scholarly journals CLPred: a sequence-based protein crystallization predictor using BLSTM neural network

2020 ◽  
Vol 36 (Supplement_2) ◽  
pp. i709-i717
Author(s):  
Wenjing Xuan ◽  
Ning Liu ◽  
Neng Huang ◽  
Yaohang Li ◽  
Jianxin Wang
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Long Range ◽  
Short Term Memory ◽  
Protein Crystallization ◽  
Predictive Performance ◽  
Attrition Rate ◽  
Multiple Time ◽  
Interaction Patterns ◽  
Range Interaction

Abstract Motivation Determining the structures of proteins is a critical step to understand their biological functions. Crystallography-based X-ray diffraction technique is the main method for experimental protein structure determination. However, the underlying crystallization process, which needs multiple time-consuming and costly experimental steps, has a high attrition rate. To overcome this issue, a series of in silico methods have been developed with the primary aim of selecting the protein sequences that are promising to be crystallized. However, the predictive performance of the current methods is modest. Results We propose a deep learning model, so-called CLPred, which uses a bidirectional recurrent neural network with long short-term memory (BLSTM) to capture the long-range interaction patterns between k-mers amino acids to predict protein crystallizability. Using sequence only information, CLPred outperforms the existing deep-learning predictors and a vast majority of sequence-based diffraction-quality crystals predictors on three independent test sets. The results highlight the effectiveness of BLSTM in capturing non-local, long-range inter-peptide interaction patterns to distinguish proteins that can result in diffraction-quality crystals from those that cannot. CLPred has been steadily improved over the previous window-based neural networks, which is able to predict crystallization propensity with high accuracy. CLPred can also be improved significantly if it incorporates additional features from pre-extracted evolutional, structural and physicochemical characteristics. The correctness of CLPred predictions is further validated by the case studies of Sox transcription factor family member proteins and Zika virus non-structural proteins. Availability and implementation https://github.com/xuanwenjing/CLPred.

scholarly journals Spatio-temporal prediction of the COVID-19 pandemic in US counties: modeling with a deep LSTM neural network

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Behnam Nikparvar ◽  
Md. Mokhlesur Rahman ◽  
Faizeh Hatami ◽  
Jean-Claude Thill
Keyword(s):  
Neural Network ◽  
Short Term Memory ◽  
Predictive Performance ◽  
Small Data ◽  
Multiple Time ◽  
Ensemble Model ◽  
Temporal Prediction ◽  
Us Counties ◽  
Spatio Temporal ◽  
Similar Accuracy

AbstractPrediction of complex epidemiological systems such as COVID-19 is challenging on many grounds. Commonly used compartmental models struggle to handle an epidemiological process that evolves rapidly and is spatially heterogeneous. On the other hand, machine learning methods are limited at the beginning of the pandemics due to small data size for training. We propose a deep learning approach to predict future COVID-19 infection cases and deaths 1 to 4 weeks ahead at the fine granularity of US counties. The multi-variate Long Short-term Memory (LSTM) recurrent neural network is trained on multiple time series samples at the same time, including a mobility series. Results show that adding mobility as a variable and using multiple samples to train the network improve predictive performance both in terms of bias and of variance of the forecasts. We also show that the predicted results have similar accuracy and spatial patterns with a standard ensemble model used as benchmark. The model is attractive in many respects, including the fine geographic granularity of predictions and great predictive performance several weeks ahead. Furthermore, data requirement and computational intensity are reduced by substituting a single model to multiple models folded in an ensemble model.

