def test_sumout_var(self):
f = Factor(self.bn,'Alarm')
f.sumout_var('Earthquake')
self.assertListEqual(f.scope,['Alarm','Burglary'])
self.assertDictEqual(f.stride,
{'Alarm':1,'Burglary':2})
self.assertListEqual(list(f.cpt),
[ 0.8545, 0.1455, 0.055 , 0.945 ])
def test_sumout_var(self):
f = Factor(self.bn,'Alarm')
f.sumout_var('Earthquake')
self.assertListEqual(f.scope,['Alarm','Burglary'])
self.assertDictEqual(f.stride,
{'Alarm':1,'Burglary':2})
self.assertListEqual(list(f.cpt),
[ 0.8545, 0.1455, 0.055 , 0.945 ])
def test_maxout_var(self):
"""
I KNOW THIS IS CORRECT.
"""
f = Factor(self.bn, 'Alarm')
f.maxout_var('Burglary')
self.assertListEqual(list(f.cpt), [0.999, 0.94, 0.71, 0.95])
self.assertListEqual(f.scope, ['Alarm', 'Earthquake'])
self.assertDictEqual(f.stride, {'Alarm': 1, 'Earthquake': 2})
def test_multiply_factor(self): f1 = Factor(self.bn,'Alarm') f2 = Factor(self.bn,'Burglary') f1.multiply_factor(f2) f3 = Factor(self.bn,'Burglary') f4 = Factor(self.bn,'Alarm') f3.multiply_factor(f4) self.assertListEqual(list(f1.cpt),list(f3.cpt))
def test_maxout_var(self):
"""
I KNOW THIS IS CORRECT.
"""
f = Factor(self.bn,'Alarm')
f.maxout_var('Burglary')
self.assertListEqual(list(f.cpt),
[ 0.999, 0.94 , 0.71 , 0.95 ])
self.assertListEqual(f.scope,['Alarm','Earthquake'])
self.assertDictEqual(f.stride,
{'Alarm':1,'Earthquake':2})
def refresh(self):
"""
Refresh Factorization attributes.
"""
self._phi = [Factor(self.bn, rv) for rv in self.bn.nodes()]
self.map_factors = OrderedDict()
self.map_assignment = dict()
self.map_prob = -1
def __init__(self, bn, nodes=None):
"""
Initialize a Factorization object.
The *nodes* argument allows you to make a Factorization object
that includes only a subset of the random variables in the
passed-in BayesNet object. This is mostly useful for CliqueTree
algorithms.
"""
self.bn = bn
if nodes is not None:
self._phi = [Factor(bn, rv) for rv in nodes]
else:
self._phi = [Factor(bn, rv) for rv in bn.nodes()]
## MAP-BASED ATTRIBUTES ##
self.map_factors = OrderedDict()
self.map_assignment = dict()
self.map_prob = -1
def test_multiply_factor(self): f1 = Factor(self.bn,'Alarm') f2 = Factor(self.bn,'Burglary') f1.multiply_factor(f2) f3 = Factor(self.bn,'Burglary') f4 = Factor(self.bn,'Alarm') f3.multiply_factor(f4) self.assertListEqual(list(f1.cpt),list(f3.cpt))
def random_sample(bn, n=1000):
"""
Take a random sample of "n" observations from a
BayesNet object. This is essentially just the
forward sample algorithm that returns the samples.
