def one_predictive_var():
Y = RandomVar('Y', 2)
X1 = RandomVar('X1', 2)
X2 = RandomVar('X2', 2)
X3 = RandomVar('X3', 2)
f_X1_Y = CPD([X1, Y], [1.0, 0.0, 0.0, 1.0])
f_X2_Y = CPD([X2, Y], [0.5, 0.5, 0.5, 0.5])
f_X3_Y = CPD([X3, Y], [0.5, 0.5, 0.5, 0.5])
f_Y = CPD([Y], [0.5, 0.5])
bn = BayesianNetwork([f_Y, f_X1_Y, f_X2_Y, f_X3_Y])
# Training the model
fs = ForwardSampler(bn)
fs.sample(1000)
scope, X = fs.samples_to_matrix()
y = X[:, -1]
X = X[:, 0:-1]
nb = NaiveBayes()
nb.fit(X, y)
# Evaluating the model
fs = ForwardSampler(bn)
fs.sample(10)
_, X = fs.samples_to_matrix()
print(nb.score(X[:, 0:-1], X[:, -1]))
print(nb.predict_proba(X[:, 0:-1]))
def main():
parents = {'alice': [], 'bob': [], 'eve': ['bob', 'alice']}
allele_freqs = [0.9, 0.1]
prob_trait_genotype = [[0.0, 0.0], [0.0, 1.0]]
bn = build_genetic_network(parents, allele_freqs, prob_trait_genotype)
# Examples
alice_trait = RandomVar('alice_trait', 2)
bob_trait = RandomVar('bob_trait', 2)
eve_trait = RandomVar('eve_trait', 2)
# alice_allele_1 = RandomVar('alice_allele_1', 2)
# alice_allele_2 = RandomVar('alice_allele_2', 2)
#
# bob_allele_1 = RandomVar('bob_allele_1', 2)
# bob_allele_2 = RandomVar('bob_allele_2', 2)
#
# eve_allele_1 = RandomVar('eve_allele_1', 2)
# eve_allele_2 = RandomVar('eve_allele_2', 2)
ve = JointMarginalization(bn)
print(ve.posterior([eve_trait]))
print(ve.posterior([eve_trait], [(bob_trait, 1)]))
print(ve.posterior([alice_trait, bob_trait], [(eve_trait, 1)]))
fs = ForwardSampler(bn)
fs.sample(1000)
print(
fs.posterior([(alice_trait, 0), (bob_trait, 0),
(eve_trait, 1)]) / fs.posterior([(eve_trait, 1)]))
print(bn.graph())
def gn():
parents = {'alice': [], 'bob': [], 'eve': ['bob', 'alice']}
allele_freqs = [0.9, 0.1]
prob_trait_genotype = [[0.0, 0.0], [0.0, 1.0]]
bn = genetic_network.build_genetic_network(parents, allele_freqs,
prob_trait_genotype)
graph = bn.graph()
fs = ForwardSampler(bn)
fs.sample(20000)
scope, X = fs.samples_to_matrix()
score_l = LikelihoodScore(scope).fit(X, graph).score
print(score_l)
score_bic = BICScore(scope).fit(X, graph).score
print(score_bic)
score_b = BayesianScore(scope).fit(X, graph).score
print(score_b)
# scorer = LikelihoodScore(scope)
# scorer = BayesianScore(scope)
scorer = BICScore(scope)
best_graph, best_score = restarting_local_search(X,
scope,
scorer,
restarts=1,
iterations=100,
epsilon=0.1,
verbose=1)
print(best_graph)
print(best_score)
def main():
x1 = RandomVar('X1', 2)
x2 = RandomVar('X2', 2)
x3 = RandomVar('X3', 2)
fx1 = CPD([x1], [0.11, 0.89])
fx2_x1 = CPD([x2, x1], [0.59, 0.22, 0.41, 0.78])
fx3_x2 = CPD([x3, x2], [0.39, 0.06, 0.61, 0.94])
bn = BayesianNetwork([fx1, fx2_x1, fx3_x2])
# mn = MarkovNetwork([fx1, fx2_x1, fx3_x2])
ve = VariableElimination(bn)
jm = JointMarginalization(bn)
