example_sample_robertson_with_dream.py 文件源码

def likelihood(parameter_vector):    

    param_dict = {pname: pvalue for pname, pvalue in zip(pysb_sampled_parameter_names, parameter_vector)}

    for pname, pvalue in param_dict.items():

        #Change model parameter values to current location in parameter space

        model.parameters[pname].value = 10**(pvalue)

    #Simulate experimentally measured Ctotal values.

    solver.run()

    #Calculate log probability contribution from simulated experimental values.

    logp_ctotal = np.sum(like_ctot.logpdf(solver.yobs['C_total']))

    #If model simulation failed due to integrator errors, return a log probability of -inf.
    if np.isnan(logp_ctotal):
        logp_ctotal = -np.inf

    return logp_ctotal


# Add vector of PySB rate parameters to be sampled as unobserved random variables to DREAM with uniform priors.