Deep-Kcr: accurate detection of lysine crotonylation sites using deep learning method

2020 ◽  
Author(s):  
Hao Lv ◽  
Fu-Ying Dao ◽  
Zheng-Xing Guan ◽  
Hui Yang ◽  
Yan-Wen Li ◽  
...  
Keyword(s):  
Deep Learning ◽  
Large Scale ◽  
Short Term Memory ◽  
Information Gain ◽  
Independent Set ◽  
Cost Effective ◽  
Cellular Regulation ◽  
Proposed Model ◽  
Experimental Approaches ◽  
Memory Network

Abstract As a newly discovered protein posttranslational modification, histone lysine crotonylation (Kcr) involved in cellular regulation and human diseases. Various proteomics technologies have been developed to detect Kcr sites. However, experimental approaches for identifying Kcr sites are often time-consuming and labor-intensive, which is difficult to widely popularize in large-scale species. Computational approaches are cost-effective and can be used in a high-throughput manner to generate relatively precise identification. In this study, we develop a deep learning-based method termed as Deep-Kcr for Kcr sites prediction by combining sequence-based features, physicochemical property-based features and numerical space-derived information with information gain feature selection. We investigate the performances of convolutional neural network (CNN) and five commonly used classifiers (long short-term memory network, random forest, LogitBoost, naive Bayes and logistic regression) using 10-fold cross-validation and independent set test. Results show that CNN could always display the best performance with high computational efficiency on large dataset. We also compare the Deep-Kcr with other existing tools to demonstrate the excellent predictive power and robustness of our method. Based on the proposed model, a webserver called Deep-Kcr was established and is freely accessible at http://lin-group.cn/server/Deep-Kcr.

scholarly journals Deep Learning based Semantic Similarity Detection using Text Data

2020 ◽  
Vol 49 (4) ◽  
pp. 495-510
Author(s):  
Muhammad Mansoor ◽  
Zahoor ur Rehman ◽  
Muhammad Shaheen ◽  
Muhammad Attique Khan ◽  
Mohamed Habib
Keyword(s):  
Deep Learning ◽  
Language Processing ◽  
Short Term Memory ◽  
Main Task ◽  
Detection Algorithms ◽  
Similarity Detection ◽  
Novel Approach ◽  
Proposed Model ◽  
Memory Network ◽  
Numeric Data

Similarity detection in the text is the main task for a number of Natural Language Processing (NLP) applications. As textual data is comparatively large in quantity and huge in volume than the numeric data, therefore measuring textual similarity is one of the important problems. Most of the similarity detection algorithms are based upon word to word matching, sentence/paragraph matching, and matching of the whole document. In this research, a novel approach is proposed using deep learning models, combining Long Short Term Memory network (LSTM) with Convolutional Neural Network (CNN) for measuring semantics similarity between two questions. The proposed model takes sentence pairs as input to measure the similarity between them. The model is tested on publicly available Quora’s dataset. The model in comparison to the existing techniques gave 87.50 % accuracy which is better than the previous approaches.

Human Activity Recognition using Fourier Transform Inspired Deep Learning Combination Model

2019 ◽  
Vol 9 (1) ◽  
pp. 16-31
Author(s):  
Kyungkoo Jun
Keyword(s):  
Fourier Transform ◽  
Deep Learning ◽  
Short Term Memory ◽  
Window Size ◽  
Sensor Data ◽  
Data Sets ◽  
Data Set ◽  
Proposed Model ◽  
Testing Data ◽  
Labeling Scheme

Background & Objective: This paper proposes a Fourier transform inspired method to classify human activities from time series sensor data. Methods: Our method begins by decomposing 1D input signal into 2D patterns, which is motivated by the Fourier conversion. The decomposition is helped by Long Short-Term Memory (LSTM) which captures the temporal dependency from the signal and then produces encoded sequences. The sequences, once arranged into the 2D array, can represent the fingerprints of the signals. The benefit of such transformation is that we can exploit the recent advances of the deep learning models for the image classification such as Convolutional Neural Network (CNN). Results: The proposed model, as a result, is the combination of LSTM and CNN. We evaluate the model over two data sets. For the first data set, which is more standardized than the other, our model outperforms previous works or at least equal. In the case of the second data set, we devise the schemes to generate training and testing data by changing the parameters of the window size, the sliding size, and the labeling scheme. Conclusion: The evaluation results show that the accuracy is over 95% for some cases. We also analyze the effect of the parameters on the performance.

Multi Disease-Prediction Framework Using Hybrid Deep Learning: An Optimal Prediction Model (Preprint)

2020 ◽  
Author(s):  
Anusha Ampavathi ◽  
Vijaya Saradhi T
Keyword(s):  
Feature Extraction ◽  
Big Data ◽  
Deep Learning ◽  
Weight Function ◽  
Optimization Algorithm ◽  
Large Scale ◽  
Heuristic Algorithms ◽  
Disease Prediction ◽  
Health Care Decisions ◽  
Proposed Model

UNSTRUCTURED Big data and its approaches are generally helpful for healthcare and biomedical sectors for predicting the disease. For trivial symptoms, the difficulty is to meet the doctors at any time in the hospital. Thus, big data provides essential data regarding the diseases on the basis of the patient’s symptoms. For several medical organizations, disease prediction is important for making the best feasible health care decisions. Conversely, the conventional medical care model offers input as structured that requires more accurate and consistent prediction. This paper is planned to develop the multi-disease prediction using the improvised deep learning concept. Here, the different datasets pertain to “Diabetes, Hepatitis, lung cancer, liver tumor, heart disease, Parkinson’s disease, and Alzheimer’s disease”, from the benchmark UCI repository is gathered for conducting the experiment. The proposed model involves three phases (a) Data normalization (b) Weighted normalized feature extraction, and (c) prediction. Initially, the dataset is normalized in order to make the attribute's range at a certain level. Further, weighted feature extraction is performed, in which a weight function is multiplied with each attribute value for making large scale deviation. Here, the weight function is optimized using the combination of two meta-heuristic algorithms termed as Jaya Algorithm-based Multi-Verse Optimization algorithm (JA-MVO). The optimally extracted features are subjected to the hybrid deep learning algorithms like “Deep Belief Network (DBN) and Recurrent Neural Network (RNN)”. As a modification to hybrid deep learning architecture, the weight of both DBN and RNN is optimized using the same hybrid optimization algorithm. Further, the comparative evaluation of the proposed prediction over the existing models certifies its effectiveness through various performance measures.

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.

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 A Hybrid Optimized LSTM Models for Human Activity Recognition with IOT Devices

2021 ◽  
pp. 182-189
Author(s):  
S. Arokiaraj ◽  
Dr. N. Viswanathan
Keyword(s):  
Deep Learning ◽  
Internet Of Things ◽  
Short Term Memory ◽  
The Other ◽  
Learning Models ◽  
Computational Overhead ◽  
Temporal Features ◽  
Human Movements ◽  
Proposed Model ◽  
Iot Devices

With the advent of Internet of things(IoT),HA (HA) recognition has contributed the more application in health care in terms of diagnosis and Clinical process. These devices must be aware of human movements to provide better aid in the clinical applications as well as user’s daily activity.Also , In addition to machine and deep learning algorithms, HA recognition systems has significantly improved in terms of high accurate recognition. However, the most of the existing models designed needs improvisation in terms of accuracy and computational overhead. In this research paper, we proposed a BAT optimized Long Short term Memory (BAT-LSTM) for an effective recognition of human activities using real time IoT systems. The data are collected by implanting the Internet of things) devices invasively. Then, proposed BAT-LSTM is deployed to extract the temporal features which are then used for classification to HA. Nearly 10,0000 dataset were collected and used for evaluating the proposed model. For the validation of proposed framework, accuracy, precision, recall, specificity and F1-score parameters are chosen and comparison is done with the other state-of-art deep learning models. The finding shows the proposed model outperforms the other learning models and finds its suitability for the HA recognition.

scholarly journals Stock Pattern Classification from Charts using Deep Learning Algorithms

2020 ◽  
Vol 3 (1) ◽  
pp. 445-454
Author(s):  
Celal Buğra Kaya ◽  
Alperen Yılmaz ◽  
Gizem Nur Uzun ◽  
Zeynep Hilal Kilimci
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
Convolutional Neural Networks ◽  
Pattern Classification ◽  
Short Term Memory ◽  
Stock Exchange ◽  
Learning Techniques ◽  
Proposed Model ◽  
Istanbul Stock Exchange

Pattern classification is related with the automatic finding of regularities in dataset through the utilization of various learning techniques. Thus, the classification of the objects into a set of categories or classes is provided. This study is undertaken to evaluate deep learning methodologies to the classification of stock patterns. In order to classify patterns that are obtained from stock charts, convolutional neural networks (CNNs), recurrent neural networks (RNNs), and long-short term memory networks (LSTMs) are employed. To demonstrate the efficiency of proposed model in categorizing patterns, hand-crafted image dataset is constructed from stock charts in Istanbul Stock Exchange and NASDAQ Stock Exchange. Experimental results show that the usage of convolutional neural networks exhibits superior classification success in recognizing patterns compared to the other deep learning methodologies.

scholarly journals Spatio-temporal deep learning model for distortion classification in laparoscopic video

F1000Research ◽  
2021 ◽  
Vol 10 ◽  
pp. 1010
Author(s):  
Nouar AlDahoul ◽  
Hezerul Abdul Karim ◽  
Abdulaziz Saleh Ba Wazir ◽  
Myles Joshua Toledo Tan ◽  
Mohammad Faizal Ahmad Fauzi
Keyword(s):  
Deep Learning ◽  
Large Scale ◽  
Spatial Information ◽  
Short Term Memory ◽  
Learning Model ◽  
Motion Blur ◽  
Video Frame ◽  
Video Enhancement ◽  
Deep Learning Model ◽  
Laparoscopic Videos

Background: Laparoscopy is a surgery performed in the abdomen without making large incisions in the skin and with the aid of a video camera, resulting in laparoscopic videos. The laparoscopic video is prone to various distortions such as noise, smoke, uneven illumination, defocus blur, and motion blur. One of the main components in the feedback loop of video enhancement systems is distortion identification, which automatically classifies the distortions affecting the videos and selects the video enhancement algorithm accordingly. This paper aims to address the laparoscopic video distortion identification problem by developing fast and accurate multi-label distortion classification using a deep learning model. Current deep learning solutions based on convolutional neural networks (CNNs) can address laparoscopic video distortion classification, but they learn only spatial information. Methods: In this paper, utilization of both spatial and temporal features in a CNN-long short-term memory (CNN-LSTM) model is proposed as a novel solution to enhance the classification. First, pre-trained ResNet50 CNN was used to extract spatial features from each video frame by transferring representation from large-scale natural images to laparoscopic images. Next, LSTM was utilized to consider the temporal relation between the features extracted from the laparoscopic video frames to produce multi-label categories. A novel laparoscopic video dataset proposed in the ICIP2020 challenge was used for training and evaluation of the proposed method. Results: The experiments conducted show that the proposed CNN-LSTM outperforms the existing solutions in terms of accuracy (85%), and F1-score (94.2%). Additionally, the proposed distortion identification model is able to run in real-time with low inference time (0.15 sec). Conclusions: The proposed CNN-LSTM model is a feasible solution to be utilized in laparoscopic videos for distortion identification.

scholarly journals Nonintrusive Load Monitoring Based on Advanced Deep Learning and Novel Signature

2017 ◽  
Vol 2017 ◽  
pp. 1-22 ◽  
Author(s):  
Jihyun Kim ◽  
Thi-Thu-Huong Le ◽  
Howon Kim
Keyword(s):  
Deep Learning ◽  
Power Consumption ◽  
Distribution System ◽  
Short Term Memory ◽  
Electrical Power ◽  
Electricity Consumption ◽  
Classification Performance ◽  
Robust Solution ◽  
Proposed Model ◽  
Load Monitoring

Monitoring electricity consumption in the home is an important way to help reduce energy usage. Nonintrusive Load Monitoring (NILM) is existing technique which helps us monitor electricity consumption effectively and costly. NILM is a promising approach to obtain estimates of the electrical power consumption of individual appliances from aggregate measurements of voltage and/or current in the distribution system. Among the previous studies, Hidden Markov Model (HMM) based models have been studied very much. However, increasing appliances, multistate of appliances, and similar power consumption of appliances are three big issues in NILM recently. In this paper, we address these problems through providing our contributions as follows. First, we proposed state-of-the-art energy disaggregation based on Long Short-Term Memory Recurrent Neural Network (LSTM-RNN) model and additional advanced deep learning. Second, we proposed a novel signature to improve classification performance of the proposed model in multistate appliance case. We applied the proposed model on two datasets such as UK-DALE and REDD. Via our experimental results, we have confirmed that our model outperforms the advanced model. Thus, we show that our combination between advanced deep learning and novel signature can be a robust solution to overcome NILM’s issues and improve the performance of load identification.

scholarly journals Forecasting Day-Ahead Hourly Photovoltaic Power Generation Using Convolutional Self-Attention Based Long Short-Term Memory

Energies ◽  
2020 ◽  
Vol 13 (15) ◽  
pp. 4017 ◽  
Author(s):  
Dukhwan Yu ◽  
Wonik Choi ◽  
Myoungsoo Kim ◽  
Ling Liu
Keyword(s):  
Power Generation ◽  
Deep Learning ◽  
Prediction Accuracy ◽  
Short Term Memory ◽  
Local Context ◽  
Short Term ◽  
Term Memory ◽  
Proposed Model ◽  
Long Short Term Memory ◽  
Pv Power Generation

The problem of Photovoltaic (PV) power generation forecasting is becoming crucial as the penetration level of Distributed Energy Resources (DERs) increases in microgrids and Virtual Power Plants (VPPs). In order to improve the stability of power systems, a fair amount of research has been proposed for increasing prediction performance in practical environments through statistical, machine learning, deep learning, and hybrid approaches. Despite these efforts, the problem of forecasting PV power generation remains to be challenging in power system operations since existing methods show limited accuracy and thus are not sufficiently practical enough to be widely deployed. Many existing methods using long historical data suffer from the long-term dependency problem and are not able to produce high prediction accuracy due to their failure to fully utilize all features of long sequence inputs. To address this problem, we propose a deep learning-based PV power generation forecasting model called Convolutional Self-Attention based Long Short-Term Memory (LSTM). By using the convolutional self-attention mechanism, we can significantly improve prediction accuracy by capturing the local context of the data and generating keys and queries that fit the local context. To validate the applicability of the proposed model, we conduct extensive experiments on both PV power generation forecasting using a real world dataset and power consumption forecasting. The experimental results of power generation forecasting using the real world datasets show that the MAPEs of the proposed model are much lower, in fact by 7.7%, 6%, 3.9% compared to the Deep Neural Network (DNN), LSTM and LSTM with the canonical self-attention, respectively. As for power consumption forecasting, the proposed model exhibits 32%, 17% and 44% lower Mean Absolute Percentage Error (MAPE) than the DNN, LSTM and LSTM with the canonical self-attention, respectively.

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