print(ve.posterior([x1, x2], [(x3, 0)]))
print(jm.posterior([x1, x2], [(x3, 0)]))
print(ve.posterior([x1, x2, x3]))
print(jm.posterior([x1, x2, x3]))
print(ve.maximum_a_posteriori(evidence=[(x3, 0)]))
print(jm.maximum_a_posteriori([x1, x2], [(x3, 0)]))
fs = ForwardSampler(bn)
fs.sample(10000)
for c in itertools.product(range(2), repeat=3):
print('{0}: {1}'.format(c, fs.posterior(zip([x1, x2, x3], c))))
px3_0 = fs.posterior([(x3, 0)])
for c in itertools.product(range(2), repeat=2):
assg = list(zip([x1, x2], c)) + [(x3, 0)]
print('{0}: {1}'.format(c, fs.posterior(assg) / px3_0))
gs = GibbsSampler(bn)
gs.sample(burn_in=1000, n=2000)
for c in itertools.product(range(2), repeat=3):
print('{0}: {1}'.format(c, gs.posterior(zip([x1, x2, x3], c))))
gs.reset()
gs.sample(burn_in=1000, n=1000, evidence=[(x3, 0)])
for c in itertools.product(range(2), repeat=2):
print('{0}: {1}'.format(c, gs.posterior(zip([x1, x2], c))))
def earthquake():
B = RandomVar('B', 2)
E = RandomVar('E', 2)
A = RandomVar('A', 2)
R = RandomVar('R', 2)
a_be = CPD([A, B, E],
[0.999, 0.01, 0.01, 0.0001, 0.001, 0.99, 0.99, 0.9999])
r_e = CPD([R, E], [1.0, 0.0, 0.0, 1.0])
b = CPD([B], [0.99, 0.01])
e = CPD([E], [0.999, 0.001])
bn = BayesianNetwork([a_be, r_e, b, e])
fs = ForwardSampler(bn)
fs.sample(1000)
scope, X = fs.samples_to_matrix()
graph = bn.graph()
# graph = {B : set(), E: set(), A: set(), R: set()}
score_l = LikelihoodScore(scope).fit(X, graph).score
print(score_l)
score_bic = BICScore(scope).fit(X, graph).score
print(score_bic)
score_b = BayesianScore(scope).fit(X, graph).score
print(score_b)
# scorer = LikelihoodScore(scope)
# scorer = BICScore(scope)
scorer = BayesianScore(scope)
best_graph, best_score = restarting_local_search(X,
scope,
scorer,
restarts=1,
iterations=100,
epsilon=0.2,
verbose=1)
print('Best:')
print(best_score)
print(best_graph)
def main():
B = RandomVar('B', 2)
E = RandomVar('E', 2)
A = RandomVar('A', 2)
R = RandomVar('R', 2)
a_be = CPD([A, B, E],
[0.999, 0.01, 0.01, 0.0001, 0.001, 0.99, 0.99, 0.9999])
r_e = CPD([R, E], [1.0, 0.0, 0.0, 1.0])
b = CPD([B], [0.99, 0.01])
e = CPD([E], [0.999, 0.001])
bn = BayesianNetwork([a_be, r_e, b, e])
ve = VariableElimination(bn)
jm = JointMarginalization(bn)
print(ve.posterior([B, E, A, R]) == jm.posterior([B, E, A, R]))
fs = ForwardSampler(bn)
fs.sample(1000)
def simple_chain():
x1 = RandomVar('X1', 2)
x2 = RandomVar('X2', 2)
x3 = RandomVar('X3', 2)
fx1 = CPD([x1], [0.11, 0.89])
fx2_x1 = CPD([x2, x1], [0.59, 0.22, 0.41, 0.78])
fx3_x2 = CPD([x3, x2], [0.39, 0.06, 0.61, 0.94])
bn = BayesianNetwork([fx1, fx2_x1, fx3_x2])
fs = ForwardSampler(bn)
fs.sample(2000)
scope, X = fs.samples_to_matrix()
graph = bn.graph()
# graph = {x1 : set(), x2: set(), x3: set()}
score_l = LikelihoodScore(scope).fit(X, graph).score
