Engineering Science and Technology, an International Journal 46 (2023) 101500

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Automated bacteria genera classification using histogram-oriented

optimized capsule network
Jitendra P. Chaudhari a , Hiren Mewada b ,∗, Amit V. Patel a , Keyur Mahant a
a
CHARUSAT Space Research and Technology Center and V. T. Patel Department of Electronics & Communication, Chandubhai S. Patel Institute of Technology,
Faculty of Technology & Engineering, Charotar University of Science and Technology, Changa, Gujarat, India
b
Electrical Engineering Department, Prince Mohammad Bin Fahd University, Al Khobar, Kingdom of Saudi Arabia

ARTICLE INFO ABSTRACT

Keywords: Identifying the nature and type of bacteria is essential in diagnosing various fatal diseases and their treatments.
Bacteria classification Biologists classify bacteria using morphological characterization from microscopic images according to their
Machine learning color and shape information. Therefore, an automated bacterial recognition and classification approach is
Deep learning
required compared to a challenging and time-consuming manual process. Much research has been carried
Capsule Network
out on bacteria classification using machine learning algorithms. However, the major weakness of these
Optimization
conventional machine learning algorithms is that they cannot differentiate pose and deformation, have
significant trainable parameters, require extensive training time, and use trial-and-error-based hyperparameter
selection. In addition, the choice of optimization function to reduce the loss is also equally important. This
paper presents an efficient capsule network that encodes information from orientation as an alternative to
these machine learning models. The proposed model is designed with histogram-based feature sets requiring
minimal parameters. Various optimization algorithms are tested to find an appropriate optimizer. 33 categories
of bacteria species are classified using the proposed method. A comprehensive analysis of popular gradient
descent optimizers is presented with a capsule network to strengthen testing and validation and benchmark
the performance. The extensive empirical study on DiBAS datasets demonstrates that the proposed network
performs 95.08% efficiency among various machine learning algorithms, including KNN, Decision Trees, Naïve
Bayes and SVM. Furthermore, the proposed model achieves better accuracy with the least training parameters
of 6.9 million.

1. Introduction
Research in bacteria classification would directly help save millions
of people’s lives. It would also be helpful in the detection of their
diseases at an early stage. Bacterial species are crucial in the field of
microorganisms, including medicine, biochemistry, veterinary science,
farming, and the food industry. Bacteria classification is essential in
medical science for identifying and treating bacterial diseases such
as cholera, pneumonia, gonorrhea, meningitis, and bacterial dysen-
tery. Their cellular envelopes have a distinctive shape that gives them
virulence and protects them from different chemicals. For scientists
and doctors, understanding these cellular processes and mitigating the
effects of these resistance properties poses a significant challenge [1].
The bacterial recognition process requires the staining of samples and
dedicated instruments to analyze the characteristics of stained samples.
Generally, bacteria can be classified in two ways: (a) using their cell
wall composition and reaction to the Gram-stain test, and (b) using
their shape and other morphological information. Fig. 1(a–b) depicts
the classification of bacteria as positive gram and negative gram based
on the Gram stain test. Fig. 1(c–d) shows the type of bacteria based on
their shapes, such as cocci and bacilli.
The laboratory staff must work with this complicated process to
classify these bacteria. Several steps in this complex process are rightly
expressed in [2]. Microscopic observation is used to classify them based
on specific characteristics in the final stage. A few features that help
to discriminate are color and shape. However, certain bacterial species
are morphologically complex, with cells of various sizes and shapes.
Therefore, manual classification is challenging and time-consuming
since they need to know multiple bacterial characteristics. On the other
hand, the convolutional neural network (CNN) is the ultimate solution
in image-based classification with its deep and self-learning abilities.
CNN’s self-learning and automated learning processes determine the

∗ Corresponding author.
E-mail addresses: jitendrapchaudhari.ec@charusat.ac.in (J.P. Chaudhari), hmewada@pmu.edu.sa (H. Mewada), amitvpatel.ec@charusat.ac.in (A.V. Patel),
keyurmahant.ec@charusat.ac.in (K. Mahant).

