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Analysis of behavioral changes of zebrafish (Danio rerio) in response to formaldehyde using Self-organizing map and a hidden Markov model

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  • Liu, Yuedan
  • Lee, Sang-Hee
  • Chon, Tae-Soo

Abstract

Two computational methods were applied to classification of movement patterns of zebrafish (Danio rerio) to elucidate Markov processes in behavioral changes before and after treatment of formaldehyde (0.1mg/L) in semi-natural conditions. The complex data of the movement tracks were initially classified by the Self-organizing map (SOM) to present different behavioral states of test individuals. Transition probabilities between behavioral states were further evaluated to fit Markov processes by using the hidden Markov model (HMM). Emission transition probability was also obtained from the observed variables (i.e., speed) for training with the HMM. Experimental transition and emission probability matrices were successfully estimated with the HMM for recognizing sequences of behavioral states with accuracy rates in acceptable ranges at central and boundary zones before (77.3–81.2%) and after (70.1–76.5%) treatment. A heuristic algorithm and a Markov model were efficiently combined to analyze movement patterns and could be a means of in situ behavioral monitoring tool.

Suggested Citation

  • Liu, Yuedan & Lee, Sang-Hee & Chon, Tae-Soo, 2011. "Analysis of behavioral changes of zebrafish (Danio rerio) in response to formaldehyde using Self-organizing map and a hidden Markov model," Ecological Modelling, Elsevier, vol. 222(14), pages 2191-2201.
    • Handle: RePEc:eee:ecomod:v:222:y:2011:i:14:p:2191-2201
    DOI: 10.1016/j.ecolmodel.2011.02.010
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    References listed on IDEAS

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    1. Walker, E. & Bez, N., 2010. "A pioneer validation of a state-space model of vessel trajectories (VMS) with observers’ data," Ecological Modelling, Elsevier, vol. 221(17), pages 2008-2017.
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    1. Ren, Zongming & Zeng, Yang & Fu, Xiu’e & Zhang, Gaosheng & Chen, Linlin & Chen, Jing & Chon, Tae-Soo & Wang, Yawei & Wei, Yuansong, 2013. "Modeling macrozooplankton and water quality relationships after wetland construction in the Wenyuhe River Basin, China," Ecological Modelling, Elsevier, vol. 252(C), pages 97-105.
    2. Li, Shangge & Chon, Tae-Soo & Park, Young-Seuk & Shi, Xiaotao & Ren, Zongming, 2020. "Application of temporal self-organizing maps to patterning short-time series of fish behavior responding to environmental stress," Ecological Modelling, Elsevier, vol. 433(C).
    3. Kim, Hungsoo & Nguyen, Tuyen Van & Uehara, Takashi & Heo, Muyoung & Chon, Tae-Soo, 2015. "Zebrafish (Danio rerio) movement in addressing stress to conflicting stimuli, foods and predators," Ecological Modelling, Elsevier, vol. 306(C), pages 257-267.

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