def test_hmm_3():
A = 20
S = 160
n = 4000
N = 10
pZ = np.repeat(1.0/S, S)
pE = util.normalized(np.random.rand(S, A))
pT = util.normalized(np.random.rand(S, S))
H = hmm.FixedHMM(
pZ = pZ,
pE = pE,
pT = pT
)
X, Z = H.generate(n)
print 'test_hmm_3'
print '----------'
print ' A = {0}'.format(A)
print ' S = {0}'.format(S)
print ' n = {0}'.format(n)
for i in range(N):
H = hmm.FixedHMM(
pZ = pZ,
pE = util.normalized(np.random.rand(S, A)),
pT = util.normalized(np.random.rand(S, S))
)
t1 = time.clock()
H.forward_backward(X)
t2 = time.clock()
print ' {0:2d}/{1:2d} FB: {2:.5f}s'.format(i + 1, N, t2 - t1)
def test_phmm_1():
W = 3
A = 4
f1 = util.normalized(np.random.rand(W+1, A))
t1 = np.random.rand(6)
t1[2:] /= t1[2:].sum()
H1 = phmm.ProfileHMM(f1, t1)
X, Z = H1.generate(10000)
f2 = util.normalized(f1 + np.random.rand(W+1, A))
t2 = t1.copy()
t2[:2] = np.random.rand(2)
t2[2:] = np.random.rand(4)
t2[2:] /= t2[2:].sum()
H2 = phmm.ProfileHMM(f2, t2)
H2.fit_em(X, precision=1e-5, max_iter=1000)
print H2.f
print H2.t
print H1.f
print H1.t
