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

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

ISBN: (纸本)9798350307306

The infection of Plasmodium vivax is relatively less virulent than the deathliest Plasmodium falciparum. However, it still can lead to a fatal case and often induces recurring malaria due to dormant parasites in the liver. Thus, the research to study the drug to treat Plasmodium vivax is essential, where the enzyme dihydroorotate dehydrogenase (DHODH) has recently become a new drug target. However, the drug-enzyme interaction study has only recently been conducted in Plasmodium falciparum (pfDHODH) due to the lack of the 3D structure of enzyme DHODH from Plasmodium vivax that is crucial for the study. Therefore, this study aimed to perform the modelling study of Plasmodium vivax DHODH (PvDHODH) to create a 3D structure as a basis for drug-protein interaction study in upcoming studies. Sequence pvDHODH (Accession: SCO68359.1) was used in homology modelling using Modeller 10.2 with the crystal structure of DHODH from DHODH (Accession: 7KZY) as a template. Overall, the model generated from the homology modelling was considered a good model, and the 3D structure was close to the native state according to several parameters, including DOPE score, GA341 score, QMEAN4 value, 3D-1D score, ERRAT2 score, and ProSA score. Ramachandran plot also revealed that almost all amino acids were distributed in the desirable and allowed area (99.1%), and only 0.9% were in generously allowed regions. Superimposition of the model with the template also indicated that the model has an almost similar structure and amino acids positioning, including in the binding pocket and active site. Therefore, the model can be used for downstream analysis in drug-protein interaction studies. Nevertheless, some improvements can still be performed to upgrade the quality of the model by deleting unaligned residues on the C-terminal and realigning the residues at the doubting site. © 2023 IEEE.

关键词： Amino acids

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Mobile applications for skin cancer detection are vulnerable to physical camera-based adversarial attacks

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Scientific reports 2025年第1期15卷 18119页

作者： Junsei Oda Kazuhiro Takemoto Department of Bioscience and Bioinformatics Kyushu Institute of Technology Iizuka Fukuoka Japan. Department of Bioscience and Bioinformatics Kyushu Institute of Technology Iizuka Fukuoka Japan. takemoto@bio.kyutech.ac.jp. Data Science and AI Research Center Kyushu Institute of Technology Iizuka Fukuoka Japan. takemoto@bio.kyutech.ac.jp.

Skin cancer is one of the most prevalent malignant tumors, and early detection is crucial for patient prognosis, leading to the development of mobile applications as screening tools. Recent advances in deep neural networks (DNNs) have accelerated the deployment of DNN-based applications for automated skin cancer detection. While DNNs have demonstrated remarkable capabilities, they are known to be vulnerable to adversarial attacks, where carefully crafted perturbations can manipulate model predictions. The vulnerability of deployed medical mobile applications to such attacks remains largely unexplored under real-world conditions. Here, we investigate the susceptibility of three DNN-based medical mobile applications to physical adversarial attacks using transparent camera stickers under black-box conditions where internal model architectures are inaccessible. Through digital experiments with various DNN architectures trained on a publicly available skin lesion dataset, we first demonstrate that camera-based adversarial patterns can achieve high transferability across different models. Using these findings, we implement physical attacks by attaching optimized transparent stickers to mobile device cameras. Our results show that these attacks successfully manipulate application predictions, particularly for melanoma images, with attack success rates reaching 50-80% across all applications while maintaining visual imperceptibility. Notably, melanoma images showed consistently higher vulnerability compared to nevus images across all tested applications. To the best of our knowledge, this is the first demonstration of real-world adversarial vulnerabilities in deployed medical mobile applications, revealing significant security concerns where prediction manipulation could affect diagnostic processes. Our study demonstrates the importance of security evaluation in deploying such applications in clinical settings.

