scholarly journals Classification and specific primer design for accurate detection of SARS-CoV-2 using deep learning

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Alejandro Lopez-Rincon ◽  
Alberto Tonda ◽  
Lucero Mendoza-Maldonado ◽  
Daphne G. J. C. Mulders ◽  
Richard Molenkamp ◽  
...  
Keyword(s):  
Deep Learning ◽  
Diagnostic Methods ◽  
Added Value ◽  
Detection Methods ◽  
Minimal Amount ◽  
Specific Detection ◽  
Data Repositories ◽  
Primer Sets ◽  
Global Initiative ◽  
Virus Strains

AbstractIn this paper, deep learning is coupled with explainable artificial intelligence techniques for the discovery of representative genomic sequences in SARS-CoV-2. A convolutional neural network classifier is first trained on 553 sequences from the National Genomics Data Center repository, separating the genome of different virus strains from the Coronavirus family with 98.73% accuracy. The network’s behavior is then analyzed, to discover sequences used by the model to identify SARS-CoV-2, ultimately uncovering sequences exclusive to it. The discovered sequences are validated on samples from the National Center for Biotechnology Information and Global Initiative on Sharing All Influenza Data repositories, and are proven to be able to separate SARS-CoV-2 from different virus strains with near-perfect accuracy. Next, one of the sequences is selected to generate a primer set, and tested against other state-of-the-art primer sets, obtaining competitive results. Finally, the primer is synthesized and tested on patient samples (n = 6 previously tested positive), delivering a sensitivity similar to routine diagnostic methods, and 100% specificity. The proposed methodology has a substantial added value over existing methods, as it is able to both automatically identify promising primer sets for a virus from a limited amount of data, and deliver effective results in a minimal amount of time. Considering the possibility of future pandemics, these characteristics are invaluable to promptly create specific detection methods for diagnostics.

scholarly journals Classification and Specific Primer Design for Accurate Detection of SARS-CoV-2 Using Deep Learning

2020 ◽  
Author(s):  
Alejandro Lopez-Rincon ◽  
Alberto Tonda ◽  
Lucero Mendoza-Maldonado ◽  
Daphne G.J.C. Mulders ◽  
Richard Molenkamp ◽  
...  
Keyword(s):  
Neural Network ◽  
Artificial Intelligence ◽  
Deep Learning ◽  
Convolutional Neural Network ◽  
State Of The Art ◽  
Diagnostic Methods ◽  
Neural Network Classifier ◽  
Explainable Artificial Intelligence ◽  
Primer Sets ◽  
Virus Strains

ABSTRACTIn this paper, deep learning is coupled with explainable artificial intelligence techniques for the discovery of representative genomic sequences in SARS-CoV-2. A convolutional neural network classifier is first trained on 553 sequences from available repositories, separating the genome of different virus strains from the Coronavirus family with considerable accuracy. The network’s behavior is then analyzed, to discover sequences used by the model to identify SARS-CoV-2, ultimately uncovering sequences exclusive to it. The discovered sequences are first validated on samples from other repositories, and proven able to separate SARS-CoV-2 from different virus strains with near-perfect accuracy. Next, one of the sequences is selected to generate a primer set, and tested against other state-of-the-art primer sets on existing datasets, obtaining competitive results. Finally, the primer is synthesized and tested on patient samples (n=6 previously tested positive), delivering a sensibility similar to routine diagnostic methods, and 100% specificity. In this paper, deep learning is coupled with explainable artificial intelligence techniques for the discovery of representative genomic sequences in SARS-CoV-2. A convolutional neural network classifier is first trained on 553 sequences from NGDC, separating the genome of different virus strains from the Coronavirus family with accuracy 98.73%. The network’s behavior is then analyzed, to discover sequences used by the model to identify SARS-CoV-2, ultimately uncovering sequences exclusive to it. The discovered sequences are validated on samples from NCBI and GISAID, and proven able to separate SARS-CoV-2 from different virus strains with near-perfect accuracy. Next, one of the sequences is selected to generate a primer set, and tested against other state-of-the-art primer sets, obtaining competitive results. Finally, the primer is synthesized and tested on patient samples (n=6 previously tested positive), delivering a sensibility similar to routine diagnostic methods, and 100% specificity. The proposed methodology has a substantial added value over existing methods, as it is able to both identify promising primer sets for a virus from a limited amount of data, and deliver effective results in a minimal amount of time. Considering the possibility of future pandemics, these characteristics are invaluable to promptly create specific detection methods for diagnostics.

