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ScalaParBiBit: scaling the binary biclustering in distributed-memory systems

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Abstract

Biclustering is a data mining technique that allows us to find groups of rows and columns that are highly correlated in a 2D dataset. Although there exist several software applications to perform biclustering, most of them suffer from a high computational complexity which prevents their use in large datasets. In this work we present ScalaParBiBit, a parallel tool to find biclusters on binary data, quite common in many research fields such as text mining, marketing or bioinformatics. ScalaParBiBit takes advantage of the special characteristics of these binary datasets, as well as of an efficient parallel implementation and algorithm, to accelerate the biclustering procedure in distributed-memory systems. The experimental evaluation proves that our tool is significantly faster and more scalable that the state-of-the-art tool ParBiBit in a cluster with 32 nodes and 768 cores. Our tool together with its reference manual are freely available at https://github.com/fraguela/ScalaParBiBit.

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Data availability

The application developed in this manuscript, together with building and usage instructions, as well as the datasets used in the experiments are publicly available under an open source license at https://github.com/fraguela/ScalaParBiBit.

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Acknowledgements

This research was supported by the Ministry of Science and Innovation of Spain (TIN2016-75845-P and PID2019-104184RB-I00, AEI/FEDER/EU, 10.13039/ 501100011033), and by the Xunta de Galicia co-founded by the European Regional Development Fund (ERDF) under the Consolidation Programme of Competitive Reference Groups (ED431C 2017/04). We acknowledge also the support from the Centro Singular de Investigación de Galicia “CITIC”, funded by Xunta de Galicia and the European Union (European Regional Development Fund- Galicia 2014-2020 Program), by grant ED431G 2019/01. We also acknowledge the Centro de Supercomputación de Galicia (CESGA) for the usage of their resources.

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Authors and Affiliations

  1. Universidade da Coruña, CITIC, Grupo de Arquitectura de Computadores, Facultade de Informática, Campus de Elviña, S/N. 15071, A Coruña, Spain

    Basilio B. Fraguela, Diego Andrade & Jorge González-Domínguez

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  1. Basilio B. Fraguela
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  2. Diego Andrade
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  3. Jorge González-Domínguez
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Correspondence to Basilio B. Fraguela.

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Fraguela, B.B., Andrade, D. & González-Domínguez, J. ScalaParBiBit: scaling the binary biclustering in distributed-memory systems. Cluster Comput 24, 2249–2268 (2021). https://doi.org/10.1007/s10586-021-03261-z

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