def run_experiment(index, dataset_name, name, constraint_getter, master_tree, X, y, out_dir, n_iters=1000, add_constraint=200, add_score=200,
add_likelihood=200, should_continue=False):
N, D = X.shape
df = Inverse(c=1)
if dataset_name == 'iris':
lm = GaussianLikelihoodModel(sigma=np.eye(D) / 9.0, sigma0=np.eye(D) / 2.0, mu0=X.mean(axis=0)).compile()
elif dataset_name == 'zoo':
lm = GaussianLikelihoodModel(sigma=np.diag(np.diag(np.cov(X.T))) / 4.0, sigma0=np.eye(D) / 2.0, mu0=X.mean(axis=0)).compile()
else:
lm = GaussianLikelihoodModel(sigma=np.diag(np.diag(np.cov(X.T))) / 2.0, sigma0=np.eye(D) / 2.0, mu0=X.mean(axis=0)).compile()
if should_continue:
with open(out_dir / name / 'scores-%u.pkl' % index, 'r') as fp:
scores = pickle.load(fp)
with open(out_dir / name / 'costs-%u.pkl' % index, 'r') as fp:
costs = pickle.load(fp)
with open(out_dir / name / 'final-tree-%u.pkl' % index, 'r') as fp:
tree = DirichletDiffusionTree(df=df, likelihood_model=lm)
tree.set_state(pickle.load(fp))
sampler = MetropolisHastingsSampler(tree, X)
else:
scores = []
costs = []
tree = DirichletDiffusionTree(df=df, likelihood_model=lm)
sampler = MetropolisHastingsSampler(tree, X)
sampler.initialize_assignments()
if dataset_name == 'zoo':
sampler.tree = sampler.tree.induced_subtree(master_tree.points())
current_run = []
for i in tqdm(xrange(n_iters + 1)):
sampler.sample()
current_run.append(sampler.tree)
if i % add_score == 0:
scores.append(dist(master_tree, sampler.tree))
if i % add_likelihood == 0:
costs.append(sampler.tree.marg_log_likelihood())
if i != 0 and i % add_constraint == 0:
if constraint_getter is not None:
constraint = constraint_getter.get_constraint(current_run)
if constraint is not None:
sampler.add_constraint(constraint)
current_run = []
# plot_tree(sampler.tree, y)
(out_dir / name).mkdir_p()
with open(out_dir / name / 'scores-%u.pkl' % index, 'w') as fp:
pickle.dump(scores, fp)
print len(costs)
with open(out_dir / name / 'costs-%u.pkl' % index, 'w') as fp:
pickle.dump(costs, fp)
# with open(out_dir / name / 'trees-%u.pkl' % index, 'r') as fp:
# previous_trees = pickle.load(fp)
# with open(out_dir / name / 'trees-%u.pkl' % index, 'w') as fp:
# pickle.dump(previous_trees + [t.get_state() for t in trees], fp)
with open(out_dir / name / 'final-tree-%u.pkl' % index, 'w') as fp:
pickle.dump(sampler.tree.get_state(), fp)
return costs, scores, sampler
X = X[idx]
y = y[idx]
constraints = set()
for constraint in interactor.current_interactions:
a, b, c = constraint
if a not in idx_map or b not in idx_map or c not in idx_map:
continue
constraints.add(tuple(map(lambda x: idx_map[x], constraint)))
logging.info("Interactions: %s", constraints)
logging.info("Interactions: %u", len(constraints))
N, D = X.shape
df = Inverse(c=2)
cov = np.cov(X.T) / 4.0 + np.eye(D) * 0.001
lm = GaussianLikelihoodModel(sigma=cov, sigma0=np.eye(D) / 2.0, mu0=X.mean(axis=0)).compile()
model = DirichletDiffusionTree(df=df,
likelihood_model=lm,
constraints=constraints)
sampler = MetropolisHastingsSampler(model, X)
sampler.initialize_assignments()
def iterate(iters):
for i in tqdm(xrange(iters)):
sampler.sample()
import numpy as np
from trees.util import plot_tree, plot_tree_2d
from trees.ddt import DirichletDiffusionTree, Inverse, GaussianLikelihoodModel
from trees.mcmc import MetropolisHastingsSampler
from tqdm import tqdm
if __name__ == "__main__":
D = 2
N = 100
X = np.random.multivariate_normal(mean=np.zeros(D), cov=np.eye(D), size=N).astype(np.float32)
df = Inverse(c=1)
lm = GaussianLikelihoodModel(sigma=np.eye(D) / 4.0, mu0=np.zeros(D), sigma0=np.eye(D))
ddt = DirichletDiffusionTree(df=df,
likelihood_model=lm)
