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

作者： Isnan, Mahmud Elwirehardja, Gregorius Natanael Pardamean, Bens Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta11480 Indonesia Computer Science Department School of Computer Science Bina Nusantara University Jakarta11480 Indonesia Cmputer Science Department BINUS Graduate Program Computer Science Program Bina Nusantara University Jakarta11480 Indonesia

When processing datasets in diabetes classification, common problems included a large number of missing values, outliers, and dataset imbalance. To deal with those issues, this study analyzed 18 studies on diabetes classification with machine learning algorithms over the past 5 years. This revealed the important role of data pre-processing in creating effective classification models, as it was found that by using different data pre-processing techniques, the same model can provide different performance. The study identified K-Nearest Neighbor (KNN) and support vector machine (SVM) as superior methods for filling in missing values, achieving an accuracy of 98.49% and 94.89%, respectively. These approaches outperformed traditional methods such as median or mean replacement. However, the challenge of imbalanced data sets remains in all studies reviewed. The common evaluation metrics used to evaluate the created models in previous studies included accuracy, precision, specificity, sensitivity/recall, and F1 Score. Overall, this review showed that the role of data pre-processing is no less important than algorithm selection to improve the performance of machine learning models in diabetes classification. © 2024 The Authors.

关键词： Adversarial machine learning

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SeqCP: A sequence-based algorithm for searching circularly permuted proteins

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Computational and Structural Biotechnology Journal 2023年 21卷 185-201页

作者： Chen, Chi-Chun Huang, Yu-Wei Huang, Hsuan-Cheng Lo, Wei-Cheng Lyu, Ping-Chiang Bioinformatics Program Institute of Information Science Taiwan International Graduate Program Academia Sinica Taipei115 Taiwan Institute of Bioinformatics and Structural Biology National Tsing Hua University Hsinchu300 Taiwan Institute of Bioinformatics and Systems Biology National Yang Ming Chiao Tung University Hsinchu300 Taiwan Institute of Biomedical Informatics National Yang Ming Chiao Tung University Taipei112 Taiwan Department of Biological Science and Technology National Yang Ming Chiao Tung University Hsinchu300 Taiwan The Center for Bioinformatics Research National Yang Ming Chiao Tung University Hsinchu Taiwan

Circular permutation (CP) is a protein sequence rearrangement in which the amino- and carboxyl-termini of a protein can be created in different positions along the imaginary circularized sequence. Circularly permutated proteins usually exhibit conserved three-dimensional structures and functions. By comparing the structures of circular permutants (CPMs), protein research and bioengineering applications can be approached in ways that are difficult to achieve by traditional mutagenesis. Most current CP detection algorithms depend on structural information. Because there is a vast number of proteins with unknown structures, many CP pairs may remain unidentified. An efficient sequence-based CP detector will help identify more CP pairs and advance many protein studies. For instance, some hypothetical proteins may have CPMs with known functions and structures that are informative for functional annotation, but existing structure-based CP search methods cannot be applied when those hypothetical proteins lack structural information. Despite the considerable potential for applications, sequence-based CP search methods have not been well developed. We present a sequence-based method, SeqCP, which analyzes normal and duplicated sequence alignments to identify CPMs and determine candidate CP sites for proteins. SeqCP was trained by data obtained from the Circular Permutation Database and tested with nonredundant datasets from the Protein Data Bank. It shows high reliability in CP identification and achieves an AUC of 0.9. SeqCP has been implemented into a web server available at: http://***/SeqCP/. © 2022 The Authors

关键词： Proteins

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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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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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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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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 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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Aggregating Structural Features for Computational Analysis of Mutations in BRCT Domains of BRCA1 Protein

Aggregating Structural Features for Computational Analysis o...

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

作者： Hidayat, Alam Ahmad Nirwantono, Rudi Isnan, Mahmud Trinugroho, Joko Pebrianto Pardamean, Bens 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 Bioinformatics and Data Science Research Center Jakarta11480 Indonesia Binus Graduate Program Bioinformatics and Data Science Research Center Computer Science Department Jakarta11480 Indonesia

ISBN: (纸本)9798350307306

Understanding the mechanistic interpretability of mutation effects in a protein can help predict the clinical implications of the genetic variants. Hence, computational variant effect predictions that involve protein structural features of the protein mutations might be suitable in this case. In this work, we focus on BRCT domains of BRCA1 gene that is widely studied in breast cancer studies. We retrieved 88 selected missense variants found in BRCT domains annotated in both ClinVar and gnomAD databases. To computationally characterize the pathogenic property of the mutations we used two types of features extracted from protein structures: a change in free Gibbs energy and a set of features derived from molecular dynamics simulations of each mutant. Using a dimensional reduction and Gaussian mixture model (GMM)-based clustering we demonstrate that the variants are segregated into two regions that may correspond to their pathogenic status. This method can be a potential computational pipeline for providing the preliminary mechanistic interpretation of mutation effects in terms of their thermodynamic and structural features. © 2023 IEEE.

关键词： Proteins

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Sentiment Analysis: Indonesia Netflix User's Comment Using Multiple Lexicon-Based Dictionaries 4

Sentiment Analysis: Indonesia Netflix User's Comment Using M...

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4th International Conference on Intelligent Cybernetics Technology and Applications, ICICyTA 2024

作者： Mola, Sebastianus Adi Santoso Widiastuti, Tiwuk Roma, Rosa V. K. Isabela Ohe Karnyoto, Andrea Stevens Pardamean, Bens University of Nusa Cendana Faculty of Science and Engineering Kupang Indonesia Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta11480 Indonesia Bina Nusantara University Binus Graduate Program Computer Science Department Jakarta11480 Indonesia

ISBN: (纸本)9798331506490

A subscription movie streaming service from the United States, Netflix, has been present in Indonesia since 2016 and provides a wide variety of films without showing any single advertisements that can be viewed from anywhere, as long as there is access to the internet. Despite these advantages, many users have complained through the Google Play Store's comments column. Some of the common complaints include frequent buffering and connectivity issues, dissatisfaction with the limited selection of Indonesian movies, lack of subtitles for specific languages, or pricing concerns have also been raised. In this study developed two combined scenario methods using the InSet and SentiStrength-id dictionary to obtain better performance and compare them against independent InSet and SentiStrength-id. This study collected users' comments for the Netflix app in the Google Play Store as a dataset using web scraping techniques through the Google Collaboration tool. The dataset contains 3250 rows spanning the period from January 22, 2024, through June 6, 2024. To ensure proper processing of the text, data cleaning, lowercasing, normalization, tokenization, stemming, and stopwords removal are conducted. The results show that most user opinions are negative. The InSet dictionary has an accuracy of 92%, SentiStrength-id 78%, Combined scenario 1 is 87%, and scenario 2 reaches the highest among others which is 92.52%. © 2024 IEEE.

关键词： Video streaming

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