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StochNetV2: A Tool for Automated Deep Abstractions for Stochastic Reaction Networks

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Quantitative Evaluation of Systems (QEST 2020)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 12289))

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We present a toolbox for stochastic simulations with CRN models and their (automated) deep abstractions: a mixture density deep neural network trained on time-series data produced by the CRN. The optimal neural network architecture is learnt along with learning the transition kernel of the abstract process. Automated search of the architecture makes the method applicable directly to any given CRN, which is time-saving for deep learning experts and crucial for non-specialists. The tool was primarily designed to efficiently reproduce simulation traces of given complex stochastic reaction networks arising in systems biology research, possibly with multi-modal emergent phenotypes. It is at the same time applicable to any other application domain, where time-series measurements of a Markovian stochastic process are available by experiment or synthesised with simulation (e.g. are obtained from a rule-based description of the CRN).

TP’s research is supported by the Ministry of Science, Research and the Arts of the state of Baden-Württemberg, and the DFG Centre of Excellence 2117 ‘Centre for the Advanced Study of Collective Behaviour’ (ID: 422037984), DR’s research is supported by Young Scholar Fund (YSF), project no. \(P83943018 FP 430\_/18\) and by the ‘Centre for the Advanced Study of Collective Behaviour’. The authors would like to thank to Luca Bortolussi for inspiring discussions on the topic.

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  1. 1.

    The tool name makes it transparent that the tool was inspired by [2] called ‘StochNet’.

  2. 2.

    While we performed specific performance evaluation, e.g. in Fig. 2 and [8], a systematic scalability analysis is beyond the scope of this tool presentation.


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Correspondence to Tatjana Petrov .

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Repin, D., Phung, NH., Petrov, T. (2020). StochNetV2: A Tool for Automated Deep Abstractions for Stochastic Reaction Networks. In: Gribaudo, M., Jansen, D.N., Remke, A. (eds) Quantitative Evaluation of Systems. QEST 2020. Lecture Notes in Computer Science(), vol 12289. Springer, Cham.

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  • Print ISBN: 978-3-030-59853-2

  • Online ISBN: 978-3-030-59854-9

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