An Explorative Parameter Sweep: Spatial-temporal Data Mining in Stochastic Reaction-diffusion Simulations

University essay from Uppsala universitet/Institutionen för biologisk grundutbildning


Stochastic reaction-diffusion simulations has become an efficient approach for modelling spatial aspects of intracellular biochemical reaction networks. By accounting for intrinsic noise due to low copy number of chemical species, stochastic reaction-diffusion simulations have the ability to more accurately predict and model biological systems. As with many simulations software, exploration of the parameters associated with the model can be needed to yield new knowledge about the underlying system. The exploration can be conducted by executing parameter sweeps for a model. However, with little or no prior knowledge about the modelled system, the effort for practitioners to explore the parameter space can get overwhelming. To account for this problem we perform a feasibility study on an explorative behavioural analysis of stochastic reaction-diffusion simulations by applying spatial-temporal data mining to large parameter sweeps. By reducing individual simulation outputs into a feature space involving simple time series and distribution analytics, we were able to find similar behaving simulations after performing an agglomerative hierarchical clustering.

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