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Mapper Interactive: A Scalable, Extendable, and Interactive Toolbox for the Visual Exploration of High-Dimensional Data [article]

Youjia Zhou, Nithin Chalapathi, Archit Rathore, Yaodong Zhao, Bei Wang
2021 arXiv   pre-print
In this paper, we present Mapper Interactive, a web-based framework for the interactive analysis and visualization of high-dimensional point cloud data.  ...  The mapper algorithm is a popular tool from topological data analysis for extracting topological summaries of high-dimensional datasets.  ...  ACKNOWLEDGMENTS The authors wish to thank Nathaniel Saul for comments on the initial prototype of our tool; Anantharaman Kalyanaraman, Methun Kamruzzaman, Bala Krishnamoorthy, and Umberto Lupo for valuable  ... 
arXiv:2011.03209v2 fatcat:pg3de5yctnelfefg4xbhe4nasm

Pheno-Mapper: An Interactive Toolbox for the Visual Exploration of Phenomics Data [article]

Youjia Zhou, Methun Kamruzzaman, Patrick Schnable, Bala Krishnamoorthy, Ananth Kalyanaraman, Bei Wang
2021 arXiv   pre-print
In this paper, we present Pheno-Mapper, an interactive toolbox for the exploratory analysis and visualization of large-scale phenomics data.  ...  In particular, Pheno-Mapper allows the interactive selection of subpopulations guided by a topological summary of the data and applies data mining and machine learning to these selected subpopulations  ...  National Science Foundation (NSF) awards DBI-1661375 and DBI-1661348.  ... 
arXiv:2106.13397v2 fatcat:sej4lq4x4jhb7oov3si53frmqq

Stitch Fix for Mapper and Topological Gains [article]

Youjia Zhou, Nathaniel Saul, Ilkin Safarli, Bala Krishnamoorthy, Bei Wang
2021 arXiv   pre-print
The mapper construction is a powerful tool from topological data analysis that is designed for the analysis and visualization of multivariate data.  ...  In this paper, we investigate a method for stitching a pair of univariate mappers together into a bivariate mapper, and study topological notions of information gains, referred to as topological gains,  ...  The tool is an extension of Mapper Interactive [50] , which is an extendable and interactive toolbox for the visual exploration of high-dimensional data using the mapper algorithm.  ... 
arXiv:2105.01961v2 fatcat:ybsv4hrmyfhz3bcpu2ibgbcafy

The Connectome Viewer Toolkit: An Open Source Framework to Manage, Analyze, and Visualize Connectomes

Stephan Gerhard, Alessandro Daducci, Alia Lemkaddem, Reto Meuli, Jean-Philippe Thiran, Patric Hagmann
2011 Frontiers in Neuroinformatics  
The efficiency of sharing data and source code would benefit if a transdisciplinary lingua franca for programming was available.  ...  Connectome mapping workflows involve image acquisition, registration and segmentation, data organization and sharing, high-throughput pipelining, analysis, and visualization.  ...  Mayavi provides Interactive manipulation of visualization parameters such as node position and coloring enables data exploration.  ... 
doi:10.3389/fninf.2011.00003 pmid:21713110 pmcid:PMC3112315 fatcat:stufldro4zaahfx3x5hzfawvs4

NeuMapper: A scalable computational framework for multiscale exploration of the brain's dynamical organization

Caleb Geniesse, Samir Chowdhury, Manish Saggar
2022 Network Neuroscience  
Despite promising results, initial applications of Mapper to neuroimaging data were constrained by (1) the need for dimensionality reduction, and (2) lack of a biologically grounded heuristic for efficiently  ...  Here, we present a novel computational framework for Mapper—designed specifically for neuroimaging data—that removes limitations and reduces computational costs associated with dimensionality reduction  ...  Acknowledgments Funding was provided by a Career Development Award (K99/R00 MH104605) and a New Innovator Award (DP2 MH119735) from the National Institute of Mental Health (NIMH); and by the Stanford University  ... 
doi:10.1162/netn_a_00229 pmid:35733428 pmcid:PMC9207992 fatcat:rz57dwfvrrbb5iyqhhmgfgf3nu

Machine Learning and Cloud Computing: Survey of Distributed and SaaS Solutions [article]

Daniel Pop
2016 arXiv   pre-print
Next on the list are libraries of distributed implementations for ML algorithms, and on-premise deployments of complex systems for data analytics and data mining.  ...  Applying popular machine learning algorithms to large amounts of data raised new challenges for the ML practitioners.  ...  Pentaho Business Analytics 22 offers a complete solution for big data analytics, supporting all phases of an analytics process, from pre-processing to advanced data exploration and visualization.  ... 
arXiv:1603.08767v1 fatcat:vuzeggijyfbb7bmlcqdnt3xdjy

The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy

Björn A. Grüning, Jörg Fallmann, Dilmurat Yusuf, Sebastian Will, Anika Erxleben, Florian Eggenhofer, Torsten Houwaart, Bérénice Batut, Pavankumar Videm, Andrea Bagnacani, Markus Wolfien, Steffen C. Lott (+8 others)
2017 Nucleic Acids Research  
for RNA data analysis.  ...  RNA-based regulation has become a major research topic in molecular biology. The analysis of epigenetic and expression data is therefore incomplete if RNAbased regulation is not taken into account.  ...  Thanks also to the BioJS community for great discussions about scientific visualizations and how we can make them more accessible.  ... 
doi:10.1093/nar/gkx409 pmid:28582575 pmcid:PMC5570170 fatcat:qhl5knnpazd3noomvloekfefsy

Precision dynamical mapping using topological data analysis reveals a unique hub-like transition state at rest [article]

