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

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

doi:10.1007/978-3-319-24282-8_25

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 proceeding › Conference article in proceedings › Scientific › peer-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 language	English
Title of host publication	Discovery Science
Publisher	Springer
Pages	299-307
ISBN (Electronic)	978-3-319-24282-8
ISBN (Print)	978-3-319-24281-1
DOIs	https://doi.org/10.1007/978-3-319-24282-8_25
Publication status	Published - 2015
MoE publication type	A4 Article in a conference publication
Event	18th International Conference on Discovery Science, DS 2015 - Banff, Canada Duration: 4 Oct 2015 → 6 Oct 2015 Conference number: 18

Publication series

Series	Lecture Notes in Computer Science
Volume	9356

Conference

Conference	18th International Conference on Discovery Science, DS 2015
Abbreviated title	DS 2015
Country/Territory	Canada
City	Banff
Period	4/10/15 → 6/10/15

Keywords

Canonical correlation
Kernel methods
Sparsity
Deep biosphere

Access to Document

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

Cite this

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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",

publisher = "Springer",

pages = "299--307",

booktitle = "Discovery Science",

address = "Germany",

note = "18th International Conference on Discovery Science, DS 2015, DS 2015 ; Conference date: 04-10-2015 Through 06-10-2015",

}

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

Research output: Chapter in Book/Report/Conference proceeding › Conference article in proceedings › Scientific › peer-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

N1 - Conference code: 18

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

SP - 299

EP - 307

BT - Discovery Science

PB - Springer

T2 - 18th International Conference on Discovery Science, DS 2015

Y2 - 4 October 2015 through 6 October 2015

ER -

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

Abstract

Publication series

Conference

Keywords

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Cite this