scholarly journals Prediction of Protein–Protein Interaction Sites Using Convolutional Neural Network and Improved Data Sets

2020 ◽  
Vol 21 (2) ◽  
pp. 467 ◽  
Author(s):  
Zengyan Xie ◽  
Xiaoya Deng ◽  
Kunxian Shu
Keyword(s):  
Neural Network ◽  
Convolutional Neural Network ◽  
Protein Interaction ◽  
Protein Complexes ◽  
Area Under The Curve ◽  
Data Sets ◽  
Data Set ◽  
Protein Protein Interaction ◽  
Interaction Sites ◽  
Remarkable Result

Protein–protein interaction (PPI) sites play a key role in the formation of protein complexes, which is the basis of a variety of biological processes. Experimental methods to solve PPI sites are expensive and time-consuming, which has led to the development of different kinds of prediction algorithms. We propose a convolutional neural network for PPI site prediction and use residue binding propensity to improve the positive samples. Our method obtains a remarkable result of the area under the curve (AUC) = 0.912 on the improved data set. In addition, it yields much better results on samples with high binding propensity than on randomly selected samples. This suggests that there are considerable false-positive PPI sites in the positive samples defined by the distance between residue atoms.

ConvsPPIS: Identifying Protein-protein Interaction Sites by an Ensemble Convolutional Neural Network with Feature Graph

2020 ◽  
Vol 15 (4) ◽  
pp. 368-378
Author(s):  
Huaixu Zhu ◽  
Xiuquan Du ◽  
Yu Yao
Keyword(s):  
Neural Network ◽  
Convolutional Neural Network ◽  
Protein Interaction ◽  
Learning Ability ◽  
Superior Performance ◽  
Model Learning ◽  
Protein Protein Interaction ◽  
Interaction Sites ◽  
Protein Interaction Sites ◽  
Interface Residues

Background/Objective: Protein-protein interactions are essentials for most cellular processes and thus, unveiling how proteins interact with is a crucial question that can be better understood by recognizing which residues participate in the interaction. Although many computational approaches have been proposed to predict interface residues, their feature perspective and model learning ability are not enough to achieve ideal results. So, our objective is to improve the predictive performance under considering feature perspective and new learning algorithm. Method: In this study, we proposed an ensemble deep convolutional neural network, which explores the context and positional context of consecutive residues within a protein sub-sequence. Specifically, unlike the feature view of previous methods, ConvsPPIS uses evolutionary, physicochemical, and structural protein characteristics to construct their own feature graph respectively. After that, three independent deep convolutional neural networks are trained on each type of feature graph for learning the underlying pattern in sub-sequence. Lastly, we integrated those three deep networks into an ensemble predictor with leveraging complementary information of those features to predict potential interface residues. Results: Some comparative experiments have conducted through 10-fold cross-validation. The results indicated that ConvsPPIS achieved superior performance on DBv5-Sel dataset with an accuracy of 88%. Additional experiments on CAPRI-Alone dataset demonstrated ConvsPPIS has also better prediction performance. Conclusion: The ConvsPPIS method provided a new perspective to capture protein feature expression for identifying protein-protein interaction sites. The results proved the superiority of this method.

scholarly journals End-to-end convolutional neural network enables COVID-19 detection from breath and cough audio: a pilot study

2021 ◽  
Vol 7 (2) ◽  
pp. 356-362
Author(s):  
Harry Coppock ◽  
Alex Gaskell ◽  
Panagiotis Tzirakis ◽  
Alice Baird ◽  
Lyn Jones ◽  
...  
Keyword(s):  
Neural Network ◽  
Convolutional Neural Network ◽  
Low Cost ◽  
Area Under The Curve ◽  
Alternative Form ◽  
Economic Damage ◽  
Audio Signals ◽  
Operating Characteristics ◽  
Data Set ◽  
Empirical Performance

BackgroundSince the emergence of COVID-19 in December 2019, multidisciplinary research teams have wrestled with how best to control the pandemic in light of its considerable physical, psychological and economic damage. Mass testing has been advocated as a potential remedy; however, mass testing using physical tests is a costly and hard-to-scale solution.MethodsThis study demonstrates the feasibility of an alternative form of COVID-19 detection, harnessing digital technology through the use of audio biomarkers and deep learning. Specifically, we show that a deep neural network based model can be trained to detect symptomatic and asymptomatic COVID-19 cases using breath and cough audio recordings.ResultsOur model, a custom convolutional neural network, demonstrates strong empirical performance on a data set consisting of 355 crowdsourced participants, achieving an area under the curve of the receiver operating characteristics of 0.846 on the task of COVID-19 classification.ConclusionThis study offers a proof of concept for diagnosing COVID-19 using cough and breath audio signals and motivates a comprehensive follow-up research study on a wider data sample, given the evident advantages of a low-cost, highly scalable digital COVID-19 diagnostic tool.

scholarly journals Core looseness fault identification model based on Mel spectrogram-CNN