Parameters
----------
*bn* : a BayesNet object from which to sample
*n* : an integer
The number of observations to take
*evidence* : a dictionary, key=rv & value=instantiation
Evidence to pass in
Returns
-------
*sample_dict* : a list of samples, where each sample
is a list of values in bn.nodes() (topsort) order
Notes
-----
"""
sample = np.empty((n, bn.num_nodes()), dtype=np.int)
rv_map = dict([(rv, idx) for idx, rv in enumerate(bn.nodes())])
factor_map = dict([(rv, Factor(bn, rv)) for rv in bn.nodes()])
for i in xrange(n):
for rv in bn.nodes():
f = deepcopy(factor_map[rv])
# reduce_factor by parent samples
for p in bn.parents(rv):
f.reduce_factor(p, bn.values(p)[sample[i][rv_map[p]]])
choice_vals = bn.values(rv)
choice_probs = f.cpt
chosen_val = np.random.choice(choice_vals, p=choice_probs)
sample[i][rv_map[rv]] = bn.values(rv).index(chosen_val)
return sample
def test_reduce_factor(self):
f = Factor(self.bn, 'Alarm')
f.reduce_factor('Burglary','Yes')
self.assertListEqual(list(f.cpt),
[ 0.06, 0.94, 0.05, 0.95])
def test_to_log(self): f = Factor(self.bn,'Earthquake') f.to_log() self.assertEqual(round(sum(f.cpt),4),-6.2166)
def lw_sample(bn, evidence={}, target=None, n=1000):
"""
Approximate Marginal probabilities from
likelihood weighted sample algorithm on
a BayesNet object.
Arguments
---------
*bn* : a BayesNet object
*n* : an integer
The number of samples to take
*evidence* : a dictionary, where
key = rv, value = instantiation
Returns
-------
*sample_dict* : a dictionary where key = rv
and value = another dictionary where
key = rv instantiation and value = marginal
probability
Effects
-------
None
Notes
-----
"""
sample_dict = {}
weight_list = np.ones(n)
# factor_dict = dict([(var,Factor(bn, var)) for var in bn.V])
# parent_dict = dict([(var, bn.data[var]['parents']) for var in bn.V])
# create sample diction
ct_discard = 0
for var in bn.nodes():
sample_dict[var] = {}
# print(var)
for val in bn.values(var):
# print (val)
sample_dict[var][val] = 0
# start to draw sample
for i in range(n):
new_sample = {}
for rv in bn.nodes(): # _get_variable_nodes()
# for rv in a:
# print(rv,'rv is variable')
f = Factor(bn, rv)
# reduce_factor by parent samples
for p in bn.parents(rv):
if p in new_sample:
f.reduce_factor(p, new_sample[p]) #this line has problem
else: #austin add this line to cheat on sampling algorithm
# pass
new_sample[p] = '1'
f.reduce_factor(p, new_sample[p])
# f2 = Factor(bn, p)
# choice_vals = bn.values(p)
# choice_probs = f2.cpt
# chosen_val = np.random.choice(choice_vals, p=choice_probs)
# new_sample[rv] = chosen_val
# if rv in evidence, choose that value and weight
if rv in evidence:
# print(rv,'in evidence')
chosen_val = evidence[rv]
# print(chosen_val,'chosen_val in evidence')
weight_list[i] *= f.cpt[bn.values(rv).index(evidence[rv])]
# print(weight_list[i],'weight')
# if rv not in evidence, sample as usual
else:
# print(new_sample)
choice_vals = bn.values(rv)
choice_probs = f.cpt
# print(choice_probs)
# print(choice_probs)
# print(len(choice_vals),len(choice_probs))
chosen_val = np.random.choice(choice_vals, p=choice_probs)
# print(weight_list)
new_sample[rv] = chosen_val
# weight the choice by the evidence likelihood
for rv in new_sample:
sample_dict[rv][new_sample[rv]] += 1 * weight_list[i]
if weight_list[i] == 0:
ct_discard += 1
weight_sum = sum(weight_list)
# print("total discard sample", ct_discard) # I only add this line
for rv in sample_dict:
for val in sample_dict[rv]:
sample_dict[rv][val] /= weight_sum
sample_dict[rv][val] = round(sample_dict[rv][val], 4)
