARVARI CHANDRASHEKHAR TAMANE 2

1Department of Computer Engineering, Reasearch Scholor, Babasaheb Ambedkar Marathwada University,

Aurangabad, India. 2Department of Computer Engineering JNEC, Babasaheb Ambedkar Marathwada University,

Aurangabad, India.

ABSTRACT: Disease diagnosis is one of the applications where machine learning algorithms are giving successful results. Different classifiers can be used to explore patients’ data and extract a predictive model. Machine learning algorithms can provide reliable performance in determining diabetes mellitus. PIMA Indian Dataset consists of women’s records. The risk of developing diabetes in Women is quite high. Hence, the idea is to Detect and Predict this Disorder with the help of Machine Learning techniques. In this study firstly PCA is used as dimensionality reduction and then KMeans is used to cluster the data set. The prime objective of this research work is to provide a better classification of diabetes. The experimental results show the performance of this work on PIDD.

Keywords: Diabetes mellitus; early diagnosis; PCA; machine learning; clustering; KMeans.

[1] INTRODUCTION

Diabetes mellitus (DM) is a group of metabolic disorders in which there are high blood

sugar levels over a prolonged period. The chronic hyperglycemia of diabetes is associated

with long-term damage, dysfunction, and failure of different organs, especially the eyes,

kidneys, nerves, heart, and blood vessels. Diabetes Mellitus is a metabolic disease where the

person will have high blood sugar due to the pancreas unable to produce sufficient insulin or

International Journal of Computer Engineering and Applications, Volume XI, Issue VIII, August 17, www.ijcea.com ISSN 2321-3469

RATNA NITIN PATIL AND Dr. SHARVARI CHANDRASHEKHAR TAMANE

77

the cells which are not responding to the insulin produced. There are three types of diabetes.

They are Type 1 diabetes, Type 2 diabetes and Gestational diabetes. Type 1 diabetes mostly

occurs in children. Its cause is an absolute deficiency of insulin secretion. Type 2 diabetes is

called adult-onset diabetes which is common in adults. The cause of Type 2 diabetes is a

combination of resistance to insulin action and an inadequate compensatory insulin secretory

response. In this category, a degree of hyperglycemia is sufficient to cause pathologic and

functional changes in various target tissues, but without clinical symptoms may be present for

a long period of time before diabetes is detected. Gestational diabetes (GDM) has been

defined as any degree of glucose intolerance with onset during pregnancy.

Diabetes is a deadly disease and a major public health challenge worldwide. The number of

diabetics in India is doubled from 32 million in 2000 to 63 million in 2013 and the figure is

projected to further increase to 102.2 million in the next 15 years. This is the latest

assessment by the World Health Organization, raising an alarm over the need to treat the

condition. The annual spend on diabetes treatment in India is pegged at Rs1.5 lakh crore,

which is 4.7 times the Centre’s allocation of Rs32000 crore for health. This cost is projected

to rise by 20-30% every year.

Diabetes disease diagnosis via proper interpretation of the Diabetes data is an important

classification problem. There are several methodologies available on classification of diabetes

disease. This work will help to develop a predictive model based on set of attributes collected

from the patients to develop a mathematical model. It is essential to find a way that can help

in detection with high accuracy and less complexity.

MATERIAL

A. DATASET

In the machine learning research community, a work is going on to solve the classification

problem. Pima Indian Dataset (PIMA) has been used to test the classification performance by

most of the scholars. It is publically available in the machine learning dataset UCI. All the

instances in this dataset are Pima Indian women of at least 21 years old and living near

Phoenix, Arizona, USA. The data is a collection of 768 records.

B. Risk Factors

The following are the parameters which contribute to the development of diabetes. The

prevalence of Type 2 diabetes is increasing at a fast pace due to obesity, physical inactivity

and unhealthy dietary habits.

Age – Indians develop diabetes earlier than western population. An early occurrence

gives abundant time for the development of prolonged complications of diabetes. The

incidence of diabetes increases with an age.

A NOVEL SCHEME FOR PREDICTING TYPE 2 DIABETES IN WOMEN:

USING KMEANS WITH PCA AS DIMENSIONALITY REDUCTION

Ratna Nitin Patil and Dr Sharvari Chandrashekhar Tamane

78

Family History – The occurrence of diabetes increases with a family history of diabetes.

A high incidence of diabetes is seen among the first degree relatives.

Lifestyle – Deskbound lifestyle is an independent factor for the growth of Type2

diabetes.

Obesity – There is a close association of obesity with Type2 diabetes. Increase in weight

increases Body Mass Index (BMI).

