scholarly journals VIDHOP, viral host prediction with Deep Learning

2019 ◽  
Author(s):  
Florian Mock ◽  
Adrian Viehweger ◽  
Emanuel Barth ◽  
Manja Marz
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
Viral Genome ◽  
Influenza A ◽  
Deep Neural Networks ◽  
Ebola Virus ◽  
Training Data ◽  
Supplementary Information ◽  
Virus Species ◽  
Rotavirus A

AbstractMotivationZoonosis, the natural transmission of infections from animals to humans, is a far-reaching global problem. The recent outbreaks of Zika virus, Ebola virus and Corona virus are examples of viral zoonosis, which occur more frequently due to globalization. In the case of a virus outbreak, it is helpful to know which host organism was the original carrier of the virus. Once the reservoir or intermediate host is known, it can be isolated to prevent further spreading of the viral infection. Recent approaches aim to predict a viral host based on the viral genome, often in combination with the potential host genome and arbitrarily selected features. These methods have a clear limitation in either the number of different hosts they can predict or the accuracy of their prediction.ResultsHere, we present a fast and accurate deep learning approach for viral host prediction, which is based on the viral genome sequence only. To ensure a high prediction accuracy, we developed an effective selection approach for the training data to avoid biases due to a highly unbalanced number of known sequences per virus-host combinations. We tested our deep neural network on three different virus species (influenza A, rabies lyssavirus, rotavirus A). We reached for each virus species an AUG between 0.93 and 0.98, outperforming previous approaches and allowing highly accurate predictions while only using fractions (100-400 bp) of the viral genome sequences. We show that deep neural networks are suitable to predict the host of a virus, even with a limited amount of sequences and highly unbalanced available data. The deep neural networks trained for this approach build the core of the virus-host predicting tool VIDHOP (Virus Deep learning HOst Prediction).AvailabilityThe trained models for the prediction of the host for the viruses influenza A, rabies lyssavirus, rotavirus A are implemented in the tool VIDHOP. This tool is freely available under https://github.com/flomock/vidhop.Supplementary informationSupplementary data are available at DOI 10.17605/OSF.IO/UXT7N

scholarly journals VIDHOP, viral host prediction with deep learning

2020 ◽  
Author(s):  
Florian Mock ◽  
Adrian Viehweger ◽  
Emanuel Barth ◽  
Manja Marz
Keyword(s):  
Deep Learning ◽  
Viral Genome ◽  
Influenza A ◽  
Deep Neural Networks ◽  
Supplementary Information ◽  
Learning Approach ◽  
Virus Species ◽  
Genome Sequences ◽  
Rotavirus A ◽  
The Core

Abstract Motivation Zoonosis, the natural transmission of infections from animals to humans, is a far-reaching global problem. The recent outbreaks of Zikavirus, Ebolavirus and Coronavirus are examples of viral zoonosis, which occur more frequently due to globalization. In case of a virus outbreak, it is helpful to know which host organism was the original carrier of the virus to prevent further spreading of viral infection. Recent approaches aim to predict a viral host based on the viral genome, often in combination with the potential host genome and arbitrarily selected features. These methods are limited in the number of different hosts they can predict or the accuracy of the prediction. Results Here, we present a fast and accurate deep learning approach for viral host prediction, which is based on the viral genome sequence only. We tested our deep neural network (DNN) on three different virus species (influenza A virus, rabies lyssavirus and rotavirus A). We achieved for each virus species an AUC between 0.93 and 0.98, allowing highly accurate predictions while using only fractions (100–400 bp) of the viral genome sequences. We show that deep neural networks are suitable to predict the host of a virus, even with a limited amount of sequences and highly unbalanced available data. The trained DNNs are the core of our virus–host prediction tool VIrus Deep learning HOst Prediction (VIDHOP). VIDHOP also allows the user to train and use models for other viruses. Availability and implementation VIDHOP is freely available under https://github.com/flomock/vidhop. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Comprehensive evaluation of deep learning architectures for prediction of DNA/RNA sequence binding specificities

2019 ◽  
Vol 35 (14) ◽  
pp. i269-i277 ◽  
Author(s):  
Ameni Trabelsi ◽  
Mohamed Chaabane ◽  
Asa Ben-Hur
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
Rna Binding ◽  
Binding Specificity ◽  
Training Data ◽  
Supplementary Information ◽  
Recurrent Networks ◽  
Dna And Rna ◽  
Learning Architectures ◽  
Dna And Rna Binding

Abstract Motivation Deep learning architectures have recently demonstrated their power in predicting DNA- and RNA-binding specificity. Existing methods fall into three classes: Some are based on convolutional neural networks (CNNs), others use recurrent neural networks (RNNs) and others rely on hybrid architectures combining CNNs and RNNs. However, based on existing studies the relative merit of the various architectures remains unclear. Results In this study we present a systematic exploration of deep learning architectures for predicting DNA- and RNA-binding specificity. For this purpose, we present deepRAM, an end-to-end deep learning tool that provides an implementation of a wide selection of architectures; its fully automatic model selection procedure allows us to perform a fair and unbiased comparison of deep learning architectures. We find that deeper more complex architectures provide a clear advantage with sufficient training data, and that hybrid CNN/RNN architectures outperform other methods in terms of accuracy. Our work provides guidelines that can assist the practitioner in choosing an appropriate network architecture, and provides insight on the difference between the models learned by convolutional and recurrent networks. In particular, we find that although recurrent networks improve model accuracy, this comes at the expense of a loss in the interpretability of the features learned by the model. Availability and implementation The source code for deepRAM is available at https://github.com/MedChaabane/deepRAM. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals On regularization properties of artificial datasets for deep learning

2019 ◽  
Vol 0 (9/2019) ◽  
pp. 13-18
Author(s):  
Karol Antczak
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
Deep Neural Networks ◽  
Real Data ◽  
Training Data ◽  
Generation Process ◽  
Data Generation ◽  
Artificial Data ◽  
High Level ◽  
Artificial Datasets

The paper discusses regularization properties of artificial data for deep learning. Artificial datasets allow to train neural networks in the case of a real data shortage. It is demonstrated that the artificial data generation process, described as injecting noise to high-level features, bears several similarities to existing regularization methods for deep neural networks. One can treat this property of artificial data as a kind of “deep” regularization. It is thus possible to regularize hidden layers of the network by generating the training data in a certain way.

scholarly journals Image Denoising Using Nonlocal Regularized Deep Image Prior

Symmetry ◽  
2021 ◽  
Vol 13 (11) ◽  
pp. 2114
Author(s):  
Zhonghua Xie ◽  
Lingjun Liu ◽  
Zhongliang Luo ◽  
Jianfeng Huang
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
Image Denoising ◽  
Deep Neural Networks ◽  
Optimization Problems ◽  
Training Data ◽  
Superior Performance ◽  
Convolutional Network ◽  
Image Prior ◽  
Deep Image

Deep neural networks have shown great potential in various low-level vision tasks, leading to several state-of-the-art image denoising techniques. Training a deep neural network in a supervised fashion usually requires the collection of a great number of examples and the consumption of a significant amount of time. However, the collection of training samples is very difficult for some application scenarios, such as the full-sampled data of magnetic resonance imaging and the data of satellite remote sensing imaging. In this paper, we overcome the problem of a lack of training data by using an unsupervised deep-learning-based method. Specifically, we propose a deep-learning-based method based on the deep image prior (DIP) method, which only requires a noisy image as training data, without any clean data. It infers the natural images with random inputs and the corrupted observation with the help of performing correction via a convolutional network. We improve the original DIP method as follows: Firstly, the original optimization objective function is modified by adding nonlocal regularizers, consisting of a spatial filter and a frequency domain filter, to promote the gradient sparsity of the solution. Secondly, we solve the optimization problem with the alternating direction method of multipliers (ADMM) framework, resulting in two separate optimization problems, including a symmetric U-Net training step and a plug-and-play proximal denoising step. As such, the proposed method exploits the powerful denoising ability of both deep neural networks and nonlocal regularizations. Experiments validate the effectiveness of leveraging a combination of DIP and nonlocal regularizers, and demonstrate the superior performance of the proposed method both quantitatively and visually compared with the original DIP method.

scholarly journals Deep Learning on Low-Resource Datasets

2018 ◽  
Author(s):  
Veronica Morfi ◽  
Dan Stowell
Keyword(s):  
Neural Network ◽  
Neural Networks ◽  
Deep Learning ◽  
Deep Neural Networks ◽  
Learning System ◽  
Training Data ◽  
Quality Performance ◽  
Training Performance ◽  
Low Resource ◽  
Advantages And Disadvantages

In training a deep learning system to perform audio transcription, two practical problems may arise. Firstly, most datasets are weakly labelled, having only a list of events present in each recording without any temporal information for training. Secondly, deep neural networks need a very large amount of labelled training data to achieve good quality performance, yet in practice it is difficult to collect enough samples for most classes of interest. In this paper, we propose factorising the final task of audio transcription into multiple intermediate tasks in order to improve the training performance when dealing with this kind of low-resource datasets. We evaluate three data-efficient approaches of training a stacked convolutional and recurrent neural network for the intermediate tasks. Our results show that different methods of training have different advantages and disadvantages.

scholarly journals Online Deep Learning: Learning Deep Neural Networks on the Fly

2018 ◽  
Author(s):  
Doyen Sahoo ◽  
Quang Pham ◽  
Jing Lu ◽  
Steven C. H. Hoi
Keyword(s):  
Neural Networks ◽  
Online Learning ◽  
Deep Learning ◽  
Deep Neural Networks ◽  
Large Data ◽  
Learning Task ◽  
Large Data Sets ◽  
Training Data ◽  
Data Sets ◽  
Online Setting

Deep Neural Networks (DNNs) are typically trained by backpropagation in a batch setting, requiring the entire training data to be made available prior to the learning task. This is not scalable for many real-world scenarios where new data arrives sequentially in a stream. We aim to address an open challenge of ``Online Deep Learning" (ODL) for learning DNNs on the fly in an online setting. Unlike traditional online learning that often optimizes some convex objective function with respect to a shallow model (e.g., a linear/kernel-based hypothesis), ODL is more challenging as the optimization objective is non-convex, and regular DNN with standard backpropagation does not work well in practice for online settings. We present a new ODL framework that attempts to tackle the challenges by learning DNN models which dynamically adapt depth from a sequence of training data in an online learning setting. Specifically, we propose a novel Hedge Backpropagation (HBP) method for online updating the parameters of DNN effectively, and validate the efficacy on large data sets (both stationary and concept drifting scenarios).

scholarly journals Automatic Detection of Arrhythmia Based on Multi-Resolution Representation of ECG Signal

Sensors ◽  
2020 ◽  
Vol 20 (6) ◽  
pp. 1579
Author(s):  
Dongqi Wang ◽  
Qinghua Meng ◽  
Dongming Chen ◽  
Hupo Zhang ◽  
Lisheng Xu
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
Deep Neural Networks ◽  
Channel Model ◽  
Expert Knowledge ◽  
Automatic Detection ◽  
Data Representation ◽  
Learning Technology ◽  
Arrhythmia Detection ◽  
Automatic Feature Extraction

Automatic detection of arrhythmia is of great significance for early prevention and diagnosis of cardiovascular disease. Traditional feature engineering methods based on expert knowledge lack multidimensional and multi-view information abstraction and data representation ability, so the traditional research on pattern recognition of arrhythmia detection cannot achieve satisfactory results. Recently, with the increase of deep learning technology, automatic feature extraction of ECG data based on deep neural networks has been widely discussed. In order to utilize the complementary strength between different schemes, in this paper, we propose an arrhythmia detection method based on the multi-resolution representation (MRR) of ECG signals. This method utilizes four different up to date deep neural networks as four channel models for ECG vector representations learning. The deep learning based representations, together with hand-crafted features of ECG, forms the MRR, which is the input of the downstream classification strategy. The experimental results of big ECG dataset multi-label classification confirm that the F1 score of the proposed method is 0.9238, which is 1.31%, 0.62%, 1.18% and 0.6% higher than that of each channel model. From the perspective of architecture, this proposed method is highly scalable and can be employed as an example for arrhythmia recognition.

scholarly journals Enabling deeper learning on big data for materials informatics applications

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Dipendra Jha ◽  
Vishu Gupta ◽  
Logan Ward ◽  
Zijiang Yang ◽  
Christopher Wolverton ◽  
...  
Keyword(s):  
Neural Networks ◽  
Big Data ◽  
Deep Learning ◽  
Deep Neural Networks ◽  
Materials Science ◽  
Prediction Models ◽  
Model Performance ◽  
Materials Informatics ◽  
Learning Framework ◽  
Significant Attention

AbstractThe application of machine learning (ML) techniques in materials science has attracted significant attention in recent years, due to their impressive ability to efficiently extract data-driven linkages from various input materials representations to their output properties. While the application of traditional ML techniques has become quite ubiquitous, there have been limited applications of more advanced deep learning (DL) techniques, primarily because big materials datasets are relatively rare. Given the demonstrated potential and advantages of DL and the increasing availability of big materials datasets, it is attractive to go for deeper neural networks in a bid to boost model performance, but in reality, it leads to performance degradation due to the vanishing gradient problem. In this paper, we address the question of how to enable deeper learning for cases where big materials data is available. Here, we present a general deep learning framework based on Individual Residual learning (IRNet) composed of very deep neural networks that can work with any vector-based materials representation as input to build accurate property prediction models. We find that the proposed IRNet models can not only successfully alleviate the vanishing gradient problem and enable deeper learning, but also lead to significantly (up to 47%) better model accuracy as compared to plain deep neural networks and traditional ML techniques for a given input materials representation in the presence of big data.

scholarly journals Laplacian networks: bounding indicator function smoothness for neural networks robustness

2021 ◽  
Vol 10 ◽  
Author(s):  
Carlos Lassance ◽  
Vincent Gripon ◽  
Antonio Ortega
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
Supervised Learning ◽  
Indicator Function ◽  
Training Data ◽  
Theoretical Justification ◽  
The Past ◽  
Noisy Examples

For the past few years, deep learning (DL) robustness (i.e. the ability to maintain the same decision when inputs are subject to perturbations) has become a question of paramount importance, in particular in settings where misclassification can have dramatic consequences. To address this question, authors have proposed different approaches, such as adding regularizers or training using noisy examples. In this paper we introduce a regularizer based on the Laplacian of similarity graphs obtained from the representation of training data at each layer of the DL architecture. This regularizer penalizes large changes (across consecutive layers in the architecture) in the distance between examples of different classes, and as such enforces smooth variations of the class boundaries. We provide theoretical justification for this regularizer and demonstrate its effectiveness to improve robustness on classical supervised learning vision datasets for various types of perturbations. We also show it can be combined with existing methods to increase overall robustness.

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