if target is not None:
return sample_dict[target]
else:
return sample_dict, ct_discard
def test_reduce_factor_by_list(self):
f = Factor(self.bn, 'Alarm')
f.reduce_factor_by_list([['Burglary','Yes'],['Earthquake','Yes']])
self.assertListEqual(list(f.cpt),[0.05,0.95])
self.assertListEqual(f.scope,['Alarm'])
self.assertDictEqual(f.stride,{'Alarm':1})
class FactorTestCase(unittest.TestCase):
def setUp(self):
self.data_path = os.path.join(dirname(dirname(dirname(dirname(__file__)))),'data')
self.bn = read_bn(os.path.join(self.data_path,'cmu.bn'))
self.f = Factor(self.bn, 'Alarm')
def tearDown(self):
pass
# Factor Creation Tests
def test_factor_init(self):
self.assertIsInstance(self.f,Factor)
def test_factor_bn(self):
self.assertListEqual(self.f.bn.V,
['Burglary', 'Earthquake', 'Alarm', 'JohnCalls', 'MaryCalls'])
def test_factor_var(self):
self.assertEqual(self.f.var, 'Alarm')
def test_factor_scope(self):
self.assertListEqual(self.f.scope,['Alarm','Earthquake','Burglary'])
def test_factor_card(self):
self.assertDictEqual(self.f.card,
{'Alarm':2, 'Burglary':2, 'Earthquake':2})
def test_factor_stride(self):
self.assertDictEqual(self.f.stride,
{'Alarm':1, 'Burglary':4, 'Earthquake':2})
def test_factor_cpt(self):
self.assertListEqual(list(self.f.cpt),
[ 0.999, 0.001, 0.71 , 0.29 , 0.06 , 0.94 , 0.05 , 0.95 ])
# Factor Operations Tests
def test_multiply_factor(self):
f1 = Factor(self.bn,'Alarm')
f2 = Factor(self.bn,'Burglary')
f1.multiply_factor(f2)
f3 = Factor(self.bn,'Burglary')
f4 = Factor(self.bn,'Alarm')
f3.multiply_factor(f4)
self.assertListEqual(list(f1.cpt),list(f3.cpt))
def test_sumover_var(self):
self.f.sumover_var('Burglary')
self.assertListEqual(list(self.f.cpt),[0.5,0.5])
def test_sumout_var_list(self):
f = Factor(self.bn,'Alarm')
f.sumout_var_list(['Burglary','Earthquake'])
self.assertListEqual(f.scope,['Alarm'])
self.assertDictEqual(f.stride,{'Alarm':1})
self.assertListEqual(list(f.cpt),[0.45475,0.54525])
def test_sumout_var(self):
f = Factor(self.bn,'Alarm')
f.sumout_var('Earthquake')
self.assertListEqual(f.scope,['Alarm','Burglary'])
self.assertDictEqual(f.stride,
{'Alarm':1,'Burglary':2})
self.assertListEqual(list(f.cpt),
[ 0.8545, 0.1455, 0.055 , 0.945 ])
def test_maxout_var(self):
"""
I KNOW THIS IS CORRECT.
"""
f = Factor(self.bn,'Alarm')
f.maxout_var('Burglary')
self.assertListEqual(list(f.cpt),
[ 0.999, 0.94 , 0.71 , 0.95 ])
self.assertListEqual(f.scope,['Alarm','Earthquake'])
self.assertDictEqual(f.stride,
{'Alarm':1,'Earthquake':2})
def test_reduce_factor_by_list(self):
f = Factor(self.bn, 'Alarm')
f.reduce_factor_by_list([['Burglary','Yes'],['Earthquake','Yes']])
self.assertListEqual(list(f.cpt),[0.05,0.95])
self.assertListEqual(f.scope,['Alarm'])
self.assertDictEqual(f.stride,{'Alarm':1})
def test_reduce_factor(self):
f = Factor(self.bn, 'Alarm')
f.reduce_factor('Burglary','Yes')
self.assertListEqual(list(f.cpt),
[ 0.06, 0.94, 0.05, 0.95])
def test_to_log(self):
f = Factor(self.bn,'Earthquake')
f.to_log()
self.assertEqual(round(sum(f.cpt),4),-6.2166)
def test_from_log(self):
f = Factor(self.bn, 'Earthquake')
f.to_log()
f.from_log()
self.assertListEqual(list(f.cpt),[0.998,0.002])
def test_normalize(self):
self.f.cpt[0]=20
self.f.cpt[1]=20
self.f.cpt[4]=0.94
self.f.cpt[7]=0.15
self.f.normalize()
self.assertListEqual(list(self.f.cpt),
[0.500,0.500,0.710,0.290,0.5,0.5,0.25,0.75])
def lw_sample(bn, evidence={}, target=None, n=1000):
"""
Approximate Marginal probabilities from
likelihood weighted sample algorithm on
a BayesNet object.