关键词： Adversarial attacks Deep neural networks Medical imaging Security and privacy

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Mapping Emergency Medicine data to the Observational Medical Outcomes Partnership Common data Model: A Gap Analysis of the American College of Emergency Physicians Clinical Emergency data Registry

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JACEP Open 2025年第1期6卷 100016-100016页

作者： Cohen, Inessa Diao, Zihan Goyal, Pawan Gupta, Aarti Hawk, Kathryn Malcom, Bill Malicki, Caitlin Sharma, Dhruv Sweeney, Brian Weiner, Scott G. Venkatesh, Arjun Taylor, R. Andrew Department of Emergency Medicine Yale School of Medicine New Haven CT United States Section for Biomedical Informatics and Data Science Yale University School of Medicine New Haven CT United States Program of Computational Biology and Bioinformatics Yale University New Haven CT United States American College of Emergency Physicians Washington DC United States Department of Emergency Medicine Brigham and Women's Hospital Boston MA United States Center for Outcomes Research and Evaluation (CORE) Section of Cardiovascular Medicine Yale School of Medicine New Haven CT United States

Objectives: This study aims to conduct a gap analysis to determine the feasibility of mapping electronic health record data from the Clinical Emergency data Registry (CEDR) to the Observational Medical Outcomes Partnership Common data Model (OMOP-CDM). Methods: We employed a structured approach using a custom-built comparison matrix. This matrix facilitated the alignment of CEDR data fields with the corresponding elements in the OMOP-CDM schema. Each field was evaluated for compatibility, with categorization into 3 distinct types: direct matches, fields requiring transformation, and fields with no OMOP-CDM equivalent. The mapping process was informed by consultations with the Observational Health data sciences and Informatics community forums and was guided by existing documentation and best practices in data harmonization. We performed descriptive analyses, quantifying the extent of direct matches and identifying the specific transformations needed for each CEDR-CDM field to ensure compliance with the OMOP-CDM model. Results: Our analysis indicates a high degree of compatibility between CEDR and OMOP, with over 90% (244/269) of CEDR fields being successfully mapped. Specifically, 173 fields had direct matches, whereas 71 required transformations. Challenges identified include addressing fields unique to CEDR with no OMOP-CDM equivalent and managing the transformations required for proper alignment. Conclusion: The OMOP-CDM presents a promising framework for standardizing emergency medicine data, thereby enhancing future query automation, analytics, and cross-institutional collaboration. Despite the potential challenges in capturing unique CEDR fields and addressing necessary transformations, most emergency department data can be standardized within the OMOP-CDM, fostering broader insights and applications in research and public health. © 2024 The Author(s)

关键词： databases electronic health records emergency service informatics opioid/adverse effects quality of health care registries

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Effects of sickle trait on maternal and perinatal outcomes among pregnant women

Blood Vessels, Thrombosis & Hemostasis

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Blood Vessels, Thrombosis & Hemostasis 2025年第2期2卷 100049-100049页

作者： Sarah Sewaralthahab Jiling Chou Stephen Fernandez Nawar Shara Hedy P. Smith Department of Medicine College of Medicine King Saud University Riyadh Saudi Arabia Division of Hematology Oncology Center King Saud University Medical City Riyadh Saudi Arabia Department of Biostatistics Bioinformatics and Biomathematics Center of Biostatistics Informatics and Data Science Medstar Research Institute Hyattsville MD Depatment of Internal Medicine Medstar Washington Hospital Center Washington DC

