scholarly journals Two particle picking procedures for filamentous proteins: SPHIRE-crYOLO filament mode and SPHIRE-STRIPER

2020 ◽  
Author(s):  
Thorsten Wagner ◽  
Luca Lusnig ◽  
Sabrina Pospich ◽  
Markus Stabrin ◽  
Fabian Schönfeld ◽  
...  
Keyword(s):  
Neural Network ◽  
Deep Neural Network ◽  
Molecular Complexes ◽  
High Accuracy ◽  
The Other ◽  
Line Detection ◽  
Data Sets ◽  
Detection Approach ◽  
Selection Of

AbstractStructure determination of filamentous molecular complexes involves the selection of filaments from cryo-EM micrographs. The automatic selection of helical specimens is particularly difficult and thus many challenging samples with issues such as contamination or aggregation are still manually picked. Here we present two approaches for selecting filamentous complexes: one uses a trained deep neural network to identify the filaments and is integrated in SPHIRE-crYOLO, the other one, called SPHIRE-STRIPER, is based on a classical line detection approach. The advantage of the crYOLO based procedure is that it accurately performs on very challenging data sets and selects filaments with high accuracy. Although STRIPER is less precise, the user benefits from less intervention, since in contrast to crYOLO, STRIPER does not require training. We evaluate the performance of both procedures on tobacco mosaic virus and filamentous F-actin data sets to demonstrate the robustness of each method.

scholarly journals Two particle-picking procedures for filamentous proteins: SPHIRE-crYOLO filament mode and SPHIRE-STRIPER

2020 ◽  
Vol 76 (7) ◽  
pp. 613-620
Author(s):  
Thorsten Wagner ◽  
Luca Lusnig ◽  
Sabrina Pospich ◽  
Markus Stabrin ◽  
Fabian Schönfeld ◽  
...  
Keyword(s):  
Neural Network ◽  
Deep Neural Network ◽  
Molecular Complexes ◽  
High Accuracy ◽  
The Other ◽  
Line Detection ◽  
Data Sets ◽  
Detection Approach ◽  
Selection Of

Structure determination of filamentous molecular complexes involves the selection of filaments from cryo-EM micrographs. The automatic selection of helical specimens is particularly difficult, and thus many challenging samples with issues such as contamination or aggregation are still manually picked. Here, two approaches for selecting filamentous complexes are presented: one uses a trained deep neural network to identify the filaments and is integrated in SPHIRE-crYOLO, while the other, called SPHIRE-STRIPER, is based on a classical line-detection approach. The advantage of the crYOLO-based procedure is that it performs accurately on very challenging data sets and selects filaments with high accuracy. Although STRIPER is less precise, the user benefits from less intervention, since in contrast to crYOLO, STRIPER does not require training. The performance of both procedures on Tobacco mosaic virus and filamentous F-actin data sets is described to demonstrate the robustness of each method.

Method of determination of the text direction on the image with the use of convolutional neural network

2020 ◽  
pp. 96-99
Author(s):  
P.L. Nikolaev
Keyword(s):  
Neural Network ◽  
Convolutional Neural Network ◽  
Deep Neural Network ◽  
Binary Classification ◽  
Synthetic Data ◽  
Real Data ◽  
Method Of Determination ◽  
Classification Of Images

This article deals with method of binary classification of images with small text on them Classification is based on the fact that the text can have 2 directions – it can be positioned horizontally and read from left to right or it can be turned 180 degrees so the image must be rotated to read the sign. This type of text can be found on the covers of a variety of books, so in case of recognizing the covers, it is necessary first to determine the direction of the text before we will directly recognize it. The article suggests the development of a deep neural network for determination of the text position in the context of book covers recognizing. The results of training and testing of a convolutional neural network on synthetic data as well as the examples of the network functioning on the real data are presented.

scholarly journals Fast Accurate and Automatic Brushstroke Extraction

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.

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 Pathway-guided deep neural network toward interpretable and predictive modeling of drug sensitivity

2020 ◽  
Author(s):  
Lei Deng ◽  
Yideng Cai ◽  
Wenhao Zhang ◽  
Wenyi Yang ◽  
Bo Gao ◽  
...  
Keyword(s):  
Neural Network ◽  
Cancer Cells ◽  
Drug Targets ◽  
Deep Neural Network ◽  
Drug Sensitivity ◽  
Predictive Ability ◽  
Biological Knowledge ◽  
Data Sets ◽  
Source Codes ◽  
Sensitivity Data

