Childhood Medulloblastoma Classification

Using EfficientNets

Chandra Mohan Bhuma

ECE Department
Bapatla Engineering College
Bapatla, India
2020 IEEE Bombay Section Signature Conference (IBSSC) | 978-1-7281-8993-2/20/$31.00 ©2020 IEEE | DOI: 10.1109/IBSSC51096.2020.9332175

chandrabhuma@gmail.com

Ramanjaneyulu Kongara
ECE Department
PVP Siddhartha Institute of
Technology
Vijayawada, India
kongara.raman@gmail.com

Abstract—In this work, a deep learning methodology for
accurate classification of histological images of the patients
suffering from childhood medulloblastoma is proposed. Pre
trained EfficientNets trained on the ImageNet dataset are
considered in this work. Features are extracted from the
average pooling layer of EfficienNets and are given to an error
correcting output code classifier. Ensemble prediction from the
selected pre-trained EfficientNets is employed. For the multi
class classification, the proposed approach is able to predict
with a mean classification accuracy of 98.78% for 10x level
images and 95.67% for the 100x level images for an 80% train
and 20% test split. The peak classification accuracy is 100%
for both binary and multiclass case at cell level and
architectural level. For the binary classification with same
split, 100% mean classification accuracy is achieved even
without ensemble prediction. The results are compared with
an existing work on a similar dataset and the significant
improvement is demonstrated with the experimental
simulations.
Keywords— Childhood Medulloblastoma, Classification,
Efficientnets, Ensemble Learning, ECOC classifier
In general, histological slides are analysed using
architectural level and cell level. The magnification factor
for the cell level is higher than architecture level. More
details can be obtained from the cell level inspection. As the
problem is basically a classification problem, the task may
be just to categorize the tumour as normal (benign) or
abnormal (malignant). This is a binary classification
problem. However, in multiclass classification, the
requirement is to identify the sub type of malignancy. There
are four subtypes in CMB i.e., Nodular, Classic, Large and
Desmoplastic.
CAD techniques are popular in histological images
classification Kather et al. [2]. Categorizing MB into
anaplastic and non-anaplastic was done by Lai et al. [3], Roa
et al. [4] and Galaro et al. [5]. Das et al. [1] used texture,
color and morphological features to identify the sub type of
childhood MB. Das et al. [6] analysed the statistical
significance of CMB and its sub types using MANOVA
(Multivariate analysis of variance).

I. INTRODUCTION Instead of using traditional feature engineering, deep

Childhood Medulloblastoma (CMB) is a type of
malignant brain tumor developed in the cerebellum of
children [1]. Typical symptoms of medulloblastoma include
headache, vomiting, and problems with vision. By using
MRI (Magnetic Resonance Imaging) and CT (Computerized
Tomography) scans, the brain tumor can be detected. In
addition to chemotherapy, medulloblastoma can be treated by
using surgery, or radiation therapy. With correct diagnosis
and proper treatment, 90% of the medulloblastoma cases can
be cured.
The histological samples from the biopsy can be used to
identify MB sub types. Visual inspection is required and
expertise is also needed in the identification of type of MB
sub type from the histological images. As the treatment
largely depends on the type of tumour, identification of the
type of tumour plays a key role. In this regard, CAD
(Computer Assisted Diagnosis) plays an important role.
learning architectures can be used for accurately classifying
the childhood MB subtypes. In recent past, deep learning
architectures i.e., Convolutional Neural Network (CNN) and
its variants are able to dominate not only in the classification
problems but also in object detection, segmentation, and
regression. Inspired by the works of Das et al., in the
classification childhood MB, a deep learning approach which
improves the classification accuracy in identifying the
childhood MB subtype is presented. EfficientNets are very
recent CNN architectures which showed improved
performance on ‘ImageNet’ dataset. Hence, features
extracted from the pre-trained EfficientNets and the
predictions from their ensembles are considered in this work.
This paper is organized as follows. A brief review of
EfficientNets is presented in section II. Ensemble learning
and various techniques in ensemble learning are presented in
section III. Details of the CMB database and the proposed