Stress – The impact of physical and mental stress along with lifestyle changes has an

effect of incidence of Type 2 diabetes from persons in a strong genetic background

[2] LITERATURE REVIEW

This section discusses about the existing techniques and algorithms used for the diagnosis of

diabetes mellitus. Each and every algorithm used for the diagnosis of diabetes mellitus has

their own limitations and advantages. This section presents an analytical study on the features

of the existing techniques.

Machine learning is an area of artificial intelligence research, which uses statistical methods

for data classification. Several machine learning techniques have been applied in clinical

settings to predict disease and have shown higher accuracy for diagnosis than classical

methods [23]. Support vector machines (SVM) and artificial neural networks (ANN) have

been widely used approaches in machine learning. They are the most frequently used

supervised learning methods for analyzing complex medical data [28].

Nirmala Devi et al [29] presented a fusion model that integrates k-means clustering and k-

Nearest Neighbor (KNN) with multi-step preprocessing. It is observed that KNN algorithm

provides significant performance on various data sets. In this fusion model, the quality of the

data is improved through eliminating noisy data thus improving the accuracy and efficiency

of the KNN algorithm. K-means clustering is determines and avoids incorrectly classified

instances. An efficient classification is carried out through KNN by taking the correctly

clustered samples with preprocessed subset as inputs for the KNN. The finest choice of k is

based on the data. The main goal of this work is to identify the value of k for PIDD for better

classification accuracy using fusion based KNN. It is observed from the results that this

fusion work based on KNN along with preprocessing provides best result for different k

values. If k value is more, the classification accuracy of the proposed fusion framework is

97.4%. The results are also compared with simple KNN and cascaded K-MEANS and KNN

for the same k values.

Literature Review on Diabetes, by National Public health: Women tend to be hardest hit by

diabetes with 9.6 million women having diabetes. This represents 8.8% of the adult

population of women 18 years of age and older in and a two fold increase from 1995 (4.7%).

By 2050, the projected number of all persons with diabetes will have increased from 17

million to 29 million. [5]

Nahla H Barakat [1] utilized SVM for the diagnosis of diabetes. This work uses an additional

intelligent module, which transforms the black box model of SVM into an intelligent SVM's

diagnostic model with adaptive results. It is observed from the results that the intelligent

International Journal of Computer Engineering and Applications, Volume XI, Issue VIII, August 17, www.ijcea.com ISSN 2321-3469

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SVMs provide a potential framework for the prediction of diabetes, where a logical rule set

have been generated,

Jayalakshmi and Santhakumaran (2010) proposed a new and efficient technique for the

classification of diagnosis of diabetes disease using Artificial Neural Network (ANN). The

methodology implemented here is based on the concept of ANN which requires a complete

set of data for the accurate classification of diabetes. The paper also implements an efficient

technique for the improvement of classification accuracy of missing values in the dataset. It

also provides a pre-processing stage during classification.

Patil et al. (2010) implements an association-rule-based technique for the classification of

type-2 diabetic patients. The methodology provides the generation of rules using apriori

algorithm on the basis of some support and confidence. In the first stage, the numeric

attributes are converted into categorical form which is based on the input parameters. Lastly

generated the association rules which are useful to identify general associations in the data, to

understand the relationship between the measured fields whether the patient goes on to

develop diabetes or not.

Meng et al. [30] compared the performance of logistic regression, ANNs, and decision tree

models for predicting diabetes or prediabetes using common risk factors in China population.

Dilip Kumar Choubey et al., [31] have applied NBs, GA_NBs method on PIMA dataset. The

classification has been done by using NBs and then using GA for Attributes selection and

there by performed classification on the selected attributes. The proposed method minimizes

the computation cost, computation time and maximizes the ROC and classification accuracy

than several other existing methods.

M. Kothainayaki, P. Thangaraj [32] presented the Classification of diabetic’s data set and the

k-means algorithm to categorical domains. Before classification the preprocessing of data set

is done to remove the noise in the data set. They have used the missing value algorithm to

replace the null values in the data set. This algorithm is also used to improve the classification

rate and cluster the data set using two attributes namely plasma and pregnancy attribute.

[3] ALGORITHEMS USED

[3.1] Principal component analysis (PCA)

PCA is used abundantly in all forms of analysis - from neuroscience to computer graphics,

because it is a simple, non-parametric method of extracting relevant information from

confusing data sets. With minimal additional effort PCA provides a roadmap for how to

reduce a complex data set to a lower dimension to reveal the sometimes hidden, simplified

dynamics that often underlie it.

Principal Component Analysis (PCA) is an unsupervised dimensionality reduction method; it

is also named the discrete Karhunen–Loève transform (KLT). Principal components analysis

is a technique that can be used to simplify a dataset. It is a linear transformation that chooses

a new coordinate system for the data set such that greatest variance by any projection of the

dataset comes to lie on the first axis (then called the first principal component), the second

greatest variance on the second axis, and so on. PCA can be used for reducing

dimensionality by eliminating the later principal components [34].

