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Making Canonical Workflow Building Blocks Interoperable across Workflow Languages

data Intelligence 2022年第2期4卷 342-357页

作者： Stian Soiland-Reyes Genis Bayarri Pau Andrio Robin Long Douglas Lowe Ania Niewielska Adam Hospital Paul Groth Department of Computer Science The University of ManchesterManchester M139PLUK Informatics Institute University of AmsterdamAmsterdam 1098 XHThe Netherlands Institute for Research in Biomedicine(IRB Barcelona) The Barcelona Institute of Science and Technology(BIST)Barcelona O8028Spain The Spanish National Bioinformatics Institute(INB) Barcelona Supercomputing Center(BSC)Barcelona 08034Spain Data Science Institute Lancaster UniversityLancasterLancashire LA14YWUK Research IT IT ServicesThe University of ManchesterManchester M139PLUK European Bioinformatics Institute(EMBL-EBI) HinxtonCambridgeshire CB101SDUK

We introduce the concept of Canonical Workflow Building Blocks(CWBB),a methodology of describing and wrapping computational tools,in order for them to be utilised in a reproducible manner from multiple workflow languages and execution *** concept is implemented and demonstrated with the BioExcel Building Blocks library(BioBB),a collection of tool wrappers in the field of computational biomolecular *** across different workflow languages is showcased through a protein Molecular Dynamics setup transversal workflow,built using this library and run with 5 different Workflow Manager Systems(WfMS).We argue such practice is a necessary requirement for FAIR Computational Workflows and an element of Canonical Workflow Frameworks for Research(CWFR)in order to improve widespread adoption and reuse of computational methods across workflow language barriers.

关键词： Scientific workflows Interoperable FAIR Computational tools Containers Software packaging FAIR digital object(FDO),BioExcel Building Blocks library(BioBB),Canonical Workflow Frameworks for Research(CWFR)

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Phylogeographic and genetic network assessment of COVID-19 mitigation protocols on SARS-CoV-2 transmission in university campus residences

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eBioMedicine 2025年 116卷 105729-105729页

作者： Wertheim, Joel O. Vasylyeva, Tetyana I. Wood, Robert J. Cantrell, Kalen Contreras, Soraya Piña Feldheim, Aryeh Goyal, Ravi Havens, Jennifer L. Knight, Rob Laurent, Louise C. Moshiri, Niema Neuhard, Robert Sathe, Shashank Satterlund, Alysson Scioscia, Angela Song, Angela Y. Aigner, Stefan Andersen, Kristian G. Baer, Nathan A. Betty, Maryann Birmingham, Amanda Castro-Martinez, Anelizze Cheung, Willi De Hoff, Peter Fisch, Kathleen M. King, Alison J. Gangavarapu, Karthik Hakim, Abbas Henson, Benjamin Jepsen, Kristen Mac, Christina H. Ngo, Toan T. Nguyen, Kelly N. Ostrander, Tyler R. Perkins, Sarah Plascencia, Ashley Rivera, Andrea Rivera, Ariana Salido, Rodolfo A. Saucedo, Kieran C. Schwab, Madison Steedman, Allison L. Veder, Anthony Weiss, Alana Yeo, Gene W. Zeller, Mark Schooley, Robert T. Anderson, Cheryl M. Martin, Natasha K. Department of Medicine University of California San Diego La Jolla CA United States Department of Population Health and Disease Prevention University of California Irvine Irvine CA United States Herbert Wertheim School of Public Health and Human Longevity Science University of California San Diego La Jolla CA United States Department of Computer Science & Engineering University of California San Diego La Jolla CA United States Bioinformatics and Systems Biology Graduate Program University of California San Diego La Jolla CA United States Department of Pediatrics University of California San Diego La Jolla CA United States Department of Bioengineering University of California San Diego La Jolla CA United States Department of Computer Science and Engineering University of California San Diego La Jolla CA United States Center for Microbiome Innovation University of California San Diego La Jolla CA United States Halıcıoğlu Data Science Institute University of California San Diego La Jolla CA United States Department of Obstetrics Gynecology and Reproductive Sciences University of California San Diego La Jolla CA United States Sanford Consortium of Regenerative Medicine University of California San Diego La Jolla CA United States University of California San Diego La Jolla CA United States