Abstract The risk of multiple adverse pregnancy outcomes and perinatal outcomes among pregnant women with sickle cell trait (SCT) is not known. Our objective was to compare differences in adverse outcomes, specifically pregnancy-related hypertensive disease (PRHD), pyelonephritis/urinary tract infection (UTI), and low birth weight (LBW), between pregnant women with SCT and healthy controls. This was a retrospective cohort study of women who delivered between 2015 and 2020. We included all women with SCT, that is, hemoglobin electrophoresis AS. Women with SCT were matched in a 1:2 to women without SCT, controlling for age, gravidity, and parity. Our primary outcomes were PRHD, pyelonephritis/UTI, and LBW baby. Multivariable logistic regression modeling examined the associations between patients’ characteristics and the primary *** were 162 women with SCT, and 324 healthy control women were enrolled. Bivariate analysis revealed that women with SCT had a higher proportion of PRHD (38.9% vs 34.9%; P = .39), pyelonephritis/UTI (11.7% vs 7.1%; P = .09), but a lower proportion of LBW (10.5% vs 16.0%; P = .1). In multivariable analysis, after controlling for confounders, SCT was not an independent predictor of PRHD. However, SCT was an independent predictor of pyelonephritis/UTI (adjusted odds ratio [aOR], 1.98; 95% confidence interval [CI], 1.02-3.85) and of a lower risk of having a LBW baby (aOR, 0.48; 95% CI, 0.25-0.94). SCT is not associated with an increased risk of PRHD. However, SCT is associated with pregnancy outcomes, including higher risk of pyelonephritis/UTI but a lower risk of LBW babies.

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Organoid morphology-guided classification for oral cancer reveals prognosis

Cell Reports Medicine

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Cell Reports Medicine 2025年第5期6卷 102129-102129页

作者： Lee, Mi Rim Kang, Sumin Lee, Jonghyun Kong, Sun-Young Kim, Youngwook Lee, Yu-Sun Shon, Hye Won Kang, Gyeongmin Lee, Jiyoung Youn, Suk Min Kwack, Da Woon Park, Joo Yong Kim, Soung Min Choi, Wonyoung Lee, Jong-Ho Shin, Dongkwan Kwon, Ik-Jae Choi, Sung-Woen Kim, Yun-Hee Molecular Imaging Branch Division of Convergence Technology Research Institute of National Cancer Center 323 Ilsan-ro Ilsandong-gu Gyeonggi-do Goyang 10408 South Korea Department of Cancer Biomedical Science National Cancer Center Graduate School of Cancer Science and Policy 323 Ilsan-ro Ilsandong-gu Gyeonggi-do Goyang 10408 South Korea Bioinformatics Branch Division of Cancer Data Science Research Institute of National Cancer Center 323 Ilsan-ro Ilsandong-gu Gyeonggi-do Goyang 10408 South Korea Targeted Therapy Branch Division of Rare and Refractory Cancer Research Institute of National Cancer Center 323 Ilsan-ro Ilsandong-gu Gyeonggi-do Goyang 10408 South Korea Department of Laboratory Medicine National Cancer Center 323 Ilsan-ro Ilsandong-gu Gyeonggi-do Goyang 10408 South Korea Oral Oncology Clinic Research Institute and Hospital National Cancer Center 323 Ilsan-ro Ilsandong-gu Gyeonggi-do Goyang 10408 South Korea Department of Oral and Maxillofacial Surgery Seoul National University Dental Hospital Dental Research Institute School of Dentistry Seoul National University 101 Daehak-ro Jongno-gu Seoul 03080 South Korea Center for Clinical Trials Research Institute and Hospital National Cancer Center 323 Ilsan-ro Ilsandong-gu Gyeonggi-do Goyang 10408 South Korea Cancer Molecular Biology Branch Division of Cancer Biology Research Institute of National Cancer Center 323 Ilsan-ro Ilsandong-gu Gyeonggi-do Goyang 10408 South Korea Rare & Pediatric Cancer Branch Division of Rare and Refractory Cancer Research Institute of National Cancer Center 323 Ilsan-ro Ilsandong-gu Gyeonggi-do Goyang 10408 South Korea

