def test_active_state_indices(oom_msm_scenario):
for msm in oom_msm_scenario.msms:
dtrajs_proj = msm.count_model.transform_discrete_trajectories_to_submodel(oom_msm_scenario.dtrajs)
indices = compute_index_states(dtrajs_proj)
np.testing.assert_equal(len(indices), msm.n_states)
hist = count_states(oom_msm_scenario.dtrajs)
for state in range(msm.n_states):
np.testing.assert_equal(indices[state].shape[0], hist[msm.count_model.state_symbols[state]])
np.testing.assert_equal(indices[state].shape[1], 2)
def test_simulate_stats(msm):
# test statistics of starting state
N = 5000
trajs = [msm.simulate(1, seed=i + 1) for i in range(N)]
ss = np.concatenate(trajs).astype(int)
pi = deeptime.markov.tools.analysis.stationary_distribution(
msm.transition_matrix)
piest = count_states(ss) / float(N)
np.testing.assert_allclose(piest, pi, atol=0.025)
def test_active_state_indices(self, setting):
scenario = make_double_well(setting)
from deeptime.markov.sample import compute_index_states
I = compute_index_states(scenario.data.dtraj, subset=scenario.msm.count_model.state_symbols)
assert (len(I) == scenario.msm.n_states)
# compare to histogram
from deeptime.markov.util import count_states
hist = count_states(scenario.data.dtraj)
# number of frames should match on active subset
A = scenario.msm.count_model.state_symbols
for i in range(A.shape[0]):
assert I[i].shape[0] == hist[A[i]]
assert I[i].shape[1] == 2
def test_observable_state_indices(self):
from deeptime.markov.sample import compute_index_states
hmsm = self.hmm_lag10_largest
I = compute_index_states(self.dtrajs, subset=hmsm.observation_symbols)
# I = hmsm.observable_state_indexes
np.testing.assert_equal(len(I), hmsm.n_observation_states)
# compare to histogram
hist = count_states(self.dtrajs)
# number of frames should match on active subset
A = hmsm.observation_symbols
for i in range(A.shape[0]):
np.testing.assert_equal(I[i].shape[0], hist[A[i]])
np.testing.assert_equal(I[i].shape[1], 2)
def fit(self, data, *args, **kw):
r""" Counts transitions at given lag time according to configuration of the estimator.
Parameters
----------
data : array_like or list of array_like
discretized trajectories
"""
dtrajs = ensure_dtraj_list(data)
# basic count statistics
histogram = count_states(dtrajs, ignore_negative=True)
# Compute count matrix
count_mode = self.count_mode
lagtime = self.lagtime
count_matrix = TransitionCountEstimator.count(count_mode,
dtrajs,
lagtime,
sparse=self.sparse)
if self.n_states is not None and self.n_states > count_matrix.shape[0]:
histogram = np.pad(histogram,
pad_width=[
(0, self.n_states - count_matrix.shape[0])
])
if issparse(count_matrix):
count_matrix = scipy.sparse.csr_matrix(
(count_matrix.data, count_matrix.indices,
count_matrix.indptr),
shape=(self.n_states, self.n_states))
else:
n_pad = self.n_states - count_matrix.shape[0]
count_matrix = np.pad(count_matrix,
pad_width=[(0, n_pad), (0, n_pad)])
# initially state symbols, full count matrix, and full histogram can be left None because they coincide
# with the input arguments
self._model = TransitionCountModel(count_matrix=count_matrix,
counting_mode=count_mode,
lagtime=lagtime,
state_histogram=histogram)
return self
def nonempty_obs(self, dtrajs) -> np.ndarray:
r"""
Computes the set of visited observable states given a set of discrete trajectories.
Parameters
----------
dtrajs : array_like
observable trajectory
Returns
-------
symbols : np.ndarray
The observation symbols which are visited.
"""
from deeptime.markov.util import compute_dtrajs_effective, count_states
if dtrajs is None:
raise ValueError("Needs nonempty dtrajs to evaluate nonempty obs.")