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algorithm are given in section IV. Experimental results are
given in section V. Conclusions are given in section VI.
II. EFFICIENTNETS
EfficientNets are scaled Convolutional neural networks
(CNNs). Number of layers in CNNs are initially fixed. They
are scaled up by increasing the number of layers and deeper
features can be extracted from the images. In general,
improvement in classification accuracy is expected with the
increase in number of layers. ResNet architecture was tested
on ‘ImageNet’ dataset with 18 layers to 200 layers. Densenet
architecture was tested on 121, 169 and 201 layers. Model
scaling offers flexibility and also compatibility with the
devices on which the model is deployed. This scaling can be
done in depth wise, width wise, and resolution wise. Instead
of randomly increasing and assigning the resolutions, a
systematic study and approach was given by M.Tan and Q V
Le. [7]. Arbitrary choosing of width, depth and resolutions is
time consuming and significant improvement is not
guaranteed. Scaling coefficients were used in systematically
scaling the baseline CNNs in the work of [7]. They
developed [7] EfficientNets, which offered superior
accuracies on ‘ImageNet’ dataset. Balancing all the
dimensions is the key in EfficientNets. EfficientNet
architecture uses mobile inverted bottleneck convolution
(MBConv). With this scaling approach, EfficientNets are
available from EfficientNetB0 to EfficientNetB7 with
varying input resolutions. Some part of basic architecture of
an EfficientNetB0 is shown below in Fig 1.
224x224x3
Conv3x3
112x112x32
MBConv1,3x3
112x112x16
MBConv6,3x3
56x56x24
MBConv6,3x3
56x56x24
MBConv6,5x5
28x28x40
MBConv6,5x5
Fig. 1 A sub section of baseline EfficientNetB0 architecture
Number of layers varies from EfficientNetB0 to B7 and
the input resolutions are also different. All the images must
be resized to these resolutions. Features are extracted from
an average pooling layer which is the last pooling layer. The
feature vector sizes are given below. It is as low as 1280 and
goes up to 2560. EfficientNetB7 is approximately 3.5 times
deeper than EfficientNetB0. Some architectural details are
given below in TABLE I.
TABLE I BRIEF ARCHITECTURAL DETAILS OF EFFICIENTNETS
Description No.of layers Input FeatureVector
Resolution Size
EfficientNetB0 240 224x224 1280
EfficientNetB1 342 240x240 1280
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EfficientNetB2 342 260x260 1408
EfficientNetB3 387 300x300 1536
EfficientNetB4 477 380x380 1792
EfficientNetB5 579 456x456 2048
EfficientNetB6 669 528x528 2304
EfficientNetB7 816 600x600 2560
III. ENSEMBLE LEARNING
Ensemble learning methods are the methods where in,
various machine learning models are combined and the
prediction is based on the combined model. Hence, it is an
algorithm based on Meta learning. The combined predictions
are more accurate than the single model prediction. The key
factor in the ensemble methods is the selection of base
models. In addition, individual base models must be accurate
in terms of classification accuracy. They should have
diversity either in the model architecture, or in the type of
classifier, or in the hyper parameters of the models [8]. If
diversity is maintained amongst the models, the way the data
is visible to the model is different. Hence, if one model fails
to understand the nature of the image, at least the other model
might do better. There are many ensemble techniques. The
simple approaches are majority voting (hard voting),
averaging and weighed averaging the posterior probabilities.
In majority voting, the class labels from each model or
classifier are computed. From the number of models chosen,
the class label having highest votes is considered as the final
prediction.
Assume that there are N models or classifiers and C
classes. Decision of a model is chosen
as d n,c  {0,1} , n 1,...N , c 1,.....C, . When a classifier or a
model predicts the labels of the test data, it is assigned [9]
with a value 1. Choose a class c * if,
N N
¦
n 1
d n,c* max c ¦d
n 1
n,c
Different variants have been attempted [9] in the voting
classification. In unanimous voting, a class label is assigned
if all the classifiers agree unanimously. In simple majority
case, if class labels are predicted by at least one more than
half the number of classifiers. In this work, the strategy
chosen is that, a class having highest number of votes is the
winner. In addition, posterior probabilities can also be
calculated from the classifiers and the sum of the
probabilities of each class is calculated. Class having the
highest sum probability across all the models is considered as
the final class. Equal weightage is given for each class
probability. However, in weighed averaging, each assigned
probability is weighed with a fraction and total sum is
computed. In addition to the techniques discussed above,
Bagging, Boosting, Blending, and Stacking are some popular
ensembling techniques.
IV. DATASET AND THE PROPOSED ALGORITHM
The database of the Childhood Medulloblastoma [10]
consists of two folders having the images acquired at
architecture level and cell level. The database images have
normal tissue samples and CMB cell samples. There are
only two images in the Nodular category at cell level. For
10x and 100x, there are 5 classes. It is a multiclass
classification problem. The classes are imbalanced. When
we want to classify them as normal and abnormal category,
there are 152 images in the abnormal and 50 in the normal 4. Three EffcientNets are selected and the trained
class for 10x. In 100x level, there are 25 images in normal features from each EfficientNet are given
and 128 abnormal classes. This is dealt as a binary independently to a multiclass ECOC (Error
classification problem. All the images in the database are in Correcting Output Code) classifier. This is the
.jpg format and are 24 bit color images. Number of images training phase. Now three models are available.
in each class are depicted in the below TABLE II. Sample 5. Similarly test image features are extracted from
images from each class are shown in Fig 2. As the EfficientNets.
EfficientNets have different input resolutions, pre- 6. By applying the test features, class labels are
processing step is necessary while extracting the features obtained from the ECOC classifier.
from EfficientNets. 7. A majority voting decision is taken from all the
TABLE II CHILDHOOD MEDULLOBLASTOMA DATASET DETAILS three models for each test image feature as
described in section III. Final class labels are
Description 10x 100x predicted from this majority voting.
Classic 59 82 Classification accuracy for the test set is
Desmoplastic 42 20 calculated.
Nodular 23 02 8. Steps 2 to 7 are repeated 10 times by randomly
Large cell 28 24
Normal 50 25
shuffling the train and test and mean
Total 202 153 classification accuracy is calculated.