Oral cancer is an aggressive malignancy with a survival rate below 50% in advanced stages due to low mutation rates, lack of molecular subtypes, and limited treatment targets. This study presents a pioneering approach to classifying oral cancer subtypes based on the morphology of patient-derived organoids (PDOs) and proposes a therapeutic strategy. We establish 76 cancer and 81 normal PDOs. For cancer PDOs, both manual classification and AI-based scoring are utilized to categorize them into three distinct subtypes: normal-like, dense, and grape-like. These subtypes correlate with unique transcriptomic profiles, genetic mutations, and clinical outcomes, with patients harboring dense and grape-like organoids exhibiting poorer prognoses. Furthermore, drug response assessments of 14 single agents and cisplatin combination therapies identify a synergistic treatment approach for resistant subtypes. This study highlights the potential of integrating morphology-based classification with genomic and transcriptomic analyses to refine oral cancer subtyping and develop effective treatment strategies. © 2025 The Author(s)

关键词： combination therapy morphology analysis oral cancer organoids

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Deep learning for oil palm fruit ripeness classification with densenet 6

Deep learning for oil palm fruit ripeness classification wit...

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6th International Conference on Information Management and Technology, ICIMTech 2021

作者： Herman, Herman Cenggoro, Tjeng Wawan Susanto, Albert Pardamean, Bens Bina Nusantara University BINUS Graduate Program - Master of Computer Science Computer Science 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 - Master of Computer Science Program Bioinformatics and Data Science Research Center Computer Science Department Jakarta11480 Indonesia

ISBN: (纸本)9781665449373

Oil palm fruit farming is one of the most leading agriculture industries in the South East Asia region. Unfortunately, most of the harvesting method is still done through manual labor. Multiple research has been conducted to help farmers automatically detect the ripeness level of the oil palm fruit. We conducted an experiment of detecting the ripeness level of oil palm fruit by using one of the state-of-the-art computer vision approaches, which was deep learning with a Convolutional Neural Network (CNN). The dataset used consists of 7 levels of ripeness with 400 images of oil palm fruits. The models used in this test scenario were both AlexNet and DenseNet. The result of this study showed that DenseNet has been proven to outperform AlexNet by 8.5% in terms of accuracy and 8% in F1 score. © 2021 IEEE.

关键词： Computer vision

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Comprehensive Analysis of Ubiquitously Expressed Genes in Humans from A data-driven Perspective

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Genomics, Proteomics & bioinformatics 2023年第1期21卷 164-176页

作者： Jianlei Gu Jiawei Dai Hui Lu Hongyu Zhao SJTU-Yale Joint Center for Biostatistics and Data Science Department of Bioinformatics and BiostatisticsSchool of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghai 200240China Center for Biomedical Informatics Shanghai Engineering Research Center for Big Data in Pediatric Precision MedicineShanghai Children’s HospitalShanghai 200040China Department of Biostatistics Yale UniversityNew HavenCT 06511USA

Comprehensive characterization of spatial and temporal gene expression patterns in humans is critical for uncovering the regulatory codes of the human genome and understanding the molecular mechanisms of human *** expressed genes(UEGs)refer to the genes expressed across a majority of,if not all,phenotypic and physiological conditions of an *** is known that many human genes are broadly expressed across ***,most previous UEG studies have only focused on providing a list of UEGs without capturing their global expression patterns,thus limiting the potential use of UEG *** this study,we proposed a novel data-driven framework to leverage the extensive collection of40,000 human transcriptomes to derive a list of UEGs and their corresponding global expression patterns,which offers a valuable resource to further characterize human *** results suggest that about half(12,234;49.01%)of the human genes are expressed in at least 80%of human transcriptomes,and the median size of the human transcriptome is 16,342 genes(65.44%).Through gene clustering,we identified a set of UEGs,named LoVarUEGs,which have stable expression across human transcriptomes and can be used as internal reference genes for expression *** further demonstrate the usefulness of this resource,we evaluated the global expression patterns for 16 previously predicted disallowed genes in islet beta cells and found that seven of these genes showed relatively more varied expression patterns,suggesting that the repression of these genes may not be unique to islet beta cells.

