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

作者： Henry, Matthew Martianus 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 Computer Science Department BINUS Graduate Program Bina Nusantara University Jakarta11480 Indonesia

In educational institutions, an educator is responsible for assessing the student's knowledge grasp through examination. Creating exam questions, even the low-level factoid questions, is time-consuming, especially for inexperienced educators. Therefore, this study aims to create a sequence-to-sequence model using CopyNet by exploiting its copying mechanism advantage to automatically generate Bahasa Indonesia factoid questions to ease the educator's burden. Indonesian records in the TyDi QA dataset are used as the model input. GRU and Bi-GRU are employed as the CopyNet encoder, while LSTM is used as the CopyNet decoder. The model that utilizes GRU as the encoder achieves BLEU1, BLEU2, BLEU3, BLEU4, and ROUGE-L scores of 0.28, 0.19, 0.14, 0.1, and 0.32, respectively. Bi-GRU utilization as the model encoder achieves BLEU1, BLEU2, BLEU3, BLEU4, and ROUGE-L scores of 0.26, 0.17, 0.12, 0.09, and 0.30, respectively. Models using either encoder still achieve low scores. However, compared with the previous work, the result is still on par regarding the BLEU score. Further examination found that the generated questions do not adhere to semantic and syntactical correctness. Adding more records to the dataset and utilizing a more advanced architecture like CopyBERT are encouraged to improve the model performance in future work. Despite the result, this study has shown that CopyNet, primarily designed for text summarization or single-turn dialogue, can be tailored for factoid question generation. © 2024 The Authors.

关键词： Semantics

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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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International Conference on Informatics, Multimedia, Cyber and Information System (ICIMCIS)

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

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.

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Automatic Multiple Choice Question Generation: A Systematic Literature Review 9

Automatic Multiple Choice Question Generation: A Systematic ...

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9th International Conference on Information Technology and Digital Applications, ICITDA 2024

作者： Henry, Matthew Martianus Heryanto, Nur Adhianti Isnan, Mahmud Nugroho, Kuncahyo Setyo Pardamean, Bens Bina Nusantara University Bioinformatics and Data Science Research Center Jakarta11480 Indonesia School of Computer Science Bina Nusantara University Computer Science Department Jakarta11480 Indonesia Bina Nusantara University Binus Graduate Program Computer Science Department Jakarta11480 Indonesia

ISBN: (纸本)9798331510732

Despite their drawbacks, multiple-choice questions (MCQ) have been widely used to assess the students' understanding of lectures through examinations. The development of automatic MCQ generation is beneficial, especially for educators. As a starting point for further development, a Systematic Literature Review (SLR) is conducted to uncover current trends, future challenges, and opportunities in automatic MCQ generation. Previously, an SLR was conducted, but it lacks coverage of the utilization of transformer-based models. This SLR covers the development of automatic MCQ generation using either traditional or advanced approaches such as Transformers. The Preferred Reporting Items for Systematic Reviews and Meta-Analyses framework was used to gather the data from Scopus, IEEE Xplore, SpringerLink, arXiv, and Semantic Scholar. The included articles must be open-access computer science conference papers or journal articles and written in English less than five years ago. Four independent reviewers analyzed the research workflow, evaluation metric, and dataset used in each study. There are 18 included studies, where 17% (n = 3) studies are from 2024, 33% (n = 6) studies are from 2023, 22% (n = 4) studies are from 2022, 11% (n = 2) studies are from 2021, and 17% (n = 3) studies are from 2020. There are 33% (n = 6) of the studies used the traditional feature-based engineering approach, 39% (n = 7) of the studies used the Transformer-based model fine-tuning approach, and the remaining used novel approaches. The study found that BERT variants are the most utilized Transformer-based model in automatic MCQ. The research notes some challenges, but also open various opportunities for further research, including Large Language Model (LLM) utilization for automatic MCQ generation, the utilization BERT-based models for standardized machine-learned evaluation metrics, and the initiative for the creation of an MCQ dataset benchmark. © 2024 IEEE.

关键词： Semantics

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Literature study of stunting supplementation in Indonesian utilizing text mining approach

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Procedia Computer Science 2023年 216卷 722-729页

作者： Digdo Sudigyo Alam Ahmad Hidayat Rudi Nirwantono Reza Rahutomo Joko Pebrianto Trinugroho Bens Pardamean Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta 11480 Indonesia Computer Science Department BINUS Graduate Program Bina Nusantara University Jakarta 11480 Indonesia

Numerous research on stunting supplementation interventions in Indonesia have been published. The information can be extracted through data mining, especially from academic research databases. In this paper, we presented a text mining-based literature review strategy to create a pipeline that researchers can use to accelerate the development of stunting supplementation intervention research in Indonesia. Utilizing various NLP (Natural Language Processing) techniques, data were crawled, processed, and visualized using Python. The crawling dataset used a module from the Pubmed API (Application programming Interface) to collect literature papers. The NLTK (Natural Language Toolkit) module and itertools were used to process text data. The n-grams model was applied to process tokens into bigrams and trigrams. Text information was visualized using Matplotlib and Word cloud packages. There is an increasing number of publication in stunting supplementation intervention according to our result, which was observed from 2015 to 2021. West Java was the province where most of the stunting research has been conducted, as determined by research abstracts. Top occurrences obtained from the bigram and trigrams models calculation produced different terms. The word pairings that occurred the most frequently in the bigram and trigram model analyses were "child-aged" and "iron-folic-acid," respectively. The findings of this study are expected to help researchers to obtain the latest research topics related to stunting supplementation interventions in Indonesia.

