def setUp(self):
self.k = 4
p = np.zeros(10)
q = np.zeros(10)
p[0:-1] = 0.5
q[1:] = 0.5
p[4] = 0.01
q[6] = 0.1
self.bdc = birth_death_chain(q, p)
self.mu = self.bdc.stationary_distribution
self.T = self.bdc.transition_matrix_sparse
R, D, L = rdl_decomposition(self.T, k=self.k)
self.L = L
self.R = R
self.ts = timescales(self.T, k=self.k)
self.times = np.array([1, 5, 10, 20, 100])
ev = np.diagonal(D)
self.ev_t = ev[np.newaxis, :]**self.times[:, np.newaxis]
obs1 = np.zeros(10)
obs1[0] = 1
obs1[1] = 1
obs2 = np.zeros(10)
obs2[8] = 1
obs2[9] = 1
self.obs1 = obs1
self.obs2 = obs2
self.one_vec = np.ones(10)
def setUp(self):
p = np.zeros(10)
q = np.zeros(10)
p[0:-1] = 0.5
q[1:] = 0.5
p[4] = 0.01
q[6] = 0.1
self.A = [0, 1]
self.B = [8, 9]
self.a = 1
self.b = 8
self.bdc = birth_death_chain(q, p)
T_dense = self.bdc.transition_matrix
T_sparse = csr_matrix(T_dense)
self.T = T_sparse
self.mu = self.bdc.stationary_distribution
self.qminus = self.bdc.committor_backward(self.a, self.b)
self.qplus = self.bdc.committor_forward(self.a, self.b)
# present results
self.fluxn = flux.flux_matrix(self.T, self.mu, self.qminus, self.qplus, netflux=False)
self.netfluxn = flux.flux_matrix(self.T, self.mu, self.qminus, self.qplus, netflux=True)
self.totalfluxn = flux.total_flux(self.netfluxn, self.A)
self.raten = flux.rate(self.totalfluxn, self.mu, self.qminus)
def setUp(self):
self.k = 4
p = np.zeros(10)
q = np.zeros(10)
p[0:-1] = 0.5
q[1:] = 0.5
p[4] = 0.01
q[6] = 0.1
self.bdc = birth_death_chain(q, p)
self.mu = self.bdc.stationary_distribution
self.T = self.bdc.transition_matrix_sparse
"""Test matrix-vector product against spectral decomposition"""
R, D, L = rdl_decomposition(self.T, k=self.k)
self.L = L
self.R = R
self.ts = timescales(self.T, k=self.k)
self.times = np.array([1, 5, 10, 20, 100])
ev = np.diagonal(D)
self.ev_t = ev[np.newaxis, :]**self.times[:, np.newaxis]
"""Observable"""
obs1 = np.zeros(10)
obs1[0] = 1
obs1[1] = 1
self.obs = obs1
"""Initial distribution"""
w0 = np.zeros(10)
w0[0:4] = 0.25
self.p0 = w0
def setUp(self):
p = np.zeros(10)
q = np.zeros(10)
p[0:-1] = 0.5
q[1:] = 0.5
p[4] = 0.01
q[6] = 0.1
self.A = [0, 1]
self.B = [8, 9]
self.a = 1
self.b = 8
self.bdc = birth_death_chain(q, p)
self.T = self.bdc.transition_matrix
"""Compute mu, qminus, qplus in constructor"""
self.tpt = compute_reactive_flux(self.T, self.A, self.B)
"""Use precomputed mu, qminus, qplus"""
self.mu = self.bdc.stationary_distribution
self.qminus = self.bdc.committor_backward(self.a, self.b)
self.qplus = self.bdc.committor_forward(self.a, self.b)
self.tpt_fast = compute_reactive_flux(self.T, self.A, self.B, stationary_distribution=self.mu,
qminus=self.qminus, qplus=self.qplus)
def setUp(self):
p = np.zeros(10)
q = np.zeros(10)
p[0:-1] = 0.5
q[1:] = 0.5
p[4] = 0.01
q[6] = 0.1
self.A = [0, 1]
self.B = [8, 9]
self.a = 1
self.b = 8
self.bdc = birth_death_chain(q, p)
self.T = self.bdc.transition_matrix