AbstractMotivationTo efficiently save cost and reduce risk in drug research and development, there is a pressing demand to develop in-silico methods to predict drug sensitivity to cancer cells. With the exponentially increasing number of multi-omics data derived from high-throughput techniques, machine learning-based methods have been applied to the prediction of drug sensitivities. However, these methods have drawbacks either in the interpretability of mechanism of drug action or limited performance in modeling drug sensitivity.ResultsIn this paper, we presented a pathway-guided deep neural network model, referred to as pathDNN, to predict the drug sensitivity to cancer cells. Biological pathways describe a group of molecules in a cell that collaborates to control various biological functions like cell proliferation and death, thereby abnormal function of pathways can result in disease. To make advantage of both the excellent predictive ability of deep neural network and the biological knowledge of pathways, we reshape the canonical DNN structure by incorporating a layer of pathway nodes and their connections to input gene nodes, which makes the DNN model more interpretable and predictive compared to canonical DNN. We have conducted extensive performance evaluations on multiple independent drug sensitivity data sets, and demonstrate that pathDNN significantly outperformed canonical DNN model and seven other classical regression models. Most importantly, we observed remarkable activity decreases of disease-related pathway nodes during forward propagation upon inputs of drug targets, which implicitly corresponds to the inhibition effect of disease-related pathways induced by drug treatment on cancer cells. Our empirical experiments show that pathDNN achieves pharmacological interpretability and predictive ability in modeling drug sensitivity to cancer cells.AvailabilityThe web server, as well as the processed data sets and source codes for reproducing our work, is available at http://pathdnn.denglab.org

scholarly journals Novel Spatiotemporal Feature Extraction Parallel Deep Neural Network for Forecasting Confirmed Cases of Coronavirus Disease 2019

2020 ◽  
Author(s):  
Chiou-Jye Huang ◽  
Yamin Shen ◽  
Ping-Huan Kuo ◽  
Yung-Hsiang Chen
Keyword(s):  
Neural Network ◽  
Deep Neural Network ◽  
Absolute Error ◽  
Mean Absolute Percentage Error ◽  
The Other ◽  
Percentage Error ◽  
Model Assessment ◽  
Absolute Percentage Error ◽  
Spatiotemporal Feature ◽  
The Mean

AbstractThe coronavirus disease 2019 pandemic continues as of March 26 and spread to Europe on approximately February 24. A report from April 29 revealed 1.26 million confirmed cases and 125 928 deaths in Europe. This study proposed a novel deep neural network framework, COVID-19Net, which parallelly combines a convolutional neural network (CNN) and bidirectional gated recurrent units (GRUs). Three European countries with severe outbreaks were studied—Germany, Italy, and Spain—to extract spatiotemporal feature and predict the number of confirmed cases. The prediction results acquired from COVID-19Net were compared to those obtained using a CNN, GRU, and CNN-GRU. The mean absolute error, mean absolute percentage error, and root mean square error, which are commonly used model assessment indices, were used to compare the accuracy of the models. The results verified that COVID-19Net was notably more accurate than the other models. The mean absolute percentage error generated by COVID-19Net was 1.447 for Germany, 1.801 for Italy, and 2.828 for Spain, which were considerably lower than those of the other models. This indicated that the proposed framework can accurately predict the accumulated number of confirmed cases in the three countries and serve as a crucial reference for devising public health strategies.

CTL-DNNet: Effective Circular Traffic Light Recognition with a Deep Neural Network

2017 ◽  
Vol 31 (11) ◽  
pp. 1750037 ◽  
Author(s):  
Di Wang ◽  
Hong Bao ◽  
Feifei Zhang
Keyword(s):  
Neural Network ◽  
Autonomous Vehicles ◽  
Deep Neural Network ◽  
Road Traffic ◽  
High Accuracy ◽  
Activation Functions ◽  
Traffic Light ◽  
Traffic Lights ◽  
Learning Network ◽  
Deep Learning Network

This paper proposed an algorithm for a deep learning network for identifying circular traffic lights (CTL-DNNet). The sample labeling process uses translation to increase the number of positive samples, and the similarity is calculated to reduce the number of negative samples, thereby reducing overfitting. We use a dataset of approximately 370[Formula: see text]000 samples, with approximately 20[Formula: see text]000 positive samples and approximately 350[Formula: see text]000 negative samples. The datasets are generated from images taken at the Beijing Garden Expo. To obtain a very robust method for the detection of traffic lights, we use different layers, different cost functions and different activation functions of the depth neural network for training and comparison. Our algorithm has evaluated autonomous vehicles in varying illumination and gets the result with high accuracy and robustness. The experimental results show that CTL-DNNet is effective at recognizing road traffic lights in the Beijing Garden Expo area.

scholarly journals Effective Methodology for Co-Referential Aspect Based Sentiment Analysis of Tourist Reviews

2020 ◽  
pp. 523-529
Author(s):  
Kamlesh A. Waghmare ◽  
Sheetal K. Bhala
Keyword(s):  
Neural Network ◽  
Machine Learning ◽  
Sentiment Analysis ◽  
High Accuracy ◽  
Machine Learning Algorithms ◽  
Data Sets ◽  
Knowledge Processing ◽  
The Neural Network ◽  
The World ◽  
Sentiment Score

Tourist reviews are the source of data that is going to be used for the travelers around the world to find the hotels for their stay according to their comfort. In this the hotels are ranked over the parameters or aspects considered keeping travelers in mind. This computation of data sets is done with the help of the machine learning algorithms and the neural network. The knowledge processing done over the reviews generates the sentiment score for each hotel with respect to the aspects defined. Here, the explicit , implicit and co-referential aspects are identified by suppressing the noise. This paper proposes the method that can be best used for the detection of the sentiments with the high accuracy.

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