scholarly journals DISTEMA: distance map-based estimation of single protein model accuracy with attentive 2D convolutional neural network

2021 ◽  
Author(s):  
Xiao Chen ◽  
Jianling Cheng
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Convolutional Neural Network ◽  
Structural Models ◽  
Model Quality ◽  
Distance Map ◽  
Protein Model ◽  
Single Protein ◽  
Ranking Loss

AbstractBackgroundEstimation of the accuracy (quality) of protein structural models is important for both prediction and use of protein structural models. Deep learning methods have been used to integrate protein structure features to predict the quality of protein models. Inter-residue distances are key information for predicting protein’s tertiary structures and therefore have good potentials to predict the quality of protein structural models. However, few methods have been developed to fully take advantage of predicted inter-residue distance maps to estimate the accuracy of a single protein structural model.ResultWe developed an attentive 2D convolutional neural network (CNN) with channel-wise attention to take only a raw difference map between the inter-residue distance map calculated from a single protein model and the distance map predicted from the protein sequence as input to predict the quality of the model. The network comprises multiple convolutional layers, batch normalization layers, dense layers, and Squeeze-and-Excitation blocks with attention to automatically extract features relevant to protein model quality from the raw input without using any expert-curated features. We evaluated DISTEMA’s capability of selecting the best models for CASP13 targets in terms of ranking loss of GDT-TS score. The ranking loss of DISTEMA is 0.079, lower than several state-of-the-art single-model quality assessment methods. The work demonstrates that using raw inter-residue distance information alone with deep learning can predict the quality of protein structural models reasonably well.

scholarly journals Protein model accuracy estimation empowered by deep learning and inter-residue distance prediction in CASP14

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Xiao Chen ◽  
Jian Liu ◽  
Zhiye Guo ◽  
Tianqi Wu ◽  
Jie Hou ◽  
...  
Keyword(s):  
Deep Learning ◽  
Structure Prediction ◽  
Structural Models ◽  
Single Model ◽  
Model Accuracy ◽  
Model Quality ◽  
Distance Information ◽  
Evaluation Of Performance ◽  
Protein Model

AbstractThe inter-residue contact prediction and deep learning showed the promise to improve the estimation of protein model accuracy (EMA) in the 13th Critical Assessment of Protein Structure Prediction (CASP13). To further leverage the improved inter-residue distance predictions to enhance EMA, during the 2020 CASP14 experiment, we integrated several new inter-residue distance features with the existing model quality assessment features in several deep learning methods to predict the quality of protein structural models. According to the evaluation of performance in selecting the best model from the models of CASP14 targets, our three multi-model predictors of estimating model accuracy (MULTICOM-CONSTRUCT, MULTICOM-AI, and MULTICOM-CLUSTER) achieve the averaged loss of 0.073, 0.079, and 0.081, respectively, in terms of the global distance test score (GDT-TS). The three methods are ranked first, second, and third out of all 68 CASP14 predictors. MULTICOM-DEEP, the single-model predictor of estimating model accuracy (EMA), is ranked within top 10 among all the single-model EMA methods according to GDT-TS score loss. The results demonstrate that inter-residue distance features are valuable inputs for deep learning to predict the quality of protein structural models. However, larger training datasets and better ways of leveraging inter-residue distance information are needed to fully explore its potentials.

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.

scholarly journals Convolutional neural-network-based classification of retinal images with different combinations of filtering techniques

2021 ◽  
Vol 11 (1) ◽  
pp. 480-490
Author(s):  
Asha Gnana Priya Henry ◽  
Anitha Jude
Keyword(s):  
Neural Network ◽  
Diabetic Retinopathy ◽  
Deep Learning ◽  
Convolutional Neural Network ◽  
Performance Metrics ◽  
Input Image ◽  
Application Techniques ◽  
Enhancement Method ◽  
Neural Network Input

Abstract Retinal image analysis is one of the important diagnosis methods in modern ophthalmology because eye information is present in the retina. The image acquisition process may have some effects and can affect the quality of the image. This can be improved by better image enhancement techniques combined with the computer-aided diagnosis system. Deep learning is one of the important computational application techniques used for a medical imaging application. The main aim of this article is to find the best enhancement techniques for the identification of diabetic retinopathy (DR) and are tested with the commonly used deep learning techniques, and the performances are measured. In this article, the input image is taken from the Indian-based database named as Indian Diabetic Retinopathy Image Dataset, and 13 filters are used including smoothing and sharpening filters for enhancing the images. Then, the quality of the enhancement techniques is compared using performance metrics and better results are obtained for Median, Gaussian, Bilateral, Wiener, and partial differential equation filters and are combined for improving the enhancement of images. The output images from all the enhanced filters are given as the convolutional neural network input and the results are compared to find the better enhancement method.