The proposed algorithm is shown in in Fig 3. Selection

Class 10x 100x
of three EfficientNets, base classifiers in ECOC, and hyper
parameter selection in step 4 is purely arbitrary. However,
proper selection of appropriate three EfficientNets is done to
Classic improve the mean classification accuracy for 10 repeats of
train and test splits. They are represented as Efx, Efy and
Efz in Fig. 3. The entire process is done for the binary
classification task also. In Fig. 3, Ef0 to Ef7 indicates
EfficientNetB0 to EfficientNetB7.
Image Database
Desmoplastic

Train/Test
Split

LargeCell
Ef0 Ef1 Ef2 Ef3 1 Ef4 Ef5 Ef6 Ef7

…… ……

Feature Extraction
Nodular Last Average
Selection of Pooling Layer
EfficientNets

Efx features Efy features Efz features

Normal

ECOC Classifier ECOC Classifier ECOC Classifier

Fig. 2 Sample images from each class of the CMB dataset [10]

The proposed algorithm consists of the following steps. Ensemble

10 times repeat Prediction
1. All the images are resized to the resolutions of
the EfficientNets.
2. The dataset is split into train and test with 80% Mean Classification
train and 20% ratio. Accuracy
3. Features are extracted from the last pooling
layer (average pooling layer) of the Efficient
Fig. 3 Proposed Algorithm
Nets

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 V. EXPERIMENTAL SIMULATIONS AND RESULTS binarycomplete