A NOVEL SCHEME FOR PREDICTING TYPE 2 DIABETES IN WOMEN:

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By finding the eigenvalues and eigenvectors of the covariance matrix, we find that the

eigenvectors with the largest eigenvalues correspond to the dimensions that have the

strongest correlation in the dataset. This is the principal component.

Listed below are the 6 general steps for performing a principal component analysis,

1. Take the whole dataset consisting of d-dimensional samples ignoring the class labels

2. Compute the d-dimensional mean vector (i.e., the means for every dimension of the

whole dataset)

3. Compute the scatter matrix (alternatively, the covariance matrix) of the whole data set

4. Compute eigenvectors (e1,e2,...,ed) and corresponding eigenvalues (λ1,λ2,...,λd) of the

covariance matrix

C = λ1> λ2>⋯>λN (eigenvalues)

C = e1, e2, …, ed (eigenvectors)

5. Sort the eigenvectors by decreasing eigenvalues and choose k eigenvectors with the

largest eigenvalues to form a d×k dimensional matrix W (where every column

represents an eigenvector)

6. Use this d×k eigenvector matrix to transform the samples onto the new subspace. This

can be summarized by the mathematical equation: y=WT×x (where x is a d×1-

dimensional vector representing one sample, and y is the transformed k×1-dimensional

sample in the new subspace.)

PCA is a useful statistical technique that has found application in:

– Fields such as face recognition and image compression

– finding patterns in data of high dimension [35].

[3.2] KMeans Clustering

KMeans is one of the simplest unsupervised learning algorithms that solve the well-known

clustering problem. The procedure follows a simple and easy way to classify a given data

set through a certain number of clusters (assume k clusters) fixed Apriori. The main idea is

to define k centers, one for each cluster. These centers should be placed in a

calculating way because of different location causes different result. So, the better choice is to

place them as much as possible far away from each other. The next step is to take each point

belonging to a given data set and associate it to the nearest center. When no

point is pending, the first step is completed. At this point we need to re-calculate k new

centroids as barycenter of the clusters resulting from the previous step. After we have these k

new centroids, a new binding has to be done between the same data set points and the nearest

new center. A loop has been generated. As a result of this loop we may notice that the k

centers change their location step by step until no more changes are done or in other words

centers do not move any more. Finally, this algorithm aims at minimizing an objective function

known as squared error function given by:

Where,

‘||xi - vj||’ is the Euclidean distance between xi and vj

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RATNA NITIN PATIL AND Dr. SHARVARI CHANDRASHEKHAR TAMANE

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‘ci’ is the number of data points in ith cluster.

‘c’ is the number of cluster centers.

Algorithmic steps for k-means clustering

Let X = {x1, x2, x3,…….., xn} be the set of data points and

V = {v1, v2,……., vc} be the set of centers.

1) Randomly select ‘c’ cluster centers.

2) Calculate the distance between each data point and cluster centers.

3) Assign the data point to the cluster center whose distance from the cluster center is minimum

of all the cluster centers.

4) Recalculate the new cluster center using:

Where, ‘ci’ represents the number of data points in ith cluster.

5) Recalculate the distance between each data point and new obtained cluster centers.

6) If no data point was reassigned then stop, otherwise repeat from step (3). [4] PROPOSED METHODOLOGY

In this paper, the proposed methodology is implemented by PCA as a Dimension Reduction and

KMeans for Clustering on PIMA which has been taken from UCI machine learning repository.

The flow of process is as follows:

1. The PIDD has been taken from UCI machine learning repository.

2. Preprocessing

3. Apply PCA as Dimension Reduction on PIMA.

4. Do the Grouping by using KMeans.

Preprocessing

Principal Component Analysis

KMeans clustering Algorithm

Formation of clusters as Diabetic

and Nondiabetic

PIMA Indian Diabetes Dataset

A NOVEL SCHEME FOR PREDICTING TYPE 2 DIABETES IN WOMEN:

USING KMEANS WITH PCA AS DIMENSIONALITY REDUCTION

Ratna Nitin Patil and Dr Sharvari Chandrashekhar Tamane

82

[5] EXPERIMENTAL RESULTS

The data set is classified using the algorithm and attain the result as tested_positive or

tested_negative.

Some notations used for performance measure:

TP – True Positives (Samples the classifier has correctly classified as positives)

TN – True Negatives (Samples the classifier has correctly classified as negatives)

FP – False Positives (Samples the classifier has incorrectly classified as positives)

FN – False Negatives (Samples the classifier has incorrectly classified as negatives)

Then calculate the classification rate using followings formulas:

Precision: Proportion of all positive predictions that are correct. Precision is a measure of how

many positive predictions were actual positive observations.