https://doi.org/10.1016/j.jestch.2023.101500
Received 9 January 2023; Received in revised form 17 May 2023; Accepted 25 July 2023
Available online 17 August 2023
2215-0986/© 2023 The Authors. Published by Elsevier B.V. on behalf of Karabuk University This is an open access article under the CC BY-NC-ND license
(http://creativecommons.org/licenses/by-nc-nd/4.0/).
J.P. Chaudhari et al.
Fig. 1. Bacteria species classification based on reaction to the Gram-stain test and
shape.
parameters that distinguish the patterns. Unfortunately, it increases
CNN’s risk of overfitting or having too many parameters. Another
disadvantage of CNN is the requirement of large datasets to train
a deeper network with significant trainable parameters. In addition,
bacteria with large cell colonies lag in high-level features associated
with adapting the convolutional networks.
Bacterial images can be differentiated using their pose and texture
pattern. CNN uses spatial and textural features independent of the
object’s pose or position in the image and can be present in different
orientations or scales. Spatial features, conversely, are highly depen-
dent on the object’s pose and orientation in the image and can vary
significantly as the object is rotated or translated. A feature detector
that relies solely on spatial information may not be able to distinguish
between different orientations of the bacteria and may confuse the
texture with changes in pose. Thus, distinguishing the pose, texture, or
deformation within an image using CNN is challenging, and only spatial
features might not be adequate for texture classification [3]. The pool-
ing operation causes the removal of some essential features. In a capsule
network, the group of neurons is expressed as a capsule that encodes the
geographical information and likelihood of finding an object [4]. On
the other hand, the vector-based datastore capability of the capsule net-
work [3] provides deeper object information. In addition, the routing
mechanism enables each capsule to keep information from the previous
capsule layers and try to find an agreement to classify an image.
Thus, their memorizing capability of orientation and components’ lo-
cations motivated us to use them for Bacteria classification. Numerous
medical imaging applications have recently utilized capsule networks,
such as biomedical image classification [5,6], bioinformatics [7], and
hyperspectral image classification [8].
This paper presents an alternate solution for CNN to mitigate the
bacteria classification problem. Usually, a capsule network is trained
using images (in the spatial domain), leading to many feature sets and
trainable parameters. In addition, for better training of the network,
it needs many images; therefore, an image augmentation process is
required. In contrast, the proposed model uses histogram-based reduced
feature sets in CNN training. Images are preprocessed to remove noise,
and histogram-oriented features are obtained from the clean images.
These features are used in capsule network training without any image
augmentation. Later, a capsule network requiring fewer parameters is
proposed for the classification process. For validation, the proposed
network is tested using different optimizers. Furthermore, the proposed
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Engineering Science and Technology, an International Journal 46 (2023) 101500
model is evaluated and compared with other machine learning-based
classifiers, including K-Nearest Neighborhood (KNN), Decision Trees
(DT), Naïve Bayes, and Support Vector Machine (SVM).
Overall main contributions of this paper are as follows:
• Over the year, learnable features replaced the handcrafted fea-
tures in the convolutional neural network. Nonetheless,
histograms play an essential role in the compact representa-
tion of statistical information. Therefore, we proposed an image
histogram-trained capsule network for bacterial colony classifica-
tion.
• Minimizing the training parameters is essential in designing a
deep neural network (DNN). Significant training parameters may
lead to overfitting and require more drop-out layers. Therefore,
the capsule network is implemented, requiring fewer trainable
parameters.
• Optimization helps to tune the weights and learning rate in DNN.
Furthermore, the selection optimization model based on the quan-
titative evaluation helps improve network performance. There-
fore, the effect of optimization model selection on classification
accuracy is presented in the paper.
• The proposed algorithm is validated using the DIBAS dataset
consisting of 33 classes of the bacterial colony. After validation,
a comparative analysis is presented with widely used machine
learning algorithms, including KNN, decision tree, Naïve Bayes,
SVM, and CNN.
• Finally, the proposed network is compared with other CNN net-
works using trainable parameters and accuracy.
The remainder of this paper is organized as follows: Section 2
presents a study of recent literature on bacterial species classifica-
tion. Section 3 explains the proposed approach with mathematical
expressions to classify bacteria into species. Section 4 contains an ex-
perimental examination of the proposed model. Finally, the conclusion
and future work are expressed in Section 5.
2. Related work
As mentioned previously, shape and color information are the main
characteristics of bacteria. Wide varieties of image classification al-
gorithms are available. These algorithms can be categorized as tra-
ditional or machine learning approaches. Further machine learning
approaches can be classified as statistical machine learning [9,10] and
neural network-based [11] machine learning models. In traditional ap-
proaches, microbiologists classify bacterial colonies using their shape,
size, and color information. Molecular and biochemical testing is used
to classify the species with huge color and shape similarities. These
methods are sensitive to the operator’s skills and expertise. Therefore,
machine learning approaches are widely adopted due to their promising
results without human intervention. This section presents machine
learning approaches.
2.1. Statistical machine learning models:
Statistical machine learning algorithms are a three-step automated
tool applying (1) segmentation: Gaussian mixture model (GMM), fuzzy
C-mean, and K-means clustering; (2) feature extraction: GMM, principle
component analysis, independent component analysis, texture features
using wavelet, local binary pattern, etc.; and (3) classification using a
supervised or unsupervised classifier, i.e., KNN, Adaboost, multiplayer
perceptron network, etc.
A comprehensive study on machine learning to classify bacteria
over the last decade was presented in [12]. All models studied in this
paper used different datasets, so a standard comparison is not shown
in this paper. In [13], authors obtained features using the Gabor filter
from the segmented images, and KNN was used for classification. Later,
J.P. Chaudhari et al.
they integrated the texture features using wavelet transform and color
information using a few statistical features to improve classification
accuracy [6,14]. Finally, the feature set was reduced using principal
component analysis (PCA), and a multi-layer perceptron network was
used as a classifier. The algorithm was tested on UTMC.V1.DB and
UTMC.V2.DB datasets and obtained an accuracy of 80.8% and 80.1%,
respectively. A similar three-step approach was presented in [15]. They
look for the primary two challenges, e.g., segmentation of the bacterial
region due to a cluttered environment and occlusion. After handling
these challenges, they extracted morphotype features and classified
them using adaptive boosting. Sajedi et al. [16] extracted features using
the Gabor transform, and XGBoost was used to classify myxobacterial
images. Their model accuracy was limited to 90.28% for three classes.
Authors in [17] identified tuberculosis, distinguished between sin-
gle and multiple tuberculosis bacteria and non-bacteria, and compared
back-propagation and KNN methods. Bacteria length and endpoint were
used as features of tuberculosis bacteria. An accuracy 93.22% was
obtained for backpropagation networks, while 94.22% accuracy was
obtained for KNN. Borowa et al. [18] presented a multistage clas-
sification model using ResNET and attention-based multiple instance
learning (AbMIL). First, they used ResNet to categorize image patches
as darker, rounded, or larger. Later, the weighted combination of this
patch representation was classified using AbMIL. Finally, they classified
the bacteria colony into three classes with an accuracy of 64.8%.
2.2. Artificial neural network-based algorithms:
Zachariou et al. [19] used morphological operations to detect tu-
berculosis bacteria and a multi-stage deep CNN to count them. This
method lacks the classification of these bacteria and needs manual
microscopy to get a bacteria region. Kim et al. [20] initially used
bacteria’s interacting components to obtain varied viscosity and surface
tension and classified it as one of the six bacterial species with an
accuracy of 85%. Jeong et al. [21] analyzed infrared (IR) spectroscopy
spectra to identify the bacteria using wavelet features. A visual inspec-
tion tool was designed considering the 32 IR spectra of E. coli and
the 40 IR spectra of Pseudomonas aeruginosa. It has been observed
that logistic regression has a better accuracy of 92.5% compared to
various machine-learning approaches. In [22], Zielinski et al. used a
computationally complex process. They integrated the SIFT features
with convolutional features obtained from the last layer of CNN, and
its fisher vector (FV) was obtained. Later, FV was concatenated with
features of CNN. The SVM was trained using these features and suc-
ceeded in achieving 97% accuracy. A bacterial strain classification
using biological microscope images was proposed by Trivedi et al. [23].
They augmented image datasets to increase the number of images in
training datasets, and CNN was developed and optimized to classify
bacterial strains.
A classification of vaginal bacteria was presented from the micro-
scopic imagery in [24]. Initially, bacterial segmentation was done, and
features obtained from these segmented images were used to train SVM.
Later, CNN was compared with the SVM classifier, and they observed
that the 3-class SVM outperformed the CNN model. Anna Plichta [25]
used seven features, including shape, color, size, number of clusters,
cluster shape, density and cell distribution. A weighted classifier was
used for the recognition. The presented algorithm obtained 90.45%
accuracy with the DIBaS dataset. Chopra and Verma [26] developed
a hybrid method to train the CNN using a genetic algorithm and clas-
sify bacteria into four species. Several regularization techniques were
introduced to tackle the overfitting problem [27]. Bacanin et al. [28]
presented a sine-cosine-based swarm intelligence model to regularize
the dropout and successfully tested it on MNIST datasets. Further test-
ing of the complex image classification model is required. An algorithm
of bacterial growth estimation over time is presented in [29]. Trained
CNNs were utilized to estimate bacterial colonies’ growth rate and
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Engineering Science and Technology, an International Journal 46 (2023) 101500
size in independent Staphylococcus aureus cultures by analyzing image
sequences.
A thin-film transistor sensor obtained the bacterial colony images
in [30]. Later, two CNNs were trained using spatiotemporal features
for early detection and classification. Khalifa et al. [31] focused on
the data augmentation process to solve the overfitting problem of
CNN. They increased the sampled images of the DIBaS dataset using
the augmentation process. The model was trained using 6600 images
and validated using 5940 images. The network achieved 98.22% ac-
curacy. The authors in [32] presented foodborne pathogenic bacteria
recognition. Using principal component analysis (PCA), they reduced
the feature sets and proposed a stacking algorithm for classification.
Further improvement in the model’s performance was obtained using
a grid search and K-fold validation. The results were compared with
KNN and SVM. The stacking algorithm achieved 95.73% accuracy
using SVM. A foodborne bacteria classification from hyperspectral mi-
croscopic images using deep learning was presented in [33]. They
compared the 1D-CNN, deep residual network (ResNet), and long short-
term memory (LSTM) network using 5000 images. 1D-CNN performed
best among all with 96.2% accuracy. The studies’ summary is tabulated
in Table 1.
The study propagates that statistical approaches have limited accu-
racy of up to 80%. On the other hand, a supervised CNN algorithm
integrating bacterial features outperformed traditional or statistical
techniques. In addition, the image augmentation process in CNN has
improved the classification rate, obtaining more than 90% accuracy.
However, using spatial features obtained from CNN makes it challeng-
ing for texture pattern classification. Further, a system is required to
evaluate the quality of the image-augmented dataset. Also, a stand-
alone CNN could obtain better accuracy at the cost of high training
times. Therefore, there is a need to design a CNN that can use texture
pose information, achieve better accuracy without the image augmen-
tation process, and offer the least number of trainable parameters,
reducing overall training time. Thus, the proposed method presents the
capsule network as an alternate solution to this heterogeneous CNN
approach, offering fewer training parameters.
3. The proposed method
This section presents the proposed classification approach using a
capsule network. Initially, the selection of the capsule network and its
architecture are explained. Subsequently, histogram features and the
network training process are described. Finally, the optimization func-
tion is essential to reducing the loss in the training phase. Therefore,
this section also presents various optimization models suitable for the
neural network.
3.1. Capsule network:
The proposed method is based on capsule networks, which can
differentiate pose and deformation compared to conventional CNNs.
The traditional CNN uses a max-pooling operation to remove crucial
attributes from the images. In contrast, the capsule network uses the
squash function, which uses all the information from the previous layer
in the classification. Therefore, the capsule network is more effective
than conventional CNNs and is more reliable when the images vary in
shape or pose. Capsule networks fetch spatial information and related
features. This information is used to overcome the loss of features in
pooling operations. The output of the capsule is a vector with direction.
For example, changing the orientation of the image will change the
vector in the same direction. The result of the neuron is a scalar. It
does not vary with a change in direction. Fig. 2 depicts the capsule
network’s architecture.
The capsule network starts with a standard convolution layer having
a size equal to the input image/signal size. An appropriate kernel at
each layer extracts the features from the image. For example, each
J.P. Chaudhari et al. Engineering Science and Technology, an International Journal 46 (2023) 101500

