scholarly journals A representation and deep learning model for annotating ubiquitylation sentences stating E3 ligase - substrate interaction

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Mengqi Luo ◽  
Zhongyan Li ◽  
Shangfu Li ◽  
Tzong-Yi Lee
Keyword(s):  
Machine Learning ◽  
Deep Learning ◽  
Language Processing ◽  
Short Term Memory ◽  
E3 Ligase ◽  
Attention Mechanism ◽  
Biomedical Literature ◽  
Learning Methods ◽  
Substrate Interactions ◽  
Substrate Interaction

Abstract Background Ubiquitylation is an important post-translational modification of proteins that not only plays a central role in cellular coding, but is also closely associated with the development of a variety of diseases. The specific selection of substrate by ligase E3 is the key in ubiquitylation. As various high-throughput analytical techniques continue to be applied to the study of ubiquitylation, a large amount of ubiquitylation site data, and records of E3-substrate interactions continue to be generated. Biomedical literature is an important vehicle for information on E3-substrate interactions in ubiquitylation and related new discoveries, as well as an important channel for researchers to obtain such up to date data. The continuous explosion of ubiquitylation related literature poses a great challenge to researchers in acquiring and analyzing the information. Therefore, automatic annotation of these E3-substrate interaction sentences from the available literature is urgently needed. Results In this research, we proposed a model based on representation and attention mechanism based deep learning methods, to automatic annotate E3-substrate interaction sentences in biomedical literature. Focusing on the sentences with E3 protein inside, we applied several natural language processing methods and a Long Short-Term Memory (LSTM)-based deep learning classifier to train the model. Experimental results had proved the effectiveness of our proposed model. And also, the proposed attention mechanism deep learning method outperforms other statistical machine learning methods. We also created a manual corpus of E3-substrate interaction sentences, in which the E3 proteins and substrate proteins are also labeled, in order to construct our model. The corpus and model proposed by our research are definitely able to be very useful and valuable resource for advancement of ubiquitylation-related research. Conclusion Having the entire manual corpus of E3-substrate interaction sentences readily available in electronic form will greatly facilitate subsequent text mining and machine learning analyses. Automatic annotating ubiquitylation sentences stating E3 ligase-substrate interaction is significantly benefited from semantic representation and deep learning. The model enables rapid information accessing and can assist in further screening of key ubiquitylation ligase substrates for in-depth studies.

scholarly journals Modulation Classification of Underwater Communication with Deep Learning Network

2019 ◽  
Vol 2019 ◽  
pp. 1-12 ◽  
Author(s):  
Yan Wang ◽  
Hao Zhang ◽  
Zhanliang Sang ◽  
Lingwei Xu ◽  
Conghui Cao ◽  
...  
Keyword(s):  
Machine Learning ◽  
Feature Extraction ◽  
Deep Learning ◽  
Language Processing ◽  
Communication Process ◽  
Underwater Acoustic Communication ◽  
Learning Method ◽  
Modulation Recognition ◽  
Learning Methods ◽  
Machine Learning Methods

Automatic modulation recognition has successfully used various machine learning methods and achieved certain results. As a subarea of machine learning, deep learning has made great progress in recent years and has made remarkable progress in the field of image and language processing. Deep learning requires a large amount of data support. As a communication field with a large amount of data, there is an inherent advantage of applying deep learning. However, the extensive application of deep learning in the field of communication has not yet been fully developed, especially in underwater acoustic communication. In this paper, we mainly discuss the modulation recognition process which is an important part of communication process by using the deep learning method. Different from the common machine learning methods that require feature extraction, the deep learning method does not require feature extraction and obtains more effects than common machine learning.

scholarly journals A Tweet Sentiment Classification Approach Using a Hybrid Stacked Ensemble Technique

Information ◽  
2021 ◽  
Vol 12 (9) ◽  
pp. 374
Author(s):  
Babacar Gaye ◽  
Dezheng Zhang ◽  
Aziguli Wulamu
Keyword(s):  
Machine Learning ◽  
Logistic Regression ◽  
Deep Learning ◽  
Sentiment Analysis ◽  
Language Processing ◽  
Short Term Memory ◽  
State Of The Art ◽  
Accuracy Score ◽  
Learning Models ◽  
Proposed Model

With the extensive availability of social media platforms, Twitter has become a significant tool for the acquisition of peoples’ views, opinions, attitudes, and emotions towards certain entities. Within this frame of reference, sentiment analysis of tweets has become one of the most fascinating research areas in the field of natural language processing. A variety of techniques have been devised for sentiment analysis, but there is still room for improvement where the accuracy and efficacy of the system are concerned. This study proposes a novel approach that exploits the advantages of the lexical dictionary, machine learning, and deep learning classifiers. We classified the tweets based on the sentiments extracted by TextBlob using a stacked ensemble of three long short-term memory (LSTM) as base classifiers and logistic regression (LR) as a meta classifier. The proposed model proved to be effective and time-saving since it does not require feature extraction, as LSTM extracts features without any human intervention. We also compared our proposed approach with conventional machine learning models such as logistic regression, AdaBoost, and random forest. We also included state-of-the-art deep learning models in comparison with the proposed model. Experiments were conducted on the sentiment140 dataset and were evaluated in terms of accuracy, precision, recall, and F1 Score. Empirical results showed that our proposed approach manifested state-of-the-art results by achieving an accuracy score of 99%.

Investigating the Feasibility of Deep Learning Methods for Urdu Word Sense Disambiguation

2022 ◽  
Vol 21 (2) ◽  
pp. 1-16
Author(s):  
Ali Saeed ◽  
Rao Muhammad Adeel Nawab ◽  
Mark Stevenson
Keyword(s):  
Deep Learning ◽  
Language Processing ◽  
Short Term Memory ◽  
Word Sense Disambiguation ◽  
Word Sense ◽  
Short Term ◽  
Learning Methods ◽  
Term Memory ◽  
Sense Disambiguation ◽  
Long Short Term Memory

Word Sense Disambiguation (WSD), the process of automatically identifying the correct meaning of a word used in a given context, is a significant challenge in Natural Language Processing. A range of approaches to the problem has been explored by the research community. The majority of these efforts has focused on a relatively small set of languages, particularly English. Research on WSD for South Asian languages, particularly Urdu, is still in its infancy. In recent years, deep learning methods have proved to be extremely successful for a range of Natural Language Processing tasks. The main aim of this study is to apply, evaluate, and compare a range of deep learning methods approaches to Urdu WSD (both Lexical Sample and All-Words) including Simple Recurrent Neural Networks, Long-Short Term Memory, Gated Recurrent Units, Bidirectional Long-Short Term Memory, and Ensemble Learning. The evaluation was carried out on two benchmark corpora: (1) the ULS-WSD-18 corpus and (2) the UAW-WSD-18 corpus. Results (Accuracy = 63.25% and F1-Measure = 0.49) show that a deep learning approach outperforms previously reported results for the Urdu All-Words WSD task, whereas performance using deep learning approaches (Accuracy = 72.63% and F1-Measure = 0.60) are low in comparison to previously reported for the Urdu Lexical Sample task.

scholarly journals Sequential Model Based Intrusion Detection System for IoT Servers Using Deep Learning Methods

Sensors ◽  
2021 ◽  
Vol 21 (4) ◽  
pp. 1113
Author(s):  
Ming Zhong ◽  
Yajin Zhou ◽  
Gang Chen
Keyword(s):  
Machine Learning ◽  
Deep Learning ◽  
Intrusion Detection ◽  
Language Processing ◽  
Intrusion Detection System ◽  
Detection System ◽  
Learning Methods ◽  
Sequential Model ◽  
Machine Learning Methods ◽  
Model Based

IoT plays an important role in daily life; commands and data transfer rapidly between the servers and objects to provide services. However, cyber threats have become a critical factor, especially for IoT servers. There should be a vigorous way to protect the network infrastructures from various attacks. IDS (Intrusion Detection System) is the invisible guardian for IoT servers. Many machine learning methods have been applied in IDS. However, there is a need to improve the IDS system for both accuracy and performance. Deep learning is a promising technique that has been used in many areas, including pattern recognition, natural language processing, etc. The deep learning reveals more potential than traditional machine learning methods. In this paper, sequential model is the key point, and new methods are proposed by the features of the model. The model can collect features from the network layer via tcpdump packets and application layer via system routines. Text-CNN and GRU methods are chosen because the can treat sequential data as a language model. The advantage compared with the traditional methods is that they can extract more features from the data and the experiments show that the deep learning methods have higher F1-score. We conclude that the sequential model-based intrusion detection system using deep learning method can contribute to the security of the IoT servers.

scholarly journals Performance Analysis of Hybrid Deep Learning Models with Attention Mechanism Positioning and Focal Loss for Text Classification

2021 ◽  
Vol 2021 ◽  
pp. 1-12
Author(s):  
Sunil Kumar Prabhakar ◽  
Harikumar Rajaguru ◽  
Dong-Ok Won
Keyword(s):  
Deep Learning ◽  
Hybrid Model ◽  
Language Processing ◽  
Text Classification ◽  
Classification Accuracy ◽  
Short Term Memory ◽  
Learning Algorithm ◽  
Attention Mechanism ◽  
Learning Models ◽  
High Classification Accuracy

Over the past few decades, text classification problems have been widely utilized in many real time applications. Leveraging the text classification methods by means of developing new applications in the field of text mining and Natural Language Processing (NLP) is very important. In order to accurately classify tasks in many applications, a deeper insight into deep learning methods is required as there is an exponential growth in the number of complex documents. The success of any deep learning algorithm depends on its capacity to understand the nonlinear relationships of the complex models within data. Thus, a huge challenge for researchers lies in the development of suitable techniques, architectures, and models for text classification. In this paper, hybrid deep learning models, with an emphasis on positioning of attention mechanism analysis, are considered and analyzed well for text classification. The first hybrid model proposed is called convolutional Bidirectional Long Short-Term Memory (Bi-LSTM) with attention mechanism and output (CBAO) model, and the second hybrid model is called convolutional attention mechanism with Bi-LSTM and output (CABO) model. In the first hybrid model, the attention mechanism is placed after the Bi-LSTM, and then the output Softmax layer is constructed. In the second hybrid model, the attention mechanism is placed after convolutional layer and followed by Bi-LSTM and the output Softmax layer. The proposed hybrid models are tested on three datasets, and the results show that when the proposed CBAO model is implemented for IMDB dataset, a high classification accuracy of 92.72% is obtained and when the proposed CABO model is implemented on the same dataset, a high classification accuracy of 90.51% is obtained.

A Deep Learning Method to Analyze and Classify Happy Moments: A Comparative Analytic Study (Preprint)

2019 ◽  
Author(s):  
Qiudan Li ◽  
Ruoran Liu ◽  
Riheng Yao ◽  
Daniel Dajun Zeng
Keyword(s):  
Machine Learning ◽  
Logistic Regression ◽  
Deep Learning ◽  
Short Term Memory ◽  
Detailed Comparison ◽  
Public Attention ◽  
Learning Methods ◽  
Policy Makers ◽  
Important Indicator ◽  
Machine Learning Methods

BACKGROUND Happiness is considered as an important indicator of users’ mental and physical health. Fostering happiness has gained increasing public attention as one of the ways to decrease health costs in the long run. Understanding what makes users feel happy may help policy makers develop policies and methods that steer users towards behaviors identified to promote happiness. OBJECTIVE This paper aimed to investigate the use of deep learning methods to analyze happy moments and compare them with the traditional machine learning methods, which may provide a mechanism to accurately classify happy moments and help understand why users feel happy. METHODS A crowdsourced corpus of happy moments, HappyDB, was used. The dataset contained 14,125 posts with category labels that described sources and reasons for happy feelings: Achievement, Affection, Bonding, Enjoy the moment, Leisure, Nature and Exercise. We compared the performance of deep learning methods such as the convolutional neural network (CNN), bidirectional long-short term memory (Bi-LSTM), and attention Bi-LSTM with that of the traditional machine learning methods including logistic regression, SVM, and naïve Bayes. Standard measures including precision, recall, and F1 were adopted for each category. Macro-precision, macro-recall, and macro-F1 were used to evaluate the overall performance of the models. RESULTS We found that CNN achieved the best performance on macro-precision, macro-recall, and macro-F1, with values of 80.8, 79.3, and 80.0, respectively. Among the traditional machine learning methods, logistic regression performed the best, with macro-precision of 80.6, macro-recall of 71.1, and macro-F1 of 75.5. A detailed comparison of CNN and logistic regression on each category showed that CNN was able to improve F1 score for all categories. Specifically, F1 improved by at least 1.8% on the Bonding category and up to 11.3% on Nature. Performance improvements mainly depended on significant improvements on recall, especially for minor categories. For example, the recall of CNN was 80.9 and 70.9 for Nature and Exercise, which was an improvement of 28.5% and 11.6% compared with logistic regression. The reason was that CNN explicitly modeled the relationship between word features and the categories of happy moments by extracting important word features through convolution and pooling operations. CONCLUSIONS This is the first study to analyze happy moments based on deep learning methods. Compared with the traditional machine learning methods, deep learning methods, especially CNN, showed superiority on classifying the happy moments, which would facilitate understanding of the reasons why users feel happy and thus help policy makers formulate targeted policies to promote happiness.

Deep Learning Based High-Resolution Remote Sensing Image classification

2017 ◽  
Vol 7 (10) ◽  
pp. 22
Author(s):  
Sumit Kaur
Keyword(s):  
Machine Learning ◽  
Remote Sensing ◽  
Deep Learning ◽  
Image Classification ◽  
Language Processing ◽  
Object Perception ◽  
Remote Sensing Image ◽  
Research Area ◽  
Remote Sensing Image Classification ◽  
Unsupervised Algorithms

Abstract- Deep learning is an emerging research area in machine learning and pattern recognition field which has been presented with the goal of drawing Machine Learning nearer to one of its unique objectives, Artificial Intelligence. It tries to mimic the human brain, which is capable of processing and learning from the complex input data and solving different kinds of complicated tasks well. Deep learning (DL) basically based on a set of supervised and unsupervised algorithms that attempt to model higher level abstractions in data and make it self-learning for hierarchical representation for classification. In the recent years, it has attracted much attention due to its state-of-the-art performance in diverse areas like object perception, speech recognition, computer vision, collaborative filtering and natural language processing. This paper will present a survey on different deep learning techniques for remote sensing image classification. 

Data Science in Economics: Comprehensive Review of Advanced Machine Learning and Deep Learning Methods

2020 ◽  
Author(s):  
Saeed Nosratabadi ◽  
Amir Mosavi ◽  
Puhong Duan ◽  
Pedram Ghamisi ◽  
Filip Ferdinand ◽  
...  
Keyword(s):  
Machine Learning ◽  
Deep Learning ◽  
Data Science ◽  
Learning Methods ◽  
Comprehensive Review

scholarly journals Integrating Machine/Deep Learning Methods and Filtering Techniques for Reliable Mineral Phase Segmentation of 3D X-ray Computed Tomography Images

Energies ◽  
2021 ◽  
Vol 14 (15) ◽  
pp. 4595
Author(s):  
Parisa Asadi ◽  
Lauren E. Beckingham
Keyword(s):  
Machine Learning ◽  
Deep Learning ◽  
Random Forest ◽  
Ct Images ◽  
Ct Imaging ◽  
Learning Method ◽  
Learning Methods ◽  
X Ray ◽  
Machine Learning Methods ◽  
Filtering Techniques

X-ray CT imaging provides a 3D view of a sample and is a powerful tool for investigating the internal features of porous rock. Reliable phase segmentation in these images is highly necessary but, like any other digital rock imaging technique, is time-consuming, labor-intensive, and subjective. Combining 3D X-ray CT imaging with machine learning methods that can simultaneously consider several extracted features in addition to color attenuation, is a promising and powerful method for reliable phase segmentation. Machine learning-based phase segmentation of X-ray CT images enables faster data collection and interpretation than traditional methods. This study investigates the performance of several filtering techniques with three machine learning methods and a deep learning method to assess the potential for reliable feature extraction and pixel-level phase segmentation of X-ray CT images. Features were first extracted from images using well-known filters and from the second convolutional layer of the pre-trained VGG16 architecture. Then, K-means clustering, Random Forest, and Feed Forward Artificial Neural Network methods, as well as the modified U-Net model, were applied to the extracted input features. The models’ performances were then compared and contrasted to determine the influence of the machine learning method and input features on reliable phase segmentation. The results showed considering more dimensionality has promising results and all classification algorithms result in high accuracy ranging from 0.87 to 0.94. Feature-based Random Forest demonstrated the best performance among the machine learning models, with an accuracy of 0.88 for Mancos and 0.94 for Marcellus. The U-Net model with the linear combination of focal and dice loss also performed well with an accuracy of 0.91 and 0.93 for Mancos and Marcellus, respectively. In general, considering more features provided promising and reliable segmentation results that are valuable for analyzing the composition of dense samples, such as shales, which are significant unconventional reservoirs in oil recovery.

Artificial Intelligence and Human Rights: Four Realms of Discussion: Summary of Remarks

2020 ◽  
Vol 114 ◽  
pp. 242-245
Author(s):  
Jootaek Lee
Keyword(s):  
Artificial Intelligence ◽  
Machine Learning ◽  
Decision Making ◽  
Deep Learning ◽  
Language Processing ◽  
Human Reasoning ◽  
The Past ◽  
Making Choices ◽  
Data Capturing ◽  
Intensive Procedures

The term, Artificial Intelligence (AI), has changed since it was first coined by John MacCarthy in 1956. AI, believed to have been created with Kurt Gödel's unprovable computational statements in 1931, is now called deep learning or machine learning. AI is defined as a computer machine with the ability to make predictions about the future and solve complex tasks, using algorithms. The AI algorithms are enhanced and become effective with big data capturing the present and the past while still necessarily reflecting human biases into models and equations. AI is also capable of making choices like humans, mirroring human reasoning. AI can help robots to efficiently repeat the same labor intensive procedures in factories and can analyze historic and present data efficiently through deep learning, natural language processing, and anomaly detection. Thus, AI covers a spectrum of augmented intelligence relating to prediction, autonomous intelligence relating to decision making, automated intelligence for labor robots, and assisted intelligence for data analysis.

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