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Graph Transformer for Communities Detection in Social Networks

computers, Materials & Continua 2022年第3期70卷 5707-5720页

作者： G.Naga Chandrika Khalid Alnowibet K.Sandeep Kautish E.Sreenivasa Reddy Adel F.Alrasheedi Ali Wagdy Mohamed Department of Computer Science and Engineering ANU College of Engineering and TechnologyGuntur522510India Statistics and Operations Research Department College of ScienceKing Saud UniversityRiyadh11451Kingdom of Saudi Arabia LBEF Campus Kathmandu44600Nepal Department of Computer Science and Engineering ANUGuntur522510India Operations Research Department Faculty of Graduate Studies for Statistical ResearchCairo UniversityGiza12613Egypt Wireless Intelligent Networks Center(WINC) School of Engineering and Applied SciencesNile UniversityGiza12588Egypt

Graphs are used in various disciplines such as telecommunication,biological networks,as well as social *** large-scale networks,it is challenging to detect the communities by learning the distinct properties of the *** deep learning hasmade contributions in a variety of domains,we try to use deep learning techniques to mine the knowledge from large-scale graph *** this paper,we aim to provide a strategy for detecting communities using deep autoencoders and obtain generic neural attention to *** advantages of neural attention are widely seen in the field of NLP and computer vision,which has low computational complexity for large-scale *** contributions of the paper are summarized as ***,a transformer is utilized to downsample the first-order proximities of the graph into a latent space,which can result in the structural properties and eventually assist in detecting the ***,the fine-tuning task is conducted by tuning variant hyperparameters cautiously,which is applied to multiple social networks(Facebook and Twitch).Furthermore,the objective function(crossentropy)is tuned by L0 ***,the reconstructed model forms communities that present the relationship between the *** proposed robust model provides good generalization and is applicable to obtaining not only the community structures in social networks but also the node *** proposed graph-transformer shows advanced performance on the social networks with the average NMIs of 0.67±0.04,0.198±0.02,0.228±0.02,and 0.68±0.03 on Wikipedia crocodiles,Github Developers,Twitch England,and Facebook Page-Page networks,respectively.

关键词： Social networks graph transformer community detection graph classification

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Cancer Prediction using Clinical and Genomic Data Fusion: A Systematic Review 6

Cancer Prediction using Clinical and Genomic Data Fusion: A ...

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6th International Conference on Cybernetics and Intelligent System, ICORIS 2024

作者： Julian, Kelvin Nugroho, Kuncahyo Setyo Nirwantono, Rudi Pardamean, Bens Computer Science Department BINUS Graduate Program Bina Nusantara University Jakarta Indonesia Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia Biotechnology Department Faculty of Engineering Bina Nusantara University Jakarta Indonesia

ISBN: (纸本)9798331539603

This systematic review provides a comprehensive overview of the methods used to integrate genomic and clinical data in cancer prediction. The review includes 19 studies across various cancers, including breast, colorectal, melanoma, lung, pancreatic, and thyroid. The studies employed different methods to combine genomic and clinical data, including weighted polygenic risk scores, genetic and non-genetic risk scores, and different machine learning algorithms. The results show significant improvements in model prediction performance accuracy across multiple studies. The review highlights the potential benefits of integrating genetic and phenotypic information to improve disease risk prediction models and inform personalized healthcare strategies. © 2024 IEEE.

关键词： Lung cancer

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Mapping the Scientific Landscape of Integrated Scheduling Towards Industry 5.0 with A Bibliometric Analysis 6

Mapping the Scientific Landscape of Integrated Scheduling To...

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6th International Conference on Industry 4.0 and Smart Manufacturing, ISM 2024

作者： Putri Ardyanti, Anak Agung Ayu Xie, Zhiqiang Karnyoto, Andrea Stevens Pardamean, Bens Estiyanti, Ni Made School of Computer Science and Technology Harbin University of Science and Technology Harbin150000 China Faculty of Information Technology and Design Primakara University Bali 80226 Indonesia Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta11480 Indonesia Computer Science Department BINUS Graduate Program Master of Computer Science Bina Nusantara University Jakarta 11480 Indonesia School of Management and Business University of Debrecen Debrecen Hungary

