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An alignment-free method for profiling microbial community 8

An alignment-free method for profiling microbial community

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8th International Conference on bioinformatics and Computational Biology, BICOB 2016

作者： Pham, Diem-Trang Gao, Shanshan Phan, Vinhthuy Bioinformatics Program University of Memphis MemphisTN38111 United States Department of Computer Science University of Memphis MemphisTN38111 United States

ISBN: (纸本)9781943436033

Determining abundances of microbial genomes in metagenomic samples is an important problem in analyzing metagenomic data. Homology-based method requires aligning reads from metagenomic samples to reference genomes and can be a computationally expensive as microbial communities usually consists of hundreds to thousands of environmental microbial species. We introduce an efficient alignment-free approach to estimate abundances of microbial genomes in metagenomic samples. The approach is based on solving linear and quadratic programs, which are represented by genome-specific markers. In a controlled study at different levels of contamination, our method was able to achieve higher accuracy compared to current composition-based methods in estimating abundances of microbial genomes. Copyright ISCA.

关键词： Microorganisms

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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...

引用

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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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...

引用

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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Toward Learning Factory for Industry 4.0: Virtual Reality (VR) for Learning Human–Robot Collaboration 1

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International Conference on Innovative Technologies in Intelligent Systems and Industrial Applications, CITISIA 2022

作者： Ariansyah, Dedy Colombo, Giorgio Pardamean, Bens Bioinformatics and Data Science Research Centre Bina Nusantara University Jakarta11480 Indonesia Department of Mechanical Engineering Politecnico di Milano Milan20156 Italy Computer Science Department BINUS Graduate Program Master of Computer Science Program Bina Nusantara University Jakarta11480 Indonesia

ISBN: (数字)9783031290787

ISBN: (纸本)9783031290770

Industry 4.0 will bring not only transformation to the manufacturing technologies but also to the profile of the workforce. Education system should be revised to prepare the future graduates embracing the knowledge of the ongoing revolution. Initiatives on the modification of curriculum and tools to deliver the concepts of Industry 4.0 must be taken. This paper examines limitations of current engineering tools and proposes a virtual reality (VR)-based learning platform to support the teaching and learning activity for Industry 4.0, focusing on the design of Human–robot Collaboration (HRC). The development process began with the identification of the general Intended Learning Outcomes (ILOs) which were extracted from the review of the HRC design issues, followed by the evaluation of the current teaching tool. From these results, the new requirements of the tools to achieve ILOs are redefined. The implementation of the system is demonstrated to show the feasibility of the proposed learning platform. This workflow can serve as initial development of another learning platform for the other innovative concepts that form the building blocks of Industry 4.0. © The Author(s), under exclusive license to Springer Nature Switzerland AG 2023.

关键词： Industry 4.0

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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 ...

引用

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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An Improved Version of Texture-based Foreground Segmentation: Block-based Adaptive Segmenter 3

An Improved Version of Texture-based Foreground Segmentation...

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3rd International Conference on computer science and Computational Intelligence, ICCSCI 2018

作者： Muchtar, Kahlil Rahman, Faris Cenggoro, Tjeng Wawan Budiarto, Arif Pardamean, Bens Nodeflux Inc. Jakarta Indonesia Syiah Kuala University Aceh 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 Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta11480 Indonesia

Foreground segmentation is one of moving object detection techniques of computer vision applications. To date, modern moving object detection methods require complex background modeling and thresholds tuning to confront illumination changes. This paper proposes an adaptive approach based on non-overlapping block texture representation. It aims to design a computationally light and efficient solution to improve the robustness of detection. We evaluate our proposed method on internal and public sequences and provide the quantitative and qualitative measurements. Experimental results show that the proposed method can improve the results of previous method and suitable for real-time challenges. © 2018 The Authors. Published by Elsevier Ltd.

关键词： Textures

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Systematic Literature Review on Metaheuristic Algorithms in SNP Analysis for Diseases 6

Systematic Literature Review on Metaheuristic Algorithms in ...

引用

6th International Conference on Cybernetics and Intelligent System, ICORIS 2024

作者： Sulistyawan, Jason Sebastian Nugroho, Kuncahyo Setyo Pardamean, Bens Computer Science Department BINUS Graduate Program Bina Nusantara University Jakarta11480 Indonesia Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta11480 Indonesia

ISBN: (纸本)9798331539603

Single-nucleotide polymorphism (SNP) analysis has become a pivotal strategy for drug discovery within bioinformatics, especially for incurable diseases like cancer. With the increasing number of researchers starting to embrace metaheuristic methods, a review was done by gathering papers from the Google Scholar database from 2018 to 2023, which resulted in 20 papers after title, abstract, and content filtering. The findings show that the Genetic Algorithm and the Harmony Search Algorithm have become popular approaches in SNP analysis, particularly in studies on breast cancer, age-related macular degeneration, and colorectal cancer. However, the review shows that while researchers have proven most methods effective in finding disease-related SNPs, a more measurable study in SNP analysis is needed, due to the lack of elaboration on measurement metrics in the found studies. © 2024 IEEE.

