ISSN: 2229-6956 (ONLINE)
DOI: 10.21917/ijsc.2019.0258 SPECIAL ISSUE ON ARTIFICIAL INTELLIGENCE AND DEEP LEARNING, JANUARY 2019, VOLUME: 09, ISSUE: 02
RECOGNITION OF PATHOGENS USING IMAGE CLASSIFICATION BASED ON
IMPROVED RECURRENT NEURAL NETWORK WITH LSTM
S. Rajanarayanan, Lea Sorilla Nisperos and J.R. Ephraim Basal
Department of Computer Science Engineering, Arba Minch University, Ethiopia
Abstract
In this paper, a technique is proposed on Recurrent Neural Network
(RNN) with the end goal to group pathogen with five Deep learning
stages: preparing dataset images, RNN training, testing the RNN
model with collected images, Apply RNN created show on testing
information lastly and evaluate the performance of the proposed
method. RNN can enhance the precision in pathogens determination
that are centered around hand-tuned include extraction suggesting
some human oversights. For our examination, we consider cholera
affected images i.e. Vibrio cholera pathogen image for minute images
classification with a significant RNN. Image classification is the
responsibility of consideration the image information and obtaining
perfect likelihood of classes that best portrays the image. In spite of
the fact that this archive tends to the order of pandemic pathogen
Images utilizing a RNN demonstrate, the hidden standards apply to
alternate fields of science and innovation, as a result of its execution
and its capacity to deal with a larger number of layers than the past
customary neural networks.
Keywords:
Images Classification, Deep Learning, Recurrent Neural Networks,
LSTM
1. INTRODUCTION
The continuous advance of wise information investigation
techniques offers new opportunities and challenges for a wide
range of logical issues, including risk management and image
review. We had linked information mining methods on the
Satellite images in previous works [16], for the disclosure of
hazardous regions in television transmission studies. The
transmission study is a tele-survey of the spread, use of data and
correspondence advances, of diseases transmitted by water, air or
vehicles identified by climate, meteorological and natural
variables [19].
In this context, the cholera plague in the region of Mali in
Mopti, West Africa, has been investigated. In order to process
Landsat satellite imaging in a similar area for different periods,
we have concentrated our efforts on guided characterization
(Maximum Likelihood) calculations [1]. In order to find
fascinating relationships among factors a standard machinery-
based learning strategy with affiliation rules were also linked.
The results from membership decisions show that the level of
the Niger River and some social components in wintering times
influence the variety of cholera disease rates in Mopti. The current
level is increasingly high and the defilement rate is high at 66
percent [16]. The idea of connecting the nature with the pandemic
has been established and such uncertain conditions will emerge
when the general public’s attention to the issue and dislike
arrangements is completely critical to mitigating the creation and
development of the plague.
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With the end goal to outflank our past outcomes and reinforce
the limit of plague emergency administration, this paper
investigates Deep Learning Images acknowledgment to naturally
characterize pestilence pathogens Images through a magnifying
instrument. We help today with the progressive substitution of
numerous applications dependent on the old traditional systems
of machine learning in PC vision by new and rising ones with
Deep learning [6] [12].
Similarly, there is as yet a need to enhance the exactness in
pathogens finding strategies that are centered around hand-tuned
highlight extraction inferring some human oversights [15]. For
example, intestinal sickness parasites might be ignored on a thin
blood film while there is a little parasitemia. Deep Recurrent
Neural Networks is the standard for Image acknowledgment for
example in manually written digit acknowledgment with a back-
spread system [12].
RNN helps to manage information inquiry issues in large
spaces by giving a calculation class to unlock the unpredictable
circumstance and by providing fascinating open doors on the basis
of the symmetry [14].
The new trend of computerized reasoning, and the important
for a few areas: the visual or visual exam, the facial recognition
[3], the acknowledgement of catastrophe [17], the recognition of
the voice, the PC's vision [10] and the manipulation of a
mechanized dialect [5], Deep learning is a calculation
arrangement, which means that information displays abnormal
status reflections using a deep chart with numerous handling
layers [7]. In the last decade, Deep learning has gained fame
because it has been able to learn information portraits in a non-
controlled and managed way and to summarize inconspicuous
information tests that use several leveled portrayals.
Our investigations are situated towards RNN approach of
Deep Learning, while much research has been led in this field, as
far as anyone is concerned uncommon of them have put a genuine
accentuation on the RNN for the recognizable proof of scourge
pathogens by minuscule examination. In this way, when a scourge
happens, tiny examinations are made to affirm or not the presence
of the pestilence pathogen in presumed cases. Be that as it may,
there is regularly an absence of masters in the treatment of
magnifying instruments, consequently the need to make the tiny
investigation abroad with extra costs [16]. This results in an
extensive loss of time and meanwhile, the pestilence keeps on
spreading. To spare time in the investigation of tests, we propose
to make the RNN to make the classification better to classify the
images with pathogens or not.
2. RELATED WORK
Deep learning is the mainstream region of machine realizing
which endeavors to learn abnormal state deliberations in
S RAJANARAYANAN et al.: RECOGNITION OF PATHOGENS USING IMAGE CLASSIFICATION BASED ON IMPROVED RECURRENT NEURAL NETWORK WITH LSTM

