Network completion using dynamic programming and least-squares fitting

Natsu Nakajima, Takeyuki Tamura, Yoshihiro Yamanishi, Katsuhisa Horimoto, Tatsuya Akutsu

Research output: Contribution to journalArticle

12 Citations (Scopus)

Abstract

We consider the problem of network completion, which is to make the minimum amount of modifications to a given network so that the resulting network is most consistent with the observed data. We employ here a certain type of differential equations as gene regulation rules in a genetic network, gene expression time series data as observed data, and deletions and additions of edges as basic modification operations. In addition, we assume that the numbers of deleted and added edges are specified. For this problem, we present a novel method using dynamic programming and least-squares fitting and show that it outputs a network with the minimum sum squared error in polynomial time if the maximum indegree of the network is bounded by a constant. We also perform computational experiments using both artificially generated and real gene expression time series data.

Original languageEnglish
Article number957620
JournalThe Scientific World Journal
Volume2012
DOIs
Publication statusPublished - Dec 3 2012

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Least-Squares Analysis
Dynamic programming
Gene expression
Time series
gene expression
Gene Expression
time series
Differential equations
Polynomials
Genes
gene
Experiments
experiment

All Science Journal Classification (ASJC) codes

  • Biochemistry, Genetics and Molecular Biology(all)
  • Environmental Science(all)

Cite this

Nakajima, N., Tamura, T., Yamanishi, Y., Horimoto, K., & Akutsu, T. (2012). Network completion using dynamic programming and least-squares fitting. The Scientific World Journal, 2012, [957620]. https://doi.org/10.1100/2012/957620

Network completion using dynamic programming and least-squares fitting. / Nakajima, Natsu; Tamura, Takeyuki; Yamanishi, Yoshihiro; Horimoto, Katsuhisa; Akutsu, Tatsuya.

In: The Scientific World Journal, Vol. 2012, 957620, 03.12.2012.

Research output: Contribution to journalArticle

Nakajima, N, Tamura, T, Yamanishi, Y, Horimoto, K & Akutsu, T 2012, 'Network completion using dynamic programming and least-squares fitting', The Scientific World Journal, vol. 2012, 957620. https://doi.org/10.1100/2012/957620
Nakajima, Natsu ; Tamura, Takeyuki ; Yamanishi, Yoshihiro ; Horimoto, Katsuhisa ; Akutsu, Tatsuya. / Network completion using dynamic programming and least-squares fitting. In: The Scientific World Journal. 2012 ; Vol. 2012.
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