ode_mcmc

Implementation of probabilistic ODE model structure inference using MCMC methods

Authors

• Juho Timonen (juho.timonen@aalto.fi)
• Based on LEM modeling implementation by Jukka Intosalmi [http://research.ics.aalto.fi/csb/software/lem/]

Main functions

Main functions for running the inference in simulated data cases where the model probabilities have been precomputed

• main_sim_1.m
• main_sim_23.m

Function for precomputing model probabilities

• precompute.m

Main functions for creating simulated data and formulating an inference problem

• defineSimProblem_1.m
• defineSimProblem_2.m
• defineSimProblem_3.m

Main function for structure inference with real data

• main_Th17.m

Requirements

• Matlab [https://se.mathworks.com/products/matlab.html]
• Sundials + sundialsTB [https://computation.llnl.gov/projects/sundials]

Tested with Matlab 2016b and sundials 2.4.0

References

• J. Timonen, H. Mannerström, H. Lähdesmäki and J. Intosalmi, "A probabilistic framework for molecular network structure inference by means of mechanistic modeling," in IEEE/ACM Transactions on Computational Biology and Bioinformatics.

URL: http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=8334413&isnumber=4359833