"""Use precomputed mu, qminus, qplus"""
self.mu = self.bdc.stationary_distribution
self.qplus = self.bdc.committor_forward(self.a, self.b)
self.qminus = self.bdc.committor_backward(self.a, self.b)
# self.qminus = committor.backward_committor(self.T, self.A, self.B, mu=self.mu)
# self.qplus = committor.forward_committor(self.T, self.A, self.B)
self.fluxn = tpt.flux_matrix(self.T,
self.mu,
self.qminus,
self.qplus,
netflux=False)
self.netfluxn = tpt.to_netflux(self.fluxn)
self.Fn = tpt.total_flux(self.fluxn, self.A)
self.kn = tpt.rate(self.Fn, self.mu, self.qminus)
def fingerprints_data(sparse_mode):
p = np.zeros(10)
q = np.zeros(10)
p[0:-1] = 0.5
q[1:] = 0.5
p[4] = 0.01
q[6] = 0.1
return birth_death_chain(q, p, sparse=sparse_mode)
def bdc(sparse_mode):
p = np.zeros(10)
q = np.zeros(10)
p[0:-1] = 0.5
q[1:] = 0.5
p[4] = 0.01
q[6] = 0.1
bdc = birth_death_chain(q, p, sparse=sparse_mode)
yield bdc
def setUp(self):
p = np.zeros(10)
q = np.zeros(10)
p[0:-1] = 0.5
q[1:] = 0.5
p[4] = 0.01
q[6] = 0.1
self.bdc = birth_death_chain(q, p)
def tpt_scenario_bd(sparse_mode):
p = np.zeros(10)
q = np.zeros(10)
p[0:-1] = 0.5
q[1:] = 0.5
p[4] = 0.01
q[6] = 0.1
bdc = birth_death_chain(q, p, sparse=sparse_mode)
tpt = bdc.msm.reactive_flux([0, 1], [8, 9])
return tpt, bdc
def test_is_reversible(sparse_mode):
p = np.zeros(10)
q = np.zeros(10)
p[0:-1] = 0.5
q[1:] = 0.5
p[4] = 0.01
q[6] = 0.1
bdc = birth_death_chain(q, p, sparse=sparse_mode)
assert_equal(sparse_mode, bdc.sparse)
assert_equal(issparse(bdc.transition_matrix), sparse_mode)
assert_(is_reversible(bdc.transition_matrix, bdc.stationary_distribution))
def setUp(self):
p = np.zeros(10)
q = np.zeros(10)
p[0:-1] = 0.5
q[1:] = 0.5
p[4] = 0.01
q[6] = 0.1
self.bdc = birth_death_chain(q, p)
self.mu = self.bdc.stationary_distribution
self.T = self.bdc.transition_matrix
def stationary_vector_data(sparse_mode):
dim = 100
"""Set up meta-stable birth-death chain"""
p = np.zeros(dim)
p[0:-1] = 0.5
q = np.zeros(dim)
q[1:] = 0.5
p[dim // 2 - 1] = 0.001
q[dim // 2 + 1] = 0.001
return birth_death_chain(q, p, sparse=sparse_mode)
def setUp(self):
self.dim = 100
self.k = 10
"""Set up meta-stable birth-death chain"""
p = np.zeros(self.dim)
p[0:-1] = 0.5
q = np.zeros(self.dim)
q[1:] = 0.5
p[self.dim // 2 - 1] = 0.001
q[self.dim // 2 + 1] = 0.001
self.bdc = birth_death_chain(q, p)
def scenario(request, sparse_mode):
dim = 100
"""Set up meta-stable birth-death chain"""
p = np.zeros(dim)
p[0:-1] = 0.5
q = np.zeros(dim)
q[1:] = 0.5
p[dim // 2 - 1] = 0.001
q[dim // 2 + 1] = 0.001
bdc = birth_death_chain(q, p, sparse=sparse_mode)
yield request.param, bdc
def test_amm_sanity(fixed_seed):
# Meta-stable birth-death chain
b = 2
q = np.zeros(7)
p = np.zeros(7)
q[1:] = 0.5
p[0:-1] = 0.5
q[2] = 1.0 - 10 ** (-b)
q[4] = 10 ** (-b)
p[2] = 10 ** (-b)
p[4] = 1.0 - 10 ** (-b)
bdc = birth_death_chain(q, p)
P = bdc.transition_matrix
dtraj = MarkovStateModel(P).simulate(n_steps=10000, start=0)
