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

作者： Trinugroho, Joko Pebrianto Hidayat, Alam Ahmad Isnan, Mahmud Pardamean, Bens Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta11480 Indonesia Department of Mathematics School of Computer Science Bina Nusantara University Jakarta11480 Indonesia Computer Science Department BINUS Graduate Program Bina Nusantara University Jakarta11480 Indonesia

Lactose intolerance is a type of digestive problem that may threaten the population because milk and dairy products compose of nutrients that are essential for human body. Genetic tests possess a great potential to detect lactose intolerance as it can be used in children and even infants. However, a new approach to analyze the genetic test results is needed to elucidate the Single Nucleotide Polymorphisms (SNPs) that are related to lactose intolerance. In this work, we utilized the machine learning based feature selection to select the SNPs associated with lactose tolerance trait from genotyping samples of direct-to-customer (DTCG genetic tests, obtained from the public database. Recursive Feature Elimination (RFE) with XGBoost model was used to perform feature selection. We also compared three different models, such as XGBoost, support vector machine (SVM), and random forest (RF) for training the selected features. Our findings revealed that 20 SNPs (out of 3501) were chosen, with rs4394668 as the most important variables (F-score 0.009). Furthermore, when compared to the RF and SVM models, the XGBoost model had the highest accuracy (0.87). Further studies should be undertaken to elucidate how the selected SNPs may lead to the lactose intolerance trait. © 2023 The Authors. Published by Elsevier B.V.

关键词： feature selection genetic test lactose intolerance SNP

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Data-driven modeling and prediction of microglial cell dynamics in the ischemic penumbra

arXiv

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arXiv 2024年

作者： Amato, Sara Arnold, Andrea Bioinformatics & Computational Biology Program Worcester Polytechnic Institute WorcesterMA United States Department of Mathematical Sciences Worcester Polytechnic Institute WorcesterMA United States

Neuroinflammation immediately follows the onset of ischemic stroke. During this process, microglial cells are activated in and recruited to the tissue surrounding the irreversibly injured infarct core, referred to as the penumbra. Microglial cells can be activated into two distinct phenotypes;however, the dynamics between the detrimental M1 phenotype and beneficial M2 phenotype are not fully understood. Using phenotype-specific cell count data obtained from experimental studies on middle cerebral artery occlusion-induced stroke in mice, we employ sparsity-promoting system identification techniques combined with Bayesian statistical methods for uncertainty quantification to generate continuous and discrete-time predictive models of the M1 and M2 microglial cell dynamics. The resulting data-driven models include constant and linear terms but do not include nonlinear interactions between the cells. Results emphasize an initial M2 dominance followed by a takeover of M1 cells, capture potential long-term dynamics of microglial cells, and suggest a persistent inflammatory response. Copyright © 2024, The Authors. All rights reserved.

关键词： Mammals

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Database Design for Indonesian Scholarship Recommender Systems 7

Database Design for Indonesian Scholarship Recommender Syste...

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7th International Conference on Information Management and Technology, ICIMTech 2022

作者： Elwirehardja, Gregorius Natanael Jason Dominic, Nicholas Pardamean, Bens BINUS Graduate Program - Master of Computer Science Bina Nusantara University Computer Science Department Jakarta11480 Indonesia Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta11480 Indonesia

ISBN: (数字)9781665450904

ISBN: (纸本)9781665450904

Following the evolution of technology, researchers have conducted several studies to propose reliable scholarship recommender systems. However, few have explored the data storage systems, which are highly beneficial to collect huge volumes of real data in training the recommender systems. In this paper, a database design for collecting such data was proposed, equipped with integer encodings for categorical variables and a method to normalize variables with varying ranges. Using Connoly and Begg's database design method, the final design consisted of a normalized Entity Relationship Diagram (ERD) and data dictionaries. The design was also constructed to support usages of various data for determining scholarship recipients, including education history, achievements, and organizational experiences. The proposed design can be implemented on information systems to allow easier information access for scholarships in Indonesia. © 2022 IEEE.

关键词： Recommender systems

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Multi-modal Multitask Learning Model for Simultaneous Classification of Two Epilepsy Biomarkers 27th

Multi-modal Multitask Learning Model for Simultaneous Classi...