scholarly journals Application of deep learning to enhance the accuracy of intrusion detection in modern computer networks

2020 ◽  
Vol 9 (3) ◽  
pp. 1137-1148
Author(s):  
Jafar Majidpour ◽  
Hiwa Hasanzadeh
Keyword(s):  
Deep Learning ◽  
Intrusion Detection ◽  
Computer Networks ◽  
Diagnostic Methods ◽  
Detection Methods ◽  
Training Time ◽  
Modern Computer ◽  
Normal Behavior ◽  
Review Protocol ◽  
Future Work

Application of deep learning to enhance the accuracy of intrusion detection in modern computer networks were studied in this paper. The identification of attacks in computer networks is divided in to two categories of intrusion detection and anomaly detection in terms of the information used in the learning phase. Intrusion detection uses both routine traffic and attack traffic. Abnormal detection methods attempt to model the normal behavior of the system, and any incident that violates this model is considered to be a suspicious behavior. For example, if the web server, which is usually passive, tries to There are many addresses that are likely to be infected with the worm. The abnormal diagnostic methods are Statistical models, Secure system approach, Review protocol, Check files, Create White list, Neural Networks, Genetic Algorithm, Vector Machines, decision tree. Our results have demonstrated that our approach offers high levels of accuracy, precision and recall together with reduced training time. In our future work, the first avenue of exploration for improvement will be to assess and extend the capability of our model to handle zero-day attacks.

scholarly journals Solar Panel Detection within Complex Backgrounds Using Thermal Images Acquired by UAVs

Sensors ◽  
2020 ◽  
Vol 20 (21) ◽  
pp. 6219
Author(s):  
Jhon Jairo Vega Díaz ◽  
Michiel Vlaminck ◽  
Dionysios Lefkaditis ◽  
Sergio Alejandro Orjuela Vargas ◽  
Hiep Luong
Keyword(s):  
Deep Learning ◽  
Edge Detection ◽  
Diagnostic Methods ◽  
Detection Methods ◽  
Support Vector ◽  
Solar Panels ◽  
Low Contrast ◽  
Whole Process ◽  
Imaging Sensors ◽  
Processing Techniques

The installation of solar plants everywhere in the world increases year by year. Automated diagnostic methods are needed to inspect the solar plants and to identify anomalies within these photovoltaic panels. The inspection is usually carried out by unmanned aerial vehicles (UAVs) using thermal imaging sensors. The first step in the whole process is to detect the solar panels in those images. However, standard image processing techniques fail in case of low-contrast images or images with complex backgrounds. Moreover, the shades of power lines or structures similar to solar panels impede the automated detection process. In this research, two self-developed methods are compared for the detection of panels in this context, one based on classical techniques and another one based on deep learning, both with a common post-processing step. The first method is based on edge detection and classification, in contrast to the second method is based on training a region based convolutional neural networks to identify a panel. The first method corrects for the low contrast of the thermal image using several preprocessing techniques. Subsequently, edge detection, segmentation and segment classification are applied. The latter is done using a support vector machine trained with an optimized texture descriptor vector. The second method is based on deep learning trained with images that have been subjected to three different pre-processing operations. The postprocessing use the detected panels to infer the location of panels that were not detected. This step selects contours from detected panels based on the panel area and the angle of rotation. Then new panels are determined by the extrapolation of these contours. The panels in 100 random images taken from eleven UAV flights over three solar plants are labeled and used to evaluate the detection methods. The metrics for the new method based on classical techniques reaches a precision of 0.997, a recall of 0.970 and a F1 score of 0.983. The metrics for the method of deep learning reaches a precision of 0.996, a recall of 0.981 and a F1 score of 0.989. The two panel detection methods are highly effective in the presence of complex backgrounds.

scholarly journals Design of Specific Primer Sets for the Detection of B.1.1.7, B.1.351 and P.1 SARS-CoV-2 Variants using Deep Learning

