Network Completion Using Dynamic Programming and Least-Squares Fitting
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...
Saved in:
| Main Authors: | , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Wiley
2012-01-01
|
| Series: | The Scientific World Journal |
| Online Access: | http://dx.doi.org/10.1100/2012/957620 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1849305349146804224 |
|---|---|
| author | Natsu Nakajima Takeyuki Tamura Yoshihiro Yamanishi Katsuhisa Horimoto Tatsuya Akutsu |
| author_facet | Natsu Nakajima Takeyuki Tamura Yoshihiro Yamanishi Katsuhisa Horimoto Tatsuya Akutsu |
| author_sort | Natsu Nakajima |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-09900602e2ec4e15829b1896621f4bdf |
| institution | Kabale University |
| issn | 1537-744X |
| language | English |
| publishDate | 2012-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | The Scientific World Journal |
| spelling | doaj-art-09900602e2ec4e15829b1896621f4bdf2025-08-20T03:55:29ZengWileyThe Scientific World Journal1537-744X2012-01-01201210.1100/2012/957620957620Network Completion Using Dynamic Programming and Least-Squares FittingNatsu Nakajima0Takeyuki Tamura1Yoshihiro Yamanishi2Katsuhisa Horimoto3Tatsuya Akutsu4Bioinformatics Center, Institute for Chemical Research, Kyoto University Gokasho, Uji, Kyoto 611-0011, JapanBioinformatics Center, Institute for Chemical Research, Kyoto University Gokasho, Uji, Kyoto 611-0011, JapanDivision of System Cohort, Multi-scale Research Center for Medical Science, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582, JapanComputational Biology Research Center, National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, JapanBioinformatics Center, Institute for Chemical Research, Kyoto University Gokasho, Uji, Kyoto 611-0011, JapanWe 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.http://dx.doi.org/10.1100/2012/957620 |
| spellingShingle | Natsu Nakajima Takeyuki Tamura Yoshihiro Yamanishi Katsuhisa Horimoto Tatsuya Akutsu Network Completion Using Dynamic Programming and Least-Squares Fitting The Scientific World Journal |
| title | Network Completion Using Dynamic Programming and Least-Squares Fitting |
| title_full | Network Completion Using Dynamic Programming and Least-Squares Fitting |
| title_fullStr | Network Completion Using Dynamic Programming and Least-Squares Fitting |
| title_full_unstemmed | Network Completion Using Dynamic Programming and Least-Squares Fitting |
| title_short | Network Completion Using Dynamic Programming and Least-Squares Fitting |
| title_sort | network completion using dynamic programming and least squares fitting |
| url | http://dx.doi.org/10.1100/2012/957620 |
| work_keys_str_mv | AT natsunakajima networkcompletionusingdynamicprogrammingandleastsquaresfitting AT takeyukitamura networkcompletionusingdynamicprogrammingandleastsquaresfitting AT yoshihiroyamanishi networkcompletionusingdynamicprogrammingandleastsquaresfitting AT katsuhisahorimoto networkcompletionusingdynamicprogrammingandleastsquaresfitting AT tatsuyaakutsu networkcompletionusingdynamicprogrammingandleastsquaresfitting |