Arguments
---------
*bn* : a BayesNet object
*n* : an integer
The number of samples to take
*evidence* : a dictionary, where
key = rv, value = instantiation
Returns
-------
*sample_dict* : a dictionary where key = rv
and value = another dictionary where
key = rv instantiation and value = marginal
probability
Effects
-------
None
Notes
-----
"""
sample_dict = {}
weight_list = np.ones(n)
#factor_dict = dict([(var,Factor(bn, var)) for var in bn.V])
#parent_dict = dict([(var, bn.data[var]['parents']) for var in bn.V])
for var in bn.nodes():
sample_dict[var] = {}
for val in bn.values(var):
sample_dict[var][val] = 0
for i in range(n):
#if i % (n/float(10)) == 0:
# print 'Sample: ' , i
new_sample = {}
for rv in bn.nodes():
f = Factor(bn, rv)
# reduce_factor by parent samples
for p in bn.parents(rv):
f.reduce_factor(p, new_sample[p])
# if rv in evidence, choose that value and weight
if rv in evidence:
chosen_val = evidence[rv]
weight_list[i] *= f.cpt[bn.values(rv).index(evidence[rv])]
# if rv not in evidence, sample as usual
else:
choice_vals = bn.values(rv)
choice_probs = f.cpt
chosen_val = np.random.choice(choice_vals, p=choice_probs)
new_sample[rv] = chosen_val
# weight the choice by the evidence likelihood
for rv in new_sample:
sample_dict[rv][new_sample[rv]] += 1 * weight_list[i]
weight_sum = sum(weight_list)
for rv in sample_dict:
for val in sample_dict[rv]:
sample_dict[rv][val] /= weight_sum
sample_dict[rv][val] = round(sample_dict[rv][val], 4)
if target is not None:
return sample_dict[target]
else:
return sample_dict
def forward_sample(bn, n=1000):
"""
Approximate marginal probabilities from
forward sampling algorithm on a BayesNet object.
This algorithm works by
repeatedly sampling from the BN and taking
the ratio of observations as their marginal probabilities.
One sample is done by first sampling from any prior random
variables, then moving down the network in topological sort
order - sampling from each successive random variable by
conditioning on its parents (which have already been sampled
higher up the network).
Note that there is no evidence to include in this algorithm -
the comparative algorithm which includes evidence is the
likelihood weighted algorithm (see "lw_sample" function).
Arguments
---------
*bn* : a BayesNet object
*n* : an integer
The number of samples to take
Returns
-------
*sample_dict* : a dictionary, where key = rv, value = another dict
where key = instance, value = its probability value
Notes
-----
- Evidence is not currently implemented.
"""
sample_dict = {}
for var in bn.nodes():
sample_dict[var] = {}
for val in bn.values(var):
sample_dict[var][val] = 0
for i in range(n):
#if i % (n/float(10)) == 0:
# print 'Sample: ' , i
new_sample = {}
for rv in bn.nodes():
f = Factor(bn, rv)
for p in bn.parents(rv):
f.reduce_factor(p, new_sample[p])
choice_vals = bn.values(rv)
choice_probs = f.cpt
chosen_val = np.random.choice(choice_vals, p=choice_probs)
sample_dict[rv][chosen_val] += 1
new_sample[rv] = chosen_val
for rv in sample_dict:
for val in sample_dict[rv]:
sample_dict[rv][val] = int(sample_dict[rv][val]) / float(n)
return sample_dict
def setUp(self): self.data_path = os.path.join(dirname(dirname(dirname(dirname(__file__)))),'data') self.bn = read_bn(os.path.join(self.data_path,'cmu.bn')) self.f = Factor(self.bn, 'Alarm')
def test_sumout_var_list(self):
f = Factor(self.bn,'Alarm')
f.sumout_var_list(['Burglary','Earthquake'])
self.assertListEqual(f.scope,['Alarm'])
self.assertDictEqual(f.stride,{'Alarm':1})
self.assertListEqual(list(f.cpt),[0.45475,0.54525])
def lw_sample(bn, evidence={}, target=None, n=1000):
"""
Approximate Marginal probabilities from
likelihood weighted sample algorithm on
a BayesNet object.
