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

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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Systematic Literature Review of Transformer Model Implementations in Detecting Depression 6

Systematic Literature Review of Transformer Model Implementa...

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6th International Conference on Computer and Informatics Engineering, IC2IE 2023

作者： Nanggala, Kenjovan Pardamean, Bens Elwirehardja, Gregorius Natanael Bina Nusantara University Binus Graduate Program - Master of Computer Science Computer Science Department Jakarta Indonesia Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia

ISBN: (纸本)9798350345162

This systematic literature review explores the application of transformer models in early detection of human depression, encompassing text, audio, and video data modalities. Transformer architectures, notably BERT for text, have proven adept at capturing crucial contextual and linguistic patterns associated with depression. For audio and video data, hybrid approaches that combine transformer models with other architectures are prevalent. Key features considered include eye gaze, head pose, facial muscle movements, and audio characteristics such as MFCC and Log-mel Spectrogram, along with text embeddings. Performance comparisons underscore the superiority of text-based data in consistently delivering the most promising results, followed by audio and video modalities when utilizing transformer models. The fusion of multiple modalities emerges as an effective strategy for enhancing predictive accuracy, with the amalgamation of audio, video, and text data yielding the most precise outcomes. However, it is noteworthy that unimodal approaches also exhibit potential, with text data exhibiting superior performance over audio and video data. Nevertheless, several challenges persist in this research domain, including imbalanced datasets, the limited availability of comprehensive and diverse samples, and the inherent complexities in interpreting visual cues. Addressing these challenges remains imperative for the continued advancement of depression detection using transformer-based models across various modalities. © 2023 IEEE.

关键词： deep learning major depressive disorder multimodal transformer unimodal

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A Systematic Literature Review of CNN Approaches in Classifying Brain Tumor 6

A Systematic Literature Review of CNN Approaches in Classify...

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6th International Conference on Computer and Informatics Engineering, IC2IE 2023

作者： Paulindino, Aedentrisa Yasmanda Pardamean, Bens Elwirehardja, Gregorius Natanael Bina Nusantara University Binus Graduate Program - Master of Computer Science Computer Science Department Jakarta Indonesia Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia

ISBN: (纸本)9798350345162

The ability of Convolutional Neural Networks (CNNs) to accurately discriminate between normal and tumorous brain tissues has been promising. The review focuses on the different CNN models, pre-processing methods, data augmentation, and Transfer Learning (TL) strategies used in this research. This Systematic Literature Review (SLR) collected the data from Google Scholar. The results of this study indicate that open-source datasets from Kaggle and Brain MRI Images for Brain Tumor Detection are the most used datasets. However, limited data and imbalanced class problems remain common challenges across various datasets. To overcome those challenges, using a larger dataset, oversampling, Generative Adversarial Network (GAN), federated learning, and Self-Supervised Learning (SSL) to handle the imbalance are the potential solution. Additionally, popular CNN architectures for brain tumor classification extensively use pre-trained models such as VGG16, VGG19, DenseNet121, DenseNet201, GoogleNet, ResNet-50, and Inception-v3. TL strategies are preferred, allowing CNNs to leverage knowledge from large datasets, improving generalization even with limited labeled data. © 2023 IEEE.

关键词： brain tumor classification cnn mri pre-trained transfer learning

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A Systematic Literature Review of Deep Learning Application in Multiclass Anomaly Detection for Chest Medical Imaging 6

A Systematic Literature Review of Deep Learning Application ...

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6th International Conference on Computer and Informatics Engineering, IC2IE 2023

作者： Philips Pardamean, Bens Elwirehardja, Gregorius Natanael Isnan, Mahmud Bina Nusantara University Binus Graduate Program - Master of Compuer Science Computer Science Department Jakarta Indonesia Bina Nusantara University Bioinformatics and Data Science Research Center Jakarta Indonesia

ISBN: (纸本)9798350345162

Medical imaging abnormality detection is challenging, but deep learning approaches have shown promise. This paper reviews the current state of the art in deep learning approaches for detecting abnormalities in chest medical imaging. To discover the trends, opportunities, and challenges associated with this field, 18 studies were selected from Google Scholar based on their titles, abstracts, and contents for extensive review to answer two research questions. The study found that the National Institutes of Health (NIH) Chest X-ray 14 dataset is the most used dataset for this task. Most research uses a single-modal approach, considering only image data as input, with X-ray being the more popular instrument. There are 8 out of 18 studies leverage the transfer learning approach, with ResN et50 being the most popular network. MobileNetV2 has demonstrated competitive results compared to more robust networks. Preprocessing techniques such as image enhancement and data augmentation are leveraged by 61.1 % of the reviewed studies and are shown to improve model performance. © 2023 IEEE.

关键词： abnormality detection attention mechanisms chest x-ray CT images deep learning transfer learning

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Pap Smear Medical Image Classification Using Deep Learning: A Systematic Review 6

Pap Smear Medical Image Classification Using Deep Learning: ...