scholarly journals Protein model accuracy estimation empowered by deep learning and inter-residue distance prediction in CASP14

2021 ◽  
Author(s):  
Xiao Chen ◽  
Jian Liu ◽  
Zhiye Guo ◽  
Tianqi Wu ◽  
Jie Hou ◽  
...  
Keyword(s):  
Deep Learning ◽  
Structure Prediction ◽  
Structural Models ◽  
Single Model ◽  
Model Accuracy ◽  
Model Quality ◽  
Residue Contact ◽  
Contact Distance ◽  
Protein Model ◽  
Contact Predictions

AbstractThe inter-residue contact prediction and deep learning showed the promise to improve the estimation of protein model accuracy (EMA) in the 13th Critical Assessment of Protein Structure Prediction (CASP13). During the 2020 CASP14 experiment, we developed and tested several EMA predictors that used deep learning with the new features based on inter-residue distance/contact predictions as well as the existing model quality features. The average global distance test (GDT-TS) score loss of ranking CASP14 structural models by three multi-model MULTICOM EMA predictors (MULTICOM-CONSTRUCT, MULTICOM-AI, and MULTICOM-CLUSTER) is 0.073, 0.079, and 0.081, respectively, which are ranked first, second, and third places out of 68 CASP14 EMA predictors. The single-model EMA predictor (MULTICOM-DEEP) is ranked 10th place among all the single-model EMA methods in terms of GDT_TS score loss. The results show that deep learning and contact/distance predictions are useful in ranking and selecting protein structural models.

scholarly journals Image classification of different clove (Syzygium aromaticum) quality using deep learning method with convolutional neural network algorithm

2021 ◽  
Vol 905 (1) ◽  
pp. 012018
Author(s):  
I Y Prayogi ◽  
Sandra ◽  
Y Hendrawan
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Convolutional Neural Network ◽  
Test Data ◽  
Training Data ◽  
Syzygium Aromaticum ◽  
Learning Method ◽  
Validation Data ◽  
Reading Accuracy

Abstract The objective of this study is to classify the quality of dried clove flowers using deep learning method with Convolutional Neural Network (CNN) algorithm, and also to perform the sensitivity analysis of CNN hyperparameters to obtain best model for clove quality classification process. The quality of clove as raw material in this study was determined according to SNI 3392-1994 by PT. Perkebunan Nusantara XII Pancusari Plantation, Malang, East Java, Indonesia. In total 1,600 images of dried clove flower were divided into 4 qualities. Each clove quality has 225 training data, 75 validation data, and 100 test data. The first step of this study is to build CNN model architecture as first model. The result of that model gives 65.25% reading accuracy. The second step is to analyze CNN sensitivity or CNN hyperparameter on the first model. The best value of CNN hyperparameter in each step then to be used in the next stage. Finally, after CNN hyperparameter carried out the reading accuracy of the test data is improved to 87.75%.

scholarly journals Deep convolutional neural networks for predicting the quality of single protein structural models

2019 ◽  
Author(s):  
Jie Hou ◽  
Renzhi Cao ◽  
Jianlin Cheng
Keyword(s):  
Structure Prediction ◽  
Structural Model ◽  
Structural Models ◽  
Structural Features ◽  
Fixed Number ◽  
Deep Convolutional Neural Networks ◽  
Global Quality ◽  
Protein Model ◽  
Single Protein

AbstractPredicting the global quality and local (residual-specific) quality of a single protein structural model is important for protein structure prediction and application. In this work, we developed a deep one-dimensional convolutional neural network (1DCNN) that predicts the absolute local quality of a single protein model as well as two 1DCNNs to predict both local and global quality simultaneously through a novel multi-task learning framework. The networks accept sequential and structural features (i.e. amino acid sequence, agreement of secondary structure and solvent accessibilities, residual disorder properties and Rosetta energies) of a protein model of any size as input to predict its quality, which is different from existing methods using a fixed number of hand-crafted features as input. Our three methods (InteractQA-net, JointQA-net and LocalQA-net) were trained on the structural models of the single-domain protein targets of CASP8, 9, 10 and evaluated on the models of CASP11 and CASP12 targets. The results show that the performance of our deep learning methods is comparable to the state-of-the-art quality assessment methods. Our study also demonstrates that combining local and global quality predictions together improves the global quality prediction accuracy. The source code and executable of our methods are available at:https://github.com/multicom-toolbox/DeepCovQA

scholarly journals Automatic vegetation identification in Google Earth images using a convolutional neural network: A case study for Japanese bamboo forests