Arguments
---------
*bn* : a BayesNet object
*n* : an integer
The number of samples to take
*evidence* : a dictionary, where
key = rv, value = instantiation
Returns
-------
*sample_dict* : a dictionary where key = rv
and value = another dictionary where
key = rv instantiation and value = marginal
probability
Effects
-------
None
Notes
-----
"""
sample_dict = {}
weight_list = np.ones(n)
#factor_dict = dict([(var,Factor(bn, var)) for var in bn.V])
#parent_dict = dict([(var, bn.data[var]['parents']) for var in bn.V])
for var in bn.nodes():
sample_dict[var] = {}
for val in bn.values(var):
sample_dict[var][val] = 0
for i in range(n):
#if i % (n/float(10)) == 0:
# print 'Sample: ' , i
new_sample = {}
for rv in bn.nodes():
f = Factor(bn,rv)
# reduce_factor by parent samples
for p in bn.parents(rv):
f.reduce_factor(p,new_sample[p])
# if rv in evidence, choose that value and weight
if rv in evidence:
chosen_val = evidence[rv]
weight_list[i] *= f.cpt[bn.values(rv).index(evidence[rv])]
# if rv not in evidence, sample as usual
else:
choice_vals = bn.values(rv)
choice_probs = f.cpt
chosen_val = np.random.choice(choice_vals, p=choice_probs)
new_sample[rv] = chosen_val
# weight the choice by the evidence likelihood
for rv in new_sample:
sample_dict[rv][new_sample[rv]] += 1*weight_list[i]
weight_sum = sum(weight_list)
for rv in sample_dict:
for val in sample_dict[rv]:
sample_dict[rv][val] /= weight_sum
sample_dict[rv][val] = round(sample_dict[rv][val],4)
if target is not None:
return sample_dict[target]
else:
return sample_dict
def test_sumout_var_list(self):
f = Factor(self.bn,'Alarm')
f.sumout_var_list(['Burglary','Earthquake'])
self.assertListEqual(f.scope,['Alarm'])
self.assertDictEqual(f.stride,{'Alarm':1})
self.assertListEqual(list(f.cpt),[0.45475,0.54525])
def test_to_log(self): f = Factor(self.bn,'Earthquake') f.to_log() self.assertEqual(round(sum(f.cpt),4),-6.2166)
def setUp(self): self.data_path = os.path.join(dirname(dirname(dirname(dirname(__file__)))),'data') self.bn = read_bn(os.path.join(self.data_path,'cmu.bn')) self.f = Factor(self.bn, 'Alarm')
def test_from_log(self): f = Factor(self.bn, 'Earthquake') f.to_log() f.from_log() self.assertListEqual(list(f.cpt),[0.998,0.002])
def test_reduce_factor(self):
f = Factor(self.bn, 'Alarm')
f.reduce_factor('Burglary','Yes')
self.assertListEqual(list(f.cpt),
[ 0.06, 0.94, 0.05, 0.95])
class FactorTestCase(unittest.TestCase):
def setUp(self):
self.data_path = os.path.join(dirname(dirname(dirname(dirname(__file__)))),'data')
self.bn = read_bn(os.path.join(self.data_path,'cmu.bn'))
self.f = Factor(self.bn, 'Alarm')
def tearDown(self):
pass
# Factor Creation Tests
def test_factor_init(self):
self.assertIsInstance(self.f,Factor)
def test_factor_bn(self):
self.assertListEqual(self.f.bn.V,
['Burglary', 'Earthquake', 'Alarm', 'JohnCalls', 'MaryCalls'])
def test_factor_var(self):