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6th International Conference on Computer and Informatics Engineering, IC2IE 2023

作者： Selvano, Elvan Elwiehardja, Gregorius Natanael Pardamean, Bens Bina Nusantara University Binus Graduate Program - Master of Computer Science Computer Science Department Jakarta Indonesia Bina Nusantara University Bioinformatics and Data Science Research Center Jakarta Indonesia

ISBN: (纸本)9798350345162

Cervical cancer has been known as one of the most prevalent medical disorders globally and a leading cause of death. Early detection, particularly through Pap tests, plays a vital role in its prevention. Previous studies have leveraged machine learning and deep learning techniques to classify the medical images obtained from Pap tests. In this study, a Systematic Literature Review methodology was used to examine 15 relevant papers that have been filtered from queries to Google Scholar which have gone through 4 stages of filtering that include: identification, screening, eligibility, and inclusion. This study addresses two research questions regarding the datasets and deep learning techniques for classifying pap smear images in recent years. The performance of the models was analyzed and potential areas for improvements are suggested. The findings of this study reveal that the Herlev University Hospital and SIPaKMed datasets are the most used. The methodologies used by researchers range from machine learning techniques, transfer learning using Convolutional Neural Networks, and utilize state-of-the-art models with novel optimizing methodology. While there are exciting opportunities in the field, challenges include model generalization and interpretability. © 2023 IEEE.

关键词： cervical cancer deep learning machine learning pap test

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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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ConvNeXt Model for Breast Cancer Image Classification 6

ConvNeXt Model for Breast Cancer Image Classification

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

作者： Setiawan, Devin Karnyoto, Andrea Stevens Intan, Indo Pardamean, Bens Department of Electrical Engineering and Computer Science University of Kansas Lawrence United States Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia Department of Informatics Engineering Universitas Dipa Makassar Makassar Indonesia Computer Science Department BINUS Graduate Program Computer Science Program Bina Nusantara University Jakarta Indonesia

ISBN: (纸本)9798331539603

Breast cancer is an occurrence of cancer that attacks breast tissue and is the most common cancer among women worldwide, affecting one in eight women. In this modern world, breast cancer image classification simplifies the process of analyzing, providing objective and accurate results. By leveraging machine learning algorithms and computer vision techniques, we developed breast cancer detection. The dataset is histopathology dataset from BreakHis and UNHAS Hospital. We chose the ConvNeXt-Tiny model then modified the classifier head as the proposed method. Before the dataset is processed by the model, we augment the images by applying random horizontal and vertical flips, adjustments to brightness, contrast, saturation, and hue using color jitter. The augmentation process simulates real-world variance and enhances the model's ability to generalize to unseen data. Our proposed model gained better performance (accuracy, F1-Score) results compared two other techniques to VGG16 and SVM. According to our experiments, the F1-Score for the ConvNeXt-Tiny model with classifier head modification is higher at 0.9516, than the gain for VGG16 at 0.9292, and the gain for the SVM at 0.83. © 2024 IEEE.

关键词： Lung cancer

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Variational quantum neural network with optimized ansatz for predicting malignant ventricular arrhythmias

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Procedia Computer Science 2024年 245卷 109-116页

作者： Nicholas Dominic Bens Pardamean Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta 11480 Indonesia Computer Science Department BINUS Graduate Program – Master of Computer Science Program Bina Nusantara University Jakarta 11480 Indonesia

Preventive strategies should be the utmost priority when dealing with diverse patients suffering from malignant ventricular arrhythmia (MVA) that can lead to sudden cardiac death (SCD). Electrocardiogram (ECG) data is commonly used as a predictor for MVA predictive models. In this study, all ECG signals from MIT-BIH databases were fragmented into five-minute durations with a frequency sampling of 128 Hz. To solve the absence of hybrid optimizations in Machine Learning (ML) models, a novel Variational Quantum Neural Network (VQNN) was invented. Empowered by deep learning capabilities and optimized quantum circuits design, VQNN achieved remarkable performances designated by an accuracy of up to 95.1%, a perfect 100% recall, and a 95.2% score of the area under the Receiver Operating Characteristic curve (AUC ROC) with Conjugate Gradient as an optimizer and EfficientSU2 as a quantum ansatz. Despite the susceptibility to quantum noise, this research settles a new trajectory of utilizing quantum variational algorithms to predict and expand its applicability for MVA cases.

关键词： Malignant Ventricular Arrhythmia Sudden Cardiac Death Variational Quantum Algorithm Quantum Computing Neural Network

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Comparison of K-Nearest Neighbor and Support Vector Regression for Predicting Oil Palm Yield 1

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

作者： Pardamean, Bens Suparyanto, Teddy Sinaga, Gokma Sahat Tua Elwirehardja, Gregorius Natanael Firmansyah, Erick Ginting, Candra Mawandha, Hangger Gahara Putra, Dian Pratama Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta11480 Indonesia Computer Science Department BINUS Graduate Program—Master of Computer Science Program Bina Nusantara University Jakarta11480 Indonesia Faculty of Agriculture Institute of Agriculture STIPER Yogyakarta55282 Indonesia

ISBN: (数字)9783031290787

ISBN: (纸本)9783031290770

With the high demand for oil palm production, implementations of Machine Learning (ML) technologies to provide accurate predictions and recommendations to assist oil palm plantation management tasks have become beneficial, such as in predicting annual oil palm. However, different geographical and meteorological conditions may result in different scales of influence for each variable. In this research, K-Nearest Neighbors (KNN) and Support Vector Regression (SVR) were used in predicting oil palm yield based on data collected in Riau, Indonesia. Pearson’s correlation coefficient was also calculated in selecting the input features for the models, whereas normalization and standardization were used in scaling the data. By setting the minimum absolute correlation threshold to 0.1 and using standardization, both models managed to obtain more than 0.81 R2, with SVR obtaining the overall best performance with 0.8709 R2, 1.372 MAE, and 1.8025 RMSE without hyperparameter fine-tuning. It was also discovered that the oil palm yield in the previous year is the variable with the most influence in estimating oil palm yield in the current year, followed by the number of plants and soil types. © The Author(s), under exclusive license to Springer Nature Switzerland AG 2023.

关键词： Machine learning

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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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