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

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 Computer Science Department BINUS Graduate Program - Master of Computer Science Program Bina Nusantara University Jakarta11480 Indonesia

TikTok, a social networking site for uploading short videos, has become one of the most popular. Despite this, not all users are happy with the app;there are criticisms and suggestions, one of which is reviewed via the TikTok app on the Google Play Store. The reviews were extracted and then used for training a sentiment analysis model. The VADER sentiment method was utilized to offer the review's initial labeling (positive, neutral, and negative). The result revealed that most reviews were classified as positive, meaning that the data were imbalanced and challenging to handle in further analysis. Therefore, Random Under-sampling (RUS) and Random Over-sampling (ROS) methods were deployed to deal with that condition. The labeled reviews were subsequently pre-processed using tools such as case folding, noise removal, normalization, and stopwords before being used for training a Support Vector Machine (SVM) model for sentiment classification. The SVM trained without resampling produced the most favorable results, with an F1-score of 0.80. © 2023 The Authors. Published by Elsevier B.V.

关键词： Google Play Store Sentiment Analysis SVM TikTok VADER Sentiment

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Enhancing Interoperability of Digital Twin in the Maintenance phase of Lifecycle 6

Enhancing Interoperability of Digital Twin in the Maintenanc...

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6th International Conference on Information Technology, Information Systems and Electrical Engineering, ICITISEE 2022

作者： Ariansyah, Dedy Pardamean, Bens Bina Nusantara University Bioinformatics and Data Science Research Centre Jakarta11480 Indonesia Bina Nusantara University BINUS Graduate Program Computer Science Program Computer Science Department Jakarta11480 Indonesia

ISBN: (纸本)9798350399615

In today's digitalization era, asset management has evolved following the rapid adoption of information systems and digital technologies. In the maintenance phase of the asset, Digital Twin (DT) emerges as an effective approach to improve failure recognition and structural damage prediction through DT-driven Prognostic and Health Monitoring (PHM). As a result, DT allows asset manager to proactively plan maintenance strategy to improve the availability of the assets. However, to reduce asset downtime in a cost-effective and time efficient manner, DT for maintenance phase needs to be integrated with other software systems that manage the provision of maintenance service and spare part such as computerized maintenance management system (CMMS) or Enterprise Resource Planning (ERP). Nevertheless, many of the developed DT in PHM were not equipped with semantic data model and hence, lacks interoperability with other systems (e.g., other DT or non-DT system) and limits the effective use of the DT. To qualify as an effective DT, it needs a semantical-enabled interface to connect with data and models from various domain to enable DT-driven decision-making. This paper leverages a rule-based ontology reasoning model to enhance DT interoperability with other maintenance software systems. The results depicts that the developed model paves a way for an effective use of DT-driven system in asset maintenance management. © 2022 IEEE.

关键词： CMMS Digital Twin ERP Maintenance Ontology

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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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Sequence to Sequence Deep Learning Architecture for Forecasting Temperature and Humidity inside Closed Space 10

Sequence to Sequence Deep Learning Architecture for Forecast...

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10th International Conference on Cyber and IT Service Management, CITSM 2022

作者： Setiawan, Karli Eka Elwirehardja, Gregorius Natanael Pardamean, Bens Bina Nusantara University Binus Graduate Program Computer Science Program Computer Science Department Jakarta11480 Indonesia Bina Nusantara University Bioinformatics and Data Science Research Center Jakarta11480 Indonesia

ISBN: (数字)9781665460743

ISBN: (纸本)9781665460743

Solar Dryer Dome (SDD), an agricultural facility for drying and preserving agricultural products, needs a smart ability to predict the future indoor climate accurately, including indoor temperature and indoor humidity, in order to optimize electricity usage. To overcome these challenges, deep learning has been a widely adopted method. This research aims to forecast the future indoor climate using time series data by implementing a sequence-to-sequence (seq2seq) architecture, which is mostly used in Natural Language Processing (NLP) tasks. The two proposed seq2seq models, Long Short-Term Memory (LSTM) seq2seq and Gated Recurrent Unit (GRU) seq2seq, have proven to be superior to the adapted LSTM and GRU. The results show that the seq2seq GRU model outperforms the adapted GRU baseline model by an average difference of 0.03013 in MAE and the seq2seq LSTM model outperforms the adapted LSTM baseline model by an average difference of 0.00941 in MAE. To the best of our knowledge, this is the first implementation of seq2seq models for indoor climate forecasting on the Room Climate dataset. © 2022 IEEE.