2021 ◽  
Vol 2137 (1) ◽  
pp. 012060
Author(s):  
Ping He ◽  
Yong Li ◽  
Shoulong Chen ◽  
Hoghua Xu ◽  
Lei Zhu ◽  
...  
Keyword(s):  
Neural Network ◽  
Convolutional Neural Network ◽  
Convolution Neural Network ◽  
Data Sets ◽  
Data Set ◽  
Recognition Model ◽  
Model Based ◽  
Fault Recognition ◽  
Transformer Core ◽  
Identification Model

Abstract In order to realize transformer voiceprint recognition, a transformer voiceprint recognition model based on Mel spectrum convolution neural network is proposed. Firstly, the transformer core looseness fault is simulated by setting different preloads, and the sound signals under different preloads are collected; Secondly, the sound signal is converted into a spectrogram that can be trained by convolutional neural network, and then the dimension is reduced by Mel filter bank to draw Mel spectrogram, which can generate spectrogram data sets under different preloads in batch; Finally, the data set is introduced into convolutional neural network for training, and the transformer voiceprint fault recognition model is obtained. The results show that the training accuracy of the proposed Mel spectrum convolution neural network transformer identification model is 99.91%, which can well identify the core loosening faults.

Vision-based automated crack detection using convolutional neural networks for condition assessment of infrastructure

2020 ◽  
pp. 147592172096544
Author(s):  
Aravinda S Rao ◽  
Tuan Nguyen ◽  
Marimuthu Palaniswami ◽  
Tuan Ngo
Keyword(s):  
Neural Network ◽  
Convolutional Neural Network ◽  
Crack Detection ◽  
Concrete Structures ◽  
Area Under The Curve ◽  
Network Models ◽  
Condition Assessment ◽  
Neural Network Models ◽  
Data Set ◽  
Inspection Method

With the growing number of aging infrastructure across the world, there is a high demand for a more effective inspection method to assess its conditions. Routine assessment of structural conditions is a necessity to ensure the safety and operation of critical infrastructure. However, the current practice to detect structural damages, such as cracks, depends on human visual observation methods, which are prone to efficiency, cost, and safety concerns. In this article, we present an automated detection method, which is based on convolutional neural network models and a non-overlapping window-based approach, to detect crack/non-crack conditions of concrete structures from images. To this end, we construct a data set of crack/non-crack concrete structures, comprising 32,704 training patches, 2074 validation patches, and 6032 test patches. We evaluate the performance of our approach using 15 state-of-the-art convolutional neural network models in terms of number of parameters required to train the models, area under the curve, and inference time. Our approach provides over 95% accuracy and over 87% precision in detecting the cracks for most of the convolutional neural network models. We also show that our approach outperforms existing models in literature in terms of accuracy and inference time. The best performance in terms of area under the curve was achieved by visual geometry group-16 model (area under the curve = 0.9805) and best inference time was provided by AlexNet (0.32 s per image in size of 256 × 256 × 3). Our evaluation shows that deeper convolutional neural network models have higher detection accuracies; however, they also require more parameters and have higher inference time. We believe that this study would act as a benchmark for real-time, automated crack detection for condition assessment of infrastructure.

Identifying Protein Complexes by Combining Network Topology and Biological Characteristics

2016 ◽  
Vol 13 (10) ◽  
pp. 7666-7675 ◽  
Author(s):  
Buwen Cao ◽  
Jiawei Luo ◽  
Cheng Liang ◽  
Shulin Wang
Keyword(s):  
Protein Interaction ◽  
Network Topology ◽  
Protein Complexes ◽  
Positive Interactions ◽  
Data Sets ◽  
Disease Treatment ◽  
Weighting Method ◽  
Protein Protein Interaction ◽  
Ppi Networks ◽  
Physical Interactions

Protein–protein interaction (PPI) data derived from biological experiments include many false-positive interactions which are treated equally as other real physical interactions, thereby complicating the detection of real protein complexes from protein–protein interaction (PPI) networks. In this paper, a new weighting method, named as cwMINE (combined weight of module identification in networks), for detecting protein complexes efficiently in protein interaction networks is presented. cwMINE has a good combination between network topology and biological feature, which can solve false positives efficiently of PPI networks and make discovered protein complexes higher quality. In addition, a new expanding rule during the detection process, namely, expanding coefficient, is developed to filter edges with lower weights. The proposed method is compared with several state- of-the-art algorithms in three yeast PPI networks with two benchmark data sets. The experimental results show that the proposed method outperforms the other algorithms in most datasets in terms of the evaluation metrics. We further validate the effectiveness of our method on a human PPI network constructed from the HPRD dataset to identify important disease-related functional modules and provided valuable indications for disease treatment.

scholarly journals Skin Cancer Detection using CNN Algorithm

2020 ◽  
Vol 9 (6) ◽  
pp. 45-49
Keyword(s):  
Neural Network ◽  
Skin Cancer ◽  
Convolutional Neural Network ◽  
Well Being ◽  
Training Data ◽  
Data Sets ◽  
Data Set ◽  
Sequential Model ◽  
Pigmented Lesions ◽  
Testing Data