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27th International Conference on Pattern Recognition, ICPR 2024

作者： Broti, Nawara Mahmood Sawada, Masaki Takayama, Yutaro Iijima, Keiya Iwasaki, Masaki Ono, Yumie Electrical Engineering Program Graduate School of Science and Technology Meiji University Kanagawa Kawasaki Japan Department of Neurosurgery Yokohama City University Hospital Kanagawa Yokohama Japan Department of Neurosurgery National Center Hospital National Center of Neurology and Psychiatry Tokyo Kodaira Japan Department of Electronics and Bioinformatics School of Science and Technology Meiji University Kanagawa Kawasaki Japan

ISBN: (纸本)9783031781971

Accurate estimation of the epileptogenic zone is critical for surgical treatment of drug-resistant epilepsy. While epilepsy biomarkers detection for epileptogenic zone localization has traditionally relied on expert clinician knowledge, the use of deep learning in this context has recently gained appeal for objective diagnosis and reducing clinician burden. However, previously proposed classifiers for electrocorticogram data focused on only single biomarkers among many types, requiring separate models and large datasets for each. To minimize clinicians’ workload and patients’ sufferings, innovative methods to classify multiple biomarkers using small training datasets and minimal computation time is required. This research marks the first implementation of multi-modal multitask learning in epilepsy biomarker classification, proposing a model to automatically classify two biomarkers—high-frequency oscillations (HFO) and interictal epileptiform discharges (IED)—from separate datasets simultaneously. We validated the proposed model on 1500 annotated HFO and IED candidate signals each, obtained from 5 patients. Our proposed model can perform both HFO and IED classification simultaneously, with cross-validation accuracies of 90.99% and 93.99%;F1 scores were reported as 0.80 and 0.82, respectively. Our leave-one-patient-out experiments achieved 78.03% and 81.19% accuracy for HFO and IED classification, respectively. Compared to existing state-of-the-art classification architectures, our model is shown to be efficient and robust, yet simple and lightweight. The usefulness of sharing parameters between the two classifiers was confirmed in this practical clinical setting of epileptic biomarker detection, potentially contributing to minimizing the number of annotated datasets and realizing robust, accurate, and simultaneous identification of two biomarkers. © The Author(s), under exclusive license to Springer Nature Switzerland AG 2025.

关键词： Deep learning

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A data-informed mathematical model of microglial cell dynamics during ischemic stroke in the middle cerebral artery

arXiv

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arXiv 2024年

Neuroinflammation immediately follows the onset of ischemic stroke in the middle cerebral artery. During this process, microglial cells are activated in and recruited to the penumbra. Microglial cells can be activated into two different phenotypes: M1, which can worsen brain injury;or M2, which can aid in long-term recovery. In this study, we contribute a summary of experimental data on microglial cell counts in the penumbra following ischemic stroke induced by middle cerebral artery occlusion (MCAO) in mice and compile available data sets into a single set suitable for time series analysis. Further, we formulate a mathematical model of microglial cells in the penumbra during ischemic stroke due to MCAO. Through use of global sensitivity analysis and Markov Chain Monte Carlo (MCMC)-based parameter estimation, we analyze the effects of the model parameters on the number of M1 and M2 cells in the penumbra and fit identifiable parameters to the compiled experimental data set. We utilize results from MCMC parameter estimation to ascertain uncertainty bounds and forward predictions for the number of M1 and M2 microglial cells over time. Results demonstrate the significance of parameters related to M1 and M2 activation on the number of M1 and M2 microglial cells. Simulations further suggest that potential outliers in the observed data may be omitted and forecast predictions suggest a lingering inflammatory response. Copyright © 2024, The Authors. All rights reserved.

关键词： Parameter estimation

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The effect of visual advanced driver assistance systems on a following human driver in a mixed-Traffic condition 7

The effect of visual advanced driver assistance systems on a...

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7th International Conference on Computer Science and Computational Intelligence, CSCI 2022

作者： Ariansyah, Dedy Pardamean, Bens Caruso, Giandomenico Bioinformatics and Data Science Research Centre Bina Nusantara University Jakarta11480 Indonesia Computer Science Department BINUS Graduate Program Master of Computer Science Program Bina Nusantara University Jakarta11480 Indonesia Department of Mechanical Engineering Politecnico di Milano Milan 20156 Italy

Rapid development in vehicular technology has caused more automated vehicle control to increase on the roads. Studies showed that driving in mixed traffic with an autonomous vehicle (AV) had a negative impact on the time headway (THW) of conventional vehicles (CVs) (i.e., driven by humans). To address this issue, there is a need to equip CV with visual advanced driver assistance systems (ADASs) that helps the driver maintain safe headway when driving near AVs. This study examines the perception of drivers using visual ADAS and their associated risk while driving behind the AV at constant and varying speeds. The preliminary results showed that while visual ADAS could help drivers keep the safe THW, it could affect drivers' ability to react to emergencies. This implies that visual modality alone might not be sufficient and therefore requires some other feedback or intelligent transport systems to help drivers maintain safe driving in a mixed-Traffic condition. © 2022 Elsevier B.V.. All rights reserved.