Precision = TP / (TP + FP)

Recall: Proportion of all real positive observations that are correct. Precision is a measure of

how many actual positive observations were predicted correctly.

Recall = TP / (TP + FN)

F1 Score: The harmonic mean of precision and recall. F1 score is an 'average' of both precision

and recall. We use the harmonic mean because it is the appropriate way to average ratios (while

arithmetic mean is appropriate when it conceptually makes sense to add things up).

F1 Score = 2*(Recall * Precision) / (Recall + Precision)

PCA is applied on the dataset and the scatter graph is plotted for known outcomes.

The output from the PCA is given to KMeans clustering algorithm. The scatter graph showing the dataset

into 2 clusters.

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The primary use of clustering algorithms is to discover the grouping structures inherent in data.

The advantage of this approach is the structures of constructed data sets can be controlled. The

confusion matrix is obtained using SCIKIT.

The confusion matrix using without PCA

Cluster1 Cluster2

Tested_negative 421 79

Tested_positive 182 86

The accuracy score is 0.66015625.

In Y, Target outcome is stored

And in kmeans.labels_ predicted class value is stored

>>> print (accuracy_score(Y, kmeans.labels_))

0.66015625

>>> print (confusion_matrix(Y, kmeans.labels_))

[[421 79]

[182 86]]

>>> print (classification_report(Y, x))

precision recall f1-score support

0.0 0.70 0.84 0.76 500

1.0 0.52 0.32 0.40 268

avg / total 0.64 0.66 0.64 768

The confusion matrix after preprocessing & PCA

Cluster1 Cluster2

Tested_negative 257 104

Tested_positive 45 136

The accuracy score is 0.725092250923

A NOVEL SCHEME FOR PREDICTING TYPE 2 DIABETES IN WOMEN:

USING KMEANS WITH PCA AS DIMENSIONALITY REDUCTION

Ratna Nitin Patil and Dr Sharvari Chandrashekhar Tamane

84

>>> print (accuracy_score(Y, x))

0.725092250923

>>> print (confusion_matrix(Y, x))

[[257 104]

[ 45 136]]

>>> print (classification_report(Y, x))

precision recall f1-score support

0.0 0.85 0.71 0.78 361

1.0 0.57 0.75 0.65 181

avg / total 0.76 0.73 0.73 542

[6] CONCLUSION AND FUTURE SCOPE

The proposed method yields better results than single classifier. In this paper we have proposed

KMeans clustering algorithm which first implements the dimensionality reduction technique

i.e., PCA and then uses KMeans algorithm to fine tune the result. Using the proposed method a

given dataset is partitioned in such a way that the sum of total clustering error is reduced to a

large extent. The limitation of this work is that it may not provide the same accuracy for any

other data set which it has provided for the Pima Indian diabetic data set in this approach. This

study can be further extended to deal datasets with multiple classes.

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A NOVEL SCHEME FOR PREDICTING TYPE 2 DIABETES IN WOMEN:

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Ratna Nitin Patil and Dr Sharvari Chandrashekhar Tamane

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Author[s] brief Introduction

Ratna Nitin Patil has obtained her Masters in Computer Engineering from Thapar

Institute, Patiala, Punjab in 2001. She is pursuing PhD from Babasaheb Ambedkar

Marathwada University, Aurangabad, India. She has worked as an Associate Professor

at Kanpur Institute of Technology, Kanpur, St Peters College of Engineering, Chennai,

Sriram College of Engineering, Chennai, Mar Baselios College of Engineering,

Trivandrum and at Vishwakarma Institute of Technology, Pune. She has 22 years of

teaching experience. Her research interest includes Machine Learning, Natural

Language Processing and Analysis of Algorithms.

Email:[email protected]

Dr. Sharavari Chandrashekhar Tamane has obtained her PhD in Computer Science

and Engineering from Babasaheb Ambedkar Marathwada University, Aurangabad,

India. She has 15 international publications. She is working as an associate professor in

Jawaharlal Nehru Engineering College, Aurangabad. She is designated as a chairperson

of Second International Conference on Internet of Things, Data and Cloud Computing

International Journal of Computer Engineering and Applications, Volume XI, Issue VIII, August 17, www.ijcea.com ISSN 2321-3469

RATNA NITIN PATIL AND Dr. SHARVARI CHANDRASHEKHAR TAMANE

87

(ICC’17), Cambridge university, United Kingdom Her research area includes Cloud Computing,

Analysis of Algorithms and Network Security.

Email: [email protected]