2018 ◽  
Author(s):  
Shuntaro Watanabe ◽  
Kazuaki Sumi ◽  
Takeshi Ise
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Convolutional Neural Network ◽  
Environmental Science ◽  
Google Earth ◽  
Image Resolution ◽  
Training Data ◽  
Identification Accuracy ◽  
Automatic Identification

ABSTRACTClassifying and mapping vegetation are very important tasks in environmental science and natural resource management. However, these tasks are not easy because conventional methods such as field surveys are highly labor intensive. Automatic identification of target objects from visual data is one of the most promising ways to reduce the costs for vegetation mapping. Although deep learning has become a new solution for image recognition and classification recently, in general, detection of ambiguous objects such as vegetation still is considered difficult. In this paper, we investigated the potential for adapting the chopped picture method, a recently described protocol for deep learning, to detect plant communities in Google Earth images. We selected bamboo forests as the target. We obtained Google Earth images from three regions in Japan. By applying the deep convolutional neural network, the model successfully learned the features of bamboo forests in Google Earth images, and the best trained model correctly detected 97% of the targets. Our results show that identification accuracy strongly depends on the image resolution and the quality of training data. Our results also highlight that deep learning and the chopped picture method can potentially become a powerful tool for high accuracy automated detection and mapping of vegetation.

scholarly journals Sentiment Analysis in Spanish for Improvement of Products and Services: A Deep Learning Approach

2017 ◽  
Vol 2017 ◽  
pp. 1-6 ◽  
Author(s):  
Mario Andrés Paredes-Valverde ◽  
Ricardo Colomo-Palacios ◽  
María del Pilar Salas-Zárate ◽  
Rafael Valencia-García
Keyword(s):  
Neural Network ◽  
Social Networks ◽  
Deep Learning ◽  
Public Opinion ◽  
Customer Satisfaction ◽  
Convolutional Neural Network ◽  
Sentiment Analysis ◽  
Learning Approach ◽  
Complete Dataset

Sentiment analysis is an important area that allows knowing public opinion of the users about several aspects. This information helps organizations to know customer satisfaction. Social networks such as Twitter are important information channels because information in real time can be obtained and processed from them. In this sense, we propose a deep-learning-based approach that allows companies and organizations to detect opportunities for improving the quality of their products or services through sentiment analysis. This approach is based on convolutional neural network (CNN) and word2vec. To determine the effectiveness of this approach for classifying tweets, we conducted experiments with different sizes of a Twitter corpus composed of 100000 tweets. We obtained encouraging results with a precision of 88.7%, a recall of 88.7%, and an F-measure of 88.7% considering the complete dataset.

scholarly journals Protein Model Accuracy Estimation Empowered by Deep Learning and Inter-residue Distance Prediction in CASP14

2021 ◽  
Author(s):  
Xiao Chen ◽  
Jian Liu ◽  
Zhiye Guo ◽  
Tianqi Wu ◽  
Jie Hou ◽  
...  
Keyword(s):  
Deep Learning ◽  
Structure Prediction ◽  
Structural Models ◽  
Single Model ◽  
Model Accuracy ◽  
Model Quality ◽  
Residue Contact ◽  
Contact Distance ◽  
Protein Model ◽  
Contact Predictions

Abstract The inter-residue contact prediction and deep learning showed the promise to improve the estimation of protein model accuracy (CASP13) in the 13th Critical Assessment of Protein Structure Prediction (CASP13). During the 2020 CASP14 experiment, we developed and tested several EMA predictors that used deep learning with the new features based on inter-residue distance/contact predictions as well as the existing model quality features. The average global distance test (GDT-TS) score loss of ranking CASP14 structural models by three multi-model MULTICOM EMA predictors (MULTICOM-CONSTRUCT, MULTICOM-AI, and MULTICOM-CLUSTER) is 0.073, 0.079, and 0.081, respectively, which are ranked first, second, and third places out of 68 CASP14 EMA predictors. The single-model EMA predictor (MULTICOM-DEEP) is ranked 10th place among all the single-model EMA methods in terms of GDT-TS score loss. The results show that deep learning and contact/distance predictions are useful in ranking and selecting protein structural models.

Convolutional Neural Network of Atomic Surface Structures to Predict Binding Energies for High-Throughput Screening of Catalysts

2019 ◽  
Author(s):  
Seoin Back ◽  
Junwoong Yoon ◽  
Nianhan Tian ◽  
Wen Zhong ◽  
Kevin Tran ◽  
...  
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Convolutional Neural Network ◽  
High Throughput ◽  
High Throughput Screening ◽  
Binding Energies ◽  
Surface Structures ◽  
Voronoi Polyhedra ◽  
Atomic Surface

We present an application of deep-learning convolutional neural network of atomic surface structures using atomic and Voronoi polyhedra-based neighbor information to predict adsorbate binding energies for the application in catalysis.

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