2021 ◽  
Author(s):  
Alejandro Lopez-Rincon ◽  
Carmina A. Perez-Romero ◽  
Alberto Tonda ◽  
Lucero Mendoza-Maldonado ◽  
Eric Claassen ◽  
...  
Keyword(s):  
Deep Learning ◽  
South African ◽  
Synonymous Mutations ◽  
Molecular Tests ◽  
Learning Techniques ◽  
New Variant ◽  
Primer Sets ◽  
Global Initiative ◽  
The Uk

ABSTRACTAs the COVID-19 pandemic persists, new SARS-CoV-2 variants with potentially dangerous features have been identified by the scientific community. Variant B.1.1.7 lineage clade GR from Global Initiative on Sharing All Influenza Data (GISAID) was first detected in the UK, and it appears to possess an increased transmissibility. At the same time, South African authorities reported variant B.1.351, that shares several mutations with B.1.1.7, and might also present high transmissibility. Even more recently, a variant labeled P.1 with 17 non-synonymous mutations was detected in Brazil. In such a situation, it is paramount to rapidly develop specific molecular tests to uniquely identify, contain, and study new variants. Using a completely automated pipeline built around deep learning techniques, we design primer sets specific to variant B.1.1.7, B.1.351, and P.1, respectively. Starting from sequences openly available in the GISAID repository, our pipeline was able to deliver the primer sets in just under 16 hours for each case study. In-silico tests show that the sequences in the primer sets present high accuracy and do not appear in samples from different viruses, nor in other coronaviruses or SARS-CoV-2 variants. The presented methodology can be exploited to swiftly obtain primer sets for each independent new variant, that can later be a part of a multiplexed approach for the initial diagnosis of COVID-19 patients. Furthermore, since our approach delivers primers able to differentiate between variants, it can be used as a second step of a diagnosis in cases already positive to COVID-19, to identify individuals carrying variants with potentially threatening features.

scholarly journals Trends in Biosensors for HPV: Identification and Diagnosis

2015 ◽  
Vol 2015 ◽  
pp. 1-16 ◽  
Author(s):  
Isaac A. M. Frías ◽  
Karen Y. P. S. Avelino ◽  
Rafael R. Silva ◽  
César A. S. Andrade ◽  
Maria D. L. Oliveira
Keyword(s):  
Piezoelectric Transducers ◽  
Diagnostic Methods ◽  
Specific Detection ◽  
Adequate Treatment ◽  
Detection And Identification ◽  
Proper Diagnosis ◽  
Recent Trends ◽  
Material Sciences ◽  
Virus Strains ◽  
Intrinsic Contradiction

The conventional methodologies used for the detection of human papillomavirus (HPV) present actually robust and reproducible advantages. However, at the same time, they involve complex protocols that sometimes are difficult to popularize. Over the first half of XX century, the adequate treatment of complex and delicate processes from a simple instrumental base seemed a fundamental and intrinsic contradiction. However, interdisciplinary trends have allowed the manipulation of tissues, proteins, and nucleic acids through innovative increasingly smaller devices. The proper diagnosis of HPV has seen great advances since biosensor researchers are employing its virus strains as models to study the interactions between the biorecognition element and the transducer. Additionally, all recent improvements and trends that material sciences, biotechnology, and data processing scientists excel for biosensors can be applied for the HPV detection platforms. In this review, we highlight the recent trends on materials, nanomaterials, and transducers for the specific detection and differentiation of HPV strains. The most influential methods for the detection and identification of these papillomaviruses include optical, electrochemical, and piezoelectric transducers; we will visit their sensibility and advantages. Additionally, we highlight the factors that contributed to the increasing importance of these biodevices as potential substitutes to conventional diagnostic methods.

