Transition Path Theory

Transition path theory is a mathematical framework to analyze MSMs to find transition pathways.

Computing Mean First Passage Times (MFPTs)

Enspara implements fast, raw-matrix transition path theory (i.e. there is no dependence on any enspara-specific objects) for use in extracting various parameters derived in TPT. Among these parameters are Mean First Passage Times, which represent the mean time required to reach a particular state from some other specific state.

First, you’ll need a transition probability matrix and (optionally) equilibrium probabilities. For this recipe, we’ll use the enspara MSM class, but any transition probability matrix and equilibrium probability distribution (as a numpy array) works.

import msmbuilder.tpt

from enspara import tpt
from enspara.msm import MSM, builders

msm = MSM(lag_time=10, method=builders.transpose)
msm.fit(a)

# mfpts is an array where mfpts[i, j] gives you the mfpt from i to j
mfpts = tpt.mfpts(tprob=msm.tprobs_, populations=msm.eq_probs_)

Extracting maximum flux pathways

You can also extract a maximum flux pathway. First need a transition probability matrix and (optionally) equilibrium probabilities.
# assuming we've fit an MSM, as above in the MFPT example
source_state = 1
sink_state = 100

# compute the net flux matrix from our msm
nfm = tpt.net_fluxes(
    msm.tprobs_,
    source_state, sink_state,
    populations=msm.eq_probs_)

path, flux = msmbuilder.tpt.top_path(maximizer_ind, minimizer_ind, nfm.todense())