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An Exploratory Computational Approach for Elucidating a Nonstructural Protein Interaction in Dengue Virus 2

Procedia Computer science 2024年 245卷 470-479页

作者： Alam Ahmad Hidayat Rudi Nirwantono Bens Pardamean Mathematics Department School of Computer Science Bina Nusantara University Indonesia 11480 Biotechnology Department Faculty of Engineering Bina Nusantara University Indonesia 11480 Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia 11480 Computer Science Department BINUS Graduate Program Bina Nusantara University Jakarta Indonesia 11480

As the dengue infection still impacts hundreds of millions of people globally, unprecedented efforts in dengue drug development have been more progressive in recent decades. Computational methods provide a fast, sustainable, and efficient screening of active compounds and newly created drug molecules, including those specifically targeting nonstructural proteins (NS) of dengue viruses. In this work, protein modeling for the NS proteins of DENV-2/16681 strain was performed using a template-based homology modeling for the NS3 protein and an Artificial Intelligence (AI)-based prediction via AlphaFold for the NS4B protein. Moreover, the protein-protein interaction between the two structures was predicted using the HADDOCK server, which employs information about active and passive residues of the interaction interface to guide the docking process. After the modeling and its respective refinement process, the predicted structures of NS3 and NS4B improved their steric clashing scoring from MolProbity assessment. The refined models were then docked, and the resulting docking pose was analyzed to extract the interacting residues based on the polar contacts within the interface of the two proteins. Our result presents a preliminary study to create a dataset related to in silico molecular interactions of the NS3-NS4B interaction of different DENV types. It is helpful for building a computational pipeline for elucidating protein-ligand problems in dengue drug screenings.

关键词： bioinformatics computational biology dengue protein docking structural biology

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Cancer Prediction Using Clinical and Genomic data Fusion: A Systematic Review

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

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International Conference on Cybernetics and Intelligent System (ICORIS)

作者： Kelvin Julian Kuncahyo Setyo Nugroho Rudi Nirwantono Bens Pardamean Computer Science Department BINUS Graduate Program - Master of Computer Science 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: (数字)9798331539603

ISBN: (纸本)9798331539610

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.

关键词： Accuracy Machine learning algorithms Genomics data integration Medical services Predictive models data models Bioinformatics Cancer Systematic literature review

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Enhanced Performance and data Privacy in Lung Nodule Classification via Federated Deep Learning Approach 24

Enhanced Performance and Data Privacy in Lung Nodule Classif...

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2024 7th International Conference on Healthcare Service Management, ICHSM 2024

作者： Nguyen, Duc-Khanh Li, Ai-Hsien Adam Lai, Yen-Jun Chiu, Yen-Ling Phan, Dinh-Van Chien, Ting-Ying Chan, Chien-Lung Department of Information Management Yuan Ze University Taoyuan Taiwan Department of Statistics and Informatics University of Economics The University of Danang Danang Viet Nam Division of Cardiology Far Eastern Memorial Hospital New Taipei Taiwan Graduate Program in Biomedical Informatics Yuan Ze University Taoyuan Taiwan Department of Radiology Far Eastern Memorial Hospital New Taipei Taiwan Graduate Institute of Medicine and Graduate Program in Biomedical Informatics Yuan Ze University Taoyuan Taiwan Department of Medical Research Far Eastern Memorial Hospital New Taipei Taiwan Department of Computer Science and Engineering Yuan Ze University Taoyuan Taiwan ZDT Group- YZU Joint Research and Development Center for Big Data Taoyuan Taiwan Yuan Ze University Taoyuan Taiwan

ISBN: (纸本)9798400710162

This study explores the feasibility of deep learning for classifying nodule neoplasms, analyzing their performance on two openly available datasets, LUNGx SPIE, and LIDC-IDRI. These datasets offer valuable diversity in image quantity, quality, and malignancy annotation methodologies, posing a real-world challenge for effective model development. To handle the disparities in these diverse datasets, we aim to develop a robust classification model trained using federated learning. This decentralized approach allows model training across datasets without sharing patient data, preserving privacy and overcoming data fragmentation. Our experiments demonstrate that federated learning enables the development of a robust and superior deep learning model compared to individual models trained on limited data. This combination of deep learning, and federated learning holds immense promise for nodule neoplasm classification and can significantly improve patient care and outcomes. © 2024 Copyright held by the owner/author(s).

关键词： Federated learning

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Development of Automated Detection Methods for Calculating Blood Vessel Width and Stenosis Rate in Cardiac Catheterization Imaging 24

Development of Automated Detection Methods for Calculating B...

