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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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Utilizing Semi-supervised Method in Predicting BRCA1 Pathogenicity Variants

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Procedia Computer Science 2023年 227卷 36-45页

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

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.

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

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

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Procedia Computer Science 2024年 245卷 470-479页

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

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.

关键词： bioinformatics computational biology dengue protein docking structural biology

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Uncertainty Quantification Using Subsampling for Assembly-Free Estimates of Genomic Distance and Phylogenetic Relationships 26th

Uncertainty Quantification Using Subsampling for Assembly-F...

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26th International Conference on Research in Computational Molecular Biology, RECOMB 2022

作者： Rachtman, Eleonora Sarmashghi, Shahab Bafna, Vineet Mirarab, Siavash Bioinformatics and Systems Biology Graduate Program UC San Diego La JollaCA United States Department of Electrical and Computer Engineering UC San Diego La JollaCA United States Department of Computer Science and Engineering UC San Diego La JollaCA United States

Computing the distance between two genomes, often without using alignments or even access to assembled sequences, is fundamental to many downstream analyses. © 2022, The Author(s), under exclusive license to Spri... 详细信息

ISBN: (纸本)9783031047480

关键词： Uncertainty analysis

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P202: Post-COVID syndrome presented with psychomotor change and suicidal ideations: a geriatric case report

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International Psychogeriatrics 2023年第S1期35卷 229-230页

作者： Lin, Ying Wang, Ying-Chi Chiang, Dai-Lun Lai, Feipei Graduate Institute of Biomedical Electronics and Bioinformatics National Taiwan University Taipei City Taiwan MacKay Memorial Hospital Department of Psychiatry Taipei Taiwan Financial Technology Applications Program Ming Chuan University Taoyuan City Taiwan

Background:COVID-19 is notorious for its neuropsychiatric sequelae. Some patients present with anosmia and cognitive and attention deficits, also known as “brain-fog”. In COVID-19 survivors, psychiatric manifestations such as depression, fatigue, anxiety, and neurocognitive impairments, also known as the “post-acute COVID-19 syndrome” or “long COVID”, were reported in 35% of the patients after the infection. New-onset anxiety, depression, psychosis, seizures, and even suicidal behaviors are also reported. Inflammation was proposed to be the *** Report:The 68 year-old married female who lived with her husband did not have psychiatric history before this year. She had covid-19 infection 3 months prior to her psychiatric hospitalization. Although she had recovered, she started to have depressed mood, disrupted sleep and anhedonia since then. She became easily anxious and could hardly feed her cats as usual. She was not able to make decisions. She no longer did house chores that she had been doing. Poor appetite led to a loss of body weight from 46 to 40kgs. She had blunted emotional response, and could not cry after her cat died. She went to clinic for help, BZD and antidepressants were given, but the condition persisted. One week prior to hospitalization, her speech became weak, murmuring and could not finish a long sentence. The physiological change can be observed using wearable device. After 3 weeks of treatment, her heat rate, activity and sleep improved. The progress was also recorded via wearable devices and clinical ***:In our patient, the depression was associated with circadian rhythm disruption, suicidal ideations and psychomotor slowing. This may reveal some special features of post-COVID depression. In previous studies, antidepressants have proved to be effective in treating post-COVID-19 depression. Sigma receptors are one of the possible mechanisms. Besides, agomelatine, with its melatonergic activity of regulating circadia

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Identification of Meteorological Parameters Affecting Dengue Hemorrhagic Fever Incidences 4

Identification of Meteorological Parameters Affecting Dengue...

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4th International Conference on Informatics, Multimedia, Cyber and Information System, ICIMCIS 2022

作者： Asadi, Faisal Trinugroho, Joko Pebrianto Hidayat, Alam Ahmad Rahutomo, Reza Pardamean, Bens Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta11480 Indonesia School of Information Systems Bina Nusantara University Information System Department Jakarta11480 Indonesia Binus Graduate Program Master of Computer Science Bina Nusantara University Computer Science Department Jakarta11480 Indonesia

ISBN: (纸本)9781665473279

Tropical disease is one of the infectious diseases that affect Indonesia. Many people die because of tropical diseases, such as dengue hemorrhagic fever (DHF), chikungunya, leprosy, lymphatic, and filariasis. The Indonesian government's lack of public policy is the main problem in treating and preventing tropical diseases. The paper aims to describe the analysis results of the incidence of DHF in Jakarta, Indonesia. The analysis used the DHF incidences data from the Jakarta Health service surveillance office representative and combined it with the meteorological parameters data. The meteorological parameters were collected from the Bureau of Meteorological Climatology and Geophysics (BMKG). The statistical analysis of this research used Pearson's correlation. The results show that the meteorological parameters affecting DHF incidences are temperature, humidity, and wind speed. © 2022 IEEE.