关键词： Ubiquitous expression Housekeeping gene Disallowed gene Expression specificity Expression variability

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Leveraging user-item interactions and hotel characteristics for hotel recommendations in Indonesia with graph neural networks 9th

Leveraging user-item interactions and hotel characteristics ...

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9th International Conference on Computer science and Computational Intelligence, ICCSCI 2024

作者： Panarto, Francis Alexander Phanghegar, Tyrone Matthew Gunardi, Vincent Cenggoro, Tjeng Wawan Computer Science Department School of Computer Science Bina Nusantara University Jakarta11480 Indonesia Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta11480 Indonesia

Travelers usually check information about the destination before they decide to go. However, sometimes the information is too much to handle and causes confusion. A filtering mechanism is needed to help them make their choices. The solution is to implement a recommendation system;some common techniques that are used for this are Collaborative Filtering and content-based filtering, but both techniques have their flaws. Therefore, we propose a solution to combine those two methods through Graph Neural Network architectures to help fix their flaws. The proposed method will be used for recommending hotels in Indonesia using the HotelRec dataset as the base dataset and hotel features acquired from the TripAdvisor API. We use several GNN architectures, such as GCN, LightGCN, GraphSAGE, and GAT, to implement our approach. Then, we compare it to several baseline models, such as SVD and NeuMF, which are common baselines in recommendation systems. The performance of these models is calculated based on three metrics: HitRate@K, NDCG@K, and Recall@K. Based on the result of this experiment, we found that incorporating hotel features into the learning process of the model, accompanied by user-item interactions, boosted the model's performance by at least 20% in all metrics, especially in datasets with a smaller number of interactions. © 2024 The Authors.

关键词： Collaborative filtering

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Deep Learning for Imbalance data Classification using Class Expert Generative Adversarial Network 3

Deep Learning for Imbalance Data Classification using Class ...

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3rd International Conference on Computer science and Computational Intelligence, ICCSCI 2018

作者： Fanny Cenggoro, Tjeng Wawan Computer Science Department School of Computer Science Bina Nusantara University Jakarta11480 Indonesia Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta11480 Indonesia

Without any specific way for imbalance data classification, artificial intelligence algorithm cannot recognize data from minority classes easily. In general, modifying the existing algorithm by assuming that the training data is imbalanced, is the only way to handle imbalance data. However, for a normal data handling, this way mostly produces a deficient result. In this research, we propose a class expert generative adversarial network (CE-GAN) as the solution for imbalance data classification. CE-GAN is a modification in deep learning algorithm architecture that does not have an assumption that the training data is imbalance data. Moreover, CE-GAN is designed to identify more detail about the character of each class before classification step. CE-GAN has been proved in this research to give a good performance for imbalance data classification. © 2018 The Authors. Published by Elsevier Ltd.

关键词： Generative adversarial networks

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On the Measurement of the Inductive Bias Impact in Convolutional Neural Networks Training for Single Image Super-Resolution 8

On the Measurement of the Inductive Bias Impact in Convoluti...

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

作者： Kwantawijaya, Aldrian Najoan, Daniel Stephanus Tamimmanar Cenggoro, Tjeng Wawan Computer Science Department School of Computer Science Bina Nusantara University Jakarta11480 Indonesia Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta11480 Indonesia

The performance of SISR models is currently growing at a rapid pace since the adoption of Convolutional Neural Networks (CNN) in the domain. Despite that, the understanding of the underlying factors of this rapid growth is still low. In this study, we proposed a study design to measure the impact of the inductive bias in CNN on its training performance, which is one of the factors of the excellent performance of CNN in SISR. With this study design, we observed that not all CNN has a supportive inductive bias to the training performance. This result can provide guidance to future research in choosing a suitable CNN architecture for optimal SISR performance. © 2023 The Authors. Published by Elsevier B.V.

关键词： Convolutional Neural Networks Deep Learning Inductive Bias Single-Image Super Resolution

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