print(score_l)
score_bic = BICScore(scope).fit(X, graph).score
print(score_bic)
score_b = BayesianScore(scope).fit(X, graph).score
print(score_b)
# scorer = LikelihoodScore(scope)
scorer = BICScore(scope)
# scorer = BayesianScore(scope)
best_graph, best_score = restarting_local_search(X,
scope,
scorer,
restarts=5,
iterations=50,
epsilon=0.2,
verbose=1)
print('Best:')
print(best_score)
print(best_graph)
def traffic():
A = RandomVar('A', 2)
T = RandomVar('T', 2)
P = RandomVar('P', 2)
fP = CPD([P], [0.99, 0.01])
fA = CPD([A], [0.9, 0.1])
fT_AP = CPD([T, P, A], [0.9, 0.5, 0.4, 0.1, 0.1, 0.5, 0.6, 0.9])
bn = BayesianNetwork([fP, fA, fT_AP])
# print(bn)
fs = ForwardSampler(bn)
fs.sample(2000)
scope, X = fs.samples_to_matrix()
graph = bn.graph()
score_l = LikelihoodScore(scope).fit(X, graph).score
print(score_l)
score_bic = BICScore(scope).fit(X, graph).score
print(score_bic)
score_b = BayesianScore(scope).fit(X, graph).score
print(score_b)
# scorer = LikelihoodScore(scope)
scorer = BICScore(scope)
# scorer = BayesianScore(scope)
best_graph, best_score = restarting_local_search(X,
scope,
scorer,
restarts=5,
iterations=50,
epsilon=0.2,
verbose=1)
print('Best:')
print(best_score)
print(best_graph)
def traffic():
A = RandomVar('A', 2)
T = RandomVar('T', 2)
P = RandomVar('P', 2)
fP = CPD([P], [0.99, 0.01])
fA = CPD([A], [0.9, 0.1])
fT_AP = CPD([T, P, A], [0.9, 0.5, 0.4, 0.1, 0.1, 0.5, 0.6, 0.9])
bn = BayesianNetwork([fP, fA, fT_AP])
print(bn)
fs = ForwardSampler(bn)
fs.sample(1000)
scope, X = fs.samples_to_matrix()
mle = MaximumLikelihood(scope)
print(mle.fit_predict(X, bn.graph()))
ud = UniformDirichlet(scope, alpha=1.0)
print(ud.fit_predict(X, bn.graph()))
def simple_chain():
x1 = RandomVar('X1', 2)
x2 = RandomVar('X2', 2)
x3 = RandomVar('X3', 2)
fx1 = CPD([x1], [0.11, 0.89])
fx2_x1 = CPD([x2, x1], [0.59, 0.22, 0.41, 0.78])
fx3_x2 = CPD([x3, x2], [0.39, 0.06, 0.61, 0.94])
bn = BayesianNetwork([fx1, fx2_x1, fx3_x2])
graph = bn.graph()
print(bn)
fs = ForwardSampler(bn)
fs.sample(1000)
scope, X = fs.samples_to_matrix()
mle = MaximumLikelihood(scope)
print(mle.fit_predict(X, graph))
ud = UniformDirichlet(scope, alpha=1.0)
print(ud.fit_predict(X, graph))
def earthquake():
B = RandomVar('B', 2)
E = RandomVar('E', 2)
A = RandomVar('A', 2)
R = RandomVar('R', 2)
a_be = CPD([A, B, E],
[0.999, 0.01, 0.01, 0.0001, 0.001, 0.99, 0.99, 0.9999])
r_e = CPD([R, E], [1.0, 0.0, 0.0, 1.0])
b = CPD([B], [0.99, 0.01])
e = CPD([E], [0.999, 0.001])
bn = BayesianNetwork([a_be, r_e, b, e])
print(bn)
fs = ForwardSampler(bn)
fs.sample(1000)
scope, X = fs.samples_to_matrix()
mle = MaximumLikelihood(scope)
print(mle.fit_predict(X, bn.graph()))
ud = UniformDirichlet(scope, alpha=1.0)
print(ud.fit_predict(X, bn.graph()))