Manish Saggar, James M Shine, Raphael Liegeois, Nico U.F. Dosenbach, Damien Fair
2021 bioRxiv   pre-print
To generate the landscape of whole-brain configurations we used Topological Data Analysis based Mapper approach.  ...  The intermediate transition state and traversal through it via a topographic gradient seemed to provide the underlying structure for the continuous evolution of brain activity patterns at rest.  ...  A web-based interface was used to interact with the Mapper-generated graphs. This implementation was developed using HTML5, Scalable Vector Graphics (SVG), CSS, and JavaScript.  ... 
doi:10.1101/2021.08.05.455149 fatcat:36bg4lb7hbbopg2snc3xfzjozm

Data-intensive applications, challenges, techniques and technologies: A survey on Big Data

C.L. Philip Chen, Chun-Yang Zhang
2014 Information Sciences  
This paper is aimed to demonstrate a close-up view about Big Data, including Big Data applications, Big Data opportunities and challenges, as well as the state-of-the-art techniques and technologies we  ...  On the other hand, Big Data also arises with many challenges, such as difficulties in data capture, data storage, data analysis and data visualization.  ...  The state-of-the-art techniques for handling high-dimensional data intuitively fall into dimension reduction.  ... 
doi:10.1016/j.ins.2014.01.015 fatcat:mdnyfqqnh5citdt4moyfcggpfi

Present State of CFD Softwares Application for Launch Vehicle Analysis
발사체 해석을 위한 CFD 소프트웨어 적용 현황

Hwanghui Jeong, Jae Yeol Kim, Jae-Ryul Shin
2020 Journal of the Korean Society of Propulsion Engineers  
This software program takes an XML representation of the contents of a Hierarchical Data Format-Earth Observing System (HDF-EOS) file and recreates the file from that description .  ...  Please visit the following URL for additional information: http://opensource .gsfc .nasa .gov/projects/xml2he/index .  ...  Government Purpose Release Viewpoints: Software for Visualization of Multivariate Data ARC-16019-1 A software application that allows the interactive visualization of multivariate data using a variety  ... 
doi:10.6108/kspe.2020.24.3.071 fatcat:trxkhiuqrjakll32bcjxskgwju

Open source molecular modeling

Somayeh Pirhadi, Jocelyn Sunseri, David Ryan Koes
2016 Journal of Molecular Graphics and Modelling  
Open source software development provides many advantages to users of modeling applications, not the least of which is that the software is free and completely extendable.  ...  The success of molecular modeling and computational chemistry efforts are, by definition, dependent on quality software applications.  ...  helpful feedback on a draft of this manuscript.  ... 
doi:10.1016/j.jmgm.2016.07.008 pmid:27631126 pmcid:PMC5037051 fatcat:jxdvghsiszadjevub22qbjywwm

Visual Computing in Materials Sciences (Dagstuhl Seminar 19151)

Christoph Heinzl, Robert Michael Kirby, Stepan V. Lomov, Guillermo Requena, Rüdiger Westermann, Michael Wagner
2019 Dagstuhl Reports  
The Quantitative Data Visualization Challenge centers around the design and implementation of tailored visual analysis systems for extracting and analyzing derived data (e.g., computed from extracted features  ...  Similarly, to a debugger in computer programming, identifying errors in the code and providing hints to improve, a visual debugger in the domain of visual computing for materials science should show the  ...  Acknowledgements This activity has received funding from the Research Foundation Flanders (FWO) and the Austrian Science Fund (FWF) under the grant numbers G0F9117N and I3261-N36 "Quantitative X-ray tomography  ... 
doi:10.4230/dagrep.9.4.1 dblp:journals/dagstuhl-reports/HeinzlKLRW19 fatcat:kjcfqsgkxzaenoxncda27ttlym

BigDataGrapes D2.3 - BigDataGrapes Software Stack Design

Panagis Katsivelis
2021 Zenodo  
Deliverable D2.3 is the first submitted iteration of a living document that will describe the components and architecture of the BigDataGrapes software stack, providing design principles and technical  ...  expectations from the platform in order for the latter to conform to the requirements of those use cases.  ...  All of them are provisioned under a common master Dashboard that will serve as a showcase of the data, analytics and visualization assets of the project, but also as a monitoring tool for the state of  ... 
doi:10.5281/zenodo.4546026 fatcat:a35e4prb5ffqjmsammsac4e52q

Parameter Settings Optimization in MapReduce Big Data processing using the MOPSO Algorithm

Lennah Etyang, Waweru Mwangi, Lawrence Nderu
2020 African Conference on Software Engineering  
MapReduce is used in parallel and distributed computing environment for large scale data processing whereas Hadoop on the other hand is for running applications and storage of data in clusters of commodity  ...  Big data is a commodity which is highly valued in the entire globe. It is not just regarded as data but in the world of experts, we can derive intelligence from it.  ...  One main advantage MapReduce is its ability to be extended for it to run in a number of computing environments [24] .  ... 
dblp:conf/seia-ws/EtyangMN20 fatcat:xz2pncgwr5eqbdjdl7sqrqnfnq

BigDataGrapes D2.3 - BigDataGrapes Software Stack Design

Pythagoras Karampiperis, Antonis Koukourikos, Raffaele Perego, Franco Maria Nardini, Nicola Tonellotto, Milena Yankova, Panagiotis Zervas, Mihalis Papakonstadinou
2019 Zenodo  
Deliverable D2.3 is the first submitted iteration of a living document that will describe the components and architecture of the BigDataGrapes software stack, providing design principles and technical  ...  expectations from the platform in order for the latter to conform to the requirements of those use cases.  ...  -MongoDB, a NoSQL document storage engine that offers data model flexibility and a very high ease of usage both for write as well as also for read data.  ... 
doi:10.5281/zenodo.3269261 fatcat:7czrc4pqb5hn5kuwh34ytuzmjq
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