Improving Sentiment Analysis using Hybrid Deep Learning Model

2020 ◽  
Vol 13 (4) ◽  
pp. 627-640 ◽  
Author(s):  
Avinash Chandra Pandey ◽  
Dharmveer Singh Rajpoot
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Sentiment Analysis ◽  
Classification Accuracy ◽  
Short Term Memory ◽  
Computational Cost ◽  
Extraction Process ◽  
Learning Model ◽  
Sentiment Classification ◽  
Deep Learning Model

Background: Sentiment analysis is a contextual mining of text which determines viewpoint of users with respect to some sentimental topics commonly present at social networking websites. Twitter is one of the social sites where people express their opinion about any topic in the form of tweets. These tweets can be examined using various sentiment classification methods to find the opinion of users. Traditional sentiment analysis methods use manually extracted features for opinion classification. The manual feature extraction process is a complicated task since it requires predefined sentiment lexicons. On the other hand, deep learning methods automatically extract relevant features from data hence; they provide better performance and richer representation competency than the traditional methods. Objective: The main aim of this paper is to enhance the sentiment classification accuracy and to reduce the computational cost. Method: To achieve the objective, a hybrid deep learning model, based on convolution neural network and bi-directional long-short term memory neural network has been introduced. Results: The proposed sentiment classification method achieves the highest accuracy for the most of the datasets. Further, from the statistical analysis efficacy of the proposed method has been validated. Conclusion: Sentiment classification accuracy can be improved by creating veracious hybrid models. Moreover, performance can also be enhanced by tuning the hyper parameters of deep leaning models.

scholarly journals Multiple Pedestrians and Vehicles Tracking in Aerial Imagery Using a Convolutional Neural Network

2021 ◽  
Vol 13 (10) ◽  
pp. 1953
Author(s):  
Seyed Majid Azimi ◽  
Maximilian Kraus ◽  
Reza Bahmanyar ◽  
Peter Reinartz
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Convolutional Neural Network ◽  
Object Tracking ◽  
Short Term Memory ◽  
Aerial Imagery ◽  
Future Research ◽  
Short Term ◽  
Term Memory ◽  
Long Short Term Memory

In this paper, we address various challenges in multi-pedestrian and vehicle tracking in high-resolution aerial imagery by intensive evaluation of a number of traditional and Deep Learning based Single- and Multi-Object Tracking methods. We also describe our proposed Deep Learning based Multi-Object Tracking method AerialMPTNet that fuses appearance, temporal, and graphical information using a Siamese Neural Network, a Long Short-Term Memory, and a Graph Convolutional Neural Network module for more accurate and stable tracking. Moreover, we investigate the influence of the Squeeze-and-Excitation layers and Online Hard Example Mining on the performance of AerialMPTNet. To the best of our knowledge, we are the first to use these two for regression-based Multi-Object Tracking. Additionally, we studied and compared the L1 and Huber loss functions. In our experiments, we extensively evaluate AerialMPTNet on three aerial Multi-Object Tracking datasets, namely AerialMPT and KIT AIS pedestrian and vehicle datasets. Qualitative and quantitative results show that AerialMPTNet outperforms all previous methods for the pedestrian datasets and achieves competitive results for the vehicle dataset. In addition, Long Short-Term Memory and Graph Convolutional Neural Network modules enhance the tracking performance. Moreover, using Squeeze-and-Excitation and Online Hard Example Mining significantly helps for some cases while degrades the results for other cases. In addition, according to the results, L1 yields better results with respect to Huber loss for most of the scenarios. The presented results provide a deep insight into challenges and opportunities of the aerial Multi-Object Tracking domain, paving the way for future research.

scholarly journals Classification of Skin Disease Using Deep Learning Neural Networks with MobileNet V2 and LSTM

Sensors ◽  
2021 ◽  
Vol 21 (8) ◽  
pp. 2852
Author(s):  
Parvathaneni Naga Srinivasu ◽  
Jalluri Gnana SivaSai ◽  
Muhammad Fazal Ijaz ◽  
Akash Kumar Bhoi ◽  
Wonjoon Kim ◽  
...  
Keyword(s):  
Neural Network ◽  
Neural Networks ◽  
Deep Learning ◽  
Convolutional Neural Network ◽  
Skin Disease ◽  
Network Architecture ◽  
Large Scale ◽  
Short Term Memory ◽  
Convolutional Networks ◽  
Occurrence Matrix