Saliency detection in deep learning era: trends of development

2019 ◽  
pp. 10-36 ◽  
Author(s):  
M. N. Favorskaya ◽  
L. C. Jain
Keyword(s):  
Deep Learning ◽  
Object Detection ◽  
Event Detection ◽  
Visual Analysis ◽  
Saliency Detection ◽  
Salient Object Detection ◽  
Public Image ◽  
Detection Methods ◽  
Salient Object ◽  
Salient Event

Introduction:Saliency detection is a fundamental task of computer vision. Its ultimate aim is to localize the objects of interest that grab human visual attention with respect to the rest of the image. A great variety of saliency models based on different approaches was developed since 1990s. In recent years, the saliency detection has become one of actively studied topic in the theory of Convolutional Neural Network (CNN). Many original decisions using CNNs were proposed for salient object detection and, even, event detection.Purpose:A detailed survey of saliency detection methods in deep learning era allows to understand the current possibilities of CNN approach for visual analysis conducted by the human eyes’ tracking and digital image processing.Results:A survey reflects the recent advances in saliency detection using CNNs. Different models available in literature, such as static and dynamic 2D CNNs for salient object detection and 3D CNNs for salient event detection are discussed in the chronological order. It is worth noting that automatic salient event detection in durable videos became possible using the recently appeared 3D CNN combining with 2D CNN for salient audio detection. Also in this article, we have presented a short description of public image and video datasets with annotated salient objects or events, as well as the often used metrics for the results’ evaluation.Practical relevance:This survey is considered as a contribution in the study of rapidly developed deep learning methods with respect to the saliency detection in the images and videos.

scholarly journals Uni-Temporal Multispectral Imagery for Burned Area Mapping with Deep Learning

2021 ◽  
Vol 13 (8) ◽  
pp. 1509
Author(s):  
Xikun Hu ◽  
Yifang Ban ◽  
Andrea Nascetti
Keyword(s):  
Deep Learning ◽  
Large Scale ◽  
Multiple Scales ◽  
Detection Methods ◽  
Burned Area ◽  
Landsat 8 ◽  
Multispectral Imagery ◽  
Burned Areas ◽  
Local Climate Zones ◽  
Sentinel 2

Accurate burned area information is needed to assess the impacts of wildfires on people, communities, and natural ecosystems. Various burned area detection methods have been developed using satellite remote sensing measurements with wide coverage and frequent revisits. Our study aims to expound on the capability of deep learning (DL) models for automatically mapping burned areas from uni-temporal multispectral imagery. Specifically, several semantic segmentation network architectures, i.e., U-Net, HRNet, Fast-SCNN, and DeepLabv3+, and machine learning (ML) algorithms were applied to Sentinel-2 imagery and Landsat-8 imagery in three wildfire sites in two different local climate zones. The validation results show that the DL algorithms outperform the ML methods in two of the three cases with the compact burned scars, while ML methods seem to be more suitable for mapping dispersed burn in boreal forests. Using Sentinel-2 images, U-Net and HRNet exhibit comparatively identical performance with higher kappa (around 0.9) in one heterogeneous Mediterranean fire site in Greece; Fast-SCNN performs better than others with kappa over 0.79 in one compact boreal forest fire with various burn severity in Sweden. Furthermore, directly transferring the trained models to corresponding Landsat-8 data, HRNet dominates in the three test sites among DL models and can preserve the high accuracy. The results demonstrated that DL models can make full use of contextual information and capture spatial details in multiple scales from fire-sensitive spectral bands to map burned areas. Using only a post-fire image, the DL methods not only provide automatic, accurate, and bias-free large-scale mapping option with cross-sensor applicability, but also have potential to be used for onboard processing in the next Earth observation satellites.

Intrusion Detection Methods Based on Integrated Deep Learning Model

2021 ◽  
pp. 102177
Author(s):  
ZHENDONG WANG ◽  
YAODI LIU ◽  
DAOJING HE ◽  
SAMMY CHAN
Keyword(s):  
Deep Learning ◽  
Intrusion Detection ◽  
Learning Model ◽  
Detection Methods ◽  
Deep Learning Model

scholarly journals High-Speed Lightweight Ship Detection Algorithm Based on YOLO-V4 for Three-Channels RGB SAR Image

2021 ◽  
Vol 13 (10) ◽  
pp. 1909
Author(s):  
Jiahuan Jiang ◽  
Xiongjun Fu ◽  
Rui Qin ◽  
Xiaoyan Wang ◽  
Zhifeng Ma
Keyword(s):  
Deep Learning ◽  
Gpu Computing ◽  
Hot Spot ◽  
Detection Algorithm ◽  
Detection Methods ◽  
Detection Accuracy ◽  
Processing Unit ◽  
Sar Image ◽  
Marine Monitoring ◽  
Ship Detection