关键词： Correlation methods

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A Design of Childhood Stunting Assessment Feature with Agile UX Approach 8

A Design of Childhood Stunting Assessment Feature with Agile...

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8th International HCI and UX Conference in Indonesia, CHIuXiD 2022

作者： Rahutomo, Reza Perbangsa, Anzaludin Samsinga Asadi, Faisal Nirwantono, Rudi Pardamean, Bens Bina Nusantara University School of Information Systems Information Systems Department Jakarta11480 Indonesia Bina Nusantara University Bioinformatics and Data Science Research Center Jakarta11480 Indonesia Bina Nusantara University BINUS Graduate Program-Master of Computer Science Computer Science Department Jakarta11480 Indonesia

ISBN: (纸本)9781665476645

multidisciplinary collaboration between public health, system engineering, and UX is able to generate a solution in healthcare problem like stunting. The principle of Agile UX gathers requirements to generate an application design. Currently, various website and mobile applications are available to be utilized for stunting research. StuntingDB is one of many web-based applications that specialized in stunting data management. The application required several types of users to operate hierarchically. This research focused on Public Health Officers' workflow that require a solution to in the form of assessment module for stunting DBMS by using Agile UX principle. The method collaborates agile team and UX team to solve Public Health Officer's difficulty in changing stunting status at pre-saved child patient's profile. Collaboration of both agile team and UX team successfully proposed an application design that system design. © 2022 IEEE.

关键词： Websites

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Identifying Important Usernames in 'Biofarma' Conversation using Twitter Network Analysis 7

Identifying Important Usernames in 'Biofarma' Conversation u...

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

作者： Rahutomo, Reza Jariyah, Ainun Trinugroho, Joko Pebrianto Pardamean, Bens School of Information Systems Bina Nusantara University Information Systems Department Jakarta11480 Indonesia Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta11480 Indonesia BINUS Graduate Program-Master of Computer Science Bina Nusantara University Computer Science Department Jakarta11480 Indonesia

ISBN: (数字)9781665450904

ISBN: (纸本)9781665450904

This study analyzed interactions between Twitter users in conversations regarding Indonesia's state-owned vaccine manufacturer 'Biofarma' in 2021. The primary objective of this study is to identify Key Opinion Leaders (KOL) due to the need of authentic and trustworthy persona in social media. A technique called network centrality was employed in this research alongside four centrality measurements, namely degree of centrality, eigenvector centrality, betweenness centrality, and closeness centrality. Focused on using a reply network interaction dataset, the research discovered several important usernames with different roles that enlivened the conversation and have a potential for social media marketing optimization. © 2022 IEEE.

关键词： Marketing

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Relabeling Metabolic Pathway Data with Groups to Improve Prediction Outcomes 11th

Relabeling Metabolic Pathway Data with Groups to Improve P...

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11th International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2021

作者： Basher, Abdur Rahman M. A. Hallam, Steven J. Graduate Program in Bioinformatics University of British Columbia VancouverBCV5Z 4S6 Canada Department of Microbiology & Immunology University of British Columbia VancouverBCV6T 1Z3 Canada

ISBN: (纸本)9783031175305

Metabolic pathway inference from genomic sequence information is an integral scientific problem with wide ranging applications in the life sciences. As sequencing throughput increases, scalable and performative methods for pathway prediction at different levels of genome complexity and completion become compulsory. In this paper, we present reMap (relabeling metabolic pathway data with groups) a simple, and yet, generic framework, that performs relabeling examples to a different set of labels, characterized as groups. A pathway group is comprised of a subset of statistically correlated pathways that can be further distributed between multiple pathway groups. This has important implications for pathway prediction, where a learning algorithm can revisit a pathway multiple times across groups to improve sensitivity. The relabeling process in reMap is achieved through an alternating feedback process. In the first feed-forward phase, a minimal subset of pathway groups is picked to label each example. In the second feed-backward phase, reMap’s internal parameters are updated to increase the accuracy of mapping examples to pathway groups. The resulting pathway group dataset is then be used to train a multi-label learning algorithm. reMap’s effectiveness was evaluated on metabolic pathway prediction where resulting performance metrics equaled or exceeded other prediction methods on organismal genomes. © 2022, The Author(s), under exclusive license to Springer Nature Switzerland AG.

关键词： Forecasting

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ConvNeXt Model for Breast Cancer Image Classification

ConvNeXt Model for Breast Cancer Image Classification

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International Conference on Cybernetics and Intelligent System (ICORIS)

作者： Devin Setiawan Andrea Stevens Karnyoto Indo Intan Bens Pardamean 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 - Master of Computer Science Program Bina Nusantara University Jakarta Indonesia

ISBN: (数字)9798331539603

ISBN: (纸本)9798331539610

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.

关键词： Support vector machines Accuracy Head Computational modeling Transfer learning Breast cancer Magnetic heads Data models Reliability Image classification

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