关键词： Long short-term memory

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Convergent Usage of Amino Acids in Human Cancers as A Reversed Process of Tissue Development

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Genomics, Proteomics & bioinformatics 2022年第1期20卷 147-162页

作者： Yikai Luo Han Liang Graduate Program in Quantitative and Computational Biosciences Baylor College of MedicineHoustonTX 77030USA Department of Bioinformatics and Computational Biology The University of Texas MD Anderson Cancer CenterHoustonTX 77030USA Department of Systems Biology The University of Texas MD Anderson Cancer CenterHoustonTX 77030USA

Genome-and transcriptome-wide amino acid usage preference across different species is a well-studied phenomenon in molecular evolution,but its characteristics and implication in cancer evolution and therapy remain largely ***,we analyzed large-scale transcriptome/proteome profiles,such as The Cancer Genome Atlas(TCGA),the Genotype-Tissue Expression(GTEx),and the Clinical Proteomic Tumor Analysis Consortium(CPTAC),and found that compared to normal tissues,different cancer types showed a convergent pattern toward using biosynthetically low-cost amino *** a pattern can be accurately captured by a single index based on the average biosynthetic energy cost of amino acids,termed energy cost per amino acid(ECPA).With this index,we further compared the trends of amino acid usage and the contributing genes in cancer and tissue development,and revealed their reversed ***,focusing on the liver,a tissue with a dramatic increase in ECPA during development,we found that ECPA represents a powerful biomarker that could distinguish liver tumors from normal liver samples consistently across 11 independent patient cohorts and outperforms any index based on single *** study reveals an important principle underlying cancer evolution and suggests the global amino acid usage as a system-level biomarker for cancer diagnosis.

关键词： Amino acid usage Tissue development Biosynthetic energy Diagnostic biomarker

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A bioinformatics Analysis and Homology 3D Modeling of Dihydroxy-orotate-dehydrogenase of Plasmodium ovale

A Bioinformatics Analysis and Homology 3D Modeling of Dihydr...

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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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Utilizing Semi-supervised Method in Predicting BRCA1 Pathogenicity Variants 8

Utilizing Semi-supervised Method in Predicting BRCA1 Pathoge...

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

作者： Hidayat, Alam Ahmad Trinugroho, Joko Pebrianto Nirwantono, Rudi Sudigyo, Digdo Pardamean, Bens Department of Mathematics School of Computer Science 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

Quantifying the effect of mutations in the BRCA1 gene is useful for understanding their clinical consequences on breast cancer. Machine learning models can be applied to predict the landscape of protein variant effects that might not be always accessible by experiments. In this work, we propose a simple semi-supervised learning method using a Gaussian mixture model to predict ~90% of the unlabeled missense variants of the BRCA1 gene collected from the ClinVar database. High-quality embeddings are used as a feature of the protein sequences, extracted using the latest pre-trained transformer-based language protein model. A statistical test show that the protein embeddings are effective and robust for predicting pathogenicity. Further, the lower representations of the features are then fed into the semi-supervised model. The prediction performance of the model only for the labeled testing data achieves an AUC score and an accuracy of 79.27% and 71.58%, respectively. Using our defined pathogenic probability score, we find that ~94% of variants in our unlabeled dataset are well-separated into either benign or pathogenic classes according to that scoring. Our scores obtain a moderate Spearman rank correlation with the results of established unsupervised variant effect models. Finally, our approach can potentially be developed for more accurate and biologically reliable predictions of the variant effects. © 2023 The Authors. Published by Elsevier B.V.

关键词： embeddings language model mutation effect protein sequence semi-supervised learning

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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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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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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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