Completing SBGN-AF networks by logic-based hypothesis finding

Yoshitaka Yamamoto; Adrien Rougny; Hidetomo Nabeshima; Katsumi Inoue; Hisao Moriya; Christine Froidevaux; Koji Iwanuma

doi:10.1007/978-3-319-10398-3_14

Completing SBGN-AF networks by logic-based hypothesis finding

Yoshitaka Yamamoto, Adrien Rougny, Hidetomo Nabeshima, Katsumi Inoue, Hisao Moriya, Christine Froidevaux, Koji Iwanuma

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

1 Citation (Scopus)

Abstract

This study considers formal methods for finding unknown interactions of incomplete molecular networks using microarray profiles. In systems biology, a challenging problem lies in the growing scale and complexity of molecular networks. Along with high-throughput experimental tools, it is not straightforward to reconstruct huge and complicated networks using observed data by hand. Thus, we address the completion problem of our target networks represented by a standard markup language, called SBGN (in particular, Activity Flow). Our proposed method is based on logic-based hypothesis finding techniques; given an input SBGN network and its profile data, missing interactions can be logically generated as hypotheses by the proposed method. In this paper, we also show empirical results that demonstrate how the proposed method works with a real network involved in the glucose repression of S. cerevisiae.

Original language	English
Title of host publication	Formal Methods in Macro-Biology - First International Conference, FMMB 2014, Proceedings
Editors	Carla Piazza, François Fages
Publisher	Springer Verlag
Pages	165-179
Number of pages	15
ISBN (Electronic)	9783319103976
ISBN (Print)	9783319103976
DOIs	https://doi.org/10.1007/978-3-319-10398-3_14
Publication status	Published - 2014
Event	1st International Conference on Formal Methods in Macro-Biology, FMMB 2014 - Noumea, New Caledonia Duration: Sep 22 2014 → Sep 24 2014

Publication series

Name	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume	8738 LNBI
ISSN (Print)	0302-9743
ISSN (Electronic)	1611-3349

Other

Other	1st International Conference on Formal Methods in Macro-Biology, FMMB 2014
Country	New Caledonia
City	Noumea
Period	9/22/14 → 9/24/14

Keywords

SBGN
completion
glucose repression
hypothesis finding

ASJC Scopus subject areas

Theoretical Computer Science
Computer Science(all)

Access to Document

10.1007/978-3-319-10398-3_14

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Cite this

Yamamoto, Y., Rougny, A., Nabeshima, H., Inoue, K., Moriya, H., Froidevaux, C., & Iwanuma, K. (2014). Completing SBGN-AF networks by logic-based hypothesis finding. In C. Piazza, & F. Fages (Eds.), Formal Methods in Macro-Biology - First International Conference, FMMB 2014, Proceedings (pp. 165-179). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 8738 LNBI). Springer Verlag. https://doi.org/10.1007/978-3-319-10398-3_14

Completing SBGN-AF networks by logic-based hypothesis finding. / Yamamoto, Yoshitaka; Rougny, Adrien; Nabeshima, Hidetomo; Inoue, Katsumi; Moriya, Hisao; Froidevaux, Christine; Iwanuma, Koji.

Formal Methods in Macro-Biology - First International Conference, FMMB 2014, Proceedings. ed. / Carla Piazza; François Fages. Springer Verlag, 2014. p. 165-179 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 8738 LNBI).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Yamamoto, Y, Rougny, A, Nabeshima, H, Inoue, K, Moriya, H, Froidevaux, C & Iwanuma, K 2014, Completing SBGN-AF networks by logic-based hypothesis finding. in C Piazza & F Fages (eds), Formal Methods in Macro-Biology - First International Conference, FMMB 2014, Proceedings. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 8738 LNBI, Springer Verlag, pp. 165-179, 1st International Conference on Formal Methods in Macro-Biology, FMMB 2014, Noumea, New Caledonia, 9/22/14. https://doi.org/10.1007/978-3-319-10398-3_14

Yamamoto Y, Rougny A, Nabeshima H, Inoue K, Moriya H, Froidevaux C et al. Completing SBGN-AF networks by logic-based hypothesis finding. In Piazza C, Fages F, editors, Formal Methods in Macro-Biology - First International Conference, FMMB 2014, Proceedings. Springer Verlag. 2014. p. 165-179. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). https://doi.org/10.1007/978-3-319-10398-3_14

Yamamoto, Yoshitaka ; Rougny, Adrien ; Nabeshima, Hidetomo ; Inoue, Katsumi ; Moriya, Hisao ; Froidevaux, Christine ; Iwanuma, Koji. / Completing SBGN-AF networks by logic-based hypothesis finding. Formal Methods in Macro-Biology - First International Conference, FMMB 2014, Proceedings. editor / Carla Piazza ; François Fages. Springer Verlag, 2014. pp. 165-179 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).

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