scholarly journals DeepDigest: prediction of protein proteolytic digestion with deep learning

2020 ◽  
Author(s):  
Jinghan Yang ◽  
Zhiqiang Gao ◽  
Xiuhan Ren ◽  
Jie Sheng ◽  
Ping Xu ◽  
...  
Keyword(s):  
Deep Learning ◽  
Short Term Memory ◽  
Shotgun Proteomics ◽  
Machine Learning Algorithms ◽  
Superior Performance ◽  
Cleavage Sites ◽  
Proteomics Research ◽  
Long Short Term Memory ◽  
Deep Learning Model ◽  
Subsequent Identification

ABSTRACTIn shotgun proteomics, it is essential to accurately determine the proteolytic products of each protein in the sample for subsequent identification and quantification, because these proteolytic products are usually taken as the surrogates of their parent proteins in the further data analysis. However, systematical studies about the commonly used proteases in proteomics research are insufficient, and there is a lack of easy-to-use tools to predict the digestibilities of these proteolytic products. Here, we propose a novel sequence-based deep learning model – DeepDigest, which integrates convolutional neural networks and long-short term memory networks for digestibility prediction of peptides. DeepDigest can predict the proteolytic cleavage sites for eight popular proteases including trypsin, ArgC, chymotrypsin, GluC, LysC, AspN, LysN and LysargiNase. Compared with traditional machine learning algorithms, DeepDigest showed superior performance for all the eight proteases on a variety of datasets. Besides, some interesting characteristics of different proteases were revealed and discussed.

scholarly journals A Hybrid Deep Learning Model for Long-Term Sentiment Classification

Webology ◽  
2020 ◽  
Vol 17 (2) ◽  
pp. 663-676
Author(s):  
Tapas Guha ◽  
K.G. Mohan
Keyword(s):  
Deep Learning ◽  
Short Term Memory ◽  
Learning Model ◽  
Optimization Techniques ◽  
Machine Learning Algorithms ◽  
Sentiment Classification ◽  
Specific Product ◽  
Long Short Term Memory ◽  
Deep Learning Model

With the omnipresence of user feedbacks in social media, mining of relevant opinion and extracting the underlying sentiment to analyze synthetic emotion towards a specific product, person, topic or event has become a vast domain of research in recent times. A thorough survey of the early unimodal and multimodal sentiment classification approaches reveals that researchers mostly relied on either corpus based techniques or those based on machine learning algorithms. Lately, Deep learning models progressed profoundly in the area of image processing. This success has been efficiently directed towards enhancements in sentiment categorization. A hybrid deep learning model consisting of Convolutional Neural Network (CNN) and stacked bidirectional Long Short Term Memory (BiLSTM) over pre-trained word vectors is proposed in this paper to achieve long-term sentiment analysis. This work experiments with various hyperparameters and optimization techniques to make the model get rid of overfitting and to achieve optimal performance. It has been validated on two standard sentiment datasets, Stanford Large Movie Review (IMDB) and Stanford Sentiment Treebank2 Dataset (SST2). It achieves a competitive advantage over other models like CNN, LSTM and ensemble of CNN-LSTM by attaining better accuracy and also produces high F measure.

scholarly journals Application of Rough and Fuzzy Set Theory for Prediction of Stochastic Wind Speed Data Using Long Short-Term Memory

Atmosphere ◽  
2021 ◽  
Vol 12 (7) ◽  
pp. 924
Author(s):  
Moslem Imani ◽  
Hoda Fakour ◽  
Wen-Hau Lan ◽  
Huan-Chin Kao ◽  
Chi Ming Lee ◽  
...  
Keyword(s):  
Deep Learning ◽  
Wind Speed ◽  
Set Theory ◽  
Rough Set ◽  
Fuzzy Set Theory ◽  
Short Term Memory ◽  
Learning Model ◽  
Short Term ◽  
Long Short Term Memory ◽  
Deep Learning Model

Despite the great significance of precisely forecasting the wind speed for development of the new and clean energy technology and stable grid operators, the stochasticity of wind speed makes the prediction a complex and challenging task. For improving the security and economic performance of power grids, accurate short-term wind power forecasting is crucial. In this paper, a deep learning model (Long Short-term Memory (LSTM)) has been proposed for wind speed prediction. Knowing that wind speed time series is nonlinear stochastic, the mutual information (MI) approach was used to find the best subset from the data by maximizing the joint MI between subset and target output. To enhance the accuracy and reduce input characteristics and data uncertainties, rough set and interval type-2 fuzzy set theory are combined in the proposed deep learning model. Wind speed data from an international airport station in the southern coast of Iran Bandar-Abbas City was used as the original input dataset for the optimized deep learning model. Based on the statistical results, the rough set LSTM (RST-LSTM) model showed better prediction accuracy than fuzzy and original LSTM, as well as traditional neural networks, with the lowest error for training and testing datasets in different time horizons. The suggested model can support the optimization of the control approach and the smooth procedure of power system. The results confirm the superior capabilities of deep learning techniques for wind speed forecasting, which could also inspire new applications in meteorology assessment.