dtrajs = ensure_dtraj_list(dtrajs)
dtrajs_lagged_strided = compute_dtrajs_effective(
dtrajs, self.transition_model.lagtime,
self.transition_model.count_model.n_states_full, self.stride)
obs = np.where(count_states(dtrajs_lagged_strided) > 0)[0]
return obs
def __init__(self, complete: bool = True):
self.complete = complete
data = np.load(os.path.join(os.path.dirname(os.path.realpath(__file__)), 'resources', 'TestData_OOM_MSM.npz'))
if complete:
self.dtrajs = [data['arr_%d' % k] for k in range(1000)]
else:
excluded = [
21, 25, 30, 40, 66, 72, 74, 91, 116, 158, 171, 175, 201, 239, 246, 280, 300, 301, 310, 318,
322, 323, 339, 352, 365, 368, 407, 412, 444, 475, 486, 494, 510, 529, 560, 617, 623, 637,
676, 689, 728, 731, 778, 780, 811, 828, 838, 845, 851, 859, 868, 874, 895, 933, 935, 938,
958, 961, 968, 974, 984, 990, 999
]
self.dtrajs = [data['arr_%d' % k] for k in np.setdiff1d(np.arange(1000), excluded)]
# Number of states:
self.N = 5
# Lag time:
self.tau = 5
self.dtrajs_lag = [traj[:-self.tau] for traj in self.dtrajs]
# Rank:
if complete:
self.rank = 3
else:
self.rank = 2
# Build models:
self.msmrev = OOMReweightedMSM(lagtime=self.tau, rank_mode='bootstrap_trajs').fit(self.dtrajs)
self.msmrev_sparse = OOMReweightedMSM(lagtime=self.tau, sparse=True, rank_mode='bootstrap_trajs') \
.fit(self.dtrajs)
self.msm = OOMReweightedMSM(lagtime=self.tau, reversible=False, rank_mode='bootstrap_trajs').fit(self.dtrajs)
self.msm_sparse = OOMReweightedMSM(lagtime=self.tau, reversible=False, sparse=True,
rank_mode='bootstrap_trajs').fit(self.dtrajs)
self.estimators = [self.msmrev, self.msm, self.msmrev_sparse, self.msm_sparse]
self.msms = [est.fetch_model() for est in self.estimators]
# Reference count matrices at lag time tau and 2*tau:
if complete:
self.C2t = data['C2t']
else:
self.C2t = data['C2t_s']
self.Ct = np.sum(self.C2t, axis=1)
if complete:
self.Ct_active = self.Ct
self.C2t_active = self.C2t
self.active_faction = 1.
else:
lcc = msmest.largest_connected_set(self.Ct)
self.Ct_active = msmest.largest_connected_submatrix(self.Ct, lcc=lcc)
self.C2t_active = self.C2t[:4, :4, :4]
self.active_fraction = np.sum(self.Ct_active) / np.sum(self.Ct)
# Compute OOM-components:
self.Xi, self.omega, self.sigma, self.l = oom_transformations(self.Ct_active, self.C2t_active, self.rank)
# Compute corrected transition matrix:
Tt_rev = compute_transition_matrix(self.Xi, self.omega, self.sigma, reversible=True)
Tt = compute_transition_matrix(self.Xi, self.omega, self.sigma, reversible=False)
# Build reference models:
self.rmsmrev = MarkovStateModel(Tt_rev)
self.rmsm = MarkovStateModel(Tt)
# Active count fraction:
self.hist = count_states(self.dtrajs)
self.active_hist = self.hist[:-1] if not complete else self.hist
self.active_count_frac = float(np.sum(self.active_hist)) / np.sum(self.hist) if not complete else 1.
self.active_state_frac = 0.8 if not complete else 1.
# Commitor and MFPT:
a = np.array([0, 1])
b = np.array([4]) if complete else np.array([3])
self.comm_forward = self.rmsm.committor_forward(a, b)
self.comm_forward_rev = self.rmsmrev.committor_forward(a, b)
self.comm_backward = self.rmsm.committor_backward(a, b)
self.comm_backward_rev = self.rmsmrev.committor_backward(a, b)
self.mfpt = self.tau * self.rmsm.mfpt(a, b)
self.mfpt_rev = self.tau * self.rmsmrev.mfpt(a, b)
# PCCA:
pcca = self.rmsmrev.pcca(3 if complete else 2)
self.pcca_ass = pcca.assignments
self.pcca_dist = pcca.metastable_distributions
self.pcca_mem = pcca.memberships
self.pcca_sets = pcca.sets
# Experimental quantities:
a = np.array([1, 2, 3, 4, 5])
b = np.array([1, -1, 0, -2, 4])
p0 = np.array([0.5, 0.2, 0.2, 0.1, 0.0])
if not complete:
a = a[:-1]
b = b[:-1]
p0 = p0[:-1]
pi = self.rmsm.stationary_distribution
pi_rev = self.rmsmrev.stationary_distribution
_, _, L_rev = ma.rdl_decomposition(Tt_rev)
self.exp = np.dot(self.rmsm.stationary_distribution, a)
self.exp_rev = np.dot(self.rmsmrev.stationary_distribution, a)
self.corr_rev = np.zeros(10)
self.rel = np.zeros(10)
self.rel_rev = np.zeros(10)
for k in range(10):
Ck_rev = np.dot(np.diag(pi_rev), np.linalg.matrix_power(Tt_rev, k))
self.corr_rev[k] = np.dot(a.T, np.dot(Ck_rev, b))
self.rel[k] = np.dot(p0.T, np.dot(np.linalg.matrix_power(Tt, k), a))
self.rel_rev[k] = np.dot(p0.T, np.dot(np.linalg.matrix_power(Tt_rev, k), a))
self.fing_cor = np.dot(a.T, L_rev.T) * np.dot(b.T, L_rev.T)
self.fing_rel = np.dot(a.T, L_rev.T) * np.dot((p0 / pi_rev).T, L_rev.T)