关键词： Advanced driver assistance systems

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Web Information System Design for Fast Protein Post-Translational Modification Site Prediction 7

Web Information System Design for Fast Protein Post-Translat...

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7th International Conference on Information Management and Technology, ICIMTech 2022

作者： Elwirehardja, Gregorius Natanael Dominic, Nicholas Pardamean, Bens BINUS Graduate Program - Master of Computer Science Bina Nusantara University Computer Science Department Jakarta11480 Indonesia Research Center Bina Nusantara University Bioinformatics and Data Science Jakarta11480 Indonesia

ISBN: (数字)9781665450904

ISBN: (纸本)9781665450904

In the field of bioinformatics, the protein Post-Translational Modification (PTM) site prediction has been widely studied and Web Information Systems (WIS) has been deployed by researchers for this task. Through a literature review and benchmarking process, we identified the requirements which included quick predictions, efficient memory usage, and input validations. However, no detailed designs have been proposed so far, which may have contributed to some requirements not being implemented in some of the websites. Therefore, we propose a detailed WIS conceptual design, which can be used for predicting the sites of multiple PTM types, equipped with a validation algorithm and compared the usage of various string searching algorithms as well as file storage formats. Experiment results showed that the linear search algorithm is the fastest for this task and storing the protein data in npz format when performing multi-PTMs site prediction can assist in reducing memory usage. The proposed design can be implemented into user-friendly web tools that are both efficient in speed and memory usage in future studies. © 2022 IEEE.

关键词： Forecasting

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An Exploratory Computational Approach for Elucidating a Nonstructural Protein Interaction in Dengue Virus 2 9th

An Exploratory Computational Approach for Elucidating a Nons...

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

作者： Hidayat, Alam Ahmad Nirwantono, Rudi Pardamean, Bens Mathematics Department School of Computer Science Bina Nusantara University 11480 Indonesia Biotechnology Department Faculty of Engineering Bina Nusantara University 11480 Indonesia Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta11480 Indonesia Computer Science Department BINUS Graduate Program Bina Nusantara University Jakarta11480 Indonesia

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. © 2024 The Authors.

关键词： Molecular docking

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LLM2Vec Sentence Embeddings Analysis in Sentiment Classification

LLM2Vec Sentence Embeddings Analysis in Sentiment Classifica...

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2024 IEEE International Conference on Data and Software Engineering, ICoDSE 2024

作者： Henry, Matthew Martianus Heryanto, Nur Adhianti Isnan, Mahmud Kurnianingrum, Dian Ratnapuri, Chyntia Ika 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 Entrepreneurship Department Bina Nusantara University Jakarta11480 Indonesia Computer Science Department BINUS Graduate Program Bina Nusantara University Jakarta11480 Indonesia

ISBN: (纸本)9798331506407

Sentiment analysis is crucial method in business intelligence to extract insights, which typically begin with sentiment classification. One of the latest frameworks for generating sentence embeddings for sentiment classification is LLM2Vec, which allows Transformer decoder-based models to generate sentence embeddings for text representation. Its capability is deemed language-agnostic, which, in this study, the framework is leveraged for Tokopedia tweet sentiment analysis to prove the claim. The base decoder models used in the LLM2Vec framework were Llama 3 8B, Llama 2 7B, Sheared Llama 1.3B, and Mistral 7B. Two BERT-based models, which are the Indonesian SBERT model and IndoBERT trained with the SimCSE approach, were employed as a comparison. The generated embeddings were classified using logistic regression, SVM, and MLP Classifier. Classifiers using embedding generated by LLM2Vec with Llama 3 8B and Mistral 7B achieves on-par performance with classifiers that utilize IndoBERT SimCSE embeddings, while classifiers using embeddings generated by LLM2Vec with Llama 2 7B and Sheared Llama 1.3B achieves much lower performance. Classifiers with Indonesian SBERT embeddings achieve the highest F1 score performance. Despite slightly lower performance, this study has proven the language-agnostic capability of LLM2Vec, especially with Llama 3 8B and Mistral 7B in colloquial Bahasa Indonesia sentiment analysis, since none of the base decoders were ever trained using the Bahasa Indonesia corpus. © 2024 IEEE.

关键词： Decoding

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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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