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8th International Conference on Medical and Health Informatics, ICMHI 2024

作者： Huang, Hsien-Cheng Chang, Hsiao-Huang Ke, Xiang-Wei Chien, Ting-Ying Department of Computer Science and Engineering Yuan Ze University Taoyuan City Taiwan Cardiovascular Surgery Department Taipei Veterans General Hospital Taipei City Taiwan Taipei Medical University Taipei City Taiwan Graduate Program in Biomedical Informatics Yuan Ze University Taoyuan City Taiwan Innovation Center for Big Data and Digital Convergence Yuan Ze University Taoyuan City Taiwan

ISBN: (纸本)9798400716874

Coronary artery disease is the most prevalent type of heart disease and has a considerable mortality rate. In diagnosing and assessing coronary artery disease, physicians must integrate a variety of clinical information and test results to evaluate the degree of coronary artery obstruction and continually learn and improve their skills in clinical practice to ensure the most accurate assessment of patients. Currently, the use of information technology to assist medical staff allows more effective and accurate analysis of symptoms. This approach not only serves as an auxiliary standard for physician diagnosis, thereby reducing the possibility of misdiagnosis, but also significantly improves patient treatment outcomes and medical quality while reducing the time burden on physicians for diagnosing patients. This study utilized image processing techniques and thinning algorithms to automate the detection of coronary artery width and, following the recommended methods of physicians in related fields, used specific vessel widths to calculate the degree of coronary artery narrowing. This provides a more accurate and efficient assessment method for evaluating the degree of vascular constriction in patients with coronary artery disease. © 2024 Copyright ACM.

关键词： Patient treatment

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Lung Nodule Analysis in CT Images: Deep Learning for Segmentation and Measurement 24

Lung Nodule Analysis in CT Images: Deep Learning for Segment...

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8th International Conference on Medical and Health Informatics, ICMHI 2024

作者： Li, Ai-Hsien Adams Aruperes, Cristian Daniel Lai, Yen-Jun Chien, Ting-Ying Chiu, Yen-Ling Chan, Chien-Lung Division of Cardiology Far Eastern Memorial Hospital New Taipei TaiwanGraduate Program in Biomedical Informatics Yuan Ze University Taoyuan Taiwan Graduate Program in Biomedical Informatics Yuan Ze University Taoyuan Taiwan TaiwanDepartment of Computer Science and Engineering Yuan Ze University Taoyuan Taiwan TaiwanInnovation Center for Big Data and Digital Convergence Yuan Ze University Taoyuan Taiwan Department of Information Management Yuan Ze University Taoyuan Taiwan Graduate Institute of Medicine and Graduate Program in Biomedical Informatics Yuan Ze University Taoyuan Taiwan TaiwanGraduate Institute of Medicine Yuan Ze University Taoyuan Taiwan TaiwanDepartment of Medical Research Far Eastern Memorial Hospital New Taipei Taiwan Department of Radiology Far Eastern Memorial Hospital New Taipei Taiwan Department of Information Management Yuan Ze University Taoyuan Taiwan

ISBN: (纸本)9798400716874

In the realm of research, the global health challenge posed by lung cancer remains pronounced, contributing substantially to annual cancer-related fatalities. The critical imperative lies in the early identification of pulmonary nodules, frequently indicative of impending lung cancer, to enhance patient outcomes and diminish mortality rates. Computed Tomography (CT) imaging stands out as a pivotal diagnostic instrument for the timely detection of these nodules. The swift proliferation of medical imaging data has underscored the pressing necessity for precise and efficient methodologies dedicated to nodule segmentation and measurement. These approaches are crucial in assisting radiologists in their diagnostic and clinical decision-making endeavors. In this study, we introduced a thorough method for analyzing lung nodules, leveraging dataset from Far Eastern Memorial Hospital (FEMH) comprising original CT images and manually annotated ground truth masks obtained with the assistance of radiologists at FEMH. This dataset is utilized for the segmentation of nodules. We employed advanced deep learning models, specifically the U-Net architecture, identified as the optimal model through our training process. We made substantial progress in nodule segmentation, attaining an Intersection over Union (IoU) score of 0.824 and a Dice Coefficient of 0.903 for the FEMH dataset. Furthermore, our performance improved when utilizing the merged dataset comprising FEMH and Luna16, yielding an IoU score of 0.862 and a Dice Coefficient of 0.926. Luna16 has been extensively utilized in numerous studies related to nodule detection and segmentation. In the next phase of the study, the best-performing model from our segmentation phase was utilized to predict nodule masks on the merged dataset. Subsequently, we measured the size of each predicted nodule by comparing it with the size ground truth mask in millimeters. In detail, this study achieved the Pearson Correlation Coefficient (PCC) at 0.

关键词： Computerized tomography

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Consideration of Constructing a Weed Detection Method for an Agricultural Robot in Perilla Fields

Consideration of Constructing a Weed Detection Method for an...