Surrounding Vehicles’ Contribution to Car-Following Models: Deep-Learning-Based Analysis

2021 ◽  
pp. 036119812110186
Author(s):  
Saeed Vasebi ◽  
Yeganeh M. Hayeri ◽  
Peter J. Jin
Keyword(s):  
Deep Learning ◽  
Traffic Flow ◽  
Short Term Memory ◽  
Data Availability ◽  
Car Following ◽  
Preceding Vehicle ◽  
Long Short Term Memory ◽  
The Right ◽  
Mean Square Errors ◽  
Deep Learning Model

Relatively recent increased computational power and extensive traffic data availability have provided a unique opportunity to re-investigate drivers’ car-following (CF) behavior. Classic CF models assume drivers’ behavior is only influenced by their preceding vehicle. Recent studies have indicated that considering surrounding vehicles’ information (e.g., multiple preceding vehicles) could affect CF models’ performance. An in-depth investigation of surrounding vehicles’ contribution to CF modeling performance has not been reported in the literature. This study uses a deep-learning model with long short-term memory (LSTM) to investigate to what extent considering surrounding vehicles could improve CF models’ performance. This investigation helps to select the right inputs for traffic flow modeling. Five CF models are compared in this study (i.e., classic, multi-anticipative, adjacent-lanes, following-vehicle, and all-surrounding-vehicles CF models). Performance of the CF models is compared in relation to accuracy, stability, and smoothness of traffic flow. The CF models are trained, validated, and tested by a large publicly available dataset. The average mean square errors (MSEs) for the classic, multi-anticipative, adjacent-lanes, following-vehicle, and all-surrounding-vehicles CF models are 1.58 × 10−3, 1.54 × 10−3, 1.56 × 10−3, 1.61 × 10−3, and 1.73 × 10−3, respectively. However, the results show insignificant performance differences between the classic CF model and multi-anticipative model or adjacent-lanes model in relation to accuracy, stability, or smoothness. The following-vehicle CF model shows similar performance to the multi-anticipative model. The all-surrounding-vehicles CF model has underperformed all the other models.

A semiautomatic annotation approach for sentiment analysis

2021 ◽  
pp. 016555152110065
Author(s):  
Rahma Alahmary ◽  
Hmood Al-Dossari
Keyword(s):  
Deep Learning ◽  
Sentiment Analysis ◽  
Short Term Memory ◽  
Machine Learning Algorithms ◽  
Support Vector ◽  
Short Term ◽  
Term Memory ◽  
Annotation Process ◽  
Learning Classifiers ◽  
Long Short Term Memory

Sentiment analysis (SA) aims to extract users’ opinions automatically from their posts and comments. Almost all prior works have used machine learning algorithms. Recently, SA research has shown promising performance in using the deep learning approach. However, deep learning is greedy and requires large datasets to learn, so it takes more time for data annotation. In this research, we proposed a semiautomatic approach using Naïve Bayes (NB) to annotate a new dataset in order to reduce the human effort and time spent on the annotation process. We created a dataset for the purpose of training and testing the classifier by collecting Saudi dialect tweets. The dataset produced from the semiautomatic model was then used to train and test deep learning classifiers to perform Saudi dialect SA. The accuracy achieved by the NB classifier was 83%. The trained semiautomatic model was used to annotate the new dataset before it was fed into the deep learning classifiers. The three deep learning classifiers tested in this research were convolutional neural network (CNN), long short-term memory (LSTM) and bidirectional long short-term memory (Bi-LSTM). Support vector machine (SVM) was used as the baseline for comparison. Overall, the performance of the deep learning classifiers exceeded that of SVM. The results showed that CNN reported the highest performance. On one hand, the performance of Bi-LSTM was higher than that of LSTM and SVM, and, on the other hand, the performance of LSTM was higher than that of SVM. The proposed semiautomatic annotation approach is usable and promising to increase speed and save time and effort in the annotation process.

scholarly journals Channel state information estimation for 5G wireless communication systems: recurrent neural networks approach

2021 ◽  
Vol 7 ◽  
pp. e682
Author(s):  
Mohamed Hassan Essai Ali ◽  
Ibrahim B.M. Taha
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Channel State Information ◽  
Short Term Memory ◽  
Superior Performance ◽  
Short Term ◽  
Channel State ◽  
State Information ◽  
Term Memory ◽  
Long Short Term Memory