The industry is rapidly transitioning from the 4.0 era to the 5.0 era, prompting renewed interest among scholars in scheduling problems. They allow operations to process and assemble various components simultaneously. This bibliometric analysis provides a comprehensive understanding of the diverse research perspectives on the potential challenges of integrated scheduling within the framework. We identified 357 Scopus articles and analysed co-occurrence keyword (CNK) by VOSViewer tools and Global Citation Score (GCS) by Scopus tools. The research data obtained from 1993 to 2023 mainly in the subject areas of Engineering, computer science, Maths, and others. CNK identified six cluster keywords, and nine most cited articles based on normalised GCS. These results contribute to our understanding of the development of scheduling algorithms, shifting from an emphasis on manufacturing transfers to contemporary demand-centric research directions. Furthermore, this research provides a valuable perspective for policymakers, plant personnel, and manufacturing managers to make informed decisions. © 2025 The Authors. Published by Elsevier B.V.

关键词： Job shop scheduling

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Expanding chiral metamaterials for retrieving fingerprints via vibrational circular dichroism

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Light(science & Applications) 2023年第7期12卷 1401-1414页

作者： Cheng Xu Zhihao Ren Hong Zhou Jingkai Zhou Chong Pei Ho Nan Wang Chengkuo Lee Department of Electrical and Computer Engineering National University of SingaporeSingapore 117583Singapore Center for Inteligent Sensors and MEMS(CISM) National University of SingaporeSingapore 117608Singapore institute of Microelectronics(IME) Agency for ScienceTechnology and Research(A*STAR)Singapore 138634Singapore NUS Graduate School for Integrative Science and Engineering Program(ISEP) National University of SingaporeSingapore 117456Singapore

Circular dichroism(CD)spectroscopy has been widely demonstrated for detecting chiral ***,the determination of chiral mixtures with various concentrations and enantiomeric ratios can be a challenging *** solve this problem,we report an enhanced vibrational circular dichroism(VCD)sensing platform based on plasmonic chiral metamaterials,which presents a 6-magnitude signal enhancement with a selectivity of chiral *** by coupled-mode theory,we leverage both in-plane and out-of-plane symmetry-breaking structures for chiral metamaterial design enabled by a two-step lithography process,which increases the near-field coupling strengths and varies the ratio between absorption and radiation loss,resulting in improved chiral light-matter interaction and enhanced molecular VCD ***,we demonstrate the thin-film sensing process of BSA andβ-lactoglobulin proteins,which contain secondary structures a-helix andβ-sheet and achieve a limit of detection down to zeptomole ***,we also,for the first time,explore the potential of enhanced VCD spectroscopy by demonstrating a selective sensing process of chiral mixtures,where the mixing ratio can be successfully differentiated with our proposed chiral *** findings improve the sensing signal of molecules and expand the extractable information,paving the way toward label-free,compact,small-volume chiral molecule detection for stereochemical and clinical diagnosisapplications.

关键词： chiral vibrational circular

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Time-series Analysis of Correlation between Climatic Parameters and Dengue Fever in Indonesia 4

Time-series Analysis of Correlation between Climatic Paramet...

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4th International Conference on Informatics, Multimedia, Cyber and Information System, ICIMCIS 2022

作者： Nirwantono, Rudi Trinugroho, Joko Pebrianto Sudigyo, Digdo Hidayat, Alam Ahmad Pardamean, Bens Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta11480 Indonesia Bina Nusantara University Binus Graduate Program Master of Computer Science Program Computer Science Department Jakarta11480 Indonesia

ISBN: (纸本)9781665473279

Dengue fever is mainly caused by female mosquitoes from the genus Aedes. It predominantly occurs in equatorial to sub-tropical regions. The weather factors play a significant role in the mosquito life cycle, so a study on the impact of climate parameters on dengue incidence is required. This study aimed to understand the statistical association between the annual fluctuation of dengue cases with climate factors in Indonesia. Climatic data, annual rainfall, and annual mean ambient temperature of Indonesia were obtained from *** from 2010 to 2020, while the data on the annual incidence of dengue fever in Indonesia were collected from the Indonesian Health Profile by the Ministry of Health of Indonesia from 2010 to 2020. The association between climatic factors with dengue cases was calculated with Spearman statistical test after the data was indicated as not normally distributed. In addition, we performed Poisson regression analysis to examine how the changes in climatic parameters affect the dengue cases. The rain precipitation was insignificantly correlated with the dengue incidence in Indonesia during the study time. In contrast, the ambient temperature statistically showed a strong association with the dengue cases. The association between climatic factors and the number of dengue cases suggests that the model would likely be prospectively applied to the dengue early warning system as a nationwide intervention to reduce the epidemic impact in Indonesia. © 2022 IEEE.

