Genetic Algorithms in Search, Optimization and Machine Learning
Genetic Algorithms in Search, Optimization and Machine Learning
Verifying Continuous Time Markov Chains
CAV '96 Proceedings of the 8th International Conference on Computer Aided Verification
Parameter estimation for models of cell signaling pathways based on semi-quantitative data
BioMed'06 Proceedings of the 24th IASTED international conference on Biomedical engineering
Bayesian ranking of biochemical system models
Bioinformatics
On the analysis of numerical data time series in temporal logic
CMSB'07 Proceedings of the 2007 international conference on Computational methods in systems biology
A unifying framework for modelling and analysing biochemical pathways using Petri nets
CMSB'07 Proceedings of the 2007 international conference on Computational methods in systems biology
Machine learning biochemical networks from temporal logic properties
Transactions on Computational Systems Biology VI
Probabilistic Model Checking of Biological Systems with Uncertain Kinetic Rates
RP '09 Proceedings of the 3rd International Workshop on Reachability Problems
Process calculi for systems biology
Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology
Component-based construction of bio-pathway models: The parameter estimation problem
Theoretical Computer Science
Model repair for probabilistic systems
TACAS'11/ETAPS'11 Proceedings of the 17th international conference on Tools and algorithms for the construction and analysis of systems: part of the joint European conferences on theory and practice of software
How might petri nets enhance your systems biology toolkit
PETRI NETS'11 Proceedings of the 32nd international conference on Applications and theory of Petri Nets
A hybrid factored frontier algorithm for dynamic Bayesian network models of biopathways
Proceedings of the 9th International Conference on Computational Methods in Systems Biology
Proceedings of the 9th International Conference on Computational Methods in Systems Biology
On Parameter Synthesis by Parallel Model Checking
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
A logic for causal inference in time series with discrete and continuous variables
IJCAI'11 Proceedings of the Twenty-Second international joint conference on Artificial Intelligence - Volume Volume Two
A Hybrid Factored Frontier Algorithm for Dynamic Bayesian Networks with a Biopathways Application
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Multi-objective optimisation, sensitivity and robustness analysis in FBA modelling
CMSB'12 Proceedings of the 10th international conference on Computational Methods in Systems Biology
Proceedings of the Winter Simulation Conference
Multiscale Modeling and Analysis of Planar Cell Polarity in the Drosophila Wing
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Modeling membrane systems using colored stochastic Petri nets
Natural Computing: an international journal
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Model checking has historically been an important tool to verify models of a wide variety of systems. Typically a model has to exhibit certain properties to be classed `acceptable'. In this work we use model checking in a new setting; parameter estimation. We characterise the desired behaviour of a model in a temporal logic property and alter the model to make it conform to the property (determined through model checking). We have implemented a computational system called MC2(GA) which pairs a model checker with a genetic algorithm. To drive parameter estimation, the fitness of set of parameters in a model is the inverse of the distance between its actual behaviour and the desired behaviour. The model checker used is the simulation-based Monte Carlo Model Checker for Probabilistic Linear-time Temporal Logic with numerical constraints, MC2(PLTLc). Numerical constraints as well as the overall probability of the behaviour expressed in temporal logic are used to minimise the behavioural distance. We define the theory underlying our parameter estimation approach in both the stochastic and continuous worlds. We apply our approach to biochemical systems and present an illustrative example where we estimate the kinetic rate constants in a continuous model of a signalling pathway.