mh = MetropolisHastingsSampler(ddt, X)
mh.initialize_assignments()
for _ in tqdm(xrange(1000)):
mh.sample()
plt.figure()
plt.plot(mh.likelihoods)
plt.figure()
plot_tree(mh.tree)
plt.figure()
plot_tree_2d(mh.tree, X)
plt.show()
N = X.shape[0]
np.random.seed(0)
# idx = np.random.permutation(np.arange(N))[:20]
# X = X[idx]
# y = np.array(y)
# y = y[idx]
N, D = X.shape
df = Inverse(c=1)
lm = GaussianLikelihoodModel(sigma=np.eye(D) / 4.0, sigma0=np.eye(D) / 2.0, mu0=X.mean(axis=0)).compile()
tree = DirichletDiffusionTree(df=df, likelihood_model=lm)
sampler = MetropolisHastingsSampler(tree, X)
sampler.initialize_assignments()
D = 1.0 / squareform(pdist(X))
def plot_tree(tree):
final_tree = tree.copy()
for node in final_tree.dfs():
if node.is_leaf():
node.point = y[node.point]
newick = final_tree.to_newick()
tree = Phylo.read(StringIO(newick), 'newick')
Phylo.draw_graphviz(tree, prog='neato')
plt.show()
master_constraints = list(master_tree.generate_constraints())
random.seed(0)
random.shuffle(master_constraints)
train_constraints, test_constraints = master_constraints[:
200], master_constraints[
200:]
test_constraints = test_constraints[:10000]
df = Inverse(c=0.9)
lm = GaussianLikelihoodModel(sigma=np.eye(D) / 4.0,
sigma0=np.eye(D) / 2.0,
mu0=X.mean(axis=0)).compile()
model = DirichletDiffusionTree(df=df, likelihood_model=lm, constraints=[])
sampler = MetropolisHastingsSampler(model, X)
sampler.initialize_assignments()
constraint_add = 500
constraint_index = 0
n_iters = 100000
score_every = 1000
likelihoods = []
scores = []
for i in tqdm(xrange(n_iters + constraint_add)):
if i != 0 and i % constraint_add == 0:
sampler.add_constraint(train_constraints[constraint_index])
constraint_index += 1
sampler.sample()
likelihoods.append(sampler.tree.marg_log_likelihood())
with open("../../scripts/zoo.tree", "rb") as fp:
master_tree = pickle.load(fp)
master_constraints = list(master_tree.generate_constraints())
random.seed(0)
random.shuffle(master_constraints)
train_constraints, test_constraints = master_constraints[:200], master_constraints[200:]
test_constraints = test_constraints[:10000]
df = Inverse(c=0.9)
lm = GaussianLikelihoodModel(sigma=np.eye(D) / 4.0, sigma0=np.eye(D) / 2.0, mu0=X.mean(axis=0)).compile()
model = DirichletDiffusionTree(df=df, likelihood_model=lm, constraints=[])
sampler = MetropolisHastingsSampler(model, X)
sampler.initialize_assignments()
constraint_add = 500
constraint_index = 0
n_iters = 100000
score_every = 1000
likelihoods = []
scores = []
for i in tqdm(xrange(n_iters + constraint_add)):
if i != 0 and i % constraint_add == 0:
sampler.add_constraint(train_constraints[constraint_index])
constraint_index += 1
sampler.sample()
from trees.util import plot_tree, plot_tree_2d
from trees.ddt import DirichletDiffusionTree, Inverse, GaussianLikelihoodModel
from trees.mcmc import MetropolisHastingsSampler
from tqdm import tqdm
if __name__ == "__main__":
D = 2
N = 100
X = np.random.multivariate_normal(mean=np.zeros(D), cov=np.eye(D),
size=N).astype(np.float32)
df = Inverse(c=1)
lm = GaussianLikelihoodModel(sigma=np.eye(D) / 4.0,
mu0=np.zeros(D),
sigma0=np.eye(D))
ddt = DirichletDiffusionTree(df=df, likelihood_model=lm)
mh = MetropolisHastingsSampler(ddt, X)
mh.initialize_assignments()
for _ in tqdm(range(1000)):
mh.sample()
plt.figure()
plt.plot(mh.likelihoods)
#plt.figure()
#plot_tree(mh.tree)
#plt.figure()
#plot_tree_2d(mh.tree, X)
plt.show()
def run_experiment(index,
dataset_name,
name,
constraint_getter,
master_tree,
X,
y,
out_dir,
n_iters=1000,
add_constraint=200,
add_score=200,
add_likelihood=200,
should_continue=False):
N, D = X.shape
df = Inverse(c=1)
if dataset_name == 'iris':
lm = GaussianLikelihoodModel(sigma=np.eye(D) / 9.0,
sigma0=np.eye(D) / 2.0,
mu0=X.mean(axis=0)).compile()
elif dataset_name == 'zoo':
lm = GaussianLikelihoodModel(sigma=np.diag(np.diag(np.cov(X.T))) / 4.0,
sigma0=np.eye(D) / 2.0,
mu0=X.mean(axis=0)).compile()
else:
lm = GaussianLikelihoodModel(sigma=np.diag(np.diag(np.cov(X.T))) / 2.0,
sigma0=np.eye(D) / 2.0,
mu0=X.mean(axis=0)).compile()
if should_continue:
with open(out_dir / name / 'scores-%u.pkl' % index, 'r') as fp:
scores = pickle.load(fp)
with open(out_dir / name / 'costs-%u.pkl' % index, 'r') as fp:
costs = pickle.load(fp)
with open(out_dir / name / 'final-tree-%u.pkl' % index, 'r') as fp:
tree = DirichletDiffusionTree(df=df, likelihood_model=lm)
tree.set_state(pickle.load(fp))
sampler = MetropolisHastingsSampler(tree, X)
else:
scores = []
costs = []
tree = DirichletDiffusionTree(df=df, likelihood_model=lm)
sampler = MetropolisHastingsSampler(tree, X)
sampler.initialize_assignments()
if dataset_name == 'zoo':
sampler.tree = sampler.tree.induced_subtree(master_tree.points())
current_run = []
for i in tqdm(xrange(n_iters + 1)):
sampler.sample()
current_run.append(sampler.tree)
if i % add_score == 0:
scores.append(dist(master_tree, sampler.tree))
if i % add_likelihood == 0:
costs.append(sampler.tree.marg_log_likelihood())
if i != 0 and i % add_constraint == 0:
if constraint_getter is not None:
constraint = constraint_getter.get_constraint(current_run)
if constraint is not None:
sampler.add_constraint(constraint)
current_run = []
# plot_tree(sampler.tree, y)
(out_dir / name).mkdir_p()
with open(out_dir / name / 'scores-%u.pkl' % index, 'w') as fp:
pickle.dump(scores, fp)
print len(costs)
with open(out_dir / name / 'costs-%u.pkl' % index, 'w') as fp:
pickle.dump(costs, fp)
# with open(out_dir / name / 'trees-%u.pkl' % index, 'r') as fp:
# previous_trees = pickle.load(fp)
# with open(out_dir / name / 'trees-%u.pkl' % index, 'w') as fp:
# pickle.dump(previous_trees + [t.get_state() for t in trees], fp)
with open(out_dir / name / 'final-tree-%u.pkl' % index, 'w') as fp:
pickle.dump(sampler.tree.get_state(), fp)
return costs, scores, sampler
'50 constraints':
DirichletDiffusionTree(df=df,
likelihood_model=lm,
constraints=train_constraints[:50]),
'100 constraints':
DirichletDiffusionTree(df=df,
likelihood_model=lm,
constraints=train_constraints[:100]),
# '150 constraints': DirichletDiffusionTree(df=df, likelihood_model=lm, constraints=train_constraints[:150]),
'200 constraints':
DirichletDiffusionTree(df=df,
likelihood_model=lm,
constraints=train_constraints),
}
samplers = {a: MetropolisHastingsSampler(d, X) for a, d in models.iteritems()}
for sampler in samplers.values():
sampler.initialize_assignments()
score_every = 1000
def iterate(n_iters):
scores = {a: [] for a in samplers}
likelihoods = {a: [] for a in samplers}
for i in tqdm(xrange(n_iters)):
for name, sampler in samplers.items():
sampler.sample()
likelihoods[name].append(sampler.tree.marg_log_likelihood())
if i % score_every == 0:
np.random.seed(0)
# idx = np.random.permutation(np.arange(N))[:20]
# X = X[idx]
# y = np.array(y)
# y = y[idx]
N, D = X.shape
df = Inverse(c=1)
lm = GaussianLikelihoodModel(sigma=np.eye(D) / 4.0,
sigma0=np.eye(D) / 2.0,
mu0=X.mean(axis=0)).compile()
tree = DirichletDiffusionTree(df=df, likelihood_model=lm)
sampler = MetropolisHastingsSampler(tree, X)
sampler.initialize_assignments()
D = 1.0 / squareform(pdist(X))
def plot_tree(tree):
final_tree = tree.copy()
for node in final_tree.dfs():
if node.is_leaf():
node.point = y[node.point]
newick = final_tree.to_newick()
tree = Phylo.read(StringIO(newick), 'newick')
Phylo.draw_graphviz(tree, prog='neato')
plt.show()