Synthetic Aperture Radar (SAR) has become one of the important technical means of marine monitoring in the field of remote sensing due to its all-day, all-weather advantage. National territorial waters to achieve ship monitoring is conducive to national maritime law enforcement, implementation of maritime traffic control, and maintenance of national maritime security, so ship detection has been a hot spot and focus of research. After the development from traditional detection methods to deep learning combined methods, most of the research always based on the evolving Graphics Processing Unit (GPU) computing power to propose more complex and computationally intensive strategies, while in the process of transplanting optical image detection ignored the low signal-to-noise ratio, low resolution, single-channel and other characteristics brought by the SAR image imaging principle. Constantly pursuing detection accuracy while ignoring the detection speed and the ultimate application of the algorithm, almost all algorithms rely on powerful clustered desktop GPUs, which cannot be implemented on the frontline of marine monitoring to cope with the changing realities. To address these issues, this paper proposes a multi-channel fusion SAR image processing method that makes full use of image information and the network’s ability to extract features; it is also based on the latest You Only Look Once version 4 (YOLO-V4) deep learning framework for modeling architecture and training models. The YOLO-V4-light network was tailored for real-time and implementation, significantly reducing the model size, detection time, number of computational parameters, and memory consumption, and refining the network for three-channel images to compensate for the loss of accuracy due to light-weighting. The test experiments were completed entirely on a portable computer and achieved an Average Precision (AP) of 90.37% on the SAR Ship Detection Dataset (SSDD), simplifying the model while ensuring a lead over most existing methods. The YOLO-V4-lightship detection algorithm proposed in this paper has great practical application in maritime safety monitoring and emergency rescue.

scholarly journals A Comparison of Deep Learning Techniques for Arterial Blood Pressure Prediction

2021 ◽  
Author(s):  
Annunziata Paviglianiti ◽  
Vincenzo Randazzo ◽  
Stefano Villata ◽  
Giansalvo Cirrincione ◽  
Eros Pasero
Keyword(s):  
Blood Pressure ◽  
Neural Networks ◽  
Deep Learning ◽  
Arterial Blood Pressure ◽  
Blood Pressure Measurement ◽  
National Standards ◽  
Detection Methods ◽  
Physiological Parameter ◽  
Arterial Blood ◽  
Learning Techniques

AbstractContinuous vital signal monitoring is becoming more relevant in preventing diseases that afflict a large part of the world’s population; for this reason, healthcare equipment should be easy to wear and simple to use. Non-intrusive and non-invasive detection methods are a basic requirement for wearable medical devices, especially when these are used in sports applications or by the elderly for self-monitoring. Arterial blood pressure (ABP) is an essential physiological parameter for health monitoring. Most blood pressure measurement devices determine the systolic and diastolic arterial blood pressure through the inflation and the deflation of a cuff. This technique is uncomfortable for the user and may result in anxiety, and consequently affect the blood pressure and its measurement. The purpose of this paper is the continuous measurement of the ABP through a cuffless, non-intrusive approach. The approach of this paper is based on deep learning techniques where several neural networks are used to infer ABP, starting from photoplethysmogram (PPG) and electrocardiogram (ECG) signals. The ABP was predicted first by utilizing only PPG and then by using both PPG and ECG. Convolutional neural networks (ResNet and WaveNet) and recurrent neural networks (LSTM) were compared and analyzed for the regression task. Results show that the use of the ECG has resulted in improved performance for every proposed configuration. The best performing configuration was obtained with a ResNet followed by three LSTM layers: this led to a mean absolute error (MAE) of 4.118 mmHg on and 2.228 mmHg on systolic and diastolic blood pressures, respectively. The results comply with the American National Standards of the Association for the Advancement of Medical Instrumentation. ECG, PPG, and ABP measurements were extracted from the MIMIC database, which contains clinical signal data reflecting real measurements. The results were validated on a custom dataset created at Neuronica Lab, Politecnico di Torino.

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