Table 1
Summary of findings from the literature.
Ref Dataset and Algorithm Finding
[13] Database: UTMC sample image Texture information is used. Accuracy is limited to 65.76%.
Features: Gabor feature Further improvement in accuracy is required.
Classifier: KNN
[14] Database: UTMC sample image Spectral features are used.
Features: Wavelet features and color information Overall accuracy on the dataset is limited to 87.81%.
The feature set reduction using PCA. Classifier: multi-layer perceptron
network
[15] Database: DIBAS The average accuracy is 79.10% for 9 classes.
Features: Morphological features using unsupervised segmentation However, for more than 10 bacterial classification,
Classifier: Adaboost algorithm fails with an accuracy of 54.2%.
[17] Database: tuberculosis bacteria The main limitation is that morphological traits are not always clear.
Features: ROI extracted using Morphological operation Two class classification is presented.
Classifier: KNN Received 94.92% accuracy for binary classification.
[19] Database: tuberculosis bacteria This method lacks the classification of these bacteria
Features: morphological features and needs manual microscopy to get a region of bacteria.
Classifier: a multi-stage deep CNN for bacteria detection
[18] Database: 3 clones of Klebsiella pneumonia Novel approach of image patch categorization using shape is presented.
Features: Patch shape obtained using ResNET
Classifier: Attention-based multiple instant learning The classification accuracy is limited to 64.8%.
The clustering of clones can help to improve classification accuracy.
[20] Database: Authors generated dataset The process of obtaining viscosity and surface tension needs a complex
Features: viscosity and surface tension chemical process.
Classifier: SVM classifier They classified it into six categories with an accuracy of 85%.
[21] Dataset: Bacterial images obtained using Fiber-Optic Fourier Transform A binary classification was proposed. Achieved 92.5% accuracy.
Infrared (FO-FTIR) Sensing Algorithm validation is required for multi-class classification.
Feature: Continuous wavelet transform-based features
Classifiers: MLP, SVM and LR
[22] Features: SIFT-based texture features, CNN’s spatial features and Fisher High classification accuracy is achieved.
vector calculation Feature size is large due to SIFT and CNN.
Classifier: Concatenation of CNN, FVFC and SVM The use of CNN for feature extraction and integrating multiple
classifiers makes the system computationally intensive.
[24] Database: Florescent microscopic images SVM outperformed CNN for 3-class classification.
Images are enhanced using dual-scale Laplacian of Gaussian
Features: morphological features
Classifier: Naïve classifier, SVM and CNN
[25] Database: DIBAS 20 classes were used for classification.
Features: shape, color, size, number of clusters, cluster shape, density The claimed accuracy is 90.45%.
and cell distribution The classifiers’ details are not provided.
Classifier: Weighted average of Seven classifiers
[26] Features: obtained using autoencoder feature extraction. Hyperparameter optimized using PSO.
Classifier: CNN Training time is reduced in GA optimization.
Genetic algorithm used to learn the best hyperparameter for CNN. Categorized data in three classes with 94.9% accuracy.
[31] Database: DIBAS A large number of training and testing datasets, i.e. 6600 images after
Features: Convolutional features augmentation, were used.
Classifier: CNN The model succeeded with an accuracy of 98.22% with a large training
Data augmentation is used in the training network. time.
[34] Database: DIBAS Atrous convolution is used in VGG16 instead of spatial convolution.
Features: Convolutional features Achieve an accuracy of 93.38%.
Classifier: pre-trained VGG16 network Large learnable parameters i.e. 134.4M
[35] Database: DIBAS Transfer-learning approach to training the networks and hence less
Features: Convolutional features training time
Classifier: Shufflenet and the squeezenet neural network The network has the least number of parameters; however, its
Data augmentation using zooming and doubling to improve the precision and recall are very low.
network accuracy.
[36] Database: DIBAS Depth-wide convolution operations were used in feature extraction.
Features: Convolutional features Accuracy is 86%.
Convolutional features without image augmentation
Classifier: CNN

