Cell neighbor determination in the metazoan embryo system

Zi Wang; Husheng Li; Dali Wang; Zhirong Bao

doi:10.1145/3107411.3107465

Cell neighbor determination in the metazoan embryo system

Zi Wang
, Husheng Li
, Dali Wang
, Zhirong Bao

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

4 Scopus citations

Abstract

Cell neighbor determination is a significant component in the simulation of a metazoan embryo system since it influences a number of fundamental biological processes, such as cell signaling, migration, and proliferation. Traditional approaches to find the neighbors of a cell such as Voronoi diagram successfully accomplish this goal, but are too time-consuming as the number of cells grows exponentially. In this paper, we propose a learning-based algorithm that determines the neighbors of specific cells in the metazoan embryo in real-time. We decrease the computational time by four orders of magnitude, and achieve an accuracy of 99.66%. For the verification purpose, the simulation results indicate that our model successfully reproduces the neighbor relationship in C. elegans Notch signaling pathways and cell-cell squeeze force modeling of the cell division process.

Original language	English
Title of host publication	ACM-BCB 2017 - Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics
Publisher	Association for Computing Machinery, Inc
Pages	305-312
Number of pages	8
ISBN (Electronic)	9781450347228
DOIs	https://doi.org/10.1145/3107411.3107465
State	Published - Aug 20 2017
Externally published	Yes
Event	8th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics, ACM-BCB 2017 - Boston, United States Duration: Aug 20 2017 → Aug 23 2017

Publication series

Name	ACM-BCB 2017 - Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics

Conference

Conference	8th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics, ACM-BCB 2017
Country/Territory	United States
City	Boston
Period	08/20/17 → 08/23/17

Funding

We thank Anthony Santella for providing the Voronoi diagrams of C. elegans embryos. This study is supported by an NIH research project grants (R01GM097576 and 2R01GM097576). Research in the Bao lab is also supported by an NIH center grant to MSKCC (P30CA008748). Dr. Wang is also a Senior RD staff at Oak Ridge National Laboratory.

Keywords

Cell neighbor determination
Cell-cell signaling
Metazoan embryo system
Support vector machine
Voronoi

Access to Document

10.1145/3107411.3107465

Cite this

Wang, Z., Li, H., Wang, D., & Bao, Z. (2017). Cell neighbor determination in the metazoan embryo system. In ACM-BCB 2017 - Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (pp. 305-312). (ACM-BCB 2017 - Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics). Association for Computing Machinery, Inc. https://doi.org/10.1145/3107411.3107465

Wang, Zi ; Li, Husheng ; Wang, Dali et al. / Cell neighbor determination in the metazoan embryo system. ACM-BCB 2017 - Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics. Association for Computing Machinery, Inc, 2017. pp. 305-312 (ACM-BCB 2017 - Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics).

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abstract = "Cell neighbor determination is a significant component in the simulation of a metazoan embryo system since it influences a number of fundamental biological processes, such as cell signaling, migration, and proliferation. Traditional approaches to find the neighbors of a cell such as Voronoi diagram successfully accomplish this goal, but are too time-consuming as the number of cells grows exponentially. In this paper, we propose a learning-based algorithm that determines the neighbors of specific cells in the metazoan embryo in real-time. We decrease the computational time by four orders of magnitude, and achieve an accuracy of 99.66\%. For the verification purpose, the simulation results indicate that our model successfully reproduces the neighbor relationship in C. elegans Notch signaling pathways and cell-cell squeeze force modeling of the cell division process.",

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author = "Zi Wang and Husheng Li and Dali Wang and Zhirong Bao",

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Wang, Z, Li, H, Wang, D & Bao, Z 2017, Cell neighbor determination in the metazoan embryo system. in ACM-BCB 2017 - Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics. ACM-BCB 2017 - Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics, Association for Computing Machinery, Inc, pp. 305-312, 8th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics, ACM-BCB 2017, Boston, United States, 08/20/17. https://doi.org/10.1145/3107411.3107465

Cell neighbor determination in the metazoan embryo system. / Wang, Zi; Li, Husheng; Wang, Dali et al.
ACM-BCB 2017 - Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics. Association for Computing Machinery, Inc, 2017. p. 305-312 (ACM-BCB 2017 - Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics).

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

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AU - Wang, Zi

AU - Li, Husheng

AU - Wang, Dali

AU - Bao, Zhirong

PY - 2017/8/20

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N2 - Cell neighbor determination is a significant component in the simulation of a metazoan embryo system since it influences a number of fundamental biological processes, such as cell signaling, migration, and proliferation. Traditional approaches to find the neighbors of a cell such as Voronoi diagram successfully accomplish this goal, but are too time-consuming as the number of cells grows exponentially. In this paper, we propose a learning-based algorithm that determines the neighbors of specific cells in the metazoan embryo in real-time. We decrease the computational time by four orders of magnitude, and achieve an accuracy of 99.66%. For the verification purpose, the simulation results indicate that our model successfully reproduces the neighbor relationship in C. elegans Notch signaling pathways and cell-cell squeeze force modeling of the cell division process.

AB - Cell neighbor determination is a significant component in the simulation of a metazoan embryo system since it influences a number of fundamental biological processes, such as cell signaling, migration, and proliferation. Traditional approaches to find the neighbors of a cell such as Voronoi diagram successfully accomplish this goal, but are too time-consuming as the number of cells grows exponentially. In this paper, we propose a learning-based algorithm that determines the neighbors of specific cells in the metazoan embryo in real-time. We decrease the computational time by four orders of magnitude, and achieve an accuracy of 99.66%. For the verification purpose, the simulation results indicate that our model successfully reproduces the neighbor relationship in C. elegans Notch signaling pathways and cell-cell squeeze force modeling of the cell division process.

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Wang Z, Li H, Wang D, Bao Z. Cell neighbor determination in the metazoan embryo system. In ACM-BCB 2017 - Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics. Association for Computing Machinery, Inc. 2017. p. 305-312. (ACM-BCB 2017 - Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics). doi: 10.1145/3107411.3107465

Cell neighbor determination in the metazoan embryo system

Abstract

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Keywords

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