information by using progressive models. From [12], the 3. METHODOLOGY TO PATHOGENS USING
achievement of Deep Learning is because of the accessibility of IMPROVED RNN
equipment (Central Processing Units (CPUs), Graphics
Processing Units (GPUs), and Hard plate, and so forth.),
Microscopic analysis will confirm whether the sample is
machine learning calculations and enormous information, for
infected with Vibrio cholera pathogen, or not [9]. The contagious
example, Mixed National Institute of Standards and Technology
epidemic of cholera mainly caused by infected water that contains
(MNIST) written by hand digit informational collections and the
Vibrio cholera, a pathogen [4]. Sudden and abundant diarrhea
ImageNet information [11]. Deep Learning is applicable for a
(gastroenteritis) leading to severe dehydration is characterized by
few areas: manually written digit grouping, the capable of being
cholera. Worldwide, there are 2.8 million cases and nearly
heard or visual flag examination, facial acknowledgment,
100,000 deaths annually are the critical victims. Vibrocholera is a
catastrophe acknowledgment, voice acknowledgment, PC
bacterium gram-negative, comma-like, mobile and humanly
vision, and robotized handling [8].
responsible for cholera that could have severe consequences as an
In horticulture zone, deep Recurrent systems are an infectious disease. The malaria is an infectious disease, with an
advantage to avert harm caused by rural irritations, this estimated 212 million cases in 2015, with 429,000 deaths in 2015,
examination enhances rural generation and the capacity of yields the world's leading cause of mortality and morbidity.
with the precision of 98.67% for 10 classes of harvest bother
Images with complex farmland foundation [5]. In a similar
territory, Grinbat [6] utilize deep Recurrent neural systems Training dataset
(DRNN) for plant distinguishing proof by grouping three using Vibrio
diverse vegetable species: white beans, red beans, and soybeans. Cholera images
For distinguishing proof of rice infections, Lu [18] likewise
utilize DRNN systems through Image acknowledgment
accomplishing the exactness of 95.48% with 500 regular Images
of unhealthy and solid rice leaves and stems. In visual RNN Training with
acknowledgment, they investigate DRNN to characterize a LSTM for
hyperspectral Image with an enhanced precision. For remote classification of
detecting scene characterization, three conceivable techniques pathogens
in particular; full preparing, tweaking, and utilizing ConvNets
as highlight extractors [7].
Testing data with
Deep Learning is a sort of Neural Network Algorithm
RNN with different
accepting metadata as an information and procedures this
sets of test data
information through a few quantities of layers of the non-direct
change the yield order. In any case, beforehand, in Traditional
Pattern Recognition (Fig.1), the procedure of highlight Evaluation of images
extraction was made by the master of the region as well as the classified
software engineer and, after that the future rundown is submitted
to establish Network Neuron for the characterization of
information. High quality Feature Extractor stage is repetitive,
requires input information learning lastly takes quite a while. Non-
Pathogens
pathogens
The basic property of Deep learning calculations is
programmed extraction of highlights (Fig.2). This implies this Fig.1. Pathogen Classification using RNN
calculation naturally gets a handle on the applicable highlights
required for the arrangement of the issue. This diminishes The proposed methodology consists of five phases:
crafted by the pro to choose includes expressly, similar to the
Step 1: Collection of Training dataset;
case with customary example acknowledgment techniques. This
can be utilized to understand regulated, unsupervised or semi- Step 2: Design of RNN classification model
administered kinds of issues. The Deep Learning Neural Step 3: Evaluation of image classification
Network has something like three concealed layers, generally a a. Provision of microscope training dataset images
few layers thus it is deep on the off chance that it has in excess
of one phase of non-direct element change [12]. Each shrouded b. Training modified RNN architecture
layer made out of an arrangement of neurons is in charge of c. Preparation of test dataset
preparing the remarkable arrangement of highlights dependent d. Testing the modified RNN model and
on the yield of the past layer. As the quantity of shrouded layers e. Classification Evaluation.
expands, the multifaceted nature and deliberation of information
additionally increment. 3.1 RNN CLASSIFICATION MODEL
The model created by the RNN is saved for loading the
considered data after training. In order to assess the accuracy of
the model, the RNN model is applied at all times with test data.
The complete RNN architecture for the classification of epidemic

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SPECIAL ISSUE ON ARTIFICIAL INTELLIGENCE AND DEEP LEARNING, JANUARY 2019, VOLUME: 09, ISSUE: 02

pathogens provides a fully connected layer to the training htl  o tanh  ctl  (6)
architecture. We have used the Softmax function for the final
classifier. where, sigm and tanh are used element-wise in Eq.(3)-Eq.(6). The
LSTM equations are shown in Fig.2.
3.2 RNN TRAINING
The RNN model is training with seven hidden layers as
follow: 6 convolution layers, with the same architecture in each
convolution layer followed by a ReLU element-wise nonlinearity
Input gate i Cell O Output
gate

and a 22 MaxPooling. The criterion for choosing of the number

Cell
of convolution layer is related to the convergence of the error rate
during the learning process. g Ct
In this case, it takes 5 or 6 iterations (particularly by increasing Input
the number of convolution layers) for the calculation to converge. Modulation
Gate
RNN training architecture for this work is summarized in (Fig.1).
Stochastic gradient descent is used for RNN training using small f Forget gate
and equal batches of random data for each iterative learning
phase.

3.3 LONG SHORT TERM MEMORY

Fig.2. A graphical representation of LSTM memory cells
A LSTM network uses various gates to control the input and
output from the recurrent units. In this section we describe the The main contribution of this document is a recipe for the
deep LSTM. Next, we show how to regularize them, and explain successful reduction in overfitting of LSTMs. The main idea is
why our regularization scheme works. only for the non-recurring connections to use the opt-out operator
We let subscripts denote timesteps and superscripts denote (Fig.3). The following is a more precise description of where D is
layers. All our states are n-dimensional. Let htl N be a hidden the drop-out operator who sets its argument to zero by random
means.
state in layer l in timestep t. Moreover, let Tn,m : N  M be an
affine transform (Wx+b for some W and b). Let ⊙ be element-  i   sigm 
wise multiplication and let ht0 be an input word vector at timestep
 f   sigm   D  htl 1  
  T   (7)
k. We use the activations htL to predict yt, since L is the number of  o   sigm  2 n ,4 n  h l 1 
     t 
layers in our deep LSTM.  g   tanh 
Deterministic transitions from previous to current hidden ctl  f ctl1  i g (8)
states can be used to describe RNN dynamics. The deterministic
change of state is a feature htl  o tanh  ctl  (9)
l 1 l 1
RNN : h , ht t 1 h l
t (1) The drop-out operator corrupts the information supplied by
This function is provided for classical RNNs the units, forcing them to perform their intermediate calculations
more robustly. At the same time, all information from the units
htl  f Tn,n htl 1  Tn,n htl1  (2) should not be deleted. It is particularly important that the units
recall events that occurred in the past many times. The Fig.4
where f {sigm, tanm}. shows how information could be transferred from an event
The LSTM has complicated dynamics, which allow occurring in step t−2 to the time t+2 forecast in our
information to be easily “specified” for a long time. The memory decommissioning execution. We can see that the information has
“long-term” is stored in a cell vector. Although many LSTM been corrupted exactly L+1 times by the drop-off operator, and
architectures differ in their connectivity and activation structure, this number is independent of the number of times the data passes.
they have explicit memory cells for long term data storage for all Standard drop-out disrupts recurring links, which makes the
LSTM architectures. The LSTM can decide whether to overwrite, LSTM difficult for long-term storage of information. The LSTM
retrieve or maintain the memory cell for the next step. The can take advantage of decrease regulating without sacrificing its
following is an indication of the LSTM architecture used in our valuable storage capability by not using drop off of recurring
experiments: connections.
LSTM : htl 1 , htl1 , ctl1  htl , ctl (3)
 i   sigm 
 f   sigm   htl 1 
  T   (4)
 o   sigm  2 n ,4 n  htl 1 
   
 g   tanh 
ctl  f ctl1  i g (5)