The project “Disease Prediction Model” focuses on predicting the type of skin cancer. It deals with constructing a Convolutional Neural Network(CNN) sequential model in order to find the type of a skin cancer which takes a huge troll on mankind well-being. Since development of programmed methods increases the accuracy at high scale for identifying the type of skin cancer, we use Convolutional Neural Network, CNN algorithm in order to build our model . For this we make use of a sequential model. The data set that we have considered for this project is collected from NCBI, which is well known as HAM10000 dataset, it consists of massive amounts of information regarding several dermatoscopic images of most trivial pigmented lesions of skin which are collected from different sufferers. Once the dataset is collected, cleaned, it is split into training and testing data sets. We used CNN to build our model and using the training data we trained the model , later using the testing data we tested the model. Once the model is implemented over the testing data, plots are made in order to analyze the relation between the echos and loss function. It is also used to analyse accuracy and echos for both training and testing data.

Performance of a convolutional neural network algorithm for tooth detection and numbering on periapical radiographs

2021 ◽  
Author(s):  
Cansu Görürgöz ◽  
Kaan Orhan ◽  
Ibrahim Sevki Bayrakdar ◽  
Özer Çelik ◽  
Elif Bilgir ◽  
...  
Keyword(s):  
Neural Network ◽  
Convolutional Neural Network ◽  
Confusion Matrix ◽  
True Positive Rate ◽  
Turnaround Time ◽  
Classification Model ◽  
Data Sets ◽  
Data Set ◽  
Region Detection ◽  
Positive Rate

Objectives: The present study aimed to evaluate the performance of a Faster Region-based Convolutional Neural Network (R-CNN) algorithm for tooth detection and numbering on periapical images. Methods: The data sets of 1686 randomly selected periapical radiographs of patients were collected retrospectively. A pre-trained model (GoogLeNet Inception v3 CNN) was employed for pre-processing, and transfer learning techniques were applied for data set training. The algorithm consisted of: (1) the Jaw classification model, (2) Region detection models, and (3) the Final algorithm using all models. Finally, an analysis of the latest model has been integrated alongside the others. The sensitivity, precision, true-positive rate, and false-positive/negative rate were computed to analyze the performance of the algorithm using a confusion matrix. Results: An artificial intelligence algorithm (CranioCatch, Eskisehir-Turkey) was designed based on R-CNN inception architecture to automatically detect and number the teeth on periapical images. Of 864 teeth in 156 periapical radiographs, 668 were correctly numbered in the test data set. The F1 score, precision, and sensitivity were 0.8720, 0.7812, and 0.9867, respectively. Conclusion: The study demonstrated the potential accuracy and efficiency of the CNN algorithm for detecting and numbering teeth. The deep learning-based methods can help clinicians reduce workloads, improve dental records, and reduce turnaround time for urgent cases. This architecture might also contribute to forensic science.

scholarly journals Application of a convolutional neural network for seismic phase picking of mining-induced seismicity

2020 ◽  
Vol 224 (1) ◽  
pp. 230-240
Author(s):  
Sean W Johnson ◽  
Derrick J A Chambers ◽  
Michael S Boltz ◽  
Keith D Koper
Keyword(s):  
Neural Network ◽  
Convolutional Neural Network ◽  
Induced Seismicity ◽  
Southern California ◽  
High Stress ◽  
Training Data ◽  
Data Sets ◽  
Residual Variance ◽  
Data Set ◽  
Mining Induced Seismicity

SUMMARY Monitoring mining-induced seismicity (MIS) can help engineers understand the rock mass response to resource extraction. With a thorough understanding of ongoing geomechanical processes, engineers can operate mines, especially those mines with the propensity for rockbursting, more safely and efficiently. Unfortunately, processing MIS data usually requires significant effort from human analysts, which can result in substantial costs and time commitments. The problem is exacerbated for operations that produce copious amounts of MIS, such as mines with high-stress and/or extraction ratios. Recently, deep learning methods have shown the ability to significantly improve the quality of automated arrival-time picking on earthquake data recorded by regional seismic networks. However, relatively little has been published on applying these techniques to MIS. In this study, we compare the performance of a convolutional neural network (CNN) originally trained to pick arrival times on the Southern California Seismic Network (SCSN) to that of human analysts on coal-mine-related MIS. We perform comparisons on several coal-related MIS data sets recorded at various network scales, sampling rates and mines. We find that the Southern-California-trained CNN does not perform well on any of our data sets without retraining. However, applying the concept of transfer learning, we retrain the SCSN model with relatively little MIS data after which the CNN performs nearly as well as a human analyst. When retrained with data from a single analyst, the analyst-CNN pick time residual variance is lower than the variance observed between human analysts. We also compare the retrained CNN to a simpler, optimized picking algorithm, which falls short of the CNN's performance. We conclude that CNNs can achieve a significant improvement in automated phase picking although some data set-specific training will usually be required. Moreover, initializing training with weights found from other, even very different, data sets can greatly reduce the amount of training data required to achieve a given performance threshold.

Sign in / Sign up

Export Citation Format

Share Document