Pub Date : 2023-06-19DOI: 10.3390/computers12060125
Firas Najjar, Q. Bsoul, H. Al-Refai
Neighbor Discovery Protocol (NDP) is a network protocol used in IPv6 networks to manage communication between neighboring devices. NDP is responsible for mapping IPv6 addresses to MAC addresses and discovering the availability of neighboring devices on the network. The main risk of deploying NDP on public networks is the potential for hackers or attackers to launch various types of attacks, such as address spoofing attacks, denial-of-service attacks, and man-in-the-middle attacks. Although Secure Neighbor Discovery (SEND) is implemented to secure NDP, its complexity and cost hinder its widespread deployment. This research emphasizes the potential hazard of deploying IPv6 networks in public spaces, such as airports, without protecting NDP messages. These risks have the potential to crash the entire local network. To demonstrate these risks, the GNS3 testbed environment is used to generate NDP attacks and capture the resulting packets using Wireshark for analysis. The analysis results reveal that with just a few commands, attackers can execute various NDP attacks. This highlights the need to protect against the potential issues that come with deploying IPv6 on widely accessible public networks. In addition, the analysis result shows that NDP attacks have behavior that can be used to define various NDP attacks.
{"title":"An Analysis of Neighbor Discovery Protocol Attacks","authors":"Firas Najjar, Q. Bsoul, H. Al-Refai","doi":"10.3390/computers12060125","DOIUrl":"https://doi.org/10.3390/computers12060125","url":null,"abstract":"Neighbor Discovery Protocol (NDP) is a network protocol used in IPv6 networks to manage communication between neighboring devices. NDP is responsible for mapping IPv6 addresses to MAC addresses and discovering the availability of neighboring devices on the network. The main risk of deploying NDP on public networks is the potential for hackers or attackers to launch various types of attacks, such as address spoofing attacks, denial-of-service attacks, and man-in-the-middle attacks. Although Secure Neighbor Discovery (SEND) is implemented to secure NDP, its complexity and cost hinder its widespread deployment. This research emphasizes the potential hazard of deploying IPv6 networks in public spaces, such as airports, without protecting NDP messages. These risks have the potential to crash the entire local network. To demonstrate these risks, the GNS3 testbed environment is used to generate NDP attacks and capture the resulting packets using Wireshark for analysis. The analysis results reveal that with just a few commands, attackers can execute various NDP attacks. This highlights the need to protect against the potential issues that come with deploying IPv6 on widely accessible public networks. In addition, the analysis result shows that NDP attacks have behavior that can be used to define various NDP attacks.","PeriodicalId":10526,"journal":{"name":"Comput.","volume":"51 1","pages":"125"},"PeriodicalIF":0.0,"publicationDate":"2023-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85294429","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-06-19DOI: 10.3390/computers12060126
Nasrin Elhassan, G. Varone, Rami Ahmed, M. Gogate, K. Dashtipour, Hani Almoamari, M. El-Affendi, B. Al-Tamimi, Faisal Albalwy, Amir Hussain
Social media networks have grown exponentially over the last two decades, providing the opportunity for users of the internet to communicate and exchange ideas on a variety of topics. The outcome is that opinion mining plays a crucial role in analyzing user opinions and applying these to guide choices, making it one of the most popular areas of research in the field of natural language processing. Despite the fact that several languages, including English, have been the subjects of several studies, not much has been conducted in the area of the Arabic language. The morphological complexities and various dialects of the language make semantic analysis particularly challenging. Moreover, the lack of accurate pre-processing tools and limited resources are constraining factors. This novel study was motivated by the accomplishments of deep learning algorithms and word embeddings in the field of English sentiment analysis. Extensive experiments were conducted based on supervised machine learning in which word embeddings were exploited to determine the sentiment of Arabic reviews. Three deep learning algorithms, convolutional neural networks (CNNs), long short-term memory (LSTM), and a hybrid CNN-LSTM, were introduced. The models used features learned by word embeddings such as Word2Vec and fastText rather than hand-crafted features. The models were tested using two benchmark Arabic datasets: Hotel Arabic Reviews Dataset (HARD) for hotel reviews and Large-Scale Arabic Book Reviews (LARB) for book reviews, with different setups. Comparative experiments utilized the three models with two-word embeddings and different setups of the datasets. The main novelty of this study is to explore the effectiveness of using various word embeddings and different setups of benchmark datasets relating to balance, imbalance, and binary and multi-classification aspects. Findings showed that the best results were obtained in most cases when applying the fastText word embedding using the HARD 2-imbalance dataset for all three proposed models: CNN, LSTM, and CNN-LSTM. Further, the proposed CNN model outperformed the LSTM and CNN-LSTM models for the benchmark HARD dataset by achieving 94.69%, 94.63%, and 94.54% accuracy with fastText, respectively. Although the worst results were obtained for the LABR 3-imbalance dataset using both Word2Vec and FastText, they still outperformed other researchers’ state-of-the-art outcomes applying the same dataset.
{"title":"Arabic Sentiment Analysis Based on Word Embeddings and Deep Learning","authors":"Nasrin Elhassan, G. Varone, Rami Ahmed, M. Gogate, K. Dashtipour, Hani Almoamari, M. El-Affendi, B. Al-Tamimi, Faisal Albalwy, Amir Hussain","doi":"10.3390/computers12060126","DOIUrl":"https://doi.org/10.3390/computers12060126","url":null,"abstract":"Social media networks have grown exponentially over the last two decades, providing the opportunity for users of the internet to communicate and exchange ideas on a variety of topics. The outcome is that opinion mining plays a crucial role in analyzing user opinions and applying these to guide choices, making it one of the most popular areas of research in the field of natural language processing. Despite the fact that several languages, including English, have been the subjects of several studies, not much has been conducted in the area of the Arabic language. The morphological complexities and various dialects of the language make semantic analysis particularly challenging. Moreover, the lack of accurate pre-processing tools and limited resources are constraining factors. This novel study was motivated by the accomplishments of deep learning algorithms and word embeddings in the field of English sentiment analysis. Extensive experiments were conducted based on supervised machine learning in which word embeddings were exploited to determine the sentiment of Arabic reviews. Three deep learning algorithms, convolutional neural networks (CNNs), long short-term memory (LSTM), and a hybrid CNN-LSTM, were introduced. The models used features learned by word embeddings such as Word2Vec and fastText rather than hand-crafted features. The models were tested using two benchmark Arabic datasets: Hotel Arabic Reviews Dataset (HARD) for hotel reviews and Large-Scale Arabic Book Reviews (LARB) for book reviews, with different setups. Comparative experiments utilized the three models with two-word embeddings and different setups of the datasets. The main novelty of this study is to explore the effectiveness of using various word embeddings and different setups of benchmark datasets relating to balance, imbalance, and binary and multi-classification aspects. Findings showed that the best results were obtained in most cases when applying the fastText word embedding using the HARD 2-imbalance dataset for all three proposed models: CNN, LSTM, and CNN-LSTM. Further, the proposed CNN model outperformed the LSTM and CNN-LSTM models for the benchmark HARD dataset by achieving 94.69%, 94.63%, and 94.54% accuracy with fastText, respectively. Although the worst results were obtained for the LABR 3-imbalance dataset using both Word2Vec and FastText, they still outperformed other researchers’ state-of-the-art outcomes applying the same dataset.","PeriodicalId":10526,"journal":{"name":"Comput.","volume":"66 1","pages":"126"},"PeriodicalIF":0.0,"publicationDate":"2023-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79535863","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-06-19DOI: 10.3390/computers12060124
Andreas Kanavos, Ioannis Karamitsos, Alaa Mohasseb
Social media platforms have revolutionized information exchange and socialization in today’s world. Twitter, as one of the prominent platforms, enables users to connect with others and express their opinions. This study focuses on analyzing user engagement levels on Twitter using graph mining and clustering techniques. We measure user engagement based on various tweet attributes, including retweets, replies, and more. Specifically, we explore the strength of user connections in Twitter networks by examining the diversity of edges. Our approach incorporates graph mining models that assign different weights to evaluate the significance of each connection. Additionally, clustering techniques are employed to group users based on their engagement patterns and behaviors. Statistical analysis was conducted to assess the similarity between user profiles, as well as attributes, such as friendship, followings, and interactions within the Twitter social network. The findings highlight the discovery of closely linked user groups and the identification of distinct clusters based on engagement levels. This research emphasizes the importance of understanding both individual and group behaviors in comprehending user engagement dynamics on Twitter.
{"title":"Exploring Clustering Techniques for Analyzing User Engagement Patterns in Twitter Data","authors":"Andreas Kanavos, Ioannis Karamitsos, Alaa Mohasseb","doi":"10.3390/computers12060124","DOIUrl":"https://doi.org/10.3390/computers12060124","url":null,"abstract":"Social media platforms have revolutionized information exchange and socialization in today’s world. Twitter, as one of the prominent platforms, enables users to connect with others and express their opinions. This study focuses on analyzing user engagement levels on Twitter using graph mining and clustering techniques. We measure user engagement based on various tweet attributes, including retweets, replies, and more. Specifically, we explore the strength of user connections in Twitter networks by examining the diversity of edges. Our approach incorporates graph mining models that assign different weights to evaluate the significance of each connection. Additionally, clustering techniques are employed to group users based on their engagement patterns and behaviors. Statistical analysis was conducted to assess the similarity between user profiles, as well as attributes, such as friendship, followings, and interactions within the Twitter social network. The findings highlight the discovery of closely linked user groups and the identification of distinct clusters based on engagement levels. This research emphasizes the importance of understanding both individual and group behaviors in comprehending user engagement dynamics on Twitter.","PeriodicalId":10526,"journal":{"name":"Comput.","volume":"59 1","pages":"124"},"PeriodicalIF":0.0,"publicationDate":"2023-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74647336","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-06-19DOI: 10.3390/computation11060120
A. Nurpeisova, A. Shaushenova, Z. Mutalova, M. Ongarbayeva, S. Niyazbekova, Anargul Bekenova, Lyazzat Zhumaliyeva, S. Zhumasseitova
The demand for online education is gradually growing. Most universities and other institutions are faced with the fact that it is almost impossible to track how honestly test takers take exams remotely. In online formats, there are many simple opportunities that allow for cheating and using the use of outside help. Online proctoring based on artificial intelligence technologies in distance education is an effective technological solution to prevent academic dishonesty. This article explores the development and implementation of an online control proctoring system using artificial intelligence technology for conducting online exams. The article discusses the proctoring systems used in Kazakhstan, compares the functional features of the selected proctoring systems, and describes the architecture of Proctor SU. A prototype of the Proctor SU proctoring system has been developed. As a pilot program, the authors used this system during an online university exam and examined the results of the test. According to the author’s examination, students have a positive attitude towards the use of Proctor SU online proctoring. The proposed proctor system includes features of face detection, face tracking, audio capture, and the active capture of system windows. Models CNN, R-CNN, and YOLOv3 were used in the development process. The YOLOv3 model processed images in real time at 45 frames per second, and CNN and R-CNN processed images in real time at 30 and 38 frames per second. The YOLOv3 model showed better results in terms of real-time face recognition. Therefore, the YOLOv3 model was implemented into the Proctor SU proctoring system.
{"title":"Research on the Development of a Proctoring System for Conducting Online Exams in Kazakhstan","authors":"A. Nurpeisova, A. Shaushenova, Z. Mutalova, M. Ongarbayeva, S. Niyazbekova, Anargul Bekenova, Lyazzat Zhumaliyeva, S. Zhumasseitova","doi":"10.3390/computation11060120","DOIUrl":"https://doi.org/10.3390/computation11060120","url":null,"abstract":"The demand for online education is gradually growing. Most universities and other institutions are faced with the fact that it is almost impossible to track how honestly test takers take exams remotely. In online formats, there are many simple opportunities that allow for cheating and using the use of outside help. Online proctoring based on artificial intelligence technologies in distance education is an effective technological solution to prevent academic dishonesty. This article explores the development and implementation of an online control proctoring system using artificial intelligence technology for conducting online exams. The article discusses the proctoring systems used in Kazakhstan, compares the functional features of the selected proctoring systems, and describes the architecture of Proctor SU. A prototype of the Proctor SU proctoring system has been developed. As a pilot program, the authors used this system during an online university exam and examined the results of the test. According to the author’s examination, students have a positive attitude towards the use of Proctor SU online proctoring. The proposed proctor system includes features of face detection, face tracking, audio capture, and the active capture of system windows. Models CNN, R-CNN, and YOLOv3 were used in the development process. The YOLOv3 model processed images in real time at 45 frames per second, and CNN and R-CNN processed images in real time at 30 and 38 frames per second. The YOLOv3 model showed better results in terms of real-time face recognition. Therefore, the YOLOv3 model was implemented into the Proctor SU proctoring system.","PeriodicalId":10526,"journal":{"name":"Comput.","volume":"13 1","pages":"120"},"PeriodicalIF":0.0,"publicationDate":"2023-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75265592","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-06-18DOI: 10.3390/computers12060123
Enrico Ferrari, Damiano Verda, Nicolò Pinna, Marco Muselli
Optimizing water distribution both from an energy-saving perspective and from a quality of service perspective is a challenging task since it involves a complex system with many nodes, many hidden variables and many operational constraints. For this reason, water distribution systems need to handle a delicate trade-off between the effectiveness and computational time of the solution. In this paper, we propose a new computationally efficient method, named rule-based control, to optimize water distribution networks without the need for a rigorous formulation of the optimization problem. As a matter of fact, since it is based on a machine learning approach, the proposed method employs only a set of historical data, where the configuration can be labeled according to a quality criterion. Since it is a data-driven approach, it could be applied to any complex network where historical labeled data are available. In particular, rule-based control exploits a rule-based classification method that allows us to retrieve the rules leading to good or bad performances of the system, even without any information about its physical laws. The evaluation of the results on some simulated scenarios shows that the proposed approach is able to reduce energy consumption while ensuring a good quality of the service. The proposed approach is currently used in the water distribution system of the Milan (Italy) water main.
{"title":"Optimizing Water Distribution through Explainable AI and Rule-Based Control","authors":"Enrico Ferrari, Damiano Verda, Nicolò Pinna, Marco Muselli","doi":"10.3390/computers12060123","DOIUrl":"https://doi.org/10.3390/computers12060123","url":null,"abstract":"Optimizing water distribution both from an energy-saving perspective and from a quality of service perspective is a challenging task since it involves a complex system with many nodes, many hidden variables and many operational constraints. For this reason, water distribution systems need to handle a delicate trade-off between the effectiveness and computational time of the solution. In this paper, we propose a new computationally efficient method, named rule-based control, to optimize water distribution networks without the need for a rigorous formulation of the optimization problem. As a matter of fact, since it is based on a machine learning approach, the proposed method employs only a set of historical data, where the configuration can be labeled according to a quality criterion. Since it is a data-driven approach, it could be applied to any complex network where historical labeled data are available. In particular, rule-based control exploits a rule-based classification method that allows us to retrieve the rules leading to good or bad performances of the system, even without any information about its physical laws. The evaluation of the results on some simulated scenarios shows that the proposed approach is able to reduce energy consumption while ensuring a good quality of the service. The proposed approach is currently used in the water distribution system of the Milan (Italy) water main.","PeriodicalId":10526,"journal":{"name":"Comput.","volume":"99 1","pages":"123"},"PeriodicalIF":0.0,"publicationDate":"2023-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85760581","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-06-15DOI: 10.3390/computers12060121
Ibrahim Ba’abbad, O. Batarfi
Several malware variants have attacked systems and data over time. Ransomware is among the most harmful malware since it causes huge losses. In order to get a ransom, ransomware is software that locks the victim’s machine or encrypts his personal information. Numerous research has been conducted to stop and quickly recognize ransomware attacks. For proactive forecasting, artificial intelligence (AI) techniques are used. Traditional machine learning/deep learning (ML/DL) techniques, however, take a lot of time and decrease the accuracy and latency performance of network monitoring. In this study, we utilized the Hoeffding trees classifier as one of the stream data mining classification techniques to detect and prevent ransomware attacks. Three Hoeffding trees classifier algorithms are selected to be applied to the Resilient Information Systems Security (RISS) research group dataset. After configuration, Massive Online Analysis (MOA) software is utilized as a testing framework. The results of Hoeffding tree classifier algorithms are then assessed to choose the enhanced model with the highest accuracy and latency performance. In conclusion, the 99.41% classification accuracy was the highest result achieved by the EFDT algorithm in 66 ms.
{"title":"Proactive Ransomware Detection Using Extremely Fast Decision Tree (EFDT) Algorithm: A Case Study","authors":"Ibrahim Ba’abbad, O. Batarfi","doi":"10.3390/computers12060121","DOIUrl":"https://doi.org/10.3390/computers12060121","url":null,"abstract":"Several malware variants have attacked systems and data over time. Ransomware is among the most harmful malware since it causes huge losses. In order to get a ransom, ransomware is software that locks the victim’s machine or encrypts his personal information. Numerous research has been conducted to stop and quickly recognize ransomware attacks. For proactive forecasting, artificial intelligence (AI) techniques are used. Traditional machine learning/deep learning (ML/DL) techniques, however, take a lot of time and decrease the accuracy and latency performance of network monitoring. In this study, we utilized the Hoeffding trees classifier as one of the stream data mining classification techniques to detect and prevent ransomware attacks. Three Hoeffding trees classifier algorithms are selected to be applied to the Resilient Information Systems Security (RISS) research group dataset. After configuration, Massive Online Analysis (MOA) software is utilized as a testing framework. The results of Hoeffding tree classifier algorithms are then assessed to choose the enhanced model with the highest accuracy and latency performance. In conclusion, the 99.41% classification accuracy was the highest result achieved by the EFDT algorithm in 66 ms.","PeriodicalId":10526,"journal":{"name":"Comput.","volume":"35 1","pages":"121"},"PeriodicalIF":0.0,"publicationDate":"2023-06-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85380269","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-06-15DOI: 10.3390/computation11060119
Á. Nagy
The recently introduced version of the density functional theory that employs a set of spherically symmetric densities instead of the density has a ‘set-representability problem’. It is not known if a density exists for a given set of the spherically symmetric densities. This problem can be eliminated if potentials are applied instead of densities as basic variables. Now, the spherical subspace potential functional theory is established.
{"title":"Spherical Subspace Potential Functional Theory","authors":"Á. Nagy","doi":"10.3390/computation11060119","DOIUrl":"https://doi.org/10.3390/computation11060119","url":null,"abstract":"The recently introduced version of the density functional theory that employs a set of spherically symmetric densities instead of the density has a ‘set-representability problem’. It is not known if a density exists for a given set of the spherically symmetric densities. This problem can be eliminated if potentials are applied instead of densities as basic variables. Now, the spherical subspace potential functional theory is established.","PeriodicalId":10526,"journal":{"name":"Comput.","volume":"7 1","pages":"119"},"PeriodicalIF":0.0,"publicationDate":"2023-06-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88820377","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-06-15DOI: 10.3390/computers12060122
João Sarraipa, Majid Zamiri, Elsa Marcelino-Jesus, Andreia Artífice, R. Jardim-Gonçalves, N. Moalla
With the increasing demand for digital transformation and (digital) technology transfer (TT), digital innovation hubs (DIHs) are the new piece of the puzzle of our economy and industries’ landscapes. Evidence shows that DIHs can provide good opportunities to access needed innovations, technologies, and resources at a higher level than other organizations that can normally access them. However, it is critically important to note that DIHs are still evolving, under research, and under development. That is, there are many substantial aspects of DIHs that should be considered. For example, DIHs must cater to a wide spectrum of needs for TT. From this perspective, the contribution of this work is proposing a generic and flexible learning framework, aiming to assist DIHs in providing suitable education, training, and learning services that support the process of (digital) TT to companies. The proposed learning framework was designed, evaluated, and improved with the support of two EU projects, and these processes are discussed in brief. The primary and leading results gained in this way show that the learning framework has immense potential for application to similar cases, and it can facilitate and expedite the process of TT to companies. The study is concluded with some directions for future works.
{"title":"A Learning Framework for Supporting Digital Innovation Hubs","authors":"João Sarraipa, Majid Zamiri, Elsa Marcelino-Jesus, Andreia Artífice, R. Jardim-Gonçalves, N. Moalla","doi":"10.3390/computers12060122","DOIUrl":"https://doi.org/10.3390/computers12060122","url":null,"abstract":"With the increasing demand for digital transformation and (digital) technology transfer (TT), digital innovation hubs (DIHs) are the new piece of the puzzle of our economy and industries’ landscapes. Evidence shows that DIHs can provide good opportunities to access needed innovations, technologies, and resources at a higher level than other organizations that can normally access them. However, it is critically important to note that DIHs are still evolving, under research, and under development. That is, there are many substantial aspects of DIHs that should be considered. For example, DIHs must cater to a wide spectrum of needs for TT. From this perspective, the contribution of this work is proposing a generic and flexible learning framework, aiming to assist DIHs in providing suitable education, training, and learning services that support the process of (digital) TT to companies. The proposed learning framework was designed, evaluated, and improved with the support of two EU projects, and these processes are discussed in brief. The primary and leading results gained in this way show that the learning framework has immense potential for application to similar cases, and it can facilitate and expedite the process of TT to companies. The study is concluded with some directions for future works.","PeriodicalId":10526,"journal":{"name":"Comput.","volume":"25 1","pages":"122"},"PeriodicalIF":0.0,"publicationDate":"2023-06-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78835578","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-06-14DOI: 10.3390/computation11060118
Chawin Metah, Amal Khalifa, Rebecca A. S. Palu
As a genetic eye disorder, retinitis pigmentosa (RP) has been a focus of researchers to find a diagnosis through either genome-wide association (GWA) or RNAseq analysis. In fact, GWA and RNAseq are considered two complementary approaches to gaining a more comprehensive understanding of the genetics of different diseases. However, RNAseq analysis can provide information about the specific mechanisms underlying the disease and the potential targets for therapy. This research proposes a new approach to differential gene expression (DGE) analysis, which is the heart of the core-analysis phase in any RNAseq study. Based on the Drosophila Genetic Reference Panel (DGRP), the gene expression dataset is computationally analyzed in light of eye-size phenotypes. We utilized the foreach and the doParallel R packages to run the code on a multicore machine to reduce the running time of the original algorithm, which exhibited an exponential time complexity. Experimental results showed an outstanding performance, reducing the running time by 95% while using 32 processes. In addition, more candidate modifier genes for RP were identified by increasing the scope of the analysis and considering more datasets that represent different phenotype models.
{"title":"A Parallel Computing Approach to Gene Expression and Phenotype Correlation for Identifying Retinitis Pigmentosa Modifiers in Drosophila","authors":"Chawin Metah, Amal Khalifa, Rebecca A. S. Palu","doi":"10.3390/computation11060118","DOIUrl":"https://doi.org/10.3390/computation11060118","url":null,"abstract":"As a genetic eye disorder, retinitis pigmentosa (RP) has been a focus of researchers to find a diagnosis through either genome-wide association (GWA) or RNAseq analysis. In fact, GWA and RNAseq are considered two complementary approaches to gaining a more comprehensive understanding of the genetics of different diseases. However, RNAseq analysis can provide information about the specific mechanisms underlying the disease and the potential targets for therapy. This research proposes a new approach to differential gene expression (DGE) analysis, which is the heart of the core-analysis phase in any RNAseq study. Based on the Drosophila Genetic Reference Panel (DGRP), the gene expression dataset is computationally analyzed in light of eye-size phenotypes. We utilized the foreach and the doParallel R packages to run the code on a multicore machine to reduce the running time of the original algorithm, which exhibited an exponential time complexity. Experimental results showed an outstanding performance, reducing the running time by 95% while using 32 processes. In addition, more candidate modifier genes for RP were identified by increasing the scope of the analysis and considering more datasets that represent different phenotype models.","PeriodicalId":10526,"journal":{"name":"Comput.","volume":"47 1","pages":"118"},"PeriodicalIF":0.0,"publicationDate":"2023-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88664895","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-06-13DOI: 10.3390/computation11060116
Zuwen Sun, N. Baddour
Time and frequency concentrations of waveforms are often of interest in engineering applications. The Slepian basis of order zero is an index-limited (finite) vector that is known to be optimally concentrated in the frequency domain. This paper proposes a method of mapping the index-limited Slepian basis to a discrete-time vector, hence obtaining a time-limited, discrete-time Slepian basis that is optimally concentrated in frequency. The main result of this note is to demonstrate that the (discrete-time) Slepian basis achieves minimum time-bandwidth compactness under certain conditions. We distinguish between the characteristic (effective) time/bandwidth of the Slepians and their defining time/bandwidth (the time and bandwidth parameters used to generate the Slepian basis). Using two different definitions of effective time and bandwidth of a signal, we show that when the defining time-bandwidth product of the Slepian basis increases, its effective time-bandwidth product tends to a minimum value. This implies that not only are the zeroth order Slepian bases known to be optimally time-limited and band-concentrated basis vectors, but also as their defining time-bandwidth products increase, their effective time-bandwidth properties approach the known minimum compactness allowed by the uncertainty principle. Conclusions are also drawn about the smallest defining time-bandwidth parameters to reach the minimum possible compactness. These conclusions give guidance for applications where the time-bandwidth product is free to be selected and hence may be selected to achieve minimum compactness.
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