bacteria has a different pose or shape. The first layer extracts features
representing different parts of the shape, for example, curves in each
shape. The layer parameters, i.e., stride and spatial dimension, are
changed accordingly. Further non-linearity is induced in the feature
map using a rectified linear unit function (ReLU). The number of
convolution layers is determined with a specific application in hand.
The obtained scaler output from the convolution layers is stacked into
tiny decks in the capsule layer, where a small subset of each deck is
referred to as a capsule. This capsule stores valuable information like
size, hue, angle, thickness, etc. Thus, this capsule gives the position
and orientation of each part in 2D space. The length of this small
deck gives the likelihood of entity presence and parameter information
encoded in its orientation [37]. The functionality of the capsule layer
is illustrated in Fig. 3, where 𝑢1 , 𝑢2 , and 𝑢3 represent the capsule, 𝑊
is the transformation matrix, 𝑉 gives the predicted features, and 𝐶 is
the assigned weight. These primary capsules create secondary capsules,
representing the probability that the input bacterial image belongs to
each possible class. The network’s final output is a set of class capsules,

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J.P. Chaudhari et al. Engineering Science and Technology, an International Journal 46 (2023) 101500

Fig. 2. Architecture overview of the proposed capsule network-based method.

operation can be expressed as:

∑
𝑠𝑗 = 𝑐𝑖,𝑗 𝑣𝑗,𝑖 (2)
𝑖

Squashing Function: The information is condensed in this last

component. The role of the squashing function is to take all the
information and convert it into a vector that is less than or equal
to 1. It also maintains the direction of the vector. Step, Sigmoid,
Tanh, and ReLu are the variants of the squashing function. ReLU
is not saturated and computationally simple; it has been used in
the proposed design. The squashing operation is obtained using
Fig. 3. Capsule layer functionality using matrix multiplication and squashing.
the following equation:
‖𝑠𝑗 ‖2 𝑠𝑗
𝑣𝑗 = (3)
each containing a probability distribution over the possible classes. The 1 + ‖𝑠𝑗 ‖2 ‖𝑠𝑗 ‖
bacterial class with the highest probability is the predicted class for the 𝑣𝑗 ≈ ‖𝑠𝑗 ‖𝑠𝑗 , for 𝑠𝑗 is small
input image. ‖𝑠𝑗 ‖ (4)
The capsule network has four significant processes which make it 𝑣𝑗 ≈ , for 𝑠𝑗 is large
𝑠𝑗
distinct from other conventional CNN:
c. Dynamic routing algorithm: The dynamic routing algorithm per-
a. Matrix Multiplication: The matrix multiplication is applied to un- mits the various components to transfer information. It is an iter-
derstand the spatial part of the image. Here, the transformation ative process where higher-level capsules get input from lower-
matrix is multiplied by the vector obtained from the preceding level capsules. This routing algorithm adjusts the weights 𝑐𝑖,𝑗
convolution layer producing the higher-level feature vector v. in the scalar weighting function. In Eq. (1) a, 𝑣𝑗,𝑖 expresses the
The matrix multiplication operation can be expressed as: prediction from capsule 𝑖 on output capsule 𝑗. The 𝑣𝑗 expresses
the similarity between the two capsules. Let the similarity vector
𝑣𝑖,𝑗 = 𝑤𝑖,𝑗 𝑢𝑖 (1) is expressed using 𝑏𝑖,𝑗 as:

b. Scalar weighting of the input: It is responsible for computing 𝑏𝑖,𝑗 = 𝑣𝑗,𝑖 𝑣𝑗 (5)
a higher-level capsule that would receive the current capsule
The weight coefficient 𝑐𝑖,𝑗 is computed using the softmax of 𝑏𝑖,𝑗
output. If all outputs 𝑣1 , 𝑣2 , 𝑣3 have the same prediction, then
as
a weighted combination of feature vectors 𝑣1 , 𝑣2 , 𝑣3 increases ∑ 𝑏
the probability of predicting the following layer features. This 𝑐𝑖,𝑗 = 𝑒𝑏𝑖,𝑗 ∕ 𝑒 𝑖,𝑗 (6)

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J.P. Chaudhari et al. Engineering Science and Technology, an International Journal 46 (2023) 101500

Fig. 4. 9-patches, 196-bins histogram of the sample image.

The architecture of capsule networks consists of six layers. The first

three layers are the encoders. Encoders convert the input image into
a vector. The last three layers are called decoders. Finally, decoders
reconstruct the image using vectors. The configuration of the capsule
network for the bacterial classification requires input data size, the total
number of classes, and the routing iteration.

3.2. Histogram-oriented feature sets:

Creating a large dataset for training the neural network is time-

consuming. And designing and training a network without a good
number of datasets is the most challenging task. Augmentation is
widely employed to increase the dataset’s size. However, the quality of
augmented datasets heavily relies on the original datasets. Therefore,
the augmentation process may need a system to evaluate the aug-
mented datasets. In the proposed network, we used histogram features
with the capsule network. The histogram of color helps the neural
network exploit color information in an image. This also reduces the
size of the features in the capsule network’s first layer.
In the image, pixel color is represented using a 3D vector, where
each vector gives red, green, and blue colors. The hue-saturation-value
(HSV) space separates color components, making the histogram less
susceptible to color variation. Therefore, an RGB color space with
three histograms for each color component is proposed. We used a
histogram of nine patches with 196 bins in the experiment. These
generated patches are shown in Fig. 4. The histogram bins used in the
experiment are 196 bins (whole image), 2 × 98 (horizontal patches),
2 × 98 (vertical patches), and 4 × 49 (horizontal and vertical corner
patches). Thus, 784 histograms are obtained as feature vectors from
the image and are used to train the capsule network.
The process using this capsule network is as follows:
• Pre-processing: In this step, bacteria images are preprocessed for
noise removal using median filtering. Median filters are applied
to each image channel separately. Then the three image channels
are combined again.
• Features Extraction: In the feature extraction phase, histogram-
based features from the noise-free images are extracted. Nine
patches are obtained, and their 196 bins are concatenated to
create the feature vector. Finally, this feature vector is resized to
an image, and a 2D capsule network is used.
• Classification: Bacteria images are classified into various types
using a capsule network. The capsule network is trained using
the histogram features of patches. Different optimization func-
tions are also tested during training to see their performance.
Finally, the proposed capsule network architecture’s performance
is compared with KNN, decision trees, Naïve Bayes, SVM, and
deep learning methods.
The proposed method for bacteria classification is depicted in Fig. 5.
Fig. 5. Flowchart of the proposed method for bacteria classification (Solid line
represents network training and dotted lines represent network testing).
optimization; (ii) optimization in the training process, i.e., optimizing
learning rate, loss function, batch size, epoch, and activation function;
and (iii) optimizing the regularization hyper-parameters, i.e., L1, L2,
and drop-out regularization values. The optimum selection of learning
rates provides faster convergence. And it tunes the weights in the
backpropagation process, improving the neural network’s performance.
Therefore, various optimizers have been tested with the proposed cap-
sule network to minimize losses. The summary of the primarily used
optimizer with CNN networks is as follows:
Loss reduction can be achieved by optimizing the network. The
optimizer adjusts or tunes the weights and learning rate to reduce loss.
However, many optimization functions keep the learning rate constant.
Therefore, various optimizers have been tested with the proposed cap-
sule network to minimize losses further. The summary of the primarily
used optimizer with CNN networks is as follows:
(a) Stochastic Gradient Decent (SGD): This model updates the net-
work’s parameter after loss computation on each training sample and
offers less convergence time. It adapts both the learning rate component
(𝛼) and gradient of the learning rate (𝜕𝐿∕𝜕𝑤) to update the weight
parameters as expressed in the equation below. But there is a high
fluctuation in the parameters; hence, it has a high variance.
𝜕𝐿
𝑤𝑡+1 = 𝑤𝑡 − 𝛼 (7)
𝜕𝑤
(b) AdaGrad: This second-order optimizer changes the learning rate
for each parameter at every step. Thus, it avoids manual tuning of the
learning rate. The weight update equation can be expressed as follows:

𝛼 𝜕𝐿
3.3. Network optimization: 𝑤𝑡+1 = 𝑤𝑡 − √ (8)
𝑣𝑡 + 𝜀 𝜕𝑤𝑡
Optimizing the network can reduce the loss. There are mainly three However, its learning rate is a monotonically decreasing function,
categories of CNN hyper-parameter optimization. (i) network structure and the second-order derivative is computationally intensive.