关键词： Data mining

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Digital Twin (DT) Smart City for Air Quality Management 8

Digital Twin (DT) Smart City for Air Quality Management

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8th International Conference on computer science and Computational Intelligence, ICCSCI 2023

作者： Ariansyah, Dedy Isnan, Mahmud Rahutomo, Reza Pardamean, Bens Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta11480 Indonesia Information Systems Department School of Information Systems Bina Nusantara University Jakarta11480 Indonesia Computer Science Department BINUS Graduate Program-Master of Computer Science Program Bina Nusantara University Jakarta11480 Indonesia

Air pollution is a pressing issue in cities, and managing air quality poses a challenge for urban designers and decision-makers. This study proposes a Digital Twin (DT) Smart City integrated with Mixed Reality technology to enhance visualization and collaboration for addressing urban air pollution. The research adopts an applied research approach, with a focus on developing a DT framework. A use case of DT development for Jakarta, the capital of Indonesia, is presented. By integrating air quality data, meteorological information, traffic patterns, and urban infrastructure data, the DT provides a comprehensive understanding of air pollution dynamics. The visualization capabilities of the DT, utilizing Mixed Reality technology, facilitate effective decision-making and the identification of strategies for managing air quality. However, further research is needed to address data management challenges to build a DT for Smart City at scale. © 2023 The Authors. Published by Elsevier B.V.

关键词： Augmented Reality Digital Twin Mixed Reality Smart City

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Systematic Literature Review on Machine Learning Predictive Models for Indoor Climate in Smart Solar Dryer Dome 4

Systematic Literature Review on Machine Learning Predictive ...

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4th International Conference on Cybernetics and Intelligent System, ICORIS 2022

作者： Setiawan, Karli Eka Elwirehardja, Gregorius Natanael Pardamean, Bens Bina Nusantara University BINUS Graduate Program Master of Computer Science Program Computer Science Department Jakarta11480 Indonesia Bina Nusantara University Bioinformatics and Data Science Research Center Jakarta11480 Indonesia

ISBN: (纸本)9781665453950

Precise predictions of indoor climate conditions are required in the implementation of Smart Solar Dryer Dome (SDD). Trend development of prediction models is discussed in this review from 15 selected research papers (2018-2022) on indoor climate prediction which was obtained from research paper databases The output shows that the most used model for predicting indoor climate is Artificial Neural Network (ANN), especially Recurrent Neural Network (RNN) such as LSTM and GRU. However, there are some potential methods such as Transformer, Combined Support Vector Machines (SVM)-Deep Learning, and sequence-to-sequence which could outperform other commonly used models. Based on findings various opportunities exist to improve the precision of indoor climate prediction, which can bring power consumption efficiency and others benefit to Smart SDD users. Such studies may further be explored to produce more accurate machine learning models. © 2022 IEEE.

关键词： Domes

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Utilizing Semi-supervised Method in Predicting BRCA1 Pathogenicity Variants 8

Utilizing Semi-supervised Method in Predicting BRCA1 Pathoge...

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8th International Conference on computer science and Computational Intelligence, ICCSCI 2023

作者： Hidayat, Alam Ahmad Trinugroho, Joko Pebrianto Nirwantono, Rudi Sudigyo, Digdo Pardamean, Bens Department of Mathematics School of Computer Science Bina Nusantara University 11480 Indonesia Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta11480 Indonesia Computer Science Department BINUS Graduate Program Bina Nusantara University Jakarta11480 Indonesia

Quantifying the effect of mutations in the BRCA1 gene is useful for understanding their clinical consequences on breast cancer. Machine learning models can be applied to predict the landscape of protein variant effects that might not be always accessible by experiments. In this work, we propose a simple semi-supervised learning method using a Gaussian mixture model to predict ~90% of the unlabeled missense variants of the BRCA1 gene collected from the ClinVar database. High-quality embeddings are used as a feature of the protein sequences, extracted using the latest pre-trained transformer-based language protein model. A statistical test show that the protein embeddings are effective and robust for predicting pathogenicity. Further, the lower representations of the features are then fed into the semi-supervised model. The prediction performance of the model only for the labeled testing data achieves an AUC score and an accuracy of 79.27% and 71.58%, respectively. Using our defined pathogenic probability score, we find that ~94% of variants in our unlabeled dataset are well-separated into either benign or pathogenic classes according to that scoring. Our scores obtain a moderate Spearman rank correlation with the results of established unsupervised variant effect models. Finally, our approach can potentially be developed for more accurate and biologically reliable predictions of the variant effects. © 2023 The Authors. Published by Elsevier B.V.

