Inference of gene regulatory networks from time course gene expression data using neural networks and swarm intelligence

H. W. Ressom; Y. Zhang; J. Xuan; Y. Wang; R. Clarke

doi:10.1109/CIBCB.2006.330969

Inference of gene regulatory networks from time course gene expression data using neural networks and swarm intelligence

H. W. Ressom, Y. Zhang, J. Xuan, Y. Wang, R. Clarke

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

15 Scopus citations

Abstract

We present a novel algorithm that combines a recurrent neural network (RNN) and two swarm intelligence (SI) methods to infer a gene regulatory network (GRN) from time course gene expression data. The algorithm uses ant colony optimization (ACO) to identify the optimal architecture of an RNN, while the weights of the RNN are optimized using particle swarm optimization (PSO). Our goal is to construct an RNN whose response mimics gene expression data generated by time course DNA microarray experiments. We observed promising results in applying the proposed hybrid SI-RNN algorithm to infer networks of interaction from simulated and real-world gene expression data.

Original language	English (US)
Title of host publication	Proceedings of the 2006 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB'06
Pages	435-442
Number of pages	8
DOIs	https://doi.org/10.1109/CIBCB.2006.330969
State	Published - 2006
Externally published	Yes
Event	3rd Computational Intelligence in Bioinformatics and Computational Biology Symposium, CIBCB - Toronto, ON, Canada Duration: Sep 28 2006 → Sep 29 2006

Publication series

Name	Proceedings of the 2006 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB'06

Conference

Conference	3rd Computational Intelligence in Bioinformatics and Computational Biology Symposium, CIBCB
Country/Territory	Canada
City	Toronto, ON
Period	9/28/06 → 9/29/06

Publisher link

10.1109/CIBCB.2006.330969

Find It

Find It at U of M Libraries

Cite this

Ressom, H. W., Zhang, Y., Xuan, J., Wang, Y., & Clarke, R. (2006). Inference of gene regulatory networks from time course gene expression data using neural networks and swarm intelligence. In Proceedings of the 2006 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB'06 (pp. 435-442). Article 4133205 (Proceedings of the 2006 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB'06). https://doi.org/10.1109/CIBCB.2006.330969

Inference of gene regulatory networks from time course gene expression data using neural networks and swarm intelligence. / Ressom, H. W.; Zhang, Y.; Xuan, J. et al.
Proceedings of the 2006 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB'06. 2006. p. 435-442 4133205 (Proceedings of the 2006 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB'06).

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

Ressom, HW, Zhang, Y, Xuan, J, Wang, Y & Clarke, R 2006, Inference of gene regulatory networks from time course gene expression data using neural networks and swarm intelligence. in Proceedings of the 2006 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB'06., 4133205, Proceedings of the 2006 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB'06, pp. 435-442, 3rd Computational Intelligence in Bioinformatics and Computational Biology Symposium, CIBCB, Toronto, ON, Canada, 9/28/06. https://doi.org/10.1109/CIBCB.2006.330969

Ressom HW, Zhang Y, Xuan J, Wang Y, Clarke R. Inference of gene regulatory networks from time course gene expression data using neural networks and swarm intelligence. In Proceedings of the 2006 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB'06. 2006. p. 435-442. 4133205. (Proceedings of the 2006 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB'06). doi: 10.1109/CIBCB.2006.330969

Ressom, H. W. ; Zhang, Y. ; Xuan, J. et al. / Inference of gene regulatory networks from time course gene expression data using neural networks and swarm intelligence. Proceedings of the 2006 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB'06. 2006. pp. 435-442 (Proceedings of the 2006 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB'06).

@inproceedings{a3454e162a6e4776a4fef0bb9b03b7ea,

title = "Inference of gene regulatory networks from time course gene expression data using neural networks and swarm intelligence",

abstract = "We present a novel algorithm that combines a recurrent neural network (RNN) and two swarm intelligence (SI) methods to infer a gene regulatory network (GRN) from time course gene expression data. The algorithm uses ant colony optimization (ACO) to identify the optimal architecture of an RNN, while the weights of the RNN are optimized using particle swarm optimization (PSO). Our goal is to construct an RNN whose response mimics gene expression data generated by time course DNA microarray experiments. We observed promising results in applying the proposed hybrid SI-RNN algorithm to infer networks of interaction from simulated and real-world gene expression data.",

author = "Ressom, {H. W.} and Y. Zhang and J. Xuan and Y. Wang and R. Clarke",

year = "2006",

doi = "10.1109/CIBCB.2006.330969",

language = "English (US)",

isbn = "1424406234",

series = "Proceedings of the 2006 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB'06",

pages = "435--442",

booktitle = "Proceedings of the 2006 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB'06",

note = "3rd Computational Intelligence in Bioinformatics and Computational Biology Symposium, CIBCB ; Conference date: 28-09-2006 Through 29-09-2006",

}

TY - GEN

T1 - Inference of gene regulatory networks from time course gene expression data using neural networks and swarm intelligence

AU - Ressom, H. W.

AU - Zhang, Y.

AU - Xuan, J.

AU - Wang, Y.

AU - Clarke, R.

PY - 2006

Y1 - 2006

N2 - We present a novel algorithm that combines a recurrent neural network (RNN) and two swarm intelligence (SI) methods to infer a gene regulatory network (GRN) from time course gene expression data. The algorithm uses ant colony optimization (ACO) to identify the optimal architecture of an RNN, while the weights of the RNN are optimized using particle swarm optimization (PSO). Our goal is to construct an RNN whose response mimics gene expression data generated by time course DNA microarray experiments. We observed promising results in applying the proposed hybrid SI-RNN algorithm to infer networks of interaction from simulated and real-world gene expression data.

AB - We present a novel algorithm that combines a recurrent neural network (RNN) and two swarm intelligence (SI) methods to infer a gene regulatory network (GRN) from time course gene expression data. The algorithm uses ant colony optimization (ACO) to identify the optimal architecture of an RNN, while the weights of the RNN are optimized using particle swarm optimization (PSO). Our goal is to construct an RNN whose response mimics gene expression data generated by time course DNA microarray experiments. We observed promising results in applying the proposed hybrid SI-RNN algorithm to infer networks of interaction from simulated and real-world gene expression data.

UR - http://www.scopus.com/inward/record.url?scp=50249154011&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=50249154011&partnerID=8YFLogxK

U2 - 10.1109/CIBCB.2006.330969

DO - 10.1109/CIBCB.2006.330969

M3 - Conference contribution

AN - SCOPUS:50249154011

SN - 1424406234

SN - 9781424406234

T3 - Proceedings of the 2006 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB'06

SP - 435

EP - 442

BT - Proceedings of the 2006 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB'06

T2 - 3rd Computational Intelligence in Bioinformatics and Computational Biology Symposium, CIBCB

Y2 - 28 September 2006 through 29 September 2006

ER -

Inference of gene regulatory networks from time course gene expression data using neural networks and swarm intelligence

Abstract

Publication series

Conference

Publisher link

Find It

Other files and links

Fingerprint

Cite this