Background: Congregate living provides an ideal setting for SARS-CoV-2 transmission in which many outbreaks and superspreading events occurred. To avoid large outbreaks, universities turned to remote operations during the initial COVID-19 pandemic waves in 2020 and 2021. In late-2021, the University of California San Diego (UC San Diego) facilitated the return of students to campus with comprehensive testing, vaccination, masking, wastewater surveillance, and isolation policies. Methods: We performed molecular epidemiological and phylogeographic analysis of 4418 SARS-CoV-2 genomes sampled from UC San Diego students during the Omicron waves between December 2021 and September 2022, representing 58% of students with confirmed SARS-CoV-2 infection. We overlaid these analyses across on-campus residential information to assess the spread and persistence of SARS-CoV-2 within university residences. Findings: Within campus residences, SARS-CoV-2 transmission was frequent among students residing in the same room or suite. However, a quarter of pairs of suitemates with concurrent infections had distantly related viruses, suggesting separate sources of infection during periods of high incidence in the surrounding community. Students with concurrent infections residing in the same building were not at substantial increased probability of being members of the same transmission cluster. Genetic network and phylogeographic inference indicated that only between 3.1 and 12.4% of infections among students could be associated with transmission within buildings outside of individual suites. The only super-spreading event we detected was related to a large event outside campus residences. Interpretation: We found little evidence for sustained SARS-CoV-2 transmission within individual buildings, aside from students who resided in the same suite. Even in the face of heightened community transmission during the 2021–2022 Omicron waves, congregate living did not result in a heightened risk

关键词： Mitigation Phylogeography SARS-CoV-2 Transmission cluster University

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Fine-scale genetic structure of Tujia and central Han Chinese revealing massive genetic admixture under language borrowing

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植物分类学报 2021年第1期59卷 1-20页

作者： Guang-Lin He Ying-Xiang Li Meng-Ge Wang Xing Zou Hui-Yuan Yeh Xiao-Min Yang Zheng Wang Ren-Kuan Tang Su-Min Zhu Jian-Xin Guo Ting Luo Jing Zhao Jin Sun Zi-Yang Xia Hao-Liang Fan Rong Hu Lan-Hai Wei Gang Chen Yi-Ping Hou Chuan-Chao Wang Department of Anthropology and Ethnology Institute of AnthropologyNational Institute for Data Science in Health and Medicineand School of Life SciencesXiamen UniversityXiamen 361005FujianChina Institute of Forensic Medicine West China School of Basic Science and Forensic Medicine Sichuan UniversityChengdu 610041China Department of Anthropology and Ethnology Institute of AnthropologyNational Institute for Data Science in Health and Medicineand School of Life SciencesXiamen UniversityXiamen 361005FujianChina Institute of Forensic Medicine West China School of Basic Science and Forensic Medicine Sichuan UniversityChengdu 610041China Institute of Forensic Medicine West China School of Basic Science and Forensic Medicine Sichuan UniversityChengdu 610041China School of Humanities Nanyang Technological UniversityNanyang 639798Singapore Department of Anthropology and Ethnology Institute of AnthropologyNational Institute for Data Science in Health and Medicineand School of Life SciencesXiamen UniversityXiamen 361005FujianChina Institute of Forensic Medicine West China School of Basic Science and Forensic Medicine Sichuan UniversityChengdu 610041China Department of Forensic Medicine College of Basic Medicine Chongqing Medical UniversityChongqing 400000China Department of Forensic Medicine College of Basic Medicine Chongqing Medical UniversityChongqing 400000China Department of Anthropology and Ethnology Institute of AnthropologyNational Institute for Data Science in Health and Medicineand School of Life SciencesXiamen UniversityXiamen 361005FujianChina Department of Anthropology and Ethnology Institute of AnthropologyNational Institute for Data Science in Health and Medicineand School of Life SciencesXiamen UniversityXiamen 361005FujianChina Department of Anthropology and Ethnology Institute of AnthropologyNational Institute for Data Science in Health and Medicineand School of Life SciencesXiamen UniversityXiamen 361005FujianChina Department of Anthropology and Ethnology In