In this study, a deep learning bidirectional long short-term memory (BiLSTM) recurrent neural network-based channel state information estimator is proposed for 5G orthogonal frequency-division multiplexing systems. The proposed estimator is a pilot-dependent estimator and follows the online learning approach in the training phase and the offline approach in the practical implementation phase. The estimator does not deal with complete a priori certainty for channels’ statistics and attains superior performance in the presence of a limited number of pilots. A comparative study is conducted using three classification layers that use loss functions: mean absolute error, cross entropy function for kth mutually exclusive classes and sum of squared of the errors. The Adam, RMSProp, SGdm, and Adadelat optimisation algorithms are used to evaluate the performance of the proposed estimator using each classification layer. In terms of symbol error rate and accuracy metrics, the proposed estimator outperforms long short-term memory (LSTM) neural network-based channel state information, least squares and minimum mean square error estimators under different simulation conditions. The computational and training time complexities for deep learning BiLSTM- and LSTM-based estimators are provided. Given that the proposed estimator relies on the deep learning neural network approach, where it can analyse massive data, recognise statistical dependencies and characteristics, develop relationships between features and generalise the accrued knowledge for new datasets that it has not seen before, the approach is promising for any 5G and beyond communication system.

scholarly journals Jamming Prediction for Radar Signals Using Machine Learning Methods

2020 ◽  
Vol 2020 ◽  
pp. 1-9 ◽  
Author(s):  
Gyeong-Hoon Lee ◽  
Jeil Jo ◽  
Cheong Hee Park
Keyword(s):  
Deep Learning ◽  
Short Term Memory ◽  
Learning Model ◽  
Training Data ◽  
Electronic Warfare ◽  
New Type ◽  
Long Short Term Memory ◽  
Radar Signals ◽  
Feature Values ◽  
Deep Learning Model

Jamming is a form of electronic warfare where jammers radiate interfering signals toward an enemy radar, disrupting the receiver. The conventional method for determining an effective jamming technique corresponding to a threat signal is based on the library which stores the appropriate jamming method for signal types. However, there is a limit to the use of a library when a threat signal of a new type or a threat signal that has been altered differently from existing types is received. In this paper, we study two methods of predicting the appropriate jamming technique for a received threat signal using deep learning: using a deep neural network on feature values extracted manually from the PDW list and using long short-term memory (LSTM) which takes the PDW list as input. Using training data consisting of pairs of threat signals and corresponding jamming techniques, a deep learning model is trained which outputs jamming techniques for threat signal inputs. Training data are constructed based on the information in the library, but the trained deep learning model is used to predict jamming techniques for received threat signals without using the library. The prediction performance and time complexity of two proposed methods are compared. In particular, the ability to predict jamming techniques for unknown types of radar signals which are not used in the stage of training the model is analyzed.

Deep Learning Model for Forecasting Financial Sales Based on Long Short-Term Memory Networks

2019 ◽  
pp. 498-506
Author(s):  
Pablo F. Ordoñez-Ordoñez ◽  
Martha C. Suntaxi Sarango ◽  
Cristian Narváez ◽  
Maria del Cisne Ruilova Sánchez ◽  
Mario Enrique Cueva-Hurtado
Keyword(s):  
Deep Learning ◽  
Short Term Memory ◽  
Learning Model ◽  
Short Term ◽  
Term Memory ◽  
Long Short Term Memory ◽  
Deep Learning Model

scholarly journals A Novel Hybrid Deep Learning Model for Detecting COVID-19-Related Rumors on Social Media Based on LSTM and Concatenated Parallel CNNs

2021 ◽  
Vol 11 (17) ◽  
pp. 7940
Author(s):  
Mohammed Al-Sarem ◽  
Abdullah Alsaeedi ◽  
Faisal Saeed ◽  
Wadii Boulila ◽  
Omair AmeerBakhsh
Keyword(s):  
Machine Learning ◽  
Social Media ◽  
Deep Learning ◽  
Short Term Memory ◽  
Learning Model ◽  
Superior Performance ◽  
Detection Methods ◽  
The Internet ◽  
Proposed Model ◽  
Deep Learning Model

Spreading rumors in social media is considered under cybercrimes that affect people, societies, and governments. For instance, some criminals create rumors and send them on the internet, then other people help them to spread it. Spreading rumors can be an example of cyber abuse, where rumors or lies about the victim are posted on the internet to send threatening messages or to share the victim’s personal information. During pandemics, a large amount of rumors spreads on social media very fast, which have dramatic effects on people’s health. Detecting these rumors manually by the authorities is very difficult in these open platforms. Therefore, several researchers conducted studies on utilizing intelligent methods for detecting such rumors. The detection methods can be classified mainly into machine learning-based and deep learning-based methods. The deep learning methods have comparative advantages against machine learning ones as they do not require preprocessing and feature engineering processes and their performance showed superior enhancements in many fields. Therefore, this paper aims to propose a Novel Hybrid Deep Learning Model for Detecting COVID-19-related Rumors on Social Media (LSTM–PCNN). The proposed model is based on a Long Short-Term Memory (LSTM) and Concatenated Parallel Convolutional Neural Networks (PCNN). The experiments were conducted on an ArCOV-19 dataset that included 3157 tweets; 1480 of them were rumors (46.87%) and 1677 tweets were non-rumors (53.12%). The findings of the proposed model showed a superior performance compared to other methods in terms of accuracy, recall, precision, and F-score.

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