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Mapper Comparison with Wasserstein Metrics [article]

Michael McCabe
2018 arXiv   pre-print
One such family of techniques, Topological Data Analysis, and the Mapper algorithm in particular, has found use in a variety of fields, but describing model drift for Mapper graphs is an understudied area  ...  for model drift analysis by using the metric to transform the model drift problem into an anomaly detection problem over dynamic graphs.  ...  Here, we adapt Koutra's graph comparison criteria from the case of general graph comparison to the case of comparing Mapper graphs specifically: 1.  ... 
arXiv:1812.06232v1 fatcat:fqpbcpqw5nbl7noyci45wnsyrq

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

Caleb Geniesse, Samir Chowdhury, Manish Saggar
2022 Network Neuroscience  
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  ...  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  ...  Supplementary Fig. 1 provides a visual summary of the standard Mapper algorithm and adaptations for NeuMapper.  ... 
doi:10.1162/netn_a_00229 pmid:35733428 pmcid:PMC9207992 fatcat:rz57dwfvrrbb5iyqhhmgfgf3nu

Topology, Computation and Data Analysis (Dagstuhl Seminar 19212)

Michael Kerber, Vijay Natarajan, Bei Wang, Michael Wagner
2019 Dagstuhl Reports  
The seminar brought together researchers with mathematical and computational backgrounds in addressing emerging directions within computational topology for data analysis in practice.  ...  facilitated close interactions among the attendees with the aim of accelerating the convergence between mathematical and computational thinking in the development of theories and scalable algorithms for  ...  Weber (Lawrence Berkeley National Laboratory, US) Persistence Meets Tensor Fields  ... 
doi:10.4230/dagrep.9.5.110 dblp:journals/dagstuhl-reports/KerberNW19 fatcat:cjmvdnglxvhfzjp6i4se2w6p6u

Fast and sensitive mapping of error-prone nanopore sequencing reads with GraphMap [article]

Ivan Sovic, Mile Sikic, Andreas Wilm, Shannon Nicole Fenlon, Swaine Chen, Niranjan Nagarajan
2015 bioRxiv   pre-print
We present the first nanopore read mapper (GraphMap) that uses a read-funneling paradigm to robustly handle variable error rates and fast graph traversal to align long reads with speed and very high precision  ...  ), precise detection of structural variants from 100bp to 4kbp in length and species and strain-specific identification of pathogens using MinION reads.  ...  In principle, the approach used in GraphMap could be adapted for the problem of computing overlaps and alignments between reads.  ... 
doi:10.1101/020719 fatcat:zby4yboit5crpkvpmd4z6xx64i

Adaptive-Miner: an efficient distributed association rule mining algorithm on Spark

Sanjay Rathee, Arti Kashyap
2018 Journal of Big Data  
Adaptive-Miner uses an adaptive strategy based on the partial processing of datasets.  ...  Association rule mining is one of the highly used methods for this purpose.  ...  PFP search for top-k patterns instead of patterns fulfilling user specified minimum support criteria which make it effective for web data mining.  ... 
doi:10.1186/s40537-018-0112-0 fatcat:jbwtloyc2fhpbac6d4m6thumji

Holistic Approach for Fault-Tolerant Network-on-Chip based Many-Core Systems [article]

Siavoosh Payandeh Azad, Behrad Niazmand, Jaan Raik, Gert Jervan, Thomas Hollstein
2016 arXiv   pre-print
A Mapper/Scheduler Unit (MSU) is used for online generation of different mapping and scheduling solutions based on the current fault configuration of the system.  ...  For detection of faults, we have leveraged concurrent online checkers, able to capture faults with low detection latency and providing the fault information for SHMU, which can be later used for the recovery  ...  Mapper Memories Most Probable Mapping (MPM) memory is used by Mapper-Scheduler Unit (MSU) to keep some mapping configurations for future use to improve the system's response to faults (please refer to  ... 
arXiv:1601.07089v1 fatcat:3wpe2zkuufch3jffdbzuwfisyu

Hands-On Experience of Crowdsourcing for Flood Risks. An Android Mobile Application Tested in Frederikssund, Denmark

Simone Frigerio, Luca Schenato, Giulia Bossi, Matteo Mantovani, Gianluca Marcato, Alessandro Pasuto
2018 International Journal of Environmental Research and Public Health  
This paper describes the design and testing of an Android application named MAppERS (Mobile Applications for Emergency Response and Support), thought to enhance active participation and response of the  ...  The idea is to exploit geospatial data gathered by citizens and volunteers with their own devices such as mobile phones to provide authorities with relevant information in case of flood emergencies.  ...  Acknowledgments: We would like to express our thanks to the partners of the MAppERS Project: Institute of International Sociology Gorizia, Frederiksborg Fire and Rescue Service, Hellenberg International  ... 
doi:10.3390/ijerph15091926 pmid:30181515 pmcid:PMC6164660 fatcat:t6qkb77rpfbl7emuzgtwpncjgq

Polyflow: a Polystore-compliant Mechanism to Provide Interoperability to Heterogeneous Provenance Graphs

Yan Mendes, Daniel De Oliveira, Victor Ströele
2021 Journal of Information and Data Management  
Polyflow was evaluated by experts using provenance data collected from real experiments that generate phylogenetic trees through workflows.  ...  However, each WfMS has a proprietary format for provenance and do it in different granularity levels.  ...  Finally, Entity Mappers are software modules that exploits encoded knowledge about certain sets or subsets of data to create information for a higher layer of applications [Wiederhold 1992 ].  ... 
doi:10.5753/jidm.2020.2017 fatcat:r4evleyx7vaobixao7lc3ejmke