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Yt-2 Yt-1 Yt Yt+1 Yt+2 flexible deep learning framework. It is based on C++, together
with python APIs, and uses data flow graphs for digital
computations in which the nodes represent multidimensional data
arrays that are communicated. TensorFlow supports several
desktop, server or mobile platform backends, CPUs or GPUs. By
running every Node on another computing device [2],
TensorFlow is extremely flexible. For this study we deploy
TensorFlow via native pip installation on Ubuntu 16.04 and then
run our RNN programme.

Table.1. Results of Accuracy and validation loss during image

Xt-2 Xt-1 Xt Xt+1 Xt+2 recognition

Fig.3. Regularized multilayer RNN (solid arrows indicate Training Validation Validation
Accuracy Loss
connections to the place of the dropout and the dashed lines step accuracy loss
indicate connections to the place of the dropout) 619 0.9405 0.23
620 (last 0.97 0.079
Yt-1 Yt Yt+1 Yt+2 0.9464 0.21
Yt-2 step)

4.1 EVALUATION METRICS

The accuracy and reminder of the labels generated are used as
measuring measures. We generate the highest-ranking labels for
each picture and compare these with the ground truth labels. The
accuracy is that of the number, divided by the number of labels
that have been produced and the number of labels that have been
correctively annotated divided by the number of ground truth
information.
Xt-2 Xt-1 Xt Xt+1 Xt+2 We also compute the per-class precision and overall precision
and per class recall and overall recall scores, where the average is
Fig.3. Dashed line shows a typical path of information flow in taken over all classes and all testing examples, respectively. The
the LSTM. The information is affected by dropout L + 1 times, study further considers the geometrical average of the precision
where L is depth of network and recall scores. We also compute the mean average precision
measure.
3.4 TESTING DATA The Fig.4 shows the per-class precision rate, Fig.5 shows
overall precision rate, Fig.6 shows per-class recall rate, Fig.7
The test data are a combination of an unlabeled Plasmodium
shows overall precision rate, Fig.8 shows geometrical average of
falciparum and vibrio cholera epidemic pathogen. The data are
the precision rate, Fig.9 shows geometrical average of the recall
inputs from the RNN model generated to predict each image's
rate, Fig.10 shows mean average precision results of various test
label that is likely to be a pathogen for Vibrio cholera. The test
image datasets.
database contains [13] 80 numerically and progressively named
images for our study. Proposed RNN
70 RNN
CNN
4. EVALUATION OF CLASSIFIED IMAGES 60
Per-class Precision Rate

50
The last step is to estimate the accuracy of the classified
images and to produce the results. In order to identify images with 40
Vibrio cholera as outputs, the testing data is the input of the
generated model. The model's accuracy, as shown in table 1, is 30
improved by 94%. 20
The TensorFlow framework is the software used in this work.
TensorBoard is a TensorFlow histogram and visualizing tool that 10
makes model parameters and their changes easy to understand 0
over time. The proposed method achieves an accuracy of 97% 100 200 300
validation and a loss of 0.079% validation to distinguish cholera Number of Testing Images
pathogen images. The pathogens microscopic diagnostics
approach to RNN can significantly improve their accuracy. Fig.4. Per-class Precision Rate
The TensorFlow framework is the software used. TensorFlow
is an open source Machine Intelligence library which is a highly

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Proposed RNN talk to small perspectives, during the accumulation period of

80 RNN image dataset from Google Images. This work was carried out
CNN
70 physically and could be considered a restriction.
Overall Precision Rate

