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A spatial genome aligner for resolving chromatin architectures from multiplexed DNA FISH (Jan, 10.1038/s41587-022-01568-9, 2023)

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NATURE BIOTECHNOLOGY 2023年第7期41卷 1027-1027页

作者： Jia, Bojing Blair Jussila, Adam Kern, Colin Zhu, Quan Ren, Bing Bioinformatics and Systems Biology Graduate Program University of California San Diego La Jolla CA USA Medical Scientist Training Program University of California San Diego La Jolla CA USA Department of Cellular and Molecular Medicine Center for Epigenomics University of California San Diego La Jolla CA USA Ludwig Institute for Cancer Research La Jolla CA USA Institute of Genomic Medicine Moores Cancer Center School of Medicine University of California San Diego La Jolla CA USA

Multiplexed fluorescence in situ hybridization (FISH) is a widely used approach for analyzing three-dimensional genome organization, but it is challenging to derive chromosomal conformations from noisy fluorescence signals, and tracing chromatin is not straightforward. Here we report a spatial genome aligner that parses true chromatin signal from noise by aligning signals to a DNA polymer model. Using genomic distances separating imaged loci, our aligner estimates spatial distances expected to separate loci on a polymer in three-dimensional space. Our aligner then evaluates the physical probability observed signals belonging to these loci are connected, thereby tracing chromatin structures. We demonstrate that this spatial genome aligner can efficiently model chromosome architectures from DNA FISH data across multiple scales and be used to predict chromosome ploidies de novo in interphase cells. Reprocessing of previous whole-genome chromosome tracing data with this method indicates the spatial aggregation of sister chromatids in S/G2 phase cells in asynchronous mouse embryonic stem cells and provides evidence for extranumerary chromosomes that remain tightly paired in postmitotic neurons of the adult mouse cortex.

关键词： Gene regulation Image processing

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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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Confidentiality. Integrity, and Availability (CIA) Approach for Private Dataset Management System Design 9

Confidentiality. Integrity, and Availability (CIA) Approach ...

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

作者： Isnan, Mahmud Elwirehardja, Gregorius Natanael Ariansyah, Dedy Rahutomo, Reza Pardamean, Bens School of Computer Science Bina Nusantara University Computer Science Department Jakarta11480 Indonesia Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta11480 Indonesia School of Information Systems Bina Nusantara University Information Systems Department Jakarta11480 Indonesia Binus Graduate Program Bina Nusantara University Computer Science Department Jakarta11480 Indonesia

ISBN: (纸本)9798331510732

Dataset management systems are essential for assisting research and development (R&D) organizations in applying data governance protocols, especially in managing the utilization of datasets. In R&D, datasets are vital sources for producing analysis, machine learning prediction, and supporting decision-making. As such, it is important to deploy dataset management systems with considerations regarding the aspects of Confidentiality, Integrity, and Availability (CIA) which is a design principle that emphasized information protection and collaboration facilitation among dataset users. The study proposed an analysis and a design for a dataset management system that takes CIA aspects into account. In the future, the proposed design will be utilized as a benchmark for building a dataset management system. In this study, the Waterfall method was adopted. A use case diagram, an ERD (Entity Relationship Diagram), and an activity diagram were constructed in the design stage. In the project implementation stage, the Laravel framework including Laravel Jetstream was considered to be used. © 2024 IEEE.

关键词： Data integrity

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Evolution Of SARS-CoV-2 In The Presence Of Vaccines.

Evolution Of SARS-CoV-2 In The Presence Of Vaccines.

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2022 IEEE International Conference on bioinformatics and Biomedicine, BIBM 2022

作者： Marathe, Vishwajeet Yan, Changhui North Dakota State University Department of Computer Scienceline FargoND United States North Dakota State University Department of Computer Science Genomics Phenomics and Bioinformatics Graduate Program FargoND United States

ISBN: (纸本)9781665468190

The COVID pandemic has caused tremendous loss worldwide. Now vaccines are the primary weapon to combat the pandemic. Understanding how SARS-CoV-2, the virus that causes the COVID, may mutate in the presence of the vaccines is critical for designing drugs and vaccines for future variants of the virus. In this study, we investigated the numbers of mutations that SARS-CoV-2 accumulated on each protein over time. We found that different proteins of the virus accumulated different levels of mutations and their mutation rates changed over time following different patterns. We also presented evidence that the mutation of the Spike protein might have been suppressed by the vaccines. This is the first time that such a relation was reported based on real world data. Although the discovery was not meant to be conclusive, this study sheds light onto how the virus may response to the vaccines. If confirmed by further studies, the discovery will have significant impacts on many fields, including drug and vaccine designs. © 2022 IEEE.

关键词： Coronavirus

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

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Procedia Computer Science 2024年 245卷 391-398页

作者： Matthew Martianus Henry Nur Adhianti Heryanto Bens Pardamean Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia 11480 Computer Science Department BINUS Graduate Program - Master of Computer Science Bina Nusantara University Jakarta Indonesia 11480

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.