self.assertEqual(self.f.var, 'Alarm')
def test_factor_scope(self):
self.assertListEqual(self.f.scope,['Alarm','Earthquake','Burglary'])
def test_factor_card(self):
self.assertDictEqual(self.f.card,
{'Alarm':2, 'Burglary':2, 'Earthquake':2})
def test_factor_stride(self):
self.assertDictEqual(self.f.stride,
{'Alarm':1, 'Burglary':4, 'Earthquake':2})
def test_factor_cpt(self):
self.assertListEqual(list(self.f.cpt),
[ 0.999, 0.001, 0.71 , 0.29 , 0.06 , 0.94 , 0.05 , 0.95 ])
# Factor Operations Tests
def test_multiply_factor(self):
f1 = Factor(self.bn,'Alarm')
f2 = Factor(self.bn,'Burglary')
f1.multiply_factor(f2)
f3 = Factor(self.bn,'Burglary')
f4 = Factor(self.bn,'Alarm')
f3.multiply_factor(f4)
self.assertListEqual(list(f1.cpt),list(f3.cpt))
def test_sumover_var(self):
self.f.sumover_var('Burglary')
self.assertListEqual(list(self.f.cpt),[0.5,0.5])
def test_sumout_var_list(self):
f = Factor(self.bn,'Alarm')
f.sumout_var_list(['Burglary','Earthquake'])
self.assertListEqual(f.scope,['Alarm'])
self.assertDictEqual(f.stride,{'Alarm':1})
self.assertListEqual(list(f.cpt),[0.45475,0.54525])
def test_sumout_var(self):
f = Factor(self.bn,'Alarm')
f.sumout_var('Earthquake')
self.assertListEqual(f.scope,['Alarm','Burglary'])
self.assertDictEqual(f.stride,
{'Alarm':1,'Burglary':2})
self.assertListEqual(list(f.cpt),
[ 0.8545, 0.1455, 0.055 , 0.945 ])
def test_maxout_var(self):
"""
I KNOW THIS IS CORRECT.
"""
f = Factor(self.bn,'Alarm')
f.maxout_var('Burglary')
self.assertListEqual(list(f.cpt),
[ 0.999, 0.94 , 0.71 , 0.95 ])
self.assertListEqual(f.scope,['Alarm','Earthquake'])
self.assertDictEqual(f.stride,
{'Alarm':1,'Earthquake':2})
def test_reduce_factor_by_list(self):
f = Factor(self.bn, 'Alarm')
f.reduce_factor_by_list([['Burglary','Yes'],['Earthquake','Yes']])
self.assertListEqual(list(f.cpt),[0.05,0.95])
self.assertListEqual(f.scope,['Alarm'])
self.assertDictEqual(f.stride,{'Alarm':1})
def test_reduce_factor(self):
f = Factor(self.bn, 'Alarm')
f.reduce_factor('Burglary','Yes')
self.assertListEqual(list(f.cpt),
[ 0.06, 0.94, 0.05, 0.95])
def test_to_log(self):
f = Factor(self.bn,'Earthquake')
f.to_log()
self.assertEqual(round(sum(f.cpt),4),-6.2166)
def test_from_log(self):
f = Factor(self.bn, 'Earthquake')
f.to_log()
f.from_log()
self.assertListEqual(list(f.cpt),[0.998,0.002])
def test_normalize(self):
self.f.cpt[0]=20
self.f.cpt[1]=20
self.f.cpt[4]=0.94
self.f.cpt[7]=0.15
self.f.normalize()
self.assertListEqual(list(self.f.cpt),
[0.500,0.500,0.710,0.290,0.5,0.5,0.25,0.75])
def test_reduce_factor_by_list(self):
f = Factor(self.bn, 'Alarm')
f.reduce_factor_by_list([['Burglary','Yes'],['Earthquake','Yes']])
self.assertListEqual(list(f.cpt),[0.05,0.95])
self.assertListEqual(f.scope,['Alarm'])
self.assertDictEqual(f.stride,{'Alarm':1})
def gibbs_sample(bn, n=1000, burn=200):
"""
Approximate Marginal probabilities from Gibbs Sampling
over a BayesNet object.