关键词： metaheuristic algorithms single nucleotide polymorphisms

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Literature study of stunting supplementation in Indonesian utilizing text mining approach 7

Literature study of stunting supplementation in Indonesian u...

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7th International Conference on computer science and Computational Intelligence, CSCI 2022

作者： Sudigyo, Digdo Hidayat, Alam Ahmad Nirwantono, Rudi Rahutomo, Reza Trinugroho, Joko Pebrianto Pardamean, Bens Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta11480 Indonesia Computer Science Department BINUS Graduate Program Bina Nusantara University Jakarta11480 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. © 2022 Elsevier B.V.. All rights reserved.

关键词： Data mining

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Exploring EfficientNet Variants for Image Encoding in Auxiliary Signal Guided Knowledge Encoder-Decoder Framework 9th

Exploring EfficientNet Variants for Image Encoding in Auxili...

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9th International Conference on computer science and Computational Intelligence, ICCSCI 2024

作者： Henry, Matthew Martianus Heryanto, Nur Adhianti Pardamean, Bens Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta11480 Indonesia Computer Science Department BINUS Graduate Program Bina Nusantara University Jakarta11480 Indonesia

The growing number of medical images has led to radiologist burnout, which seriously impacts the radiologist's performance. To address the previously mentioned issue, an Auxiliary Signal Guided Knowledge (ASGK) multimodal encoder-decoder framework was designed to automatically generate the medical report based on the proposed medical graph and natural language decoder. It utilizes DenseNet-121 as the image encoder. With DenseNet-121 lack of computational and memory efficiency, this study aims to explore the potential of EfficientNetB0 to EfficientNetB4 as an ASGK image encoder substitute. The framework is trained with IU X-Ray dataset for 30 epochs, with Adam optimizer, a learning rate of 0.01 with 0.8 decay rate, binary cross entropy loss for the medical tags, and cross-entropy loss for the generated medical captions. During the framework training process with each image encoder, the parameter that achieves the highest CIDEr score on the validation set is considered the best image encoder parameter and will be used on the test set. On the test set, EfficientNetB3 as an ASGK image encoder has been shown to increase the CIDEr score to 0.35, a significant increase from the 0.28 CIDEr score obtained by the ASGK using DenseNet-121. This score is only a 1% decrease from the best validation score. It suggests that not only EfficientNetB3 increases the framework's performance, it is also less prone to overfitting. This study has demonstrated that EfficientNetB3 is a potential image encoder substitute for DenseNet-121 in the ASGK framework. © 2024 The Authors.

关键词： Medical imaging

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HAsh-MaP-ERadicator: Filtering Non-Target Sequences from Next Generation Sequencing Reads

HAsh-MaP-ERadicator: Filtering Non-Target Sequences from Nex...

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IEEE International Conference on bioinformatics and Biomedicine

作者： Jonathon Brenner Catherine Putonti Department of Computer Science Bioinformatics Program Loyola University Chicago Departments of Biology and Computer Science Bioinformatics Program Loyola University Chicago

ISBN: (纸本)9781467368001

Contemporary DNA sequencing technologies are continuously increasing throughput at ever decreasing costs. Moreover, due to recent advances in sequencing technology new platforms are emerging. As such computational challenges persist. The average read length possible has taken a giant leap forward with the PacBio and Nanopore solutions. Regardless of the platform used, impurities within the DNA preparation of the sample - be it from unintentional contaminants or pervasive symbiots - remains an issue. We have developed a new tool, HAsh-MaP-ERadicator (HAMPER), for the detection and removal of non-target, contaminating DNA sequences. Integrating hash-based and mapping-based strategies, HAMPER is both memory and time efficient while maintaining a high level of sensitivity. Moreover, HAMPER was designed for flexibility: reads of any size can be efficiently examined and the user can set parameters specific for the analysis of reads produced by a particular sequencer. To evaluate our method, mock sequencing runs were generated including various contaminating species and with variable rates of mutation revealing a high level of sensitivity and specificity. Reads that are not of interest can quickly be removed using HAMPER thus improving downstream analyses.

关键词： Sequence contamination Sequence homology Hash-mapping Homologous Sequences Pollutant rise level Filtration Platform Throughput Analyses, Sequence sequencer Flexibility

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