All the simulations for extracting the features from the
EfficientNets are carried using Keras 2.3.0 in Google Colab
Environment without using GPU. Features are calculated at
once and they are stored in .mat files in MATLAB R2019b.
Ensemble prediction is done using the shuffling, splitting the
.mat files of EfficientNets as it is computationally expensive
to compute the features each time for all the images. There
are only two images in the 100x nodular category. Hence,
they are not included in the multiclass classification of 100x
images. However, in the binary classification of 100x
images, they are included.
With an aim of improving the mean classification
accuracy, three EfficientNets are selected at random
manually. Other hyper parameters tuned are
‘KernelFunction’, ‘KernelScale’, in the Support Vector
Machine (SVM) classifier, and the ‘Distance’ metric in the
K Nearest Neighborhood (KNN) classifier. For the 10x
level and 100x level images, the details of the chosen pre-
trained networks and the classifiers are given below in
TABLES III and IV.
TABLE III DETAILS OF THE NETWORKS AND THE CLASSIFIERS FOR 10X
LEVEL IMAGES
Distance=seuclidean
EfficientNetB7 KNN 89.67
Coding: onevsone
Ensemble Mean Accuracy 95.67
The combination of EfficientNetB3,B0,B7 worked well for
10x level images, with the bases learners being SVM
(Support Vector Machine) offering a mean classification
accuracy of 98.78%. However, for 100x level images,
ensemble of EfficientNetB4, B0, B7 did a fair job offering
95.67% mean classification accuracy. When the train and
test data are shuffled for each repeat, the classification
accuracy varies for each network and in turn, the mean
accuracy also varies. For 10x level images, over 10
iterations, the classification accuracy varies as shown in the
Fig. 4. In Fig. 5, the classification accuracies for the 100x
level images are shown.

Architectural Level (10x) Multiclass Classification

Mean
Base Classification
Network Options Accuracy of
Classifier of each Network
ECOC
(%)
Kernel Scale=2
Linear Kernel
EfficientNetB3 SVM 96.34
Coding:
onevsone
Kernel Scale=2
Linear Kernel Fig. 4 Range of classification accuracies for the 10x images
EfficientNetB0 SVM 97.32
Coding:
onevsone
Kernel Scale=2
Linear Kernel
EfficientNetB7 SVM 95.85
Coding:
onevsone
Ensemble Mean Accuracy 98.78

TABLE IV DETAILS OF THE NETWORKS AND THE CLASSIFIERS FOR

100X LEVEL IMAGES
Cell Level (100x) Multiclass Classification
Mean
Classification
Base
Network Options Accuracy of
Classifier each Network
Fig. 5 Range of classification accuracies for the 100x images
(%)
Kernel Scale=3 From Fig. 4, it can be inferred that the ensemble prediction
assures us the combined model is more general not having
EfficientNetB4 SVM Linear Kernel 93.00 any over fit problem. Another observation from Fig. 4 is
Coding: onevsall that, for certain iterations, the classification accuracy is
Kernel Scale=3 100%. For binary classification of 10x and 100x images as
EfficientNetB0 SVM
normal and abnormal, EfficientNets are able to classify them
Linear Kernel 90.67 effectively. For 10x images, mean classification accuracy of
Coding: EfficientNetB1, B2, and B3 is 100%. However, for 100x

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images, EfficientnetB2 and B7 are able to offer 100% mean binary classification, the classification accuracy is 100% for
classification accuracy. Hence, ensemble of the a 80% train and 20% test split even without ensemble
EfficientNets is not required for binary classification. prediction. As EfficientNets have different resolutions,
different number of layers, the improved accuracy due to
Authors of [6] have also used similar dataset but the ensemble prediction is attributed to the diversity in the
number of images is different. They have used traditional EfficientNet models chosen.
feature i.e., texture, color and shape and applied MANOVA
on the features to identify the significant features. Compared REFERENCES
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made publicly available with some modifications [10]. The
comparison is given in TABLE VI. Results reported by the
authors of [6] in TABLE VI are after feature reduction.

TABLE VI COMPARISON OF THE PROPOSED WORK WITH AN EXISTING

WORK
Authors Level Classification Accuracy
65.21% Multiclass
Das et al., [6] Architecture
100% Binary
83.6% Multiclass
Cell
92.6% Binary
98.78% Multiclass
Proposed Architecture
100% Binary
95.67% Multiclass
Cell
100% Binary

VI. CONCLUSIONS
In this work, an algorithm is proposed for multiclass
classification of histological images of Childhood
Medulloblastoma into sub types. Binary classification of
normal tissue cells and abnormal ones is also presented. For
multiclass classification, mean classification accuracies (10
repeats) achieved with the ensemble of EfficientNets is
98.78% at architectural level and 95.67% at cell level. For

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