scholarly journals DeepSV: Accurate calling of genomic deletions from high-throughput sequencing data using deep convolutional neural network

2019 ◽  
Author(s):  
Lei Cai ◽  
Yufeng Wu ◽  
Jingyang Gao
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
High Throughput Sequencing ◽  
Sequence Data ◽  
Research Question ◽  
Genetic Variations ◽  
Training Data ◽  
Sources Of Information ◽  
Structural Variations ◽  
Genomic Deletions

AbstractBackgroundCalling genetic variations from sequence reads is an important problem in genomics. There are many existing methods for calling various types of variations. Recently, Google developed a method for calling single nucleotide polymorphisms (SNPs) based on deep learning. Their method visualizes sequence reads in the forms of images. These images are then used to train a deep neural network model, which is used to call SNPs. This raises a research question: can deep learning be used to call more complex genetic variations such as structural variations (SVs) from sequence data?ResultsIn this paper, we extend this high-level approach to the problem of calling structural variations. We present DeepSV, an approach based on deep learning for calling long deletions from sequence reads. DeepSV is based on a novel method of visualizing sequence reads. The visualization is designed to capture multiple sources of information in the sequence data that are relevant to long deletions. DeepSV also implements techniques for working with noisy training data. DeepSV trains a model from the visualized sequence reads and calls deletions based on this model. We demonstrate that DeepSV outperforms existing methods in terms of accuracy and efficiency of deletion calling on the data from the 1000 Genomes Project.ConclutionsOur work shows that deep learning can potentially lead to effective calling of different types of genetic variations that are complex than SNPs.Availability and implementationDeepSV’s source code and sample result as part of this project are readily available from GitHub at https://github.com/CSuperlei/DeepSV/.

scholarly journals DeepSV: accurate calling of genomic deletions from high-throughput sequencing data using deep convolutional neural network

2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Lei Cai ◽  
Yufeng Wu ◽  
Jingyang Gao
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
High Throughput Sequencing ◽  
Sequence Data ◽  
Research Question ◽  
Genetic Variations ◽  
Training Data ◽  
Sources Of Information ◽  
Structural Variations ◽  
Genomic Deletions

Abstract Background Calling genetic variations from sequence reads is an important problem in genomics. There are many existing methods for calling various types of variations. Recently, Google developed a method for calling single nucleotide polymorphisms (SNPs) based on deep learning. Their method visualizes sequence reads in the forms of images. These images are then used to train a deep neural network model, which is used to call SNPs. This raises a research question: can deep learning be used to call more complex genetic variations such as structural variations (SVs) from sequence data? Results In this paper, we extend this high-level approach to the problem of calling structural variations. We present DeepSV, an approach based on deep learning for calling long deletions from sequence reads. DeepSV is based on a novel method of visualizing sequence reads. The visualization is designed to capture multiple sources of information in the sequence data that are relevant to long deletions. DeepSV also implements techniques for working with noisy training data. DeepSV trains a model from the visualized sequence reads and calls deletions based on this model. We demonstrate that DeepSV outperforms existing methods in terms of accuracy and efficiency of deletion calling on the data from the 1000 Genomes Project. Conclusions Our work shows that deep learning can potentially lead to effective calling of different types of genetic variations that are complex than SNPs.

scholarly journals Robust Approach to Supervised Deep Neural Network Training for Real-Time Object Classification in Cluttered Indoor Environment

2021 ◽  
Vol 11 (15) ◽  
pp. 7148
Author(s):  
Bedada Endale ◽  
Abera Tullu ◽  
Hayoung Shi ◽  
Beom-Soo Kang
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Real Time ◽  
Network Architecture ◽  
Input Data ◽  
Deep Neural Network ◽  
Data Augmentation ◽  
Object Classification ◽  
Training Data ◽  
Gradient Descent Algorithm

Unmanned aerial vehicles (UAVs) are being widely utilized for various missions: in both civilian and military sectors. Many of these missions demand UAVs to acquire artificial intelligence about the environments they are navigating in. This perception can be realized by training a computing machine to classify objects in the environment. One of the well known machine training approaches is supervised deep learning, which enables a machine to classify objects. However, supervised deep learning comes with huge sacrifice in terms of time and computational resources. Collecting big input data, pre-training processes, such as labeling training data, and the need for a high performance computer for training are some of the challenges that supervised deep learning poses. To address these setbacks, this study proposes mission specific input data augmentation techniques and the design of light-weight deep neural network architecture that is capable of real-time object classification. Semi-direct visual odometry (SVO) data of augmented images are used to train the network for object classification. Ten classes of 10,000 different images in each class were used as input data where 80% were for training the network and the remaining 20% were used for network validation. For the optimization of the designed deep neural network, a sequential gradient descent algorithm was implemented. This algorithm has the advantage of handling redundancy in the data more efficiently than other algorithms.

scholarly journals Real-Time Automated Classification of Sky Conditions Using Deep Learning and Edge Computing

2021 ◽  
Vol 13 (19) ◽  
pp. 3859
Author(s):  
Joby M. Prince Czarnecki ◽  
Sathishkumar Samiappan ◽  
Meilun Zhou ◽  
Cary Daniel McCraine ◽  
Louis L. Wasson
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Image Quality ◽  
Convolutional Neural Network ◽  
Precision Agriculture ◽  
Edge Computing ◽  
Training Data ◽  
Learning Approaches ◽  
Sky Conditions

The radiometric quality of remotely sensed imagery is crucial for precision agriculture applications because estimations of plant health rely on the underlying quality. Sky conditions, and specifically shadowing from clouds, are critical determinants in the quality of images that can be obtained from low-altitude sensing platforms. In this work, we first compare common deep learning approaches to classify sky conditions with regard to cloud shadows in agricultural fields using a visible spectrum camera. We then develop an artificial-intelligence-based edge computing system to fully automate the classification process. Training data consisting of 100 oblique angle images of the sky were provided to a convolutional neural network and two deep residual neural networks (ResNet18 and ResNet34) to facilitate learning two classes, namely (1) good image quality expected, and (2) degraded image quality expected. The expectation of quality stemmed from the sky condition (i.e., density, coverage, and thickness of clouds) present at the time of the image capture. These networks were tested using a set of 13,000 images. Our results demonstrated that ResNet18 and ResNet34 classifiers produced better classification accuracy when compared to a convolutional neural network classifier. The best overall accuracy was obtained by ResNet34, which was 92% accurate, with a Kappa statistic of 0.77. These results demonstrate a low-cost solution to quality control for future autonomous farming systems that will operate without human intervention and supervision.

Deep Learning Based Adaptive Recurrent Neural Network for Detection of Myocardial Infarction

2021 ◽  
Vol 11 (12) ◽  
pp. 3044-3053
Author(s):  
Rakesh Kumar Mahendran ◽  
V. Prabhu ◽  
V. Parthasarathy ◽  
A. Mary Judith
Keyword(s):  
Neural Network ◽  
Myocardial Infarction ◽  
Deep Learning ◽  
Recurrent Neural Network ◽  
Classification Accuracy ◽  
Learning Algorithm ◽  
Training Data ◽  
Discrete Wavelet ◽  
Ecg Signal ◽  
Detection Techniques

Myocardial infarction (MI) may precipitate severe health damage and lead to irreversible death of the heart muscle, the result of prolonged lack of oxygen if it is not treated in a timely manner. Lack of accurate and early detection techniques for this heart disease has reduced the efficiency of MI diagnosis. In this paper, the design, and implementation of an efficient deep learning algorithm called Adaptive Recurrent neural network (ARNN) is proposed for the MI detection. The main objective of the proposed work is the accurate identification of MI disease using ECG signals. ECG signal denoising has been performed using the Multi-Notch filter, which removes the specified noise frequency range. Discrete wavelet transform (DWT) is utilized for performing the feature extraction that decomposes the ECG signal into varied scales with waveletfiltering bank. After the extraction of specific QRS features, classification of the defected and normal ECG arrhythmic beat has been performed using the deep learning-based ARNN classifier. The MIT-BIH database has been used for testing and training data. The performance of the proposed algorithm is evaluated based on classification accuracy. Results that are attained include the classification accuracy of about 99.21%, 99% of sensitivity and 99.4% of specificity with PPV and NPV of about 99.4 and 99.01 values indicate the enhanced performance of our proposed work compared with the conventional LSTM-CAE and LSTM-CNN techniques.

Oversampling Based on Data Augmentation in Convolutional Neural Network for Silicon Wafer Defect Classification

2020 ◽  
Author(s):  
Uzma Batool ◽  
Mohd Ibrahim Shapiai ◽  
Nordinah Ismail ◽  
Hilman Fauzi ◽  
Syahrizal Salleh
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Convolutional Neural Network ◽  
Silicon Wafer ◽  
Data Augmentation ◽  
Imbalanced Data ◽  
Training Data ◽  
Defect Classification ◽  
Learning Method ◽  
Test Set

Silicon wafer defect data collected from fabrication facilities is intrinsically imbalanced because of the variable frequencies of defect types. Frequently occurring types will have more influence on the classification predictions if a model gets trained on such skewed data. A fair classifier for such imbalanced data requires a mechanism to deal with type imbalance in order to avoid biased results. This study has proposed a convolutional neural network for wafer map defect classification, employing oversampling as an imbalance addressing technique. To have an equal participation of all classes in the classifier’s training, data augmentation has been employed, generating more samples in minor classes. The proposed deep learning method has been evaluated on a real wafer map defect dataset and its classification results on the test set returned a 97.91% accuracy. The results were compared with another deep learning based auto-encoder model demonstrating the proposed method, a potential approach for silicon wafer defect classification that needs to be investigated further for its robustness.

Convolutional Neural Network

2022 ◽  
pp. 1559-1575
Author(s):  
Mário Pereira Véstias
Keyword(s):  
Neural Network ◽  
Machine Learning ◽  
Neural Networks ◽  
Artificial Neural Networks ◽  
Deep Learning ◽  
Convolutional Neural Network ◽  
Machine Learning Algorithms ◽  
Training Data ◽  
Machine Learning Model ◽  
Artificial Neural

Machine learning is the study of algorithms and models for computing systems to do tasks based on pattern identification and inference. When it is difficult or infeasible to develop an algorithm to do a particular task, machine learning algorithms can provide an output based on previous training data. A well-known machine learning model is deep learning. The most recent deep learning models are based on artificial neural networks (ANN). There exist several types of artificial neural networks including the feedforward neural network, the Kohonen self-organizing neural network, the recurrent neural network, the convolutional neural network, the modular neural network, among others. This article focuses on convolutional neural networks with a description of the model, the training and inference processes and its applicability. It will also give an overview of the most used CNN models and what to expect from the next generation of CNN models.

scholarly journals Empirical Evaluation of the Effect of Optimization and Regularization Techniques on the Generalization Performance of Deep Convolutional Neural Network

2020 ◽  
Vol 10 (21) ◽  
pp. 7817
Author(s):  
Ivana Marin ◽  
Ana Kuzmanic Skelin ◽  
Tamara Grujic
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Convolutional Neural Network ◽  
Empirical Evaluation ◽  
Training Data ◽  
Generalization Performance ◽  
Deep Model ◽  
Unseen Data ◽  
Regularization Techniques ◽  
Learning Architectures

The main goal of any classification or regression task is to obtain a model that will generalize well on new, previously unseen data. Due to the recent rise of deep learning and many state-of-the-art results obtained with deep models, deep learning architectures have become one of the most used model architectures nowadays. To generalize well, a deep model needs to learn the training data well without overfitting. The latter implies a correlation of deep model optimization and regularization with generalization performance. In this work, we explore the effect of the used optimization algorithm and regularization techniques on the final generalization performance of the model with convolutional neural network (CNN) architecture widely used in the field of computer vision. We give a detailed overview of optimization and regularization techniques with a comparative analysis of their performance with three CNNs on the CIFAR-10 and Fashion-MNIST image datasets.

scholarly journals Analysis of COVID-19 Infections on a CT Image Using DeepSense Model

2020 ◽  
Vol 8 ◽  
Author(s):  
Adil Khadidos ◽  
Alaa O. Khadidos ◽  
Srihari Kannan ◽  
Yuvaraj Natarajan ◽  
Sachi Nandan Mohanty ◽  
...  
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Input Data ◽  
Training Data ◽  
Learning Framework ◽  
Learning Classifiers ◽  
Tomography Image ◽  
Mining Model ◽  
Deep Learning Model

In this paper, a data mining model on a hybrid deep learning framework is designed to diagnose the medical conditions of patients infected with the coronavirus disease 2019 (COVID-19) virus. The hybrid deep learning model is designed as a combination of convolutional neural network (CNN) and recurrent neural network (RNN) and named as DeepSense method. It is designed as a series of layers to extract and classify the related features of COVID-19 infections from the lungs. The computerized tomography image is used as an input data, and hence, the classifier is designed to ease the process of classification on learning the multidimensional input data using the Expert Hidden layers. The validation of the model is conducted against the medical image datasets to predict the infections using deep learning classifiers. The results show that the DeepSense classifier offers accuracy in an improved manner than the conventional deep and machine learning classifiers. The proposed method is validated against three different datasets, where the training data are compared with 70%, 80%, and 90% training data. It specifically provides the quality of the diagnostic method adopted for the prediction of COVID-19 infections in a patient.

scholarly journals Utilizing the Road Mark Training Set from Ground-Based Mapping System to Airborne Imagery in Deep Learning Framework

2019 ◽  
Vol 1 ◽  
pp. 1-1
Author(s):  
Tee-Ann Teo
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Spatial Resolution ◽  
Image Features ◽  
Training Data ◽  
Training Set ◽  
Data Set ◽  
The Road ◽  
Mapping System ◽  
Close Range

<p><strong>Abstract.</strong> Deep Learning is a kind of Machine Learning technology which utilizing the deep neural network to learn a promising model from a large training data set. Convolutional Neural Network (CNN) has been successfully applied in image segmentation and classification with high accuracy results. The CNN applies multiple kernels (also called filters) to extract image features via image convolution. It is able to determine multiscale features through the multiple layers of convolution and pooling processes. The variety of training data plays an important role to determine a reliable CNN model. The benchmarking training data for road mark extraction is mainly focused on close-range imagery because it is easier to obtain a close-range image rather than an airborne image. For example, KITTI Vision Benchmark Suite. This study aims to transfer the road mark training data from mobile lidar system to aerial orthoimage in Fully Convolutional Networks (FCN). The transformation of the training data from ground-based system to airborne system may reduce the effort of producing a large training data set.</p><p>This study uses FCN technology and aerial orthoimage to localize road marks on the road regions. The road regions are first extracted from 2-D large-scale vector map. The input aerial orthoimage is 10&amp;thinsp;cm spatial resolution and the non-road regions are masked out before the road mark localization. The training data are road mark’s polygons, which are originally digitized from ground-based mobile lidar and prepared for the road mark extraction using mobile mapping system. This study reuses these training data and applies them for the road mark extraction using aerial orthoimage. The digitized training road marks are then transformed to road polygon based on mapping coordinates. As the detail of ground-based lidar is much better than the airborne system, the partially occulted parking lot in aerial orthoimage can also be obtained from the ground-based system. The labels (also called annotations) for FCN include road region, non-regions and road mark. The size of a training batch is 500&amp;thinsp;pixel by 500&amp;thinsp;pixel (50&amp;thinsp;m by 50&amp;thinsp;m on the ground), and the total number of training batches for training is 75 batches. After the FCN training stage, an independent aerial orthoimage (Figure 1a) is applied to predict the road marks. The results of FCN provide initial regions for road marks (Figure 1b). Usually, road marks show higher reflectance than road asphalts. Therefore, this study uses this characteristic to refine the road marks (Figure 1c) by a binary classification inside the initial road mark’s region.</p><p>To compare the automatically extracted road marks (Figure 1c) and manually digitized road marks (Figure 1d), most road marks can be extracted using the training set from ground-based system. This study also selects an area of 600&amp;thinsp;m&amp;thinsp;&amp;times;&amp;thinsp;200&amp;thinsp;m in quantitative analysis. Among the 371 reference road marks, 332 can be extracted from proposed scheme, and the completeness reached 89%. The preliminary experiment demonstrated that most road marks can be successfully extracted by the proposed scheme. Therefore, the training data from the ground-based mapping system can be utilized in airborne orthoimage in similar spatial resolution.</p>

scholarly journals Deep Learning Neural Networks to Predict Serious Complications After Bariatric Surgery: Analysis of Scandinavian Obesity Surgery Registry Data (Preprint)

2019 ◽  
Author(s):  
Yang Cao ◽  
Scott Montgomery ◽  
Johan Ottosson ◽  
Erik Näslund ◽  
Erik Stenberg
Keyword(s):  
Neural Network ◽  
Neural Networks ◽  
Bariatric Surgery ◽  
Deep Learning ◽  
Postoperative Complications ◽  
Obesity Surgery ◽  
Test Data ◽  
Registry Data ◽  
Training Data ◽  
Complications After Bariatric Surgery

BACKGROUND Obesity is one of today’s most visible public health problems worldwide. Although modern bariatric surgery is ostensibly considered safe, serious complications and mortality still occur in some patients. OBJECTIVE This study aimed to explore whether serious postoperative complications of bariatric surgery recorded in a national quality registry can be predicted preoperatively using deep learning methods. METHODS Patients who were registered in the Scandinavian Obesity Surgery Registry (SOReg) between 2010 and 2015 were included in this study. The patients who underwent a bariatric procedure between 2010 and 2014 were used as training data, and those who underwent a bariatric procedure in 2015 were used as test data. Postoperative complications were graded according to the Clavien-Dindo classification, and complications requiring intervention under general anesthesia or resulting in organ failure or death were considered serious. Three supervised deep learning neural networks were applied and compared in our study: multilayer perceptron (MLP), convolutional neural network (CNN), and recurrent neural network (RNN). The synthetic minority oversampling technique (SMOTE) was used to artificially augment the patients with serious complications. The performances of the neural networks were evaluated using accuracy, sensitivity, specificity, Matthews correlation coefficient, and area under the receiver operating characteristic curve. RESULTS In total, 37,811 and 6250 patients were used as the training data and test data, with incidence rates of serious complication of 3.2% (1220/37,811) and 3.0% (188/6250), respectively. When trained using the SMOTE data, the MLP appeared to have a desirable performance, with an area under curve (AUC) of 0.84 (95% CI 0.83-0.85). However, its performance was low for the test data, with an AUC of 0.54 (95% CI 0.53-0.55). The performance of CNN was similar to that of MLP. It generated AUCs of 0.79 (95% CI 0.78-0.80) and 0.57 (95% CI 0.59-0.61) for the SMOTE data and test data, respectively. Compared with the MLP and CNN, the RNN showed worse performance, with AUCs of 0.65 (95% CI 0.64-0.66) and 0.55 (95% CI 0.53-0.57) for the SMOTE data and test data, respectively. CONCLUSIONS MLP and CNN showed improved, but limited, ability for predicting the postoperative serious complications after bariatric surgery in the Scandinavian Obesity Surgery Registry data. However, the overfitting issue is still apparent and needs to be overcome by incorporating intra- and perioperative information. CLINICALTRIAL

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