关键词： Automated medical report generation DenseNet-121 EfficientNet Encoder-decoder framework

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A Bayesian-based approach for extracting the pion charge radius from electron-electron scattering data

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Chinese Physics C 2021年第8期45卷 12-27页

作者： Alam A Hidayat Bens Pardamean Bioinformatics and Data Science Research Center Bina Nusantara UniversityJakarta 11480Indonesia Computer Science Department BINUS Graduate Program-Master of Computer ScienceBina Nusantara UniversityJakarta 11480Indonesia

In this study,we utilize a potentially versatile Bayesian parameter approach to compute the value of the pion charge radius and quantify its uncertainty from several experimental e^(+)e^(-) datasets for the pion vector form *** employ dispersion relations to model the pion vector form factor to extract the *** model selection is used to determine the order of polynomial appearing in the form factor formulation that can be supported by the data,adapting the computation of Bayes evidence and Bayesian effective complexity based on Occam's *** findings indicate that five out of six used datasets favor the nine-parameter model for radius extraction,and accordingly,we average the radii from the *** some inconsistencies with the most updated radius values,our approach may serve as a more intuitive method of addressing parameter estimations in dispersion theory.

关键词： Bayesian complexity dispersion hadron pion

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LDA Topic Modeling for bioinformatics Terms in arXiv Documents

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Procedia Computer Science 2024年 245卷 229-238页

作者： Andrea Stevens Karnyoto Matthew Martianus Henry Bens Pardamean Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia 11480 Computer Science Department BINUS Graduate Program - Master of Computer Science Bina Nusantara University Jakarta Indonesia 11480

A wide variety of disciplines contribute to bioinformatics research, including computer science, biology, chemistry, mathematics, and physics. This study determines the number of research articles published on arXiv classified as bioinformatics topics and the most frequently used bioinformatics terms using topic modeling, Latent Dirichlet Allocation (LDA). An algorithm based on LDA is used to discover topics hidden within large collections of documents through the use of statistical analysis. Our research examined 226453 articles on arXiv between January 2023 and January 2024. As a result, there are more than 10521 articles categorized into bioinformatics topics. Most commonly, 6352 documents are in the "Mathematical Physics" category. The second most popular category is "Computer Science," with 2950 documents. Accordingly, the terms 'RNA,' 'sequence,' 'tree,' and 'homology' are the three most commonly used terms in bioinformatics. The study of RNA plays a vital role in molecular biology; thus, the study of RNA is prevalent in bioinformatics. Sequential data refer to the order in which nucleotides or amino acids can be found in a DNA molecule or a protein.

关键词： arXiv bioinformatics Latent Dirichlet Allocation

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Semi-automated meningioma segmentation with bounding boxes

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Procedia Computer Science 2024年 245卷 583-590页

作者： Nur Adhianti Heryanto Mahmud Isnan Matthew Martianus Henry Bens Pardamean Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia 11480 Computer Science Department BINUS Graduate Program - Master of Computer Science Bina Nusantara University Jakarta Indonesia 11480

Segmentation is manually performed by physicians, which takes considerable time and may be subject to observers. Automating this task can increase efficiency and consistency. Existing studies on meningioma segmentation used data from limited study centers, indicating the need for research on multi-center data to assess generalizability. In this work, two semi-automated methods with bounding box priors, LiteMedSAM and BBU-Net, are evaluated on the brain tumor segmentation (BraTS) 2023 meningioma dataset collected from five study-centers. Preprocessing included exclusion of small tumors, z-score normalization, and extraction of slices that contain tumors, generating 25,602 2D axial magnetic resonance imaging (MRI) scans. A fine-tuning strategy is adopted for LiteMedSAM while BBU-Net is trained from scratch. The models are evaluated using a five-fold cross-validation, with data split at the case level. Results show that while U-Net models can achieve performance close to LiteMedSAM, the foundation model has overall better performance, with more than 90% in all evaluation scores.

关键词： Bounding boxes Meningioma Semi-automated segmentation

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Systematic Literature Review on Statistics and Machine Learning Predictive Models for Rice Phenotypes 8

Systematic Literature Review on Statistics and Machine Learn...

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

作者： Dominic, Nicholas Cenggoro, Tjeng Wawan 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 Bina Nusantara University Jakarta11480 Indonesia

Predicting the best-quality of rice phenotypes is the priority among agricultural researchers to fulfill worldwide food security. Trend development of predictive models from statistics to machine learning is the subject of this review. Gathered from the Google Scholar database, 14 appropriate papers (2016-2020) related to the rice phenotypes prediction were selected through title and abstract content filtering. The outputs show that Support Vector Machine, Multi-layer Perceptron, and regression are the most used models, while yield is the priority prediction point besides tiller, panicle, and 1000-grain weight of rice. However, finding the accurate predictor is invariably challenging due to distinct rice varieties in the world and high confounding factors. Thus, developing an advanced deep learning model that accommodates these needs is worth considering further. © 2023 The Authors. Published by Elsevier B.V.

关键词： machine learning rice phenotypes prediction statistics

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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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