关键词： embeddings language model mutation effect protein sequence semi-supervised learning

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Machine Learning Approach for Single Nucleotide Polymorphism Selection in Genetic Testing Results 8

Machine Learning Approach for Single Nucleotide Polymorphism...

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8th International Conference on computer science and Computational Intelligence, ICCSCI 2023

作者： Trinugroho, Joko Pebrianto Hidayat, Alam Ahmad Isnan, Mahmud Pardamean, Bens Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta11480 Indonesia Department of Mathematics School of Computer Science Bina Nusantara University Jakarta11480 Indonesia Computer Science Department BINUS Graduate Program Bina Nusantara University Jakarta11480 Indonesia

Lactose intolerance is a type of digestive problem that may threaten the population because milk and dairy products compose of nutrients that are essential for human body. Genetic tests possess a great potential to detect lactose intolerance as it can be used in children and even infants. However, a new approach to analyze the genetic test results is needed to elucidate the Single Nucleotide Polymorphisms (SNPs) that are related to lactose intolerance. In this work, we utilized the machine learning based feature selection to select the SNPs associated with lactose tolerance trait from genotyping samples of direct-to-customer (DTCG genetic tests, obtained from the public database. Recursive Feature Elimination (RFE) with XGBoost model was used to perform feature selection. We also compared three different models, such as XGBoost, support vector machine (SVM), and random forest (RF) for training the selected features. Our findings revealed that 20 SNPs (out of 3501) were chosen, with rs4394668 as the most important variables (F-score 0.009). Furthermore, when compared to the RF and SVM models, the XGBoost model had the highest accuracy (0.87). Further studies should be undertaken to elucidate how the selected SNPs may lead to the lactose intolerance trait. © 2023 The Authors. Published by Elsevier B.V.

关键词： feature selection genetic test lactose intolerance SNP

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Data Mining and Bioinformatics Approaches to Elucidate Bacterial Communities in the Extreme Environment

Data Mining and Bioinformatics Approaches to Elucidate Bacte...

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2023 International Conference on Informatics, Multimedia, Cyber and Information Systems, ICIMCIS 2023

作者： Trinugroho, Joko Pebrianto Hidayat, Alam Ahmad Nirwantono, Rudi Asadi, Faisal Pardamean, Bens Bina Nusantara University Bioinformatics and Data Science Research Center Jakarta11480 Indonesia Bina Nusantara University School of Computer Science Bioinformatics and Data Science Research Center Mathematics Department Jakarta11480 Indonesia Bina Nusantara University Faculty of Engineering Bioinformatics and Data Science Research Center Biotechnology Department Jakarta11480 Indonesia Bina Nusantara University School of Computer Science Bioinformatics and Data Science Research Center Computer Science Department Jakarta11480 Indonesia Bina Nusantara University Binus Graduate Program Computer Science Computer Science Department Jakarta11480 Indonesia

ISBN: (纸本)9798350307306

Bacteria are microscopic organisms that can be found in many environments. They are abundant and have many roles in our life. Studying bacteria is essential so that we can identify the bacteria that are needed for many industrial applications. However, the main problem is that majority of the bacteria are unculturable, hampering the exploration of bacteria from different environments. Metagenomics approach which employs Next Generation Sequencing technology could help study bacteria by utilizing 16S rRNA marker gene. This study aims to demonstrate data mining and bioinformatics approaches to analyze 16S rRNA sequencing data. The raw sequencing data of 16S rRNA was collected from biological database. Then, the data were trimmed, denoised, and clustered to generate Amplicon Sequence Variants (ASVs). Diversity (alpha and beta) and taxonomic analyses were then conducted to elucidate the bacterial diversity and taxonomic profile of ASVs. The results of this work showed that Shannon and PD indices in China's hot spring were higher than Singapore and the USA. Furthermore, a significant difference was observed in the PD index. The unweighted UniFrac distance also showed there was a significant difference of the bacterial communities between the three locations. In addition, the taxonomic investigation unveiled prevalent bacterial groups in the ecosystem, namely Proteobacteria, Chloroflexi, Cyanobacteria, and Crenarchaeota. The research outcomes have the potential to serve as a foundational resource for subsequent bacterial metagenomic research, particularly the hot spring environment. © 2023 IEEE.

关键词： Bacteria

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