scholarly journals R-CRISPR: A Deep Learning Network to Predict Off-Target Activities with Mismatch, Insertion and Deletion in CRISPR-Cas9 System

Genes ◽  
2021 ◽  
Vol 12 (12) ◽  
pp. 1878
Author(s):  
Rui Niu ◽  
Jiajie Peng ◽  
Zhipeng Zhang ◽  
Xuequn Shang
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
In Silico ◽  
Prediction Method ◽  
Training Data ◽  
Prediction Methods ◽  
In Silico Prediction ◽  
Guide Rnas ◽  
Insertion And Deletion ◽  
Deep Learning Network

The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)—associated protein 9 (Cas9) system is a groundbreaking gene-editing tool, which has been widely adopted in biomedical research. However, the guide RNAs in CRISPR-Cas9 system may induce unwanted off-target activities and further affect the practical application of the technique. Most existing in silico prediction methods that focused on off-target activities possess limited predictive precision and remain to be improved. Hence, it is necessary to propose a new in silico prediction method to address this problem. In this work, a deep learning framework named R-CRISPR is presented, which devises an encoding scheme to encode gRNA-target sequences into binary matrices, a convolutional neural network as feature extractor, and a recurrent neural network to predict off-target activities with mismatch, insertion, or deletion. It is demonstrated that R-CRISPR surpasses six mainstream prediction methods with a significant improvement on mismatch-only datasets verified by GUIDE-seq. Compared with the state-of-art prediction methods, R-CRISPR also achieves competitive performance on datasets with mismatch, insertion, and deletion. Furthermore, experiments show that data concatenate could influence the quality of training data, and investigate the optimal combination of datasets.

scholarly journals Toxicity Prediction Method Based on Multi-Channel Convolutional Neural Network

Molecules ◽  
2019 ◽  
Vol 24 (18) ◽  
pp. 3383 ◽  
Author(s):  
Yuan ◽  
Wei ◽  
Guan ◽  
Jiang ◽  
Wang ◽  
...  
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Convolutional Neural Network ◽  
Prediction Method ◽  
Toxicity Prediction ◽  
Learning Network ◽  
Machine Learning Methods ◽  
Molecular Information ◽  
Molecular Toxicity ◽  
Deep Learning Network

Molecular toxicity prediction is one of the key studies in drug design. In this paper, a deep learning network based on a two-dimension grid of molecules is proposed to predict toxicity. At first, the van der Waals force and hydrogen bond were calculated according to different descriptors of molecules, and multi-channel grids were generated, which could discover more detail and helpful molecular information for toxicity prediction. The generated grids were fed into a convolutional neural network to obtain the result. A Tox21 dataset was used for the evaluation. This dataset contains more than 12,000 molecules. It can be seen from the experiment that the proposed method performs better compared to other traditional deep learning and machine learning methods.

scholarly journals A Deep Learning Method for ECG Signal Prediction Based on VMD, Cao Method, and LSTM Neural Network

2021 ◽  
Author(s):  
Fuying Huang ◽  
Tuanfa Qin ◽  
Limei Wang ◽  
Haibin Wan
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Prediction Accuracy ◽  
Prediction Method ◽  
Prediction Methods ◽  
Ecg Signal ◽  
Learning Method ◽  
Signal Prediction ◽  
Input Layer ◽  
Ecg Data

Abstract Background: In body area network (BAN), accurate prediction of ECG signal can not only let doctors know the patient's condition in advance, but also help to reduce the energy consumption of sensors. In order to improve the accuracy of ECG signal prediction, this paper proposes a deep learning method for ECG signal prediction. Methods: The proposed prediction method combines variational mode decomposition (VMD), Cao method and a long short-term memory (LSTM) neural network. In the method, VMD decomposes ECG data into a series of intrinsic mode functions (IMFs), which reduces the non-stationary character of ECG signals and helps to improve the prediction accuracy. Cao method is used to determine the input dimension of LSTM input layer, namely, the minimum embedding dimension of each IMF is the input dimension of LSTM input layer. Each IMF is predicted by a LSTM neural network which adopts Adam optimizer. All IMFs predictions are aggregated to get the final prediction result. Results: To evaluate the prediction accuracy of the proposed method, simulation experiments are carried out on ECG data from the MIT-BIH Arrhythmia Database. Experimental results show that the RMSE (root mean square error) and MAE (mean absolute error) of the proposed model are 0.001326 and 0.001044 respectively, which are more than 10 percent lower than the traditional prediction methods.Conclusions: Compared with some traditional prediction methods, the proposed prediction method improves the prediction accuracy obviously.

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.

Accurate refinement of docked protein complexes using evolutionary information and deep learning

2016 ◽  
Vol 14 (03) ◽  
pp. 1642002 ◽  
Author(s):  
Bahar Akbal-Delibas ◽  
Roshanak Farhoodi ◽  
Marc Pomplun ◽  
Nurit Haspel
Keyword(s):  
Deep Learning ◽  
Protein Complexes ◽  
Scoring Function ◽  
Protein Docking ◽  
Training Data ◽  
Evolutionary Information ◽  
Native Structure ◽  
Learning Network ◽  
Small Set ◽  
Deep Learning Network

One of the major challenges for protein docking methods is to accurately discriminate native-like structures from false positives. Docking methods are often inaccurate and the results have to be refined and re-ranked to obtain native-like complexes and remove outliers. In a previous work, we introduced AccuRefiner, a machine learning based tool for refining protein–protein complexes. Given a docked complex, the refinement tool produces a small set of refined versions of the input complex, with lower root-mean-square-deviation (RMSD) of atomic positions with respect to the native structure. The method employs a unique ranking tool that accurately predicts the RMSD of docked complexes with respect to the native structure. In this work, we use a deep learning network with a similar set of features and five layers. We show that a properly trained deep learning network can accurately predict the RMSD of a docked complex with 1.40 Å error margin on average, by approximating the complex relationship between a wide set of scoring function terms and the RMSD of a docked structure. The network was trained on 35000 unbound docking complexes generated by RosettaDock. We tested our method on 25 different putative docked complexes produced also by RosettaDock for five proteins that were not included in the training data. The results demonstrate that the high accuracy of the ranking tool enables AccuRefiner to consistently choose the refinement candidates with lower RMSD values compared to the coarsely docked input structures.

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.

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