Deep learning models are efficient in learning the features that assist in understanding complex patterns precisely. This study proposed a computerized process of classifying skin disease through deep learning based MobileNet V2 and Long Short Term Memory (LSTM). The MobileNet V2 model proved to be efficient with a better accuracy that can work on lightweight computational devices. The proposed model is efficient in maintaining stateful information for precise predictions. A grey-level co-occurrence matrix is used for assessing the progress of diseased growth. The performance has been compared against other state-of-the-art models such as Fine-Tuned Neural Networks (FTNN), Convolutional Neural Network (CNN), Very Deep Convolutional Networks for Large-Scale Image Recognition developed by Visual Geometry Group (VGG), and convolutional neural network architecture that expanded with few changes. The HAM10000 dataset is used and the proposed method has outperformed other methods with more than 85% accuracy. Its robustness in recognizing the affected region much faster with almost 2× lesser computations than the conventional MobileNet model results in minimal computational efforts. Furthermore, a mobile application is designed for instant and proper action. It helps the patient and dermatologists identify the type of disease from the affected region’s image at the initial stage of the skin disease. These findings suggest that the proposed system can help general practitioners efficiently and effectively diagnose skin conditions, thereby reducing further complications and morbidity.

scholarly journals Real-Time Detection of Dictionary DGA Network Traffic Using Deep Learning

2021 ◽  
Vol 2 (2) ◽  
Author(s):  
Kate Highnam ◽  
Domenic Puzio ◽  
Song Luo ◽  
Nicholas R. Jennings
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Real Time ◽  
Network Traffic ◽  
Short Term Memory ◽  
Domain Names ◽  
Control Networks ◽  
Detection Techniques ◽  
Lstm Network ◽  
And Control

AbstractBotnets and malware continue to avoid detection by static rule engines when using domain generation algorithms (DGAs) for callouts to unique, dynamically generated web addresses. Common DGA detection techniques fail to reliably detect DGA variants that combine random dictionary words to create domain names that closely mirror legitimate domains. To combat this, we created a novel hybrid neural network, Bilbo the “bagging” model, that analyses domains and scores the likelihood they are generated by such algorithms and therefore are potentially malicious. Bilbo is the first parallel usage of a convolutional neural network (CNN) and a long short-term memory (LSTM) network for DGA detection. Our unique architecture is found to be the most consistent in performance in terms of AUC, $$F_1$$ F 1 score, and accuracy when generalising across different dictionary DGA classification tasks compared to current state-of-the-art deep learning architectures. We validate using reverse-engineered dictionary DGA domains and detail our real-time implementation strategy for scoring real-world network logs within a large enterprise. In 4 h of actual network traffic, the model discovered at least five potential command-and-control networks that commercial vendor tools did not flag.

scholarly journals Neural Network for Metal Detection Based on Magnetic Impedance Sensor

Sensors ◽  
2021 ◽  
Vol 21 (13) ◽  
pp. 4456
Author(s):  
Sungjae Ha ◽  
Dongwoo Lee ◽  
Hoijun Kim ◽  
Soonchul Kwon ◽  
EungJo Kim ◽  
...  
Keyword(s):  
Neural Network ◽  
Magnetic Field ◽  
Deep Learning ◽  
Short Term Memory ◽  
Magnetic Impedance ◽  
Detection Technology ◽  
Metal Detection ◽  
Long Short Term Memory ◽  
Impedance Sensor ◽  
The Magnetic Field

The efficiency of the metal detection method using deep learning with data obtained from multiple magnetic impedance (MI) sensors was investigated. The MI sensor is a passive sensor that detects metal objects and magnetic field changes. However, when detecting a metal object, the amount of change in the magnetic field caused by the metal is small and unstable with noise. Consequently, there is a limit to the detectable distance. To effectively detect and analyze this distance, a method using deep learning was applied. The detection performances of a convolutional neural network (CNN) and a recurrent neural network (RNN) were compared from the data extracted from a self-impedance sensor. The RNN model showed better performance than the CNN model. However, in the shallow stage, the CNN model was superior compared to the RNN model. The performance of a deep-learning-based (DLB) metal detection network using multiple MI sensors was compared and analyzed. The network was detected using long short-term memory and CNN. The performance was compared according to the number of layers and the size of the metal sheet. The results are expected to contribute to sensor-based DLB detection technology.

scholarly journals Near Real-Time Global Solar Radiation Forecasting at Multiple Time-Step Horizons Using the Long Short-Term Memory Network

Energies ◽  
2020 ◽  
Vol 13 (14) ◽  
pp. 3517 ◽  
Author(s):  
Anh Ngoc-Lan Huynh ◽  
Ravinesh C. Deo ◽  
Duc-Anh An-Vo ◽  
Mumtaz Ali ◽  
Nawin Raj ◽  
...  
Keyword(s):  
Deep Learning ◽  
Solar Radiation ◽  
Short Term Memory ◽  
Global Solar Radiation ◽  
Multiple Time ◽  
Short Term ◽  
Time Step ◽  
Term Memory ◽  
Multiple Time Step ◽  
Long Short Term Memory

This paper aims to develop the long short-term memory (LSTM) network modelling strategy based on deep learning principles, tailored for the very short-term, near-real-time global solar radiation (GSR) forecasting. To build the prescribed LSTM model, the partial autocorrelation function is applied to the high resolution, 1 min scaled solar radiation dataset that generates statistically significant lagged predictor variables describing the antecedent behaviour of GSR. The LSTM algorithm is adopted to capture the short- and the long-term dependencies within the GSR data series patterns to accurately predict the future GSR at 1, 5, 10, 15, and 30 min forecasting horizons. This objective model is benchmarked at a solar energy resource rich study site (Bac-Ninh, Vietnam) against the competing counterpart methods employing other deep learning, a statistical model, a single hidden layer and a machine learning-based model. The LSTM model generates satisfactory predictions at multiple-time step horizons, achieving a correlation coefficient exceeding 0.90, outperforming all of the counterparts. In accordance with robust statistical metrics and visual analysis of all tested data, the study ascertains the practicality of the proposed LSTM approach to generate reliable GSR forecasts. The Diebold–Mariano statistic test also shows LSTM outperforms the counterparts in most cases. The study confirms the practical utility of LSTM in renewable energy studies, and broadly in energy-monitoring devices tailored for other energy variables (e.g., hydro and wind energy).

SHEDR: An End-to-End Deep Neural Event Detection and Recommendation Framework for Hyperlocal News Using Social Media

2021 ◽  
Author(s):  
Yuheng Hu ◽  
Yili Hong
Keyword(s):  
Neural Network ◽  
Social Media ◽  
Deep Learning ◽  
Event Detection ◽  
Large Scale ◽  
Short Term Memory ◽  
State Of The Art ◽  
Neural Network Models ◽  
Neural Event ◽  
End To End

Residents often rely on newspapers and television to gather hyperlocal news for community awareness and engagement. More recently, social media have emerged as an increasingly important source of hyperlocal news. Thus far, the literature on using social media to create desirable societal benefits, such as civic awareness and engagement, is still in its infancy. One key challenge in this research stream is to timely and accurately distill information from noisy social media data streams to community members. In this work, we develop SHEDR (social media–based hyperlocal event detection and recommendation), an end-to-end neural event detection and recommendation framework with a particular use case for Twitter to facilitate residents’ information seeking of hyperlocal events. The key model innovation in SHEDR lies in the design of the hyperlocal event detector and the event recommender. First, we harness the power of two popular deep neural network models, the convolutional neural network (CNN) and long short-term memory (LSTM), in a novel joint CNN-LSTM model to characterize spatiotemporal dependencies for capturing unusualness in a region of interest, which is classified as a hyperlocal event. Next, we develop a neural pairwise ranking algorithm for recommending detected hyperlocal events to residents based on their interests. To alleviate the sparsity issue and improve personalization, our algorithm incorporates several types of contextual information covering topic, social, and geographical proximities. We perform comprehensive evaluations based on two large-scale data sets comprising geotagged tweets covering Seattle and Chicago. We demonstrate the effectiveness of our framework in comparison with several state-of-the-art approaches. We show that our hyperlocal event detection and recommendation models consistently and significantly outperform other approaches in terms of precision, recall, and F-1 scores. Summary of Contribution: In this paper, we focus on a novel and important, yet largely underexplored application of computing—how to improve civic engagement in local neighborhoods via local news sharing and consumption based on social media feeds. To address this question, we propose two new computational and data-driven methods: (1) a deep learning–based hyperlocal event detection algorithm that scans spatially and temporally to detect hyperlocal events from geotagged Twitter feeds; and (2) A personalized deep learning–based hyperlocal event recommender system that systematically integrates several contextual cues such as topical, geographical, and social proximity to recommend the detected hyperlocal events to potential users. We conduct a series of experiments to examine our proposed models. The outcomes demonstrate that our algorithms are significantly better than the state-of-the-art models and can provide users with more relevant information about the local neighborhoods that they live in, which in turn may boost their community engagement.

scholarly journals Learners Demographics Classification on MOOCs During the COVID-19: Author Profiling via Deep Learning Based on Semantic and Syntactic Representations

2021 ◽  
Vol 6 ◽  
Author(s):  
Tahani Aljohani ◽  
Alexandra I. Cristea
Keyword(s):  
Neural Network ◽  
Neural Networks ◽  
Deep Learning ◽  
Prediction Models ◽  
Short Term Memory ◽  
Methodological Approach ◽  
High Accuracy ◽  
Directional Model ◽  
Textual Representations ◽  
The One

Massive Open Online Courses (MOOCs) have become universal learning resources, and the COVID-19 pandemic is rendering these platforms even more necessary. In this paper, we seek to improve Learner Profiling (LP), i.e. estimating the demographic characteristics of learners in MOOC platforms. We have focused on examining models which show promise elsewhere, but were never examined in the LP area (deep learning models) based on effective textual representations. As LP characteristics, we predict here the employment status of learners. We compare sequential and parallel ensemble deep learning architectures based on Convolutional Neural Networks and Recurrent Neural Networks, obtaining an average high accuracy of 96.3% for our best method. Next, we predict the gender of learners based on syntactic knowledge from the text. We compare different tree-structured Long-Short-Term Memory models (as state-of-the-art candidates) and provide our novel version of a Bi-directional composition function for existing architectures. In addition, we evaluate 18 different combinations of word-level encoding and sentence-level encoding functions. Based on these results, we show that our Bi-directional model outperforms all other models and the highest accuracy result among our models is the one based on the combination of FeedForward Neural Network and the Stack-augmented Parser-Interpreter Neural Network (82.60% prediction accuracy). We argue that our prediction models recommended for both demographics characteristics examined in this study can achieve high accuracy. This is additionally also the first time a sound methodological approach toward improving accuracy for learner demographics classification on MOOCs was proposed.

scholarly journals Flutter speed prediction by using deep learning

2021 ◽  
Vol 13 (11) ◽  
pp. 168781402110622
Author(s):  
Yi-Ren Wang ◽  
Yi-Jyun Wang
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Short Term Memory ◽  
Learning Technology ◽  
Memory Space ◽  
Flutter Speed ◽  
Aeroelastic Flutter ◽  
Speed Prediction ◽  
Computational Fluid Dynamics Cfd ◽  
Cfd Method

Deep learning technology has been widely used in various field in recent years. This study intends to use deep learning algorithms to analyze the aeroelastic phenomenon and compare the differences between Deep Neural Network (DNN) and Long Short-term Memory (LSTM) applied on the flutter speed prediction. In this present work, DNN and LSTM are used to address complex aeroelastic systems by superimposing multi-layer Artificial Neural Network. Under such an architecture, the neurons in neural network can extract features from various flight data. Instead of time-consuming high-fidelity computational fluid dynamics (CFD) method, this study uses the K method to build the aeroelastic flutter speed big data for different flight conditions. The flutter speeds for various flight conditions are predicted by the deep learning methods and verified by the K method. The detailed physical meaning of aerodynamics and aeroelasticity of the prediction results are studied. The LSTM model has a cyclic architecture, which enables it to store information and update it with the latest information at the same time. Although the training of the model is more time-consuming than DNN, this method can increase the memory space. The results of this work show that the LSTM model established in this study can provide more accurate flutter speed prediction than the DNN algorithm.

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