Segmentation of High Resolution Satellite images SPOT applied to Lake Detection

T. Habib, M. Gay, J. Chanussot, P. Bertolino
2006 2006 IEEE International Symposium on Geoscience and Remote Sensing  
High resolution satellite imagery are widely used in many applications. One of the main applications is planet monitoring for hazard assessment.  ...  In this context three different methods are investigated on a SPOT2 image, namely: the spectral angle mapper, the irregular pyramid and the watershed with markers.  ...  The spectral angle mapper exploits the spectral information of each pixel, the irregular pyramid uses both the spectral information and the spatial information by considering each pixel neighbourhood before  ... 
doi:10.1109/igarss.2006.943 fatcat:m6jvcy2ppjcwthrxg437dbve2e

Fast and sensitive mapping of nanopore sequencing reads with GraphMap

Ivan Sović, Mile Šikić, Andreas Wilm, Shannon Nicole Fenlon, Swaine Chen, Niranjan Nagarajan
2016 Nature Communications  
Science, Technology and Research (A*STAR), Singapore, and funding from the Croatian Science Foundation (Project no. 7353-Algorithms for Genome Sequence Analysis).  ...  This work was supported by the IMaGIN platform (project no. 102 101 0025), through a grant from the Science and Engineering Research Council, funding to the Genome Institute of Singapore from the Agency for  ...  In principle, the approach used in GraphMap could be adapted for the problem of computing overlaps and alignments between reads.  ... 
doi:10.1038/ncomms11307 pmid:27079541 pmcid:PMC4835549 fatcat:ll4lrvbdqnaxxgr372bzzloemi

Junction Mapper is a novel computer vision tool to decipher cell-cell contact phenotypes

Helena Brezovjakova, Chris Tomlinson, Noor Mohd Naim, Pamela Swiatlowska, Jennifer E Erasmus, Stephan Huveneers, Julia Gorelik, Susann Bruche, Vania MM Braga
2019 eLife  
Junction Mapper is thus a powerful, unbiased and highly applicable software for profiling cell-cell adhesion phenotypes and facilitate studies on junction dynamics in health and disease.  ...  Quantification of junctions of mammalian epithelia requires laborious manual measurements that are a major roadblock for mechanistic studies.  ...  The Facility for Imaging by Light Microscopy (FILM) at Imperial College London is part supported by funding from the Wellcome Trust (grant 104931/Z/14/Z) and BBSRC (grant BB/L015129/1).  ... 
doi:10.7554/elife.45413 pmid:31793877 pmcid:PMC7034980 fatcat:4qpiuvwogrgtdbclarxo2fv7xy

Query optimization for massively parallel data processing

Sai Wu, Feng Li, Sharad Mehrotra, Beng Chin Ooi
2011 Proceedings of the 2nd ACM Symposium on Cloud Computing - SOCC '11  
MapReduce has been widely recognized as an efficient tool for large-scale data analysis.  ...  In this paper, we propose a query optimization scheme for MapReduce-based processing systems.  ...  We also thank the anonymous reviewers for their insightful comments.  ... 
doi:10.1145/2038916.2038928 dblp:conf/cloud/WuLMO11 fatcat:wrk3tn2o5zfwtc2ascmgsvyr2a

A survey of mapping algorithms in the long-reads era [article]

Kristoffer Sahlin, Thomas Baudeau, Bastien Cazaux, Camille Marchet
2022 bioRxiv   pre-print
The unprecedented characteristics of this new type of sequencing data created a shift, and methods moved on from the seed-and-extend framework previously used for short reads to a seed-and-chain framework  ...  Therefore, in this survey article, we provide an overview of existing mapping methods for long reads with insights into algorithmic details.  ...  A survey of long-read mapping MinHash) to construct fuzzy seeds over subsampled k-mers using the minimizer technique [62] .  ... 
doi:10.1101/2022.05.21.492932 fatcat:imvu5kim2za3nkdbpeyiyngzmm

Automated test mapping and coverage for network topologies

Per Erik Strandberg, Thomas J. Ostrand, Elaine J. Weyuker, Daniel Sundmark, Wasif Afzal
2018 Proceedings of the 27th ACM SIGSOFT International Symposium on Software Testing and Analysis - ISSTA 2018  
An individual physical network topology can be used as the basis for a test system that can execute many test cases, by identifying the part of the physical network topology that corresponds to the configuration  ...  Given a set of available test systems and a large number of test cases, the problem is to determine for each test case, which of the test systems are suitable for executing the test case, and to provide  ...  For example, in early work, Stickney [7] used control flow graphs and cyclomatic trees as test data selection criteria.  ... 
doi:10.1145/3213846.3213859 dblp:conf/issta/StrandbergOWSA18 fatcat:pxktjiwrmzdjbav5mpejzujuzu

Land cover change impact on urban flood modeling (case study: Upper Citarum watershed)

R I Siregar
2018 IOP Conference Series: Earth and Environment  
Land cover changes for the floods increased dramatically to a flow coefficient for 2001 is 0.65 and in 2010 at 0.69.  ...  This study aims to analyze the condition of flooding in urban areas caused by upper Citarum watershed land-use change in 2001 with the land cover change in 2010.  ...  Thanks to Major River Basin Organization of Citarum, Public Work Ministry, for providing the data and others.  ... 
doi:10.1088/1755-1315/126/1/012027 fatcat:vzfocs3nabgkvftdjeafrh5dja
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