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J.P. Chaudhari et al. Engineering Science and Technology, an International Journal 46 (2023) 101500

(c) AdaDelta: AdaDelta solves the decaying problem of learning rate 4. Experiments and results
by accumulating all past squares of gradients over a fixed window
size. The equation below replaces the learning rate component with 4.1. Experiment setup:
the exponential moving average of the square delta (𝐷). However, it is
computationally expensive. The proposed experiment integrates color information into the cap-
√ sule network for classification. The proposed method is tested on the
𝐷𝑡+1 + 𝜀 𝜕𝐿
𝑤𝑡+1 = 𝑤𝑡 − √ (9) DIBaS dataset [22] with 660 (33 bacteria species 𝑥 20 images per
𝑣𝑡 + 𝜀 𝜕𝑤𝑡
species) images. The image resolution is 2048 × 1532 pixels. The sam-
Where, ple images from the dataset are shown in Fig. 6. Parameters are tuned to
[ ] obtain better accuracy. The bacteria images obtained from the dataset
𝐷𝑡 = 𝛽𝐷𝑡−1 + (1 − 𝛽) 𝛥𝑤𝑡 (10)
are preprocessed for noise removal. Median filtering is applied for
[ ] each channel separately. Then, the noise-free image is merged. During
𝜕𝐿
𝑣𝑡 = 𝛽𝑣𝑡−1 + (1 − 𝛽) (11) the feature extraction phase, histogram-based color feature extraction
𝜕𝑤𝑡
is performed. As explained in Section 3, nine patches representing
𝛥𝑤 = 𝑤𝑡+1 − 𝑤𝑡 (12) global and local histograms of color images are used as a feature
vector. Eventually, because of the patch generation, the experiment
(d) Root Mean Square Propagation (RMSP): RMSP is an adaptive
does not require augmentation to overcome the overfitting problem due
learning approach for improving AdaGrad. A cumulative sum of a
to limited datasets. These features are used for training the system. The
gradient in AdaGrad may become a stuck model when close to con-
train–test split algorithm randomly splits the test and train data. We
vergence. RMSP overcame this problem using exponential moving and
have used 70% data for training and 30% of the data for testing the
avoided the aggressive decay in the learning rate. Update the weight
network during our experimentation. Various classification algorithms
as follows:
are trained, including KNN, decision trees, Naïve Bayes (NB), SVM, and
𝛼 𝜕𝐿 conventional CNN. The performance of the trained system is evaluated
𝑤𝑡+1 = 𝑤𝑡 − √ (13)
𝑣𝑡 + 𝜀 𝜕𝑤𝑡 using 30% test data in terms of accuracy, precision, recall and f-
(e) Adaptive moment estimation (Adam) combines the gradient measure. The hyperparameters of each classifier are listed in Table 2.
descent function with momentum and RMSP. Thus, using these two The hyper-parameters are tuned using a grid search algorithm, and a
methods’ advantages optimizes gradient descent more. In addition, it 10 K-fold cross-validation is used to validate the models.
offers fast convergence and resolves the learning rate. The weight can A conventional CNN network is designed with four hidden layers
be updated by using and a max-pooling operation. The last two layers are dense, and the
𝛼 overall trainable parameters for this CNN are 27727. The structure of
𝑤𝑡+1 = 𝑤𝑡 − √ 𝑚
̂𝑡 (14) the capsule network used for the proposed experiment is presented in
𝑣̂𝑡 + 𝜀
Table 3.
where,
𝑚𝑡 𝑣𝑡 4.2. Results and discussion:
̂𝑡 =
𝑚 and 𝑣̂𝑡 = (15)
1 − 𝛽1𝑡 1 − 𝛽2𝑡
(f) AdaMax: Adam’s generalization is AdaMax, where the l2-norm The capsule network is trained with 100 iterations. Training can run
of Adam is changed to 𝑙∞ , and sometimes, it can produce better well if we also use validation data. The learning rate value is initialized
optimization than Adam. Therefore, the weight is updated as follows: to 1e-3, which adjusts the speed of the parameter to be updated. The
𝛼 experiment is performed with 30 epochs; images are shuffled in each
𝑤𝑡+1 = 𝑤𝑡 − 𝑚 ̂ (16) epoch, and validation data is used with a validation frequency 30. The
𝑣𝑡 𝑡
model is further evaluated to find the best optimizer. All quantitative
where,
parameters are assessed and listed in Table 3. Informally, accuracy
𝑚𝑡
̂𝑡 =
𝑚 (17) refers to the percentage of correct predictions made by our model. The
1 − 𝛽1𝑡 following is the formal concept of accuracy:
𝜕𝐿
𝑚𝑡 = 𝛽1 𝑚𝑡−1 + (1 − 𝛽1 ) (18) Number of correct prediction
𝜕𝑤𝑡 Accuracy =
( ) Total number of prediction (21)
| 𝜕𝐿 |
𝑣𝑡 = 𝑚𝑎𝑥 𝛽2 𝑣𝑡−1 , || |
| (19) =
𝑇𝑃 + 𝑇𝑁
| 𝜕𝑤𝑡 | 𝑇𝑃 + 𝑇𝑁 + 𝐹𝑃 + 𝐹𝑁
(g) NAdam: The inclusion of Nesterov momentum in ADAM instead Where true positive (TP) is the correct prediction of bacteria, false
of RMSP creates a NAdan optimizer. Two problems in ADAM sometimes negative (FN) gives sensitivity to the model, false positive (FP) pro-
cause worse optimization. Firstly, the stochastic gradient update is not vides specificity to the model, and true negative (TN) gives a correct
within the historical gradient span. Secondly, magnitude parameters prediction of the negative bacteria. Using these parameters, precision,
cause variation in network function; however, the magnitude of Adam recall, and F-Score, exactness and completeness can be measured using
parameters is unaffected by the gradient descaling. Therefore, tweaking the Eqs. (22) and (24).
Adam is proposed [38] considering the 𝑙2 -norm of the gradient vector 𝑇𝑃
instead of the magnitude of the gradient vector. The NAdam optimizer Precision = (22)
𝑇𝑃 + 𝐹𝑃
is expressed as follows:
( ) Recall =
𝑇𝑃
(23)
𝛼 1 − 𝛽1 𝜕𝐿 𝑇𝑃 + 𝐹𝑁
𝑤𝑡+1 = 𝑤𝑡 − √ ̂𝑡 +
𝛽1 𝑚 (20)
𝑣̂ + 𝜀
𝑡
1 − 𝛽 𝑡 𝜕𝑤𝑡 1 Precision x Recall
F-Score = 2 ∗ (24)
where 𝑚𝑡 is expressed in Eq. (18) and 𝑣𝑡 is obtained using Eq. (11). Precision + Recall
Optimizers mentioned above have been widely used in many CNN- Better optimizers are primarily concerned with being quicker and
based applications. The selection of a particular optimizer can lead to more effective, but they are also frequently recognized for being more
better loss reduction. Therefore, the proposed model is tested with these generalizable (less overfitting) than others. The selected optimizer has
optimizers and finds the best fit for classification. a significant impact on how well the model works.