60 In the stage of convolution we stopped in six layers because

the order accuracy was not increased in the past. In the final
50 analysis, we can note that the underlying objective has been
40 largely achieved to the extent that we are able to achieve
intriguing results from the RNN display, which achieved the order
30
precision of 94%. These crucial results are firmly identified with
20 image data sets of great quality, which confirm the importance of
10
pretreatment of information.
Deep learning has upset the image group, especially in
0
100 200 300 therapeutic image examinations, in a number of areas. An optical
Number of Testing Images microscopy is used in finding human intestinal parasites Image
examination method for finding parasites Image highlights from
Fig.5. Overall Precision Rate a small set of preparations. The division of images is the way to
break the whole image into few subsections. In addition, Quinn
Proposed RNN evaluate the implementation in certain unique microscopy
70 RNN assignments of deep Recurrent neural systems.
CNN
60 They have only two convergence layers in RNN engineering
Per-class Recall Rate

and are also prepared for sections of the pictures. This

50 preprocessing affects image quality, which may be an obstacle to
40 the accuracy of the order. We can identify a few types of
pathogens in our philosophy because it gives a comparison of
30 image data. The philosophy of microscopy and PC vision is
particularly suited to nation building. This complies with the
20
absence of magnification and also encourages an unlimited
10 examination for exact analysis, and thus provides an adequate
consideration for a few unfortunate casualties during pestilence
0 emergencies in case of absence of talented experts in minute
100 200 300
Number of Testing Images control.
The results of Fig.4-Fig.10 shows that the proposed method
Fig.6. Per-class Recall Rate achieves higher precision (overall, average and per-class), higher
recall (overall, average and per-class) and MAP.
Proposed RNN Proposed RNN
70 RNN 70 RNN
CNN CNN
60
60
Average Precision Rate
Overall Recall Rate

50
50
40
40
30 30
20 20
10 10
0 0
100 200 300 100 200 300
Number of Testing Images
Number of Testing Images
Fig.7. Overall Precision Rate Fig.8. Geometrical average of the precision rate
4.2 DISCUSSIONS
RNN systems have turned into a decision-making approach
for breaking down restorative images Investigation, in particular
pestilence pathogen Images in magnifying instruments. Within
the framework of this work, we note that images of terrible
features affect the precision of characterization. This is why we
have expelled images not critical, in particular those which do not

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Proposed RNN Earth Observation and Geoinformation, Vol. 2, No. 2, pp.

80 RNN 104-119, 2000
CNN
70 [2] S. Bahrampour et al., “Comparative study of Deep Learning
Software Frameworks”, Available at:
Average Recall Rate

60
https://arxiv.org/pdf/1511.06435.pdf, 2015.
50 [3] J.G.A. Barbedo, “Digital Image Processing Techniques for
Detecting, Quantifying and Classifying Plant Diseases”,
40
SpringerPlus, Vol. 2, pp. 660-667, 2013.
30 [4] H.G. Davies, C. Bowman, S.P. Luby, “Cholera-
20 Management and Prevention”, Journal of Infection, Vol. 74,
pp. 66-73, 2017.
10 [5] El Hatri and C., Boumhidi, “Fuzzy Deep Learning based
0 Urban Traffic Incident Detection”, Cognitive Systems
100 200 300 Research, Vol. 50, pp. 206-213, 2017.
Number of Testing Images [6] G.L. Grinblat et al., “Deep Learning for Plant Identification
Fig.9. Geometrical average of the recall rate using Vein Morphological Patterns”, Computers and
Electronics in Agriculture, Vol. 127, pp. 418-424, 2016.
Proposed RNN
[7] Y. Guo et al., “Deep Learning for Visual Understanding: A
70 RNN Review”, Neurocomputing, Vol. 187, pp. 27-48, 2016.
CNN [8] G.E. Hinton, “A Fast Learning Algorithm for Deep Belief
60 Nets”, Neural Computing, Vol. 18, pp. 1527-1554, 2006.
50
[9] I.I. Hirschman, I.I. Widder, “The Convolution Transform”,
Courier Corporation, 2012.
40 [10] A. Karpathy et al., “Largescale Video Classification with
MAP

Recurrent Neural Networks”, Proceedings of IEEE

30
20
10
0
100 200
Number of Testing Images
Fig.10. Mean Average Precision
5. CONCLUSIONS
In this paper we have shown a methodology for the
recognition of images which depends on Deep Recurrent Neural
system. The aim of this method was to establish whether small
images contain a pathogen called vibrio cholera, either for cholera
or for intestinal disease. The RNN proposed engineering provides
the best results for characteristic accuracy of 94%, with Vibrio
200 cholera image and 200 for dataset and 80 images for test
information. This work is accompanied by the main
commitments. A help for the basic leadership process, since it
enhances the administration of a scourge emergencies by sparing
time and cost in minute investigations. Moreover, the proposed
system has intelligent instruments to incorporate this arrangement
into future magnifying instruments.
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