tau = 1
k = 3
# Predictions and experimental data
E = np.vstack((np.linspace(-0.1, 1., 7), np.linspace(1.5, -0.1, 7))).T
m = np.array([0.0, 0.0])
w = np.array([2.0, 2.5])
sigmas = 1. / np.sqrt(2) / np.sqrt(w)
""" Feature trajectory """
ftraj = E[dtraj, :]
amm_estimator = AugmentedMSMEstimator(expectations_by_state=E, experimental_measurements=m,
experimental_measurement_weights=w)
counts = TransitionCountEstimator(lagtime=tau, count_mode="sliding").fit(dtraj).fetch_model()
amm = amm_estimator.fit(counts).fetch_model()
amm_convenience_estimator = AugmentedMSMEstimator.estimator_from_feature_trajectories(
dtraj, ftraj, n_states=counts.n_states_full, experimental_measurements=m, sigmas=sigmas)
amm_convenience = amm_convenience_estimator.fit(counts).fetch_model()
assert_equal(tau, amm.lagtime)
assert_array_almost_equal(E, amm_estimator.expectations_by_state)
assert_array_almost_equal(E, amm_convenience_estimator.expectations_by_state, decimal=4)
assert_array_almost_equal(m, amm_estimator.experimental_measurements)
assert_array_almost_equal(m, amm_convenience_estimator.experimental_measurements)
assert_array_almost_equal(w, amm_estimator.experimental_measurement_weights)
assert_array_almost_equal(w, amm_convenience_estimator.experimental_measurement_weights)
assert_array_almost_equal(amm.transition_matrix, amm_convenience.transition_matrix, decimal=4)
assert_array_almost_equal(amm.stationary_distribution, amm_convenience.stationary_distribution, decimal=4)
assert_array_almost_equal(amm.optimizer_state.lagrange, amm_convenience.optimizer_state.lagrange, decimal=4)
def setUp(self):
self.k = 4
p = np.zeros(10)
q = np.zeros(10)
p[0:-1] = 0.5
q[1:] = 0.5
p[4] = 0.01
q[6] = 0.1
self.bdc = birth_death_chain(q, p)
self.mu = self.bdc.stationary_distribution
self.T = self.bdc.transition_matrix_sparse
R, D, L = rdl_decomposition(self.T, k=self.k)
self.L = L
self.R = R
self.ts = timescales(self.T, k=self.k)
self.times = np.array([1, 5, 10, 20])
ev = np.diagonal(D)
self.ev_t = ev[np.newaxis, :]**self.times[:, np.newaxis]
self.tau = 7.5
"""Observables"""
obs1 = np.zeros(10)
obs1[0] = 1
obs1[1] = 1
obs2 = np.zeros(10)
obs2[8] = 1
obs2[9] = 1
self.obs1 = obs1
self.obs2 = obs2
"""Initial vector for relaxation"""
w0 = np.zeros(10)
w0[0:4] = 0.25
self.p0 = w0
import matplotlib.pyplot as plt
from deeptime.data import birth_death_chain
n_states = 7
b = 2
q = np.zeros(n_states)
p = np.zeros(n_states)
q[1:] = 0.5
p[0:-1] = 0.5
q[2] = 1.0 - 10**(-b)
q[4] = 10**(-b)
p[2] = 10**(-b)
p[4] = 1.0 - 10**(-b)
bd = birth_death_chain(q, p)
dtraj = bd.msm.simulate(100000)
bins = np.arange(0, dtraj.max() + 1.5) - 0.5
fig, ax = plt.subplots()
ax.set_xticks(bins + 0.5)
ax.vlines(bins, ymin=0, ymax=.3, zorder=1, color='black', linestyles='dashed')
ax.hist(dtraj,
bins,
density=True,
alpha=.5,
color='C0',
label='Empirical distribution')
ax.bar(np.arange(n_states),
bd.stationary_distribution,