关键词： text mining data mining literature study stunting supplementation Indonesian

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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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Data Mining for the Global Multiplex Weekly Average Income Analysis

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Procedia Computer Science 2023年 219卷 52-59页

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

The box office (BO) income had significantly declined up to 80% in 2020, as the COVID-19 pandemic emerged. To minimize further financial risks, multiplex (multiple cinema complexes) owners need to analyze their potential income for each movie, each week. Therefore, we developed a proper data mining strategy that allows multiplex owners to analyze and discover insights on how successfully produced movies could be. The methodology comprises (1) data loading and exploration, (2) data cleaning, (3) data selection, integration, and transformation using Pentaho, (4) data mining in which the results were stored in the MySQL database, and (5) pattern evaluation and presentation using Qlik Sense as the Business Intelligence (BI) dashboard. Based on our data mining methodology, we revealed that drama, comedy, action, and thriller are favorite genres. We also found that DreamWorks Animation and Pixar Animation Studios are both the most popular production houses, even Apatow Productions and Escape Artists still have the biggest revenue on average.

关键词： movie multiplex income data mining Business Intelligence dashboard

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Hybrid support vector regression in electric load during national holiday season

Hybrid support vector regression in electric load during nat...

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2017 International Conference on Innovative and Creative Information Technology: Computational Intelligence and IoT, ICITech 2017

作者： Caraka, Rezzy Eko Bakar, Sakhinah Abu Pardamean, Bens Budiarto, Arif School of Mathematical Sciences Faculty of Science and Technology National University of Malaysia Malaysia Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta11480 Indonesia Computer Science Department BINUS Graduate Program-Master of Computer Science Bina Nusantara University Jakarta11480 Indonesia

ISBN: (纸本)9781538640456

This paper studies non-parametric time-series approach to electric load in national holiday seasons based on historical hourly data in state electric company of Indonesia consisting of historical data of the Northern Sumatera also South and Central Sumatra electricity load. Given a baseline for forecasting performance, we apply our hybrid models and computation platform with combining parameter of the kernel. To facilitate comparison to results of our analysis, we highlighted the results around MAPE-based and R2-based techniques. In order to get more accurate results, we need to improve, investigate, also develop the appropriate statistical tools. Electric load forecasting is a fundamental aspect of infrastructure development decisions and can reduce the energy usage of the nation. © 2017 IEEE.

关键词： Time series

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Mutual dependency between lncRNA LETN and protein NPM1 in controlling the nucleolar structure and functions sustaining cell proliferation

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细胞研究（英文版） 2021年第6期31卷 664-683页

作者： Xianteng Wang Xiaolin Hu Wanlu Song Hui Xu Zhengtao Xiao Rongyao Huang Qingran Bai Fan Zhang Yongzhen Chen Yu Liu Jianhuo Fang Xin Li Qin Shen Haitao Zhao Xuerui Yang MOE Key Laboratory of Bioinformatics Tsinghua UniversityBeijing 100084China Center for Synthetic & Systems Biology Tsinghua UniversityBeijing 100084China School of Life Sciences Tsinghua UniversityBeijing 100084China MOE Key Laboratory of Bioinformatics Tsinghua UniversityBeijing 100084China Center for Synthetic & Systems Biology Tsinghua UniversityBeijing 100084China School of Life Sciences Tsinghua UniversityBeijing 100084China Joint Graduate Program of Peking-Tsinghua-National Institute of Biological Science Beijing 100084China Brain and Spinal Cord Innovative Research Center of Tongji Hospital School of Life Sciences and TechnologyTongji University and Frontier Science Research Center for Stem Cells of Ministry of EducationShanghai 200092China Department of Liver Surgery Peking Union Medical College HospitalChinese Academy of Medical Sciences & Peking Union Medical College (CAMS & PUMC)Beijing 100730China

Fundamental processes such as ribosomal RNA synthesis and chromatin remodeling take place in the nucleolus,which is hyperactive in fast-proliferating *** sophisticated regulatory mechanism underlying the dynamic nucleolar structure and functions is yet to be fully *** present study uncovers the mutual functional dependency between a previously uncharacterized human long non-coding RNA,which we renamed LETN,and a key nucleolar protein,***,being upregulated in multiple types of cancer,LETN resides in the nucleolus via direct binding with *** plays a critical role in facilitating the formation of NPM1 pentamers,which are essential building blocks of the nucleolar granular component and control the nucleolar *** of LETN or NPM1 led to similar and profound changes of the nucleolar morphology and arrest of the nucleolar functions,which led to proliferation inhibition of human cancer cells and neural progenitor ***,this inter-dependency between LETN and NPM1 is associated with the evolutionarily new variations of NPM1 and the coincidental emergence of LETN in higher *** propose that this human-specific protein-lncRNA axis renders an additional yet critical layer of regulation with high physiological relevance in both cancerous and normal developmental processes that require hyperactive nucleoli.

关键词： Cell division Long non-coding RNAs

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Decision Theory and Risk Simulation Analysis for Optimizing Profit in PayLater Services

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Procedia Computer Science 2023年 219卷 60-67页

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

The projected increase in PayLater utilization reaches up to five million people by 2025. To optimize the yearly profit from their PayLater service, fintech companies must examine all possible risks before a unanimous decision is taken. Therefore, we proposed a unified decision framework derived from decision theory and the Monte Carlo simulation technique. Two schemes were coined: (1) a decision-making scheme, and (2) a risk simulation scheme. Throughout experiments, the framework was able to estimate several alternative decisions and their impacts, analyze the causes of failure and delays in the development of the PayLater service, and execute Monte Carlo simulations in up to 10,000 trials. Outputs of this study will benefit decision-makers in the fintech initiative before launching their PayLater products.

关键词： PayLater decision-making Bayesian analysis fault tree analysis critical path method Monte Carlo simulation

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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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