Arguments
---------
*bn* : a BayesNet object
*n* : an integer
The number of samples to take
*burn* : an integer
The number of beginning samples to
throw away for the MCMC mixing.
Returns
-------
*sample_dict* : a dictionary where key = rv
and value = another dictionary where
key = rv instantiation and value = marginal
probability
Notes
-----
"""
sample_dict ={}
for rv in bn.nodes():
sample_dict[rv]={}
for val in bn.values(rv):
sample_dict[rv][val] = 0
state = {}
for rv in bn.nodes():
state[rv] = np.random.choice(bn.values(rv)) # uniform sample
for i in range(n):
#if i % (n/float(10)) == 0:
# print 'Sample: ' , i
for rv in bn.nodes():
# get possible values conditioned on everything else
parents = bn.parents(rv)
# no parents - prior
if len(parents) == 0:
choice_vals = bn.values(rv)
choice_probs = bn.cpt(rv)
# has parent - filter cpt
else:
f = Factor(bn,rv)
for p in parents:
f.reduce_factor(p,state[p])
choice_vals = bn.values(rv)
choice_probs = f.cpt
# sample over remaining possibilities
chosen_val = np.random.choice(choice_vals,p=choice_probs)
state[rv]=chosen_val
# update sample_dict dictionary
if i > burn:
for rv,val in state.items():
sample_dict[rv][val] +=1
for rv in sample_dict:
for val in sample_dict[rv]:
sample_dict[rv][val] = round(int(sample_dict[rv][val]) / float(n-burn),4)
return sample_dict
def test_from_log(self): f = Factor(self.bn, 'Earthquake') f.to_log() f.from_log() self.assertListEqual(list(f.cpt),[0.998,0.002])
def gibbs_sample(bn, n=1000, burn=200):
"""
Approximate Marginal probabilities from Gibbs Sampling
over a BayesNet object.
Arguments
---------
*bn* : a BayesNet object
*n* : an integer
The number of samples to take
*burn* : an integer
The number of beginning samples to
throw away for the MCMC mixing.
Returns
-------
*sample_dict* : a dictionary where key = rv
and value = another dictionary where
key = rv instantiation and value = marginal
probability
Notes
-----
"""
sample_dict = {}
for rv in bn.nodes():
sample_dict[rv] = {}
for val in bn.values(rv):
sample_dict[rv][val] = 0
state = {}
for rv in bn.nodes():
state[rv] = np.random.choice(bn.values(rv)) # uniform sample
for i in range(n):
#if i % (n/float(10)) == 0:
# print 'Sample: ' , i
for rv in bn.nodes():
# get possible values conditioned on everything else
parents = bn.parents(rv)
# no parents - prior
if len(parents) == 0:
choice_vals = bn.values(rv)
choice_probs = bn.cpt(rv)
# has parent - filter cpt
else:
f = Factor(bn, rv)
for p in parents:
f.reduce_factor(p, state[p])
choice_vals = bn.values(rv)
choice_probs = f.cpt
# sample over remaining possibilities
chosen_val = np.random.choice(choice_vals, p=choice_probs)
state[rv] = chosen_val
# update sample_dict dictionary
if i > burn:
for rv, val in state.items():
sample_dict[rv][val] += 1
for rv in sample_dict:
for val in sample_dict[rv]:
sample_dict[rv][val] = round(
int(sample_dict[rv][val]) / float(n - burn), 4)
return sample_dict
def forward_sample(bn, n=1000):
"""
Approximate marginal probabilities from
forward sampling algorithm on a BayesNet object.
This algorithm works by
repeatedly sampling from the BN and taking
the ratio of observations as their marginal probabilities.
One sample is done by first sampling from any prior random
variables, then moving down the network in topological sort
order - sampling from each successive random variable by
conditioning on its parents (which have already been sampled
higher up the network).
Note that there is no evidence to include in this algorithm -
the comparative algorithm which includes evidence is the
likelihood weighted algorithm (see "lw_sample" function).
Arