High-Quality Genomes of Nanopore Sequencing by Homologous Polishing

AbstractNanopore sequencing has been widely used for reconstruction of a variety of microbial genomes. Owing to the higher error rate, the assembled genome requires further error correction. Existing methods erase many of these errors via deep neural network trained from Nanopore reads. However, quite a few systematic errors are still left on the genome. This paper proposed a new model trained from homologous sequences extracted from closely-related genomes, which provides valuable features missed in Nanopore reads. The developed program (called Homopolish) outperforms the state-of-the-art Racon/Medaka and MarginPolish/HELEN pipelines in metagenomic and isolates of bacteria, viruses and fungi. When Homopolish is combined with Medaka or with HELEN, the genomes quality can exceed Q50 on R9.4 flowcells. The genome quality can be also improved on R10.3 flowcells (Q50-Q90). We proved that Nanopore-only sequencing can now produce high-quality genomes without the need of Illumina hybrid sequencing.

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Homopolish: a method for the removal of systematic errors in nanopore sequencing by homologous polishing

Genome Biology ◽

10.1186/s13059-021-02282-6 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Yao-Ting Huang ◽

Po-Yu Liu ◽

Pei-Wen Shih

Keyword(s):

Neural Networks ◽

Systematic Errors ◽

Error Rates ◽

Nanopore Sequencing ◽

High Quality ◽

Flow Cells ◽

Microbial Genomes ◽

Homologous Sequences ◽

Downstream Analysis

AbstractNanopore sequencing has been widely used for the reconstruction of microbial genomes. Owing to higher error rates, errors on the genome are corrected via neural networks trained by Nanopore reads. However, the systematic errors usually remain uncorrected. This paper designs a model that is trained by homologous sequences for the correction of Nanopore systematic errors. The developed program, Homopolish, outperforms Medaka and HELEN in bacteria, viruses, fungi, and metagenomic datasets. When combined with Medaka/HELEN, the genome quality can exceed Q50 on R9.4 flow cells. We show that Nanopore-only sequencing can produce high-quality microbial genomes sufficient for downstream analysis.

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Tri-net for Semi-Supervised Deep Learning

Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence ◽

10.24963/ijcai.2018/278 ◽

2018 ◽

Cited By ~ 11

Author(s):

Dong-Dong Chen ◽

Wei Wang ◽

Wei Gao ◽

Zhi-Hua Zhou

Keyword(s):

Neural Network ◽

Neural Networks ◽

Deep Learning ◽

Error Rate ◽

Deep Neural Network ◽

Deep Neural Networks ◽

State Of The Art ◽

Fine Tuning ◽

Learning Methods ◽

Model Initialization

Deep neural networks have witnessed great successes in various real applications, but it requires a large number of labeled data for training. In this paper, we propose tri-net, a deep neural network which is able to use massive unlabeled data to help learning with limited labeled data. We consider model initialization, diversity augmentation and pseudo-label editing simultaneously. In our work, we utilize output smearing to initialize modules, use fine-tuning on labeled data to augment diversity and eliminate unstable pseudo-labels to alleviate the influence of suspicious pseudo-labeled data. Experiments show that our method achieves the best performance in comparison with state-of-the-art semi-supervised deep learning methods. In particular, it achieves 8.30% error rate on CIFAR-10 by using only 4000 labeled examples.

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Fast Accurate and Automatic Brushstroke Extraction

ACM Transactions on Multimedia Computing Communications and Applications ◽

10.1145/3429742 ◽

2021 ◽

Vol 17 (2) ◽

pp. 1-24

Author(s):

Yunfei Fu ◽

Hongchuan Yu ◽

Chih-Kuo Yeh ◽

Tong-Yee Lee ◽

Jian J. Zhang

Keyword(s):

Neural Network ◽

Efficient Algorithm ◽

Deep Neural Network ◽

High Efficiency ◽

State Of The Art ◽

High Reliability ◽

The Other ◽

Manual Annotation ◽

Stroke Extraction ◽

Art Research

Brushstrokes are viewed as the artist’s “handwriting” in a painting. In many applications such as style learning and transfer, mimicking painting, and painting authentication, it is highly desired to quantitatively and accurately identify brushstroke characteristics from old masters’ pieces using computer programs. However, due to the nature of hundreds or thousands of intermingling brushstrokes in the painting, it still remains challenging. This article proposes an efficient algorithm for brush Stroke extraction based on a Deep neural network, i.e., DStroke. Compared to the state-of-the-art research, the main merit of the proposed DStroke is to automatically and rapidly extract brushstrokes from a painting without manual annotation, while accurately approximating the real brushstrokes with high reliability. Herein, recovering the faithful soft transitions between brushstrokes is often ignored by the other methods. In fact, the details of brushstrokes in a master piece of painting (e.g., shapes, colors, texture, overlaps) are highly desired by artists since they hold promise to enhance and extend the artists’ powers, just like microscopes extend biologists’ powers. To demonstrate the high efficiency of the proposed DStroke, we perform it on a set of real scans of paintings and a set of synthetic paintings, respectively. Experiments show that the proposed DStroke is noticeably faster and more accurate at identifying and extracting brushstrokes, outperforming the other methods.

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An Efficient Method for Detection of DDoS Attacks on the Web Using Deep Learning Algorithms

International Journal of Advanced Trends in Computer Science and Engineering ◽

10.30534/ijatcse/2021/271042021 ◽

2021 ◽

Vol 10 (4) ◽

pp. 2821-2829

Keyword(s):

Neural Network ◽

Deep Learning ◽

Deep Neural Network ◽

State Of The Art ◽

Ddos Attacks ◽

Problem Statement ◽

Neural Network Approach ◽

Learning Techniques ◽

Attack Data ◽

Deep Learning Neural Network

Recently, DDoS attacks is the most significant threat in network security. Both industry and academia are currently debating how to detect and protect against DDoS attacks. Many studies are provided to detect these types of attacks. Deep learning techniques are the most suitable and efficient algorithm for categorizing normal and attack data. Hence, a deep neural network approach is proposed in this study to mitigate DDoS attacks effectively. We used a deep learning neural network to identify and classify traffic as benign or one of four different DDoS attacks. We will concentrate on four different DDoS types: Slowloris, Slowhttptest, DDoS Hulk, and GoldenEye. The rest of the paper is organized as follow: Firstly, we introduce the work, Section 2 defines the related works, Section 3 presents the problem statement, Section 4 describes the proposed methodology, Section 5 illustrate the results of the proposed methodology and shows how the proposed methodology outperforms state-of-the-art work and finally Section VI concludes the paper.

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An Analysis of State-of-the-art Activation Functions For Supervised Deep Neural Network

10.31219/osf.io/2zk6a ◽

2021 ◽

Author(s):

Anh Nguyen ◽

Khoa Pham ◽

Dat Ngo ◽

Thanh Ngo ◽

Lam Pham

Keyword(s):

Neural Network ◽

Supervised Classification ◽

Deep Neural Network ◽

State Of The Art ◽

Network Architectures ◽

Activation Functions ◽

Scene Classification ◽

Learning Network ◽

Deep Learning Network

This paper provides an analysis of state-of-the-art activation functions with respect to supervised classification of deep neural network. These activation functions comprise of Rectified Linear Units (ReLU), Exponential Linear Unit (ELU), Scaled Exponential Linear Unit (SELU), Gaussian Error Linear Unit (GELU), and the Inverse Square Root Linear Unit (ISRLU). To evaluate, experiments over two deep learning network architectures integrating these activation functions are conducted. The first model, basing on Multilayer Perceptron (MLP), is evaluated with MNIST dataset to perform these activation functions.Meanwhile, the second model, likely VGGish-based architecture, is applied for Acoustic Scene Classification (ASC) Task 1A in DCASE 2018 challenge, thus evaluate whether these activation functions work well in different datasets as well as different network architectures.

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Regularized Training and Tight Certification for Randomized Smoothed Classifier with Provable Robustness

Proceedings of the AAAI Conference on Artificial Intelligence ◽

10.1609/aaai.v34i04.5798 ◽

2020 ◽

Vol 34 (04) ◽

pp. 3858-3865

Author(s):

Huijie Feng ◽

Chunpeng Wu ◽

Guoyang Chen ◽

Weifeng Zhang ◽

Yang Ning

Keyword(s):

Neural Network ◽

High Probability ◽

Deep Neural Network ◽

State Of The Art ◽

Computationally Efficient ◽

Base Classifier ◽

Training Scheme ◽

Adversarial Training ◽

Gaussian Perturbation ◽

Probabilistic Robustness

Recently smoothing deep neural network based classifiers via isotropic Gaussian perturbation is shown to be an effective and scalable way to provide state-of-the-art probabilistic robustness guarantee against ℓ2 norm bounded adversarial perturbations. However, how to train a good base classifier that is accurate and robust when smoothed has not been fully investigated. In this work, we derive a new regularized risk, in which the regularizer can adaptively encourage the accuracy and robustness of the smoothed counterpart when training the base classifier. It is computationally efficient and can be implemented in parallel with other empirical defense methods. We discuss how to implement it under both standard (non-adversarial) and adversarial training scheme. At the same time, we also design a new certification algorithm, which can leverage the regularization effect to provide tighter robustness lower bound that holds with high probability. Our extensive experimentation demonstrates the effectiveness of the proposed training and certification approaches on CIFAR-10 and ImageNet datasets.

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Covid-19 detection via deep neural network and occlusion sensitivity maps

10.36227/techrxiv.14100890 ◽

2021 ◽

Author(s):

Noor Ahmad ◽

Muhammad Aminu ◽

Mohd Halim Mohd Noor

Keyword(s):

Neural Network ◽

Deep Learning ◽

Deep Neural Network ◽

State Of The Art ◽

Color Images ◽

Fine Tuning ◽

Training Dataset ◽

Learning Approaches ◽

Learning Models ◽

Sensitivity Maps

Deep learning approaches have attracted a lot of attention in the automatic detection of Covid-19 and transfer learning is the most common approach. However, majority of the pre-trained models are trained on color images, which can cause inefficiencies when fine-tuning the models on Covid-19 images which are often grayscale. To address this issue, we propose a deep learning architecture called CovidNet which requires a relatively smaller number of parameters. CovidNet accepts grayscale images as inputs and is suitable for training with limited training dataset. Experimental results show that CovidNet outperforms other state-of-the-art deep learning models for Covid-19 detection.

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