def test_normal_mixture(self):
with Model() as model:
w = Dirichlet('w', np.ones_like(self.norm_w))
mu = Normal('mu', 0., 10., shape=self.norm_w.size)
tau = Gamma('tau', 1., 1., shape=self.norm_w.size)
x_obs = NormalMixture('x_obs',
w,
mu,
tau=tau,
observed=self.norm_x)
step = Metropolis()
trace = sample(5000,
step,
random_seed=self.random_seed,
progressbar=False)
assert_allclose(np.sort(trace['w'].mean(axis=0)),
np.sort(self.norm_w),
rtol=0.1,
atol=0.1)
assert_allclose(np.sort(trace['mu'].mean(axis=0)),
np.sort(self.norm_mu),
rtol=0.1,
atol=0.1)
def test_normal_mixture_nd(self):
nd, ncomp = 3, 5
with Model() as model0:
mus = Normal('mus', shape=(nd, ncomp))
taus = Gamma('taus', alpha=1, beta=1, shape=(nd, ncomp))
ws = Dirichlet('ws', np.ones(ncomp))
mixture0 = NormalMixture('m', w=ws, mu=mus, tau=taus, shape=nd)
with Model() as model1:
mus = Normal('mus', shape=(nd, ncomp))
taus = Gamma('taus', alpha=1, beta=1, shape=(nd, ncomp))
ws = Dirichlet('ws', np.ones(ncomp))
comp_dist = [Normal.dist(mu=mus[:, i], tau=taus[:, i])
for i in range(ncomp)]
mixture1 = Mixture('m', w=ws, comp_dists=comp_dist, shape=nd)
testpoint = model0.test_point
testpoint['mus'] = np.random.randn(nd, ncomp)
assert_allclose(model0.logp(testpoint), model1.logp(testpoint))
assert_allclose(mixture0.logp(testpoint), mixture1.logp(testpoint))
def test_normal_mixture(self):
with Model() as model:
w = Dirichlet("w", floatX(np.ones_like(self.norm_w)), shape=self.norm_w.size)
mu = Normal("mu", 0.0, 10.0, shape=self.norm_w.size)
tau = Gamma("tau", 1.0, 1.0, shape=self.norm_w.size)
NormalMixture("x_obs", w, mu, tau=tau, observed=self.norm_x)
step = Metropolis()
trace = sample(5000, step, random_seed=self.random_seed, progressbar=False, chains=1)
assert_allclose(np.sort(trace["w"].mean(axis=0)), np.sort(self.norm_w), rtol=0.1, atol=0.1)
assert_allclose(
np.sort(trace["mu"].mean(axis=0)), np.sort(self.norm_mu), rtol=0.1, atol=0.1
)
def test_normal_mixture_nd(self):
nd, ncomp = 3, 5
with Model() as model0:
mus = Normal('mus', shape=(nd, ncomp))
taus = Gamma('taus', alpha=1, beta=1, shape=(nd, ncomp))
ws = Dirichlet('ws', np.ones(ncomp))
mixture0 = NormalMixture('m', w=ws, mu=mus, tau=taus, shape=nd)
with Model() as model1:
mus = Normal('mus', shape=(nd, ncomp))
taus = Gamma('taus', alpha=1, beta=1, shape=(nd, ncomp))
ws = Dirichlet('ws', np.ones(ncomp))
comp_dist = [
Normal.dist(mu=mus[:, i], tau=taus[:, i]) for i in range(ncomp)
]
mixture1 = Mixture('m', w=ws, comp_dists=comp_dist, shape=nd)
testpoint = model0.test_point
testpoint['mus'] = np.random.randn(nd, ncomp)
assert_allclose(model0.logp(testpoint), model1.logp(testpoint))
assert_allclose(mixture0.logp(testpoint), mixture1.logp(testpoint))
def test_normal_mixture_nd(self, nd, ncomp):
nd = to_tuple(nd)
ncomp = int(ncomp)
comp_shape = nd + (ncomp, )
test_mus = np.random.randn(*comp_shape)
test_taus = np.random.gamma(1, 1, size=comp_shape)
observed = generate_normal_mixture_data(w=np.ones(ncomp) / ncomp,
mu=test_mus,
sd=1 / np.sqrt(test_taus),
size=10)
with Model() as model0:
mus = Normal("mus", shape=comp_shape)
taus = Gamma("taus", alpha=1, beta=1, shape=comp_shape)
ws = Dirichlet("ws", np.ones(ncomp), shape=(ncomp, ))
mixture0 = NormalMixture("m",
w=ws,
mu=mus,
tau=taus,
shape=nd,
comp_shape=comp_shape)
obs0 = NormalMixture("obs",
w=ws,
mu=mus,
tau=taus,
shape=nd,
comp_shape=comp_shape,
observed=observed)
with Model() as model1:
mus = Normal("mus", shape=comp_shape)
taus = Gamma("taus", alpha=1, beta=1, shape=comp_shape)
ws = Dirichlet("ws", np.ones(ncomp), shape=(ncomp, ))
comp_dist = [
Normal.dist(mu=mus[..., i], tau=taus[..., i], shape=nd)
for i in range(ncomp)
]
mixture1 = Mixture("m", w=ws, comp_dists=comp_dist, shape=nd)
obs1 = Mixture("obs",
w=ws,
comp_dists=comp_dist,
shape=nd,
observed=observed)
with Model() as model2:
# Expected to fail if comp_shape is not provided,
# nd is multidim and it does not broadcast with ncomp. If by chance
# it does broadcast, an error is raised if the mixture is given
# observed data.
# Furthermore, the Mixture will also raise errors when the observed
# data is multidimensional but it does not broadcast well with
# comp_dists.
mus = Normal("mus", shape=comp_shape)
taus = Gamma("taus", alpha=1, beta=1, shape=comp_shape)
ws = Dirichlet("ws", np.ones(ncomp), shape=(ncomp, ))
if len(nd) > 1:
if nd[-1] != ncomp:
with pytest.raises(ValueError):
NormalMixture("m", w=ws, mu=mus, tau=taus, shape=nd)
mixture2 = None
else:
mixture2 = NormalMixture("m",
w=ws,
mu=mus,
tau=taus,
shape=nd)
else:
mixture2 = NormalMixture("m", w=ws, mu=mus, tau=taus, shape=nd)
observed_fails = False
if len(nd) >= 1 and nd != (1, ):
try:
np.broadcast(np.empty(comp_shape), observed)
except Exception:
observed_fails = True
if observed_fails:
with pytest.raises(ValueError):
NormalMixture("obs",
w=ws,
mu=mus,
tau=taus,
shape=nd,
observed=observed)
obs2 = None
else:
obs2 = NormalMixture("obs",
w=ws,
mu=mus,
tau=taus,
shape=nd,
observed=observed)
testpoint = model0.test_point
testpoint["mus"] = test_mus
testpoint["taus"] = test_taus
assert_allclose(model0.logp(testpoint), model1.logp(testpoint))
assert_allclose(mixture0.logp(testpoint), mixture1.logp(testpoint))
assert_allclose(obs0.logp(testpoint), obs1.logp(testpoint))
if mixture2 is not None and obs2 is not None:
assert_allclose(model0.logp(testpoint), model2.logp(testpoint))
if mixture2 is not None:
assert_allclose(mixture0.logp(testpoint), mixture2.logp(testpoint))
if obs2 is not None:
assert_allclose(obs0.logp(testpoint), obs2.logp(testpoint))
def test_normal_mixture_nd(self, nd, ncomp):
nd = to_tuple(nd)
ncomp = int(ncomp)
comp_shape = nd + (ncomp,)
test_mus = np.random.randn(*comp_shape)
test_taus = np.random.gamma(1, 1, size=comp_shape)
observed = generate_normal_mixture_data(w=np.ones(ncomp)/ncomp,
mu=test_mus,
sd=1/np.sqrt(test_taus),
size=10)
with Model() as model0:
mus = Normal('mus', shape=comp_shape)
taus = Gamma('taus', alpha=1, beta=1, shape=comp_shape)
ws = Dirichlet('ws', np.ones(ncomp))
mixture0 = NormalMixture('m', w=ws, mu=mus, tau=taus, shape=nd,
comp_shape=comp_shape)
obs0 = NormalMixture('obs', w=ws, mu=mus, tau=taus, shape=nd,
comp_shape=comp_shape,
observed=observed)
with Model() as model1:
mus = Normal('mus', shape=comp_shape)
taus = Gamma('taus', alpha=1, beta=1, shape=comp_shape)
ws = Dirichlet('ws', np.ones(ncomp))
comp_dist = [Normal.dist(mu=mus[..., i], tau=taus[..., i],
shape=nd)
for i in range(ncomp)]
mixture1 = Mixture('m', w=ws, comp_dists=comp_dist, shape=nd)
obs1 = Mixture('obs', w=ws, comp_dists=comp_dist, shape=nd,
observed=observed)
with Model() as model2:
# Expected to fail if comp_shape is not provided,
# nd is multidim and it does not broadcast with ncomp. If by chance
# it does broadcast, an error is raised if the mixture is given
# observed data.
# Furthermore, the Mixture will also raise errors when the observed
# data is multidimensional but it does not broadcast well with
# comp_dists.
mus = Normal('mus', shape=comp_shape)
taus = Gamma('taus', alpha=1, beta=1, shape=comp_shape)
ws = Dirichlet('ws', np.ones(ncomp))
if len(nd) > 1:
if nd[-1] != ncomp:
with pytest.raises(ValueError):
NormalMixture('m', w=ws, mu=mus, tau=taus,
shape=nd)
mixture2 = None
else:
mixture2 = NormalMixture('m', w=ws, mu=mus, tau=taus,
shape=nd)
else:
mixture2 = NormalMixture('m', w=ws, mu=mus, tau=taus,
shape=nd)
observed_fails = False
if len(nd) >= 1 and nd != (1,):
try:
np.broadcast(np.empty(comp_shape), observed)
except Exception:
observed_fails = True
if observed_fails:
with pytest.raises(ValueError):
NormalMixture('obs', w=ws, mu=mus, tau=taus,
shape=nd,
observed=observed)
obs2 = None
else:
obs2 = NormalMixture('obs', w=ws, mu=mus, tau=taus,
shape=nd,
observed=observed)
testpoint = model0.test_point
testpoint['mus'] = test_mus
testpoint['taus'] = test_taus
assert_allclose(model0.logp(testpoint), model1.logp(testpoint))
assert_allclose(mixture0.logp(testpoint), mixture1.logp(testpoint))
assert_allclose(obs0.logp(testpoint), obs1.logp(testpoint))
if mixture2 is not None and obs2 is not None:
assert_allclose(model0.logp(testpoint), model2.logp(testpoint))
if mixture2 is not None:
assert_allclose(mixture0.logp(testpoint), mixture2.logp(testpoint))
if obs2 is not None:
assert_allclose(obs0.logp(testpoint), obs2.logp(testpoint))