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J.P. Chaudhari et al. Engineering Science and Technology, an International Journal 46 (2023) 101500

Fig. 6. Sample images from DIBaS dataset used in experiments.

Table 2
Hyper-parameters for classifiers.
KNN: LDA:
N 5 No of components 2
Nayeve Base: SVM:
Variance 1e−9 Kernel RBF
Capsule:
Batch size 100 Epoch 50
Learning rate 0.001 Routing 3
Node in primary caps 256 Dimension of each capsule 8
Routing time 5 Batch Size 100

Table 3
Layer structure of the proposed capsule.
Layer Output Shape Parameters Connected to
input_1 (Input Layer) (None, 28, 28, 1) 0
Convolution layer (None, 20, 20, 256) 20992 Input Layer
Primarycap_conv2D (None, 6, 6, 256) 5308672 Convolution layer
primarycap_reshape (None, 1152, 8) 0 Primarycap_conv2D
primarycap_squash (None, 1152, 8) 0 primarycap_reshape
Secondarycap_conv2D (None, 2, 16) 294912 primarycap_squash
input_2 (InputLayer) (None, 2) 0
Mask (None, 32) 0 Secondarycap_conv2Dinput_2 (InputLayer)
capsnet (Length) (None, 32) 0 Secondarycap_conv2D
decoder (Sequential) (None, 28, 28, 1) 1345808 Mask
Total parameters 6,970,384
Trainable parameters 6,970,384
Non-trainable parameters 0

however, NADAM trained the model faster than other optimizers. On

Fig. 7. Accuracy analysis over the epochs of various optimizer.
Fig. 7 shows the convergence of the various optimizers over the
epoch. The ADAM takes time to converge but obtains the best accuracy
among all. The performance of NADAM, RMSP, and ADAMAX is close;
the other hand, SGD and Adadelta have the lowest performance com-
pared to other optimization functions. The obtained training loss and
testing loss graph for ADAM is presented in Fig. 8.
A confusion matrix obtained from a proposed network gives valu-
able insights into the model’s performance in classifying images into
their respective categories. A five-fold confusion matrix in Fig. 9 shows
the model’s performance for each class. A few types are not classified,
for example, Staphylococcus aureus and Staphylococcus saprophyticus,
because of their color, shape, and orientation similarity.
The precision vs recall curve (PR curve) can provide insights into
the performance of the CNN for different classification thresholds.
A high precision value indicates that the CNN correctly classifies a
high proportion of predicted positive cases. In contrast, a high recall
value suggests that CNN correctly classifies a high proportion of actual
positive cases. Fig. 10 shows the PR curve for validation datasets.
Further analysis using precision, recall, F1-score, and accuracy for
each optimizer is presented in Table 4. ADAM provides the best perfor-
mance among all optimization models. Therefore, ADAM is used with
the capsule network to obtain a better classification rate.
Further, various classifiers, i.e., KNN, decision trees, Naïve Bayes,
and SVM, have been considered to validate the model. The histogram-
based features are obtained from the noise removal images in all these

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J.P. Chaudhari et al. Engineering Science and Technology, an International Journal 46 (2023) 101500

Table 4
Performance evaluation of capsule network with different optimizer.
Optimizers Precision Recall FMeasure Accuracy
Adadelta 0.59106 0.49751 0.44701 0.49751
Adagrad 0.734236 0.676617 0.650898 0.676617
Adam 0.959886 0.960796 0.942739 0.950796
Adamax 0.774883 0.716418 0.704564 0.716418
Nadam 0.764819 0.721393 0.695114 0.721393
RMSP 0.751382 0.726368 0.708243 0.7263
SGD 0.131922 0.447761 0.195412 0.44776

