dynamo.vf.MFPT

dynamo.vf.MFPT(X_input, F, D=0.1, lambda_=1)[source]

Calculate the MFPT (mean first passage time) to convert from one cell state to another cell state by taking the optimal path.

The mean first-passage time (MFPT) defines an average timescale for a stochastic event to first occur. The MFPT maps a multi-step kinetic process to a coarse-grained timescale for reaching a final state, having started at some initial state. The inverse of the MFPT is an effective rate of the overall reaction. (reference: Mean First-Passage Times in Biology Nicholas F. Polizzi,a Michael J. Therien,b and David N. Beratan)

Parameters:

  • X_input (numpy.ndarray) – The initial guess of the least action path. Default is a straight line connecting the starting and end path.

  • F (Function) – The reconstructed vector field function

  • D (float) – The diffusion constant. Note that this can be a space-dependent matrix.

  • lamada (float) – Regularization parameter

Returns:

The transition to convert from one cell state to another.