Canonical correlation methods for exploring microbe-environment interactions in deep subsurface

Viivi Uurtio, Malin Bomberg, Kristian Nybo, Merja Itävaara, Juho Rousu

Research output: Chapter in Book/Report/Conference proceedingConference article in proceedingsScientificpeer-review

2 Citations (Scopus)

Abstract

In this study, we apply non-linear kernelized canonical correlation analysis (KCCA) as well as primal-dual sparse canonical correlation analysis (SCCA) to the discovery of correlations between sulphate reducing bacterial taxa and their geochemical environment in the deep biosphere. For visualization of canonical patterns, we demonstrate the applicability of the correlation plot technique on kernelized data. Finally, we provide an extension to the visual analysis by clustergrams. The presented framework and visualization tools enabled extraction of latent canonical correlation patterns between the salinity of the groundwater and the bacterial taxonomic orders Desulfobacterales, Desulfovibrionales and Clostridiales.
Original languageEnglish
Title of host publicationDiscovery Science
PublisherSpringer
Pages299-307
ISBN (Electronic)978-3-319-24282-8
ISBN (Print)978-3-319-24281-1
DOIs
Publication statusPublished - 2015
MoE publication typeA4 Article in a conference publication
Event18th International Conference on Discovery Science, DS 2015 - Banff, Canada
Duration: 4 Oct 20156 Oct 2015
Conference number: 18

Publication series

NameLecture Notes in Computer Science LNCS
PublisherSpringer
Volume9356

Conference

Conference18th International Conference on Discovery Science, DS 2015
Abbreviated titleDS 2015
CountryCanada
CityBanff
Period4/10/156/10/15

Fingerprint

visualization
visual analysis
biosphere
method
sulfate
salinity
groundwater
analysis

Keywords

  • Canonical correlation
  • Kernel methods
  • Sparsity
  • Deep biosphere

Cite this

Uurtio, V., Bomberg, M., Nybo, K., Itävaara, M., & Rousu, J. (2015). Canonical correlation methods for exploring microbe-environment interactions in deep subsurface. In Discovery Science (pp. 299-307). Springer. Lecture Notes in Computer Science, Vol.. 9356 https://doi.org/10.1007/978-3-319-24282-8_25
Uurtio, Viivi ; Bomberg, Malin ; Nybo, Kristian ; Itävaara, Merja ; Rousu, Juho. / Canonical correlation methods for exploring microbe-environment interactions in deep subsurface. Discovery Science. Springer, 2015. pp. 299-307 (Lecture Notes in Computer Science, Vol. 9356).
@inproceedings{5053b8326b1b426f9243216ebd944d1c,
title = "Canonical correlation methods for exploring microbe-environment interactions in deep subsurface",
abstract = "In this study, we apply non-linear kernelized canonical correlation analysis (KCCA) as well as primal-dual sparse canonical correlation analysis (SCCA) to the discovery of correlations between sulphate reducing bacterial taxa and their geochemical environment in the deep biosphere. For visualization of canonical patterns, we demonstrate the applicability of the correlation plot technique on kernelized data. Finally, we provide an extension to the visual analysis by clustergrams. The presented framework and visualization tools enabled extraction of latent canonical correlation patterns between the salinity of the groundwater and the bacterial taxonomic orders Desulfobacterales, Desulfovibrionales and Clostridiales.",
keywords = "Canonical correlation, Kernel methods, Sparsity, Deep biosphere",
author = "Viivi Uurtio and Malin Bomberg and Kristian Nybo and Merja It{\"a}vaara and Juho Rousu",
year = "2015",
doi = "10.1007/978-3-319-24282-8_25",
language = "English",
isbn = "978-3-319-24281-1",
series = "Lecture Notes in Computer Science LNCS",
publisher = "Springer",
pages = "299--307",
booktitle = "Discovery Science",
address = "Germany",

}

Uurtio, V, Bomberg, M, Nybo, K, Itävaara, M & Rousu, J 2015, Canonical correlation methods for exploring microbe-environment interactions in deep subsurface. in Discovery Science. Springer, Lecture Notes in Computer Science, vol. 9356, pp. 299-307, 18th International Conference on Discovery Science, DS 2015, Banff, Canada, 4/10/15. https://doi.org/10.1007/978-3-319-24282-8_25

Canonical correlation methods for exploring microbe-environment interactions in deep subsurface. / Uurtio, Viivi; Bomberg, Malin; Nybo, Kristian; Itävaara, Merja; Rousu, Juho.

Discovery Science. Springer, 2015. p. 299-307 (Lecture Notes in Computer Science, Vol. 9356).

Research output: Chapter in Book/Report/Conference proceedingConference article in proceedingsScientificpeer-review

TY - GEN

T1 - Canonical correlation methods for exploring microbe-environment interactions in deep subsurface

AU - Uurtio, Viivi

AU - Bomberg, Malin

AU - Nybo, Kristian

AU - Itävaara, Merja

AU - Rousu, Juho

PY - 2015

Y1 - 2015

N2 - In this study, we apply non-linear kernelized canonical correlation analysis (KCCA) as well as primal-dual sparse canonical correlation analysis (SCCA) to the discovery of correlations between sulphate reducing bacterial taxa and their geochemical environment in the deep biosphere. For visualization of canonical patterns, we demonstrate the applicability of the correlation plot technique on kernelized data. Finally, we provide an extension to the visual analysis by clustergrams. The presented framework and visualization tools enabled extraction of latent canonical correlation patterns between the salinity of the groundwater and the bacterial taxonomic orders Desulfobacterales, Desulfovibrionales and Clostridiales.

AB - In this study, we apply non-linear kernelized canonical correlation analysis (KCCA) as well as primal-dual sparse canonical correlation analysis (SCCA) to the discovery of correlations between sulphate reducing bacterial taxa and their geochemical environment in the deep biosphere. For visualization of canonical patterns, we demonstrate the applicability of the correlation plot technique on kernelized data. Finally, we provide an extension to the visual analysis by clustergrams. The presented framework and visualization tools enabled extraction of latent canonical correlation patterns between the salinity of the groundwater and the bacterial taxonomic orders Desulfobacterales, Desulfovibrionales and Clostridiales.

KW - Canonical correlation

KW - Kernel methods

KW - Sparsity

KW - Deep biosphere

U2 - 10.1007/978-3-319-24282-8_25

DO - 10.1007/978-3-319-24282-8_25

M3 - Conference article in proceedings

SN - 978-3-319-24281-1

T3 - Lecture Notes in Computer Science LNCS

SP - 299

EP - 307

BT - Discovery Science

PB - Springer

ER -

Uurtio V, Bomberg M, Nybo K, Itävaara M, Rousu J. Canonical correlation methods for exploring microbe-environment interactions in deep subsurface. In Discovery Science. Springer. 2015. p. 299-307. (Lecture Notes in Computer Science, Vol. 9356). https://doi.org/10.1007/978-3-319-24282-8_25