Table 5
Performance measurement of various machine learning algorithms.
Parameter Precision Recall F Measure
KNN 0.78312 0.731343 0.717629
DT 0.660978 0.616915 0.614203
Fig. 8. Training and Testing loss of proposed model using ADAM. NB 0.652992 0.59204 0.586787
SVM 0.722511 0.686567 0.66932
Deep Learning CNN 0.709105 0.656716 0.640989
Capsule networks 0. 959886 0. 960796 0. 942739

classifiers. Table 5 presents the performance using precision, recall,

Fig. 9. Confusion matrix for 33 classes.
and F-measure. As depicted in Table 5, capsule network-based classi-
fication performance is better than other supervised machine learning
techniques.
Further, a comparison of the proposed model with literature hav-
ing a CNN-based bacterial species classification model is presented
in Table 6. The results reported in Table 6 show that the proposed
capsule network generates consistent results with one or more param-
eters better than other implemented methods. In [34], Patel performed
atrous convolution using VGG 16 to achieve an accuracy of 93.38%.
In contrast, Garcia et al. [35] used a transfer-learning approach to
train the shufflenet and the squeezenet neural networks. Their model
has the least parameters; however, its precision and recall are very
low. In [39], Talo used the 5-fold cross-compilation technique and
achieved an accuracy of 99.10%. In [36], CNN was modified using a
depth-wide convolution operation and validated using augmentation
and without augmentation. They succeeded in obtaining 86% accuracy
without image augmentation. In [22], the authors extracted features
using a Fisher vector, and SVM was used for classification. They re-
ceived 83.4% accuracy among all classes. A conventional convolution
operation is replaced with depth-wise convolution in CNN, and species
classification is presented with an overall accuracy of 86%. The number
of parameters for each model is also listed in Table 3. It suggests that
the proposed model successfully maintains an accuracy of 95.08% and
requires few training parameters, i.e., 6.9 M, compared to other models.

5. Conclusions and future works

In the medical domain, diseases are predicted by analyzing patient

Fig. 10. Precision vs. Recall curve.
classifiers. It has been observed that a histogram-oriented capsule net-
work provides maximum accuracy compared to other machine-learning
samples. Identification of appropriate bacteria types and microorgan-
isms plays an important role. In earlier days, this was done manually
using microscopic image observation. But the manual process is time-
consuming and complex. In this paper, we have proposed an automated
methodology for classifying bacteria images into the appropriate type.
Thirty-three bacteria species were used for analysis and classifica-
tion. In this study, capsule network-based bacteria classification using
histogram-based features is employed to classify bacteria species into
33 classes. This model has reached an average classification accuracy of
95.07%, and the total training parameters are 6.9M. The performance
of the proposed system is compared with that of various classifiers,
including KNN, decision trees, Naïve Bayes, SVM, and deep learning.
The proposed model uses histogram features in classification. The
similarity in shape and orientation in a few classes has a similar
histogram; therefore, the model fails to classify such classes. So global
and local histogram concatenated feature sets can be used in the future

9
J.P. Chaudhari et al.
Table 6
A quantitative comparison with various machine learning frameworks without image augmentation.
CNN Methods No of images Parameters
Atrous convolution based VGG 16 [34] 660 134.5 M
Squeeznet_1_0 [35] 669 0.751 M
Shufflenet_V2 [35] 669 5.543 M
FisherVector SIFT + SVM [22] 660 58.42 M
Depthwise Separable CNN [36] 689 3.23M
Proposed Capsule network 689 6.9M
to improve performance. Further used datasets have a limited set of
images for each class, which may weaken the model in the training
process. A further extension of datasets with appropriate preprocessing
algorithms needs to be investigated. Thus, the main focus is to improve
the system’s performance by considering different combinations of
features, reductions in execution time, and extensions of datasets.
CRediT authorship contribution statement
Jitendra P. Chaudhari: Conceptualization of this study, Methodol-
ogy. Hiren Mewada: Software, Writing – original draft. Amit V. Patel:
Software, Writing. Keyur Mahant: Modification for the final layout.
Declaration of competing interest
The authors declare that they have no known competing finan-
cial interests or personal relationships that could have appeared to
influence the work reported in this paper.
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Jitendra P. Chaudhari received the B.E. degree in Electronics Engineering from
Nagpur University, Nagpur, M.E. degree in Industrial Electronics engineering from M.S.
University, Baroda, Gujarat, India and Ph.D. from Charotar University of Science and
Technology in 1996, 2001 and 2016 respectively. He is working as Associate Professor
in Department of Electronics and Communication Engineering at Charotar University
of Science and Technology, Changa, Gujarat. Presently he is deputed as Coordinator,
CHARUSAT Space Research Technology Center. He is member of IE(I) and IETE. His
research interest includes, Image Processing, RF and Microwave.
11
Engineering Science and Technology, an International Journal 46 (2023) 101500
Hiren K. Mewada has obtained his M.Tech. and Ph.D. degree from Sardar Vallbhbhai
National Institute of Technology — Surat, Gujarat, India. Presently he is Assistant
Research Professor at Prince Mohammad Bin Fahd University, Kingdom of Saudi Arabia.
Previously he was associate professor at Charotar University of Science and Technology,
Gujarat, India. He has more than 17 years teaching experience. His current areas of
interest are computer vision, signal processing, machine learning and Embedded System
design. He has published more than 60 research papers and completed several funded
research projects. He is coauthor of one book and published five book chapters. He is
member of IETE and ISTE.
Amit Patel completed his Ph.D. from Charusat University in 2015. He is presently
working as an Associate scientist in Charusat Space Research and Technology center
and Assistant Professor in Electronics and Communication Engineering Department,
CSPIT change. He is associated with a number of research projects sponsored by the
Board of Research in Nuclear Science and SAC-ISRO, Govt. of India. He has published
more than 40 research papers in various international journals and conferences.
Keyur Mahant is an Assistant Scientist/ Professor at CHARUSAT Space Research and
Technology Center, Changa, Gujarat, India. He received B.Tech. in Electronics and
communication from C U Shah College of engineering and technology, India in 2008.
He has also received M.Tech. in Communication system from CHARUSAT University,
India in 2011. He is currently involved with the microwave filters, power dividers
and circulator design using SIW technology for FMCW Radar Application, funded by
Board of Research in Nuclear Sciences (BRNS), Department of Atomic Energy (DAE),
Government of India.