Archaeological,genetic,and linguistic evidence has supported the idea that northern China is the original center of modern Sino-Tibetan-speaking ***,the demographic history of subsequent southward migration and genetic admixture of Han Chinese with surrounding indigenous populations remain uncharacterized,and the language shifts and assimilations accompanied by movement of people,or just an adaptation of cultural ideas among populations in central China is still unclear,especially for Tibeto-Burman-speaking Tujia and central Han Chinese *** resolve this,we genotyped over 60K genome-wide markers in 505 unrelated individuals from 63 indigenous *** results showed both studied Han and Tujia were at the intermediate position in the modern East Asian North-South genetic cline and there was a correlation between the genetic composition and the *** observed the strong genetic assimilation between Tujia people and central Han Chinese,which suggested massive population movements and genetic admixture under language *** and central Han Chinese could be modeled as a two-way admixture deriving primary ancestry from a northern ancestral population closely related to the ancient DevilsCave and present-day Tibetans and a southern ancestral population closely related to the present-day Tai-Kadai and Austronesian-speaking *** ancestral northern population we suspect to be related to the Neolithic millet farming groups in the Yellow River Basin or central *** showed that the newly genotyped populations in Hubei Province had a higher proportion of DevilsCave or modern Tungusic/Mongolic-related northern ancestries,while the Hunan populations harbored a higher proportion of Austronesian/Tai-Kadai-related southern ancestries.

关键词： demographic history gene flow genetic admixture language borrowing Tibeto-Burman Tujia

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Novel loci and potential mechanisms of major depressive disorder,bipolar disorder,and schizophrenia

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science China(Life sciences) 2022年第1期65卷 167-183页

作者： He Wang Zhenghui Yi Tieliu Shi Center for Bioinformatics and Computational Biology Institute of Biomedical Sciences and School of Life SciencesEast China Normal UniversityShanghai 200241China Shanghai Mental Health Center Shanghai Jiao Tong University School of MedicineShanghai 200030China Key Laboratory of Advanced Theory and Application in Statistics and Data Science-MOE School of StatisticsEast China Normal UniversityShanghai 200062China Beijing Advanced Innovation Center for Big Data-Based Precision Medicine Beihang University&Capital Medical UniversityBeijing 100083China

Different psychiatric disorders share genetic relationships and pleiotropic loci to certain *** integrated and analyzed datasets related to major depressive disorder(MDD),bipolar disorder(BIP),and schizophrenia(SCZ)from the Psychiatric Genomics Consortium using multitrait analysis of genome-wide association analysis(MTAG).MTAG significantly increased the effective sample size from 99,773 to 119,754 for MDD,from 909,061 to 1,450,972 for BIP,and from 856,677 to 940,613 for *** discovered 7,32,and 43 novel lead single nucleotide polymorphisms(SNPs)and 1,6,and 3 novel causal SNPs for MDD,BIP,and SCZ,respectively,after *** identified rs8039305 in the FURIN gene as a novel pleiotropic locus across the three *** performed marker analysis of genomic annotation(MAGMA)and Hi-C-coupled MAGMA(H-MAGMA)based gene-set analysis and identified 101 genes associated with the three disorders,which were enriched in the regulation of postsynaptic membranes,postsynaptic membrane dopaminergic synapses,and Notch signaling ***,we performed Mendelian randomization analysis using different tools and detected a causal effect of BIP on ***,we demonstrated the usage of combined genome-wide association studies summary statistics for exploring potential novel mechanisms of the three psychiatric disorders,providing an alternative approach to integrate publicly available summary data.

关键词： psychiatric disorders multitrait analysis of genome-wide association analysis novel loci Mendelian randomization causal effects

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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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Long Short-Term Memory-based Models for Sleep Quality Prediction from Wearable Device Time Series data 8

Long Short-Term Memory-based Models for Sleep Quality Predic...

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

作者： Hidayat, Alam Ahmad Budiarto, Arif Pardamean, Bens Mathematics Department School of Computer Science Bina Nusantara University Jakarta11480 Indonesia 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

Several studies suggest that sleep quality is associated with physical activities. Moreover, deep sleep time can be used to determine the sleep quality of an individual. In this work, we aim to find the association between physical activities and deep sleep time by modeling the time series data such as heart rate and a number of steps captured from a commercial wearable device. Our previous study demonstrates that deep learning-based time series modeling is well suited for our problem since the temporal patterns in the two physical parameters need to be captured to obtain more accurate results. We first preprocess our series data to have a time-step size of 10 minutes. To improve our previous effort in this modeling, we compare four different variants of Long Short-Term Memory (LSTM)-based models, ranging from single input to dual input models. Our result shows that the simple stacked LSTM model performs better for our data because the remaining models suffer from overfitting due to a larger number of the trained parameters. © 2023 The Authors. Published by Elsevier B.V.

关键词： deep learning forecasting sleep quality time series wearable devices

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TENSOR-ON-TENSOR REGRESSION: RIEMANNIAN OPTIMIZATION, OVER-PARAMETERIZATION, STATISTICAL-COMPUTATIONAL GAP, AND THEIR INTERPLAY

arXiv

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arXiv 2022年

作者： Luo, Yuetian Zhang, Anru R. Data Science Institute University of Chicago United States Department of Biostatistics & Bioinformatics Department of Computer Science Duke University United States

We study the tensor-on-tensor regression, where the goal is to connect tensor responses to tensor covariates with a low Tucker rank parameter tensor/matrix without prior knowledge of its intrinsic rank. We propose the Riemannian gradient descent (RGD) and Riemannian Gauss-Newton (RGN) methods and cope with the challenge of unknown rank by studying the effect of rank over-parameterization. We provide the first convergence guarantee for the general tensor-on-tensor regression by showing that RGD and RGN respectively converge linearly and quadratically to a statistically optimal estimate in both rank correctly-parameterized and over-parameterized settings. Our theory reveals an intriguing phenomenon: Riemannian optimization methods naturally adapt to over-parameterization without modifications to their implementation. We also prove the statistical-computational gap in scalar-on-tensor regression by a direct low-degree polynomial argument. Our theory demonstrates a "blessing of statistical-computational gap" phenomenon: in a wide range of scenarios in tensor-on-tensor regression for tensors of order three or higher, the computationally required sample size matches what is needed by moderate rank over-parameterization when considering computationally feasible estimators, while there are no such benefits in the matrix settings. This shows moderate rank over-parameterization is essentially "cost-free" in terms of sample size in tensor-on-tensor regression of order three or higher. Finally, we conduct simulation studies to show the advantages of our proposed methods and to corroborate our theoretical findings. © 2022, CC BY.

关键词： Tensors

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Grid-connected microgrid:design and feasibility analysis for a local community in Bangladesh

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Clean Energy 2022年第3期6卷 447-459页

作者： Dewan Mahnaaz Mahmud S.M.Masum Ahmed Sayeed Hasan Mohammad Zeyad Energy and Technology Research Division Advanced BioinformaticsComputational Biology and Data Science LaboratoryBangladesh Faculty of Engineering Erasmus Mundus Joint MSc in Smart Cities and Communities(SMACCs)University of Mons(UMONS)Belgium School of Engineering and Physical Sciences(EPS) Erasmus Mundus Joint MSc in Smart Cities and Communities(SMACCs)Heriot-Watt University(HWU)UK

Global demand for electricity is growing significantly in developing *** energy accounts for barely 3%of total energy consumption in *** of renewable energy,***,are increasingly being acknowledged as viable supply-side choices for *** article presents a grid-connected microgrid design based on meteorological data for a local community situated in Mohammadpur,*** study presents a feasible design of a system that gives the lowest cost of energy production and emissions that is evaluated using software named Hybrid Optimization Multiple Energy Resources(HOMER Pro).Comparison and assessment of the net present cost,cost of energy,operating cost and environmental emission for five different feasible microgrids are analysed concerning real-time ***,a suitable case is sorted out and proposed for the local community for *** proposed case offers a$0.0442/kWh cost of energy,which is~32%cheaper than the current rate with a 57.5%renewable fraction and a payback period of 16.86 *** of this local community will have access to considerably more clean energy at a lower price by this study;also this design could sell the excess energy to the grid to avoid frequent electricity outages.

关键词： renewable energy communities microgrid community energy photovoltaic batteries emission cost of energy

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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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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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