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International Conference on Machine Learning and Cybernetics (ICMLC)

作者： Tatsuya Sugie Noboru Takagi Tatsuo Motoyoshi Kei Sawai Hiroyuki Masuta Graduate School of Intelligent Robotics Program Toyama Prefectural University Toyama Japan Department of Data Science Toyama Prefectural University Toyama Japan Department of Intelligent Robotics Toyama Prefectural University Toyama Japan

ISBN: (数字)9798331528041

ISBN: (纸本)9798331528058

In recent years, the number of farmers in Japan has been decreasing, and the automation of agriculture using robots, AI, and IoT, known as “smart agriculture,” is being promoted. In this context, Toyama city is promoting a project to build a robot for automatic weeding between plants in a perilla fields. In this research, we are in charge of the system part that detects weeding regions and informs the weeding mechanism. In the field, a wide variety of weeds form vegetation, and it is necessary to prevent food crops from being cut. Therefore, we detect crop regions and the rest of the area should be the weeding regions. In this study, we construct a system to detect crop regions by transfer learning the object detection model YOLO-v8, which is a convolutional neural network (CNN), and evaluate the system in terms of detection accuracy and processing speed.

关键词： Smart agriculture Accuracy Transfer learning Urban areas Crops Vegetation mapping Object detection Real-time systems Convolutional neural networks Object recognition

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Investigation of Robot's Eye Gaze Affecting Human Pedestrian Behavior by Robot in Virtual Space

Investigation of Robot's Eye Gaze Affecting Human Pedestrian...

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International Conference on Machine Learning and Cybernetics (ICMLC)

作者： RYO TAKATA YOTARO FUSE NOBORU TAKAGI BILGUUNMAA MYAGMARDULAM TATSUO MOTOYOSHI KEI SAWAI HIROYUKI MASUTA Graduate School of Intelligent Robotics Program Toyama Prefectural University Toyama Japan Department of Data Science Toyama Prefectural University Toyama Japan Department of Intelligent Robotics Toyama Prefectural University Toyama Japan

ISBN: (数字)9798331528041

ISBN: (纸本)9798331528058

We investigate the effects of robot's gaze on human behavior when a human and a robot pass each other in a virtual reality space (VR). Nonverbal communication, particularly eye contact, influences physical proximity between individuals in human-to-human interaction. Results of a study indicate that the robot's gaze affects the physical distance between a human and a robot in human-robot communication. Studies on robot's gaze tend to focus on experimental scenarios in which robots and humans communicate. However, robot's gaze in environments with interactions, such as crossing paths, has not been extensively investigated. Therefore, we hypothesize that the robot's gaze exhibits an influence on the physical distance between humans and robots during encounters. In our experiment, we compare three conditions: a robot with a rotating neck and gaze directed at the subject, a faceless robot with a rotating neck, and a faceless robot with a rotating neck and gaze directed at the subject. We analyze the subject's paths of movement and physical distance between the subjects and the robot. Results suggest that the hypothesis that “intimacy equilibrium model” works when humans and robot's cross paths in the VR environment is not supported.

关键词： Solid modeling Pedestrians Human-robot interaction Virtual reality Machine learning Neck Behavioral sciences Mobile robots Robots Cybernetics

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Sample Complexity of Kernel-Based Q-Learning

arXiv

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arXiv 2023年

作者： Yeh, Sing-Yuan Chang, Fu-Chieh Yueh, Chang-Wei Wu, Pei-Yuan Bernacchia, Alberto Vakili, Sattar MediaTek Research Graduate Program of Data Science National Taiwan University Academia Sinica Taiwan Graduate Institute of Communication Engineering National Taiwan University Taiwan Department of Electrical Engineering National Taiwan University Taiwan

Modern reinforcement learning (RL) often faces an enormous state-action space. Existing analytical results are typically for settings with a small number of state-actions, or simple models such as linearly modeled Q-functions. To derive statistically efficient RL policies handling large state-action spaces, with more general Q-functions, some recent works have considered nonlinear function approximation using kernel ridge regression. In this work, we derive sample complexities for kernel based Q-learning when a generative model exists. We propose a nonparametric Q-learning algorithm which finds an ǫ-optimal policy in an arbitrarily large scale discounted MDP. The sample complexity of the proposed algorithm is order optimal with respect to ǫ and the complexity of the kernel (in terms of its information gain). To the best of our knowledge, this is the first result showing a finite sample complexity under such a general model. © 2023, CC BY.

关键词： Reinforcement learning

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The largest genome-wide association study for breast cancer in Taiwanese Han population

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Breast Cancer Research and Treatment 2024年第2期203卷 291-306页

作者： Hsu, Yu-Ching Chen, Hung-Lin Cheng, Chi-Fung Chattopadhyay, Amrita Chen, Pei-Shan Lin, Che-Chen Chiang, Hsiu-Yin Liu, Ting-Yuan Huang, Chi-Hao Kuo, Chin-Chi Chuang, Eric Y. Lu, Tzu-Pin Tsai, Fuu-Jen Bioinformatics Program Taiwan International Graduate Program National Taiwan University Taipei Taiwan Bioinformatics Program Institute of Statistical Science Taiwan International Graduate Program Academia Sinica Taipei Taiwan Institute of Health Data Analytics and Statistics Department of Public Health College of Public Health National Taiwan University Taipei Taiwan Big Data Center China Medical University Hospital Taichung Taiwan Center for Translational Genomic Research Department of Medical Research China Medical University Hospital Taichung Taiwan Million-Person Precision Medicine Initiative Department of Medical Research China Medical University Hospital Taichung Taiwan Division of Breast Surgery Department of Surgery China Medical University Hospital Taichung Taiwan Division of Nephrology Department of Internal Medicine China Medical University Hospital Taichung Taiwan Department of Medical Research China Medical University Hospital Taichung Taiwan Bioinformatics and Biostatistics Core Center of Genomic and Precision Medicine National Taiwan University Taipei Taiwan Graduate Institute of Biomedical Electronics and Bioinformatics National Taiwan University Taipei Taiwan Biomedical Technology and Device Research Laboratories Industrial Technology Research Institute Hsinchu Taiwan Genetic Center Department of Medical Research China Medical University Hospital Taichung Taiwan

Purpose: Breast cancer is a molecularly heterogeneous disease, and multiple genetic variants contribute to its development and prognosis. Most of previous genome-wide association studies (GWASs) and polygenic risk scores (PRSs) analyses focused on studying breast cancers of Caucasian populations, which may not be applicable to other population. Therefore, we conducted the largest breast cancer cohort of Taiwanese population to fill in the knowledge gap. Methods: A total of 152,534 Participants recruited by China Medical University Hospital between 2003 and 2019 were filtered by several patient selection criteria and GWAS quality control steps, resulting in the inclusion of 2496 cases and 9984 controls for this study. We then conducted GWAS for all breast cancers and PRS analyses for all breast cancers and the four breast cancer subtypes, including luminal A, luminal B, basal-like, and HER2-enriched. Results: The GWAS analyses identified 113 SNPs, 50 of which were novel. The PRS models for all breast cancers and the luminal A subtype showed positively correlated trends between the PRS and the risk of developing breast cancer. The odds ratios (95% confidence intervals) for the groups with the highest PRS in all breast cancers and the luminal A subtype were 5.33 (3.79–7.66) and 3.55 (2.13–6.14), respectively. Conclusion: In summary, we explored the association of genetic variants with breast cancer in the largest Taiwanese cohort and developed two PRS models that can predict the risk of developing any breast cancer and the luminal A subtype in Taiwanese women. © 2023, The Author(s), under exclusive licence to Springer science+Business Media, LLC, part of Springer Nature.

关键词： Breast cancer Genome-wide association study Polygenic risk score Taiwanese population

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Society with Trust: A Scientometrics Review of Zero-Knowledge Proof Advanced Applications in Preserving Digital Privacy for Society 5.0 1

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International Conference on Innovative Technologies in Intelligent Systems and Industrial Applications, CITISIA 2022

作者： Dominic, Nicholas Pratama, Naufal Rizqi Cornelius, Kenny Senewe, Shavellin Herliman Pardamean, Bens Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta11480 Indonesia Information System Department School of Information Systems Bina Nusantara University Jakarta11480 Indonesia Department of Computer Science Universitas Multimedia Nusantara Tangerang15111 Indonesia Psychology Department Faculty of Humanities Bina Nusantara University Jakarta11480 Indonesia BINUS Graduate Program Bina Nusantara University Jakarta11480 Indonesia

ISBN: (数字)9783031290787

ISBN: (纸本)9783031290770

Society 5.0 focuses on human productivity in the midst of advanced technological services. While the concept has human trust at its core, technology development is now leading to zero-trust architecture. In this scientometrics review, 107 selected papers were analyzed to obtain the nature of the Zero-knowledge Proof (ZKP) theory and its advanced applications to favor digital privacy in greater society. With the common literature review strategy, it was found that the most citations in this field appeared in 2018, with IEEE, Springer, and Elsevier as the top three publishers. By affiliations, China and United States are both leading countries where the researcher comes from. And as the positive trend emerged, the ZKP mechanism will keep being leveraged as one of the cryptographic toolsets in the cloud services, Internet of Things (IoT), smart contracts, healthcare, electronic systems, and many other industrial needs. © The Author(s), under exclusive license to Springer Nature Switzerland AG 2023.

关键词： Smart contract

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