scholarly journals IAV-CNN: a 2D convolutional neural network model to predict antigenic variants of influenza A virus

2020 ◽  
Author(s):  
Rui Yin ◽  
Nyi Nyi Thwin ◽  
Pei Zhuang ◽  
Yu Zhang ◽  
Zhuoyi Lin ◽  
...  
Keyword(s):  
Neural Network ◽  
Convolutional Neural Network ◽  
Influenza A ◽  
Computational Models ◽  
Rapid Evolution ◽  
Predictive Performance ◽  
Influenza Viruses ◽  
Distributed Representation ◽  
Similar Distribution ◽  
Feature Maps

The rapid evolution of influenza viruses constantly leads to the emergence of novel influenza strains that are capable of escaping from population immunity. The timely determination of antigenic variants is critical to vaccine design. Empirical experimental methods like hemagglutination inhibition (HI) assays are time-consuming and labor-intensive, requiring live viruses. Recently, many computational models have been developed to predict the antigenic variants without considerations of explicitly modeling the interdependencies between the channels of feature maps. Moreover, the influenza sequences consisting of similar distribution of residues will have high degrees of similarity and will affect the prediction outcome. Consequently, it is challenging but vital to determine the importance of different residue sites and enhance the predictive performance of influenza antigenicity. We have proposed a 2D convolutional neural network (CNN) model to infer influenza antigenic variants (IAV-CNN). Specifically, we introduce a new distributed representation of amino acids, named ProtVec that can be applied to a variety of downstream proteomic machine learning tasks. After splittings and embeddings of influenza strains, a 2D squeeze-and-excitation CNN architecture is constructed that enables networks to focus on informative residue features by fusing both spatial and channel-wise information with local receptive fields at each layer. Experimental results on three influenza datasets show IAV-CNN achieves state-of-the-art performance combing the new distributed representation with our proposed architecture. It outperforms both traditional machine algorithms with the same feature representations and the majority of existing models in the independent test data. Therefore we believe that our model can be served as a reliable and robust tool for the prediction of antigenic variants.

scholarly journals VirPreNet: A weighted ensemble convolutional neural network for the virulence prediction of influenza A virus using all 8 segments

2020 ◽  
Author(s):  
Rui Yin ◽  
Zihan Luo ◽  
Pei Zhuang ◽  
Zhuoyi Lin ◽  
Chee Keong Kwoh
Keyword(s):  
Public Health ◽  
Neural Network ◽  
Convolutional Neural Network ◽  
Influenza A Virus ◽  
Influenza A ◽  
Lethal Dose ◽  
Influenza Viruses ◽  
Numerical Representation ◽  
Influenza A Viruses ◽  
Linear Layer

AbstractMotivationInfluenza viruses are persistently threatening public health, causing annual epidemics and sporadic pandemics. The evolution of influenza viruses remains to be the main obstacle in the effectiveness of antiviral treatments due to rapid mutations. Previous work has been investigated to reveal the determinants of virulence of the influenza A virus. To further facilitate flu surveillance, explicit detection of influenza virulence is crucial to protect public health from potential future pandemics.ResultsIn this paper, we propose a weighted ensemble convolutional neural network for the virulence prediction of influenza A viruses named VirPreNet that uses all 8 segments. Firstly, mouse lethal dose 50 is exerted to label the virulence of infections into two classes, namely avirulent and virulent. A numerical representation of amino acids named ProtVec is applied to the 8-segments in a distributed manner to encode the biological sequences. After splittings and embeddings of influenza strains, the ensemble convolutional neural network is constructed as the base model on the influenza dataset of each segment, which serves as the VirPreNet’s main part. Followed by a linear layer, the initial predictive outcomes are integrated and assigned with different weights for the final prediction. The experimental results on the collected influenza dataset indicate that VirPreNet achieves state-of-the-art performance combining ProtVec with our proposed architecture. It outperforms baseline methods on the independent testing data. Moreover, our proposed model reveals the importance of PB2 and HA segments on the virulence prediction. We believe that our model may provide new insights into the investigation of influenza [email protected] and ImplementationCodes and data to generate the VirPreNet are publicly available at https://github.com/Rayin-saber/VirPreNet

scholarly journals VirPreNet: a weighted ensemble convolutional neural network for the virulence prediction of influenza A virus using all eight segments

2020 ◽  
Author(s):  
Rui Yin ◽  
Zihan Luo ◽  
Pei Zhuang ◽  
Zhuoyi Lin ◽  
Chee Keong Kwoh
Keyword(s):  
Public Health ◽  
Neural Network ◽  
Convolutional Neural Network ◽  
Influenza A Virus ◽  
Influenza A ◽  
Lethal Dose ◽  
Influenza Viruses ◽  
Supplementary Information ◽  
Numerical Representation ◽  
Influenza A Viruses

Abstract Motivation Influenza viruses are persistently threatening public health, causing annual epidemics and sporadic pandemics. The evolution of influenza viruses remains to be the main obstacle in the effectiveness of antiviral treatments due to rapid mutations. Previous work has been investigated to reveal the determinants of virulence of the influenza A virus. To further facilitate flu surveillance, explicit detection of influenza virulence is crucial to protect public health from potential future pandemics. Results In this article, we propose a weighted ensemble convolutional neural network (CNN) for the virulence prediction of influenza A viruses named VirPreNet that uses all eight segments. Firstly, mouse lethal dose 50 is exerted to label the virulence of infections into two classes, namely avirulent and virulent. A numerical representation of amino acids named ProtVec is applied to the eight-segments in a distributed manner to encode the biological sequences. After splittings and embeddings of influenza strains, the ensemble CNN is constructed as the base model on the influenza dataset of each segment, which serves as the VirPreNet’s main part. Followed by a linear layer, the initial predictive outcomes are integrated and assigned with different weights for the final prediction. The experimental results on the collected influenza dataset indicate that VirPreNet achieves state-of-the-art performance combining ProtVec with our proposed architecture. It outperforms baseline methods on the independent testing data. Moreover, our proposed model reveals the importance of PB2 and HA segments on the virulence prediction. We believe that our model may provide new insights into the investigation of influenza virulence. Availability and implementation Codes and data to generate the VirPreNet are publicly available at https://github.com/Rayin-saber/VirPreNet. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals AFibNet: an implementation of atrial fibrillation detection with convolutional neural network

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Bambang Tutuko ◽  
Siti Nurmaini ◽  
Alexander Edo Tondas ◽  
Muhammad Naufal Rachmatullah ◽  
Annisa Darmawahyuni ◽  
...  
Keyword(s):  
Neural Network ◽  
Atrial Fibrillation ◽  
Convolutional Neural Network ◽  
Learning System ◽  
Single Frequency ◽  
Feature Maps ◽  
Normal Sinus ◽  
Unseen Data ◽  
Specific Device ◽  
Model Formation

Abstract Background Generalization model capacity of deep learning (DL) approach for atrial fibrillation (AF) detection remains lacking. It can be seen from previous researches, the DL model formation used only a single frequency sampling of the specific device. Besides, each electrocardiogram (ECG) acquisition dataset produces a different length and sampling frequency to ensure sufficient precision of the R–R intervals to determine the heart rate variability (HRV). An accurate HRV is the gold standard for predicting the AF condition; therefore, a current challenge is to determine whether a DL approach can be used to analyze raw ECG data in a broad range of devices. This paper demonstrates powerful results for end-to-end implementation of AF detection based on a convolutional neural network (AFibNet). The method used a single learning system without considering the variety of signal lengths and frequency samplings. For implementation, the AFibNet is processed with a computational cloud-based DL approach. This study utilized a one-dimension convolutional neural networks (1D-CNNs) model for 11,842 subjects. It was trained and validated with 8232 records based on three datasets and tested with 3610 records based on eight datasets. The predicted results, when compared with the diagnosis results indicated by human practitioners, showed a 99.80% accuracy, sensitivity, and specificity. Result Meanwhile, when tested using unseen data, the AF detection reaches 98.94% accuracy, 98.97% sensitivity, and 98.97% specificity at a sample period of 0.02 seconds using the DL Cloud System. To improve the confidence of the AFibNet model, it also validated with 18 arrhythmias condition defined as Non-AF-class. Thus, the data is increased from 11,842 to 26,349 instances for three-class, i.e., Normal sinus (N), AF and Non-AF. The result found 96.36% accuracy, 93.65% sensitivity, and 96.92% specificity. Conclusion These findings demonstrate that the proposed approach can use unknown data to derive feature maps and reliably detect the AF periods. We have found that our cloud-DL system is suitable for practical deployment

scholarly journals Spectral Convolution Feature-Based SPD Matrix Representation for Signal Detection Using a Deep Neural Network

Entropy ◽  
2020 ◽  
Vol 22 (9) ◽  
pp. 949
Author(s):  
Jiangyi Wang ◽  
Min Liu ◽  
Xinwu Zeng ◽  
Xiaoqiang Hua
Keyword(s):  
Neural Network ◽  
Signal Detection ◽  
Convolutional Neural Network ◽  
Deep Neural Network ◽  
Detection Method ◽  
Learning Algorithm ◽  
Simulated Data ◽  
Data Sets ◽  
Feature Maps ◽  
Simulated Data Sets

Convolutional neural networks have powerful performances in many visual tasks because of their hierarchical structures and powerful feature extraction capabilities. SPD (symmetric positive definition) matrix is paid attention to in visual classification, because it has excellent ability to learn proper statistical representation and distinguish samples with different information. In this paper, a deep neural network signal detection method based on spectral convolution features is proposed. In this method, local features extracted from convolutional neural network are used to construct the SPD matrix, and a deep learning algorithm for the SPD matrix is used to detect target signals. Feature maps extracted by two kinds of convolutional neural network models are applied in this study. Based on this method, signal detection has become a binary classification problem of signals in samples. In order to prove the availability and superiority of this method, simulated and semi-physical simulated data sets are used. The results show that, under low SCR (signal-to-clutter ratio), compared with the spectral signal detection method based on the deep neural network, this method can obtain a gain of 0.5–2 dB on simulated data sets and semi-physical simulated data sets.

scholarly journals PedNet: A Spatio-Temporal Deep Convolutional Neural Network for Pedestrian Segmentation

2018 ◽  
Vol 4 (9) ◽  
pp. 107 ◽  
Author(s):  
Mohib Ullah ◽  
Ahmed Mohammed ◽  
Faouzi Alaya Cheikh
Keyword(s):  
Neural Network ◽  
Convolutional Neural Network ◽  
Performance Metrics ◽  
State Of The Art ◽  
Temporal Information ◽  
Feature Maps ◽  
Current Frame ◽  
Low Level ◽  
Art Methods ◽  
Spatio Temporal

Articulation modeling, feature extraction, and classification are the important components of pedestrian segmentation. Usually, these components are modeled independently from each other and then combined in a sequential way. However, this approach is prone to poor segmentation if any individual component is weakly designed. To cope with this problem, we proposed a spatio-temporal convolutional neural network named PedNet which exploits temporal information for spatial segmentation. The backbone of the PedNet consists of an encoder–decoder network for downsampling and upsampling the feature maps, respectively. The input to the network is a set of three frames and the output is a binary mask of the segmented regions in the middle frame. Irrespective of classical deep models where the convolution layers are followed by a fully connected layer for classification, PedNet is a Fully Convolutional Network (FCN). It is trained end-to-end and the segmentation is achieved without the need of any pre- or post-processing. The main characteristic of PedNet is its unique design where it performs segmentation on a frame-by-frame basis but it uses the temporal information from the previous and the future frame for segmenting the pedestrian in the current frame. Moreover, to combine the low-level features with the high-level semantic information learned by the deeper layers, we used long-skip connections from the encoder to decoder network and concatenate the output of low-level layers with the higher level layers. This approach helps to get segmentation map with sharp boundaries. To show the potential benefits of temporal information, we also visualized different layers of the network. The visualization showed that the network learned different information from the consecutive frames and then combined the information optimally to segment the middle frame. We evaluated our approach on eight challenging datasets where humans are involved in different activities with severe articulation (football, road crossing, surveillance). The most common CamVid dataset which is used for calculating the performance of the segmentation algorithm is evaluated against seven state-of-the-art methods. The performance is shown on precision/recall, F 1 , F 2 , and mIoU. The qualitative and quantitative results show that PedNet achieves promising results against state-of-the-art methods with substantial improvement in terms of all the performance metrics.

scholarly journals Permutation Entropy-Based Interpretability of Convolutional Neural Network Models for Interictal EEG Discrimination of Subjects with Epileptic Seizures vs. Psychogenic Non-Epileptic Seizures

Entropy ◽  
2022 ◽  
Vol 24 (1) ◽  
pp. 102
Author(s):  
Michele Lo Giudice ◽  
Giuseppe Varone ◽  
Cosimo Ieracitano ◽  
Nadia Mammone ◽  
Giovanbattista Gaspare Tripodi ◽  
...  
Keyword(s):  
Neural Network ◽  
Discriminant Analysis ◽  
Convolutional Neural Network ◽  
Epileptic Seizures ◽  
Permutation Entropy ◽  
Diagnostic Tools ◽  
Support Vector ◽  
Feature Maps ◽  
Time Frequency ◽  
Interictal Eeg

The differential diagnosis of epileptic seizures (ES) and psychogenic non-epileptic seizures (PNES) may be difficult, due to the lack of distinctive clinical features. The interictal electroencephalographic (EEG) signal may also be normal in patients with ES. Innovative diagnostic tools that exploit non-linear EEG analysis and deep learning (DL) could provide important support to physicians for clinical diagnosis. In this work, 18 patients with new-onset ES (12 males, 6 females) and 18 patients with video-recorded PNES (2 males, 16 females) with normal interictal EEG at visual inspection were enrolled. None of them was taking psychotropic drugs. A convolutional neural network (CNN) scheme using DL classification was designed to classify the two categories of subjects (ES vs. PNES). The proposed architecture performs an EEG time-frequency transformation and a classification step with a CNN. The CNN was able to classify the EEG recordings of subjects with ES vs. subjects with PNES with 94.4% accuracy. CNN provided high performance in the assigned binary classification when compared to standard learning algorithms (multi-layer perceptron, support vector machine, linear discriminant analysis and quadratic discriminant analysis). In order to interpret how the CNN achieved this performance, information theoretical analysis was carried out. Specifically, the permutation entropy (PE) of the feature maps was evaluated and compared in the two classes. The achieved results, although preliminary, encourage the use of these innovative techniques to support neurologists in early diagnoses.

scholarly journals Block-Based Compression and Corresponding Hardware Circuits for Sparse Activations

Sensors ◽  
2021 ◽  
Vol 21 (22) ◽  
pp. 7468
Author(s):  
Yui-Kai Weng ◽  
Shih-Hsu Huang ◽  
Hsu-Yu Kao
Keyword(s):  
Neural Network ◽  
Power Consumption ◽  
Convolutional Neural Network ◽  
Feature Maps ◽  
Benchmark Data ◽  
Data Volume ◽  
Block Based

In a CNN (convolutional neural network) accelerator, to reduce memory traffic and power consumption, there is a need to exploit the sparsity of activation values. Therefore, some research efforts have been paid to skip ineffectual computations (i.e., multiplications by zero). Different from previous works, in this paper, we point out the similarity of activation values: (1) in the same layer of a CNN model, most feature maps are either highly dense or highly sparse; (2) in the same layer of a CNN model, feature maps in different channels are often similar. Based on the two observations, we propose a block-based compression approach, which utilizes both the sparsity and the similarity of activation values to further reduce the data volume. Moreover, we also design an encoder, a decoder and an indexing module to support the proposed approach. The encoder is used to translate output activations into the proposed block-based compression format, while both the decoder and the indexing module are used to align nonzero values for effectual computations. Compared with previous works, benchmark data consistently show that the proposed approach can greatly reduce both memory traffic and power consumption.

Classification and grading of diabetic retinopathy images using mixture of ensemble classifiers

2021 ◽  
pp. 1-13
Author(s):  
R. Bhuvaneswari ◽  
S. Ganesh Vaidyanathan
Keyword(s):  
Neural Network ◽  
Diabetic Retinopathy ◽  
Convolutional Neural Network ◽  
Blood Vessels ◽  
Support Vector ◽  
Network Architectures ◽  
Ensemble Classifiers ◽  
Feature Maps ◽  
Class Labels ◽  
Hierarchical Features

Diabetic Retinopathy (DR) is one of the most common diabetic diseases that affect the retina’s blood vessels. Too much of the glucose level in blood leads to blockage of blood vessels in the retina, weakening and damaging the retina. Automatic classification of diabetic retinopathy is a challenging task in medical research. This work proposes a Mixture of Ensemble Classifiers (MEC) to classify and grade diabetic retinopathy images using hierarchical features. We use an ensemble of classifiers such as support vector machine, random forest, and Adaboost classifiers that use the hierarchical feature maps obtained at every pooling layer of a convolutional neural network (CNN) for training. The feature maps are generated by applying the filters to the output of the previous layer. Lastly, we predict the class label or the grade for the given test diabetic retinopathy image by considering the class labels of all the ensembled classifiers. We have tested our approaches on the E-ophtha dataset for the classification task and the Messidor dataset for the grading task. We achieved an accuracy of 95.8% and 96.2% for the E-ophtha and Messidor datasets, respectively. A comparison among prominent convolutional neural network architectures and the proposed approach is provided.

Deep Convolutional Neural Network for Object Classification

2021 ◽  
pp. 317-343
Author(s):  
Amira Ahmad Al-Sharkawy ◽  
Gehan A. Bahgat ◽  
Elsayed E. Hemayed ◽  
Samia Abdel-Razik Mashali
Keyword(s):  
Neural Network ◽  
Neural Networks ◽  
Convolutional Neural Network ◽  
Computational Models ◽  
Human Performance ◽  
Deep Neural Networks ◽  
Object Classification ◽  
Classification Problem ◽  
Deep Convolutional Neural Network ◽  
Object Appearance

Object classification problem is essential in many applications nowadays. Human can easily classify objects in unconstrained environments easily. Classical classification techniques were far away from human performance. Thus, researchers try to mimic the human visual system till they reached the deep neural networks. This chapter gives a review and analysis in the field of the deep convolutional neural network usage in object classification under constrained and unconstrained environment. The chapter gives a brief review on the classical techniques of object classification and the development of bio-inspired computational models from neuroscience till the creation of deep neural networks. A review is given on the constrained environment issues: the hardware computing resources and memory, the object appearance and background, and the training and processing time. Datasets that are used to test the performance are analyzed according to the images environmental conditions, besides the dataset biasing is discussed.

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