scholarly journals DeePVP: Identification and classification of phage virion protein using deep learning

2021 ◽  
Author(s):  
Zhencheng Fang ◽  
Tao Feng ◽  
Hongwei Zhou
Keyword(s):  
Deep Learning ◽  
Phage Genome ◽  
State Of The Art ◽  
Viral Evolution ◽  
Antibacterial Drug ◽  
Specific Class ◽  
Virion Protein ◽  
Host Identification ◽  
Main Module

The poor annotation of phage virion protein (PVP) is the bottleneck of many areas of viral research, such as viral phylogenetic analysis, viral host identification and antibacterial drug design. Because of the high diversity of the PVP sequences, the PVP annotation remains a great challenging bioinformatic task. Based on deep learning, we present DeePVP that contains a main module and an extended module. The main module aims to identify the PVPs from non-PVP over a phage genome, while the extended module can further classify the predicted PVP into one of the ten major classes of PVP. Compared with the state-of-the-art tools that can distinguish PVP from non-PVP, DeePVP's main module performs much better, with an F1-score 9.05% higher in the PVP identification task. Compared with PhANNs, a tool that can further classify the predicted PVP into a specific class, the overall accuracy of DeePVP's extended module is approximately 3.72% higher in the PVP classification task. Two application cases on the genome of mycobacteriophage PDRPxv and Escherichia phage HP3 show that the predictions of DeePVP are much more reliable and can better reveal the compact PVP-enriched region, which may be conserved during the viral evolution process, over the phage genome.

scholarly journals Visual-Based Defect Detection and Classification Approaches for Industrial Applications—A SURVEY

Sensors ◽  
2020 ◽  
Vol 20 (5) ◽  
pp. 1459 ◽  
Author(s):  
Tamás Czimmermann ◽  
Gastone Ciuti ◽  
Mario Milazzo ◽  
Marcello Chiurazzi ◽  
Stefano Roccella ◽  
...  
Keyword(s):  
Deep Learning ◽  
Defect Detection ◽  
Visual Processing ◽  
State Of The Art ◽  
Industrial Applications ◽  
The State ◽  
Shape Error ◽  
Supervised Classifiers ◽  
Processing Techniques

This paper reviews automated visual-based defect detection approaches applicable to various materials, such as metals, ceramics and textiles. In the first part of the paper, we present a general taxonomy of the different defects that fall in two classes: visible (e.g., scratches, shape error, etc.) and palpable (e.g., crack, bump, etc.) defects. Then, we describe artificial visual processing techniques that are aimed at understanding of the captured scenery in a mathematical/logical way. We continue with a survey of textural defect detection based on statistical, structural and other approaches. Finally, we report the state of the art for approaching the detection and classification of defects through supervised and non-supervised classifiers and deep learning.

scholarly journals Review of the State of the Art of Deep Learning for Plant Diseases: A Broad Analysis and Discussion

Plants ◽  
2020 ◽  
Vol 9 (10) ◽  
pp. 1302 ◽  
Author(s):  
Reem Ibrahim Hasan ◽  
Suhaila Mohd Yusuf ◽  
Laith Alzubaidi
Keyword(s):  
Machine Learning ◽  
Deep Learning ◽  
Early Detection ◽  
Feature Fusion ◽  
State Of The Art ◽  
Vital Role ◽  
Considerable Improvement ◽  
Plant Diseases ◽  
Recent Emergence

Deep learning (DL) represents the golden era in the machine learning (ML) domain, and it has gradually become the leading approach in many fields. It is currently playing a vital role in the early detection and classification of plant diseases. The use of ML techniques in this field is viewed as having brought considerable improvement in cultivation productivity sectors, particularly with the recent emergence of DL, which seems to have increased accuracy levels. Recently, many DL architectures have been implemented accompanying visualisation techniques that are essential for determining symptoms and classifying plant diseases. This review investigates and analyses the most recent methods, developed over three years leading up to 2020, for training, augmentation, feature fusion and extraction, recognising and counting crops, and detecting plant diseases, including how these methods can be harnessed to feed deep classifiers and their effects on classifier accuracy.

scholarly journals Cycle-Consistent Adversarial GAN: The Integration of Adversarial Attack and Defense

2020 ◽  
Vol 2020 ◽  
pp. 1-9 ◽  
Author(s):  
Lingyun Jiang ◽  
Kai Qiao ◽  
Ruoxi Qin ◽  
Linyuan Wang ◽  
Wanting Yu ◽  
...  
Keyword(s):  
Deep Learning ◽  
Deep Neural Networks ◽  
State Of The Art ◽  
Small Magnitude ◽  
Defense Strategies ◽  
Adversarial Examples ◽  
Adversarial Attack ◽  
Public Datasets ◽  
Attack And Defense

In image classification of deep learning, adversarial examples where input is intended to add small magnitude perturbations may mislead deep neural networks (DNNs) to incorrect results, which means DNNs are vulnerable to them. Different attack and defense strategies have been proposed to better research the mechanism of deep learning. However, those researches in these networks are only for one aspect, either an attack or a defense. There is in the improvement of offensive and defensive performance, and it is difficult to promote each other in the same framework. In this paper, we propose Cycle-Consistent Adversarial GAN (CycleAdvGAN) to generate adversarial examples, which can learn and approximate the distribution of the original instances and adversarial examples, especially promoting attackers and defenders to confront each other and improve their ability. For CycleAdvGAN, once the GeneratorA and D are trained, GA can generate adversarial perturbations efficiently for any instance, improving the performance of the existing attack methods, and GD can generate recovery adversarial examples to clean instances, defending against existing attack methods. We apply CycleAdvGAN under semiwhite-box and black-box settings on two public datasets MNIST and CIFAR10. Using the extensive experiments, we show that our method has achieved the state-of-the-art adversarial attack method and also has efficiently improved the defense ability, which made the integration of adversarial attack and defense come true. In addition, it has improved the attack effect only trained on the adversarial dataset generated by any kind of adversarial attack.

scholarly journals Classification of Hyperspectral Image Based on Double-Branch Dual-Attention Mechanism Network

2020 ◽  
Vol 12 (3) ◽  
pp. 582 ◽  
Author(s):  
Rui Li ◽  
Shunyi Zheng ◽  
Chenxi Duan ◽  
Yang Yang ◽  
Xiqi Wang
Keyword(s):  
Deep Learning ◽  
Hyperspectral Image ◽  
State Of The Art ◽  
Attention Mechanism ◽  
Superior Performance ◽  
Feature Maps ◽  
Spatial Features ◽  
Training Samples ◽  
Series Of Experiments

In recent years, researchers have paid increasing attention on hyperspectral image (HSI) classification using deep learning methods. To improve the accuracy and reduce the training samples, we propose a double-branch dual-attention mechanism network (DBDA) for HSI classification in this paper. Two branches are designed in DBDA to capture plenty of spectral and spatial features contained in HSI. Furthermore, a channel attention block and a spatial attention block are applied to these two branches respectively, which enables DBDA to refine and optimize the extracted feature maps. A series of experiments on four hyperspectral datasets show that the proposed framework has superior performance to the state-of-the-art algorithm, especially when the training samples are signally lacking.

scholarly journals Investigating Deep Feedforward Neural Networks for Classification of Transposon-Derived piRNAs

2020 ◽  
Author(s):  
Alisson Hayasi da Costa ◽  
Renato Augusto C. dos Santos ◽  
Ricardo Cerri
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
State Of The Art ◽  
Feedforward Neural Networks ◽  
The State ◽  
Machine Learning Algorithms ◽  
Support Vector ◽  
Advantages And Disadvantages ◽  
Large Application

AbstractPIWI-Interacting RNAs (piRNAs) form an important class of non-coding RNAs that play a key role in the genome integrity through the silencing of transposable elements. However, despite their importance and the large application of deep learning in computational biology for classification tasks, there are few studies of deep learning and neural networks for piRNAs prediction. Therefore, this paper presents an investigation on deep feedforward networks models for classification of transposon-derived piRNAs. We analyze and compare the results of the neural networks in different hyperparameters choices, such as number of layers, activation functions and optimizers, clarifying the advantages and disadvantages of each configuration. From this analysis, we propose a model for human piRNAs classification and compare our method with the state-of-the-art deep neural network for piRNA prediction in the literature and also traditional machine learning algorithms, such as Support Vector Machines and Random Forests, showing that our model has achieved a great performance with an F-measure value of 0.872, outperforming the state-of-the-art method in the literature.

scholarly journals Formulation of probability-based pervasive information set features and Hanman transform classifier for the categorization of mammograms

2021 ◽  
Vol 3 (6) ◽  
Author(s):  
Jyoti Dabass ◽  
M. Hanmandlu ◽  
Rekha Vig
Keyword(s):  
Breast Cancer ◽  
Deep Learning ◽  
Statistical Analysis ◽  
Fuzzy Set ◽  
State Of The Art ◽  
Entropy Function ◽  
Information Set ◽  
Learning Architectures

AbstractWith aim of detecting breast cancer at the early stages using mammograms, this study presents the formulation of five feature types by extending the information set to encompass the concept of an intuitionist fuzzy set. The resulting pervasive information set gives not only the certainty of the pixel intensities of mammograms to a class but also the deficiency in the fuzzy modeling referred to as the hesitancy. The generalized adaptive Hanman Anirban fuzzy entropy function is shown to be equivalent to the hesitancy entropy function. The probability-based fuzzy Hanman transform and the pervasive Information with probability taking the role of hesitancy degree help derive the above five feature types termed as probability-based pervasive Information set features. The effectiveness of each feature type is demonstrated on the mini-MIAS and DDSM databases for the multi-class categorization of mammograms using the Hanman transform classifier. The statistical analysis by ANOVA test proves that the features are statistically significant and the experimental results are shown to be clinically relevant by the expert radiologists. The performance of the five feature types is either superior to or equal to that of some deep learning architectures on comparison but they outperform the state-of-the-art literature methods in the classification of breast cancer using mammograms.

scholarly journals MP19-20 STATE-OF-THE-ART WEAKLY SUPERVISED AUTOMATED CLASSIFICATION OF PROSTATE CANCER TISSUE MICROARRAYS VIA DEEP LEARNING

2020 ◽  
Vol 203 ◽  
pp. e306
Author(s):  
Sami-Ramzi Leyh-Bannurah* ◽  
Ulrich Wolffgang ◽  
Jonathan Schmitz ◽  
Veronique Ouellet ◽  
Feryel Azzi ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Deep Learning ◽  
State Of The Art ◽  
Tissue Microarrays ◽  
Cancer Tissue ◽  
Automated Classification ◽  
Prostate Cancer Tissue ◽  
Weakly Supervised

scholarly journals An Automated Classification of Mammals and Reptiles Animal Classes Using Deep Learning

2020 ◽  
pp. 2361-2370
Author(s):  
Elham Mohammed Thabit A. ALSAADI ◽  
Nidhal K. El Abbadi
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
State Of The Art ◽  
Target Object ◽  
Automated Classification ◽  
High Learning ◽  
Deep Convolutional Neural Networks ◽  
Learning Capacity ◽  
Typical Object

Detection and classification of animals is a major challenge that is facing the researchers. There are five classes of vertebrate animals, namely the Mammals, Amphibians, Reptiles, Birds, and Fish, and each type includes many thousands of different animals. In this paper, we propose a new model based on the training of deep convolutional neural networks (CNN) to detect and classify two classes of vertebrate animals (Mammals and Reptiles). Deep CNNs are the state of the art in image recognition and are known for their high learning capacity, accuracy, and robustness to typical object recognition challenges. The dataset of this system contains 6000 images, including 4800 images for training. The proposed algorithm was tested by using 1200 images. The accuracy of the system’s prediction for the target object was 97.5%.

scholarly journals Assessing the combination of DistilBERT news representations and difusion topological features to classify fake news

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Carlos Abel Córdova Sáenz ◽  
Marcelo Dias ◽  
Karin Becker
Keyword(s):  
Social Media ◽  
Deep Learning ◽  
State Of The Art ◽  
Fake News ◽  
Topological Features ◽  
Compact Representations ◽  
Fact Checking ◽  
Textual Features ◽  
Propagation Network

Fake news (FN) have affected people’s lives in unimaginable ways. The automatic classification of FN is a vital tool to prevent their dissemination and support fact-checking. Related work has shown that FN spread faster, deeper, and more broadly than truthful news on social media. Deep learning has produced state-of-the-art solutions in this field, mainly based on textual attributes. In this paper, we propose to combine compact representations of the textual news properties generated using DistilBERT, with topological metrics extracted from their propagation network in social media. Using a dataset related to politics and distinct learning algorithms, we extensively assessed the components of the proposed solution. Regarding the textual attributes, we reached results comparable to stateof-the-art solutions using only the news title and contents, which is useful for FN early detection. We assessed the influential topological metrics, and the effect of their combination with the news textual features. We also explored the use of ensembles. Our results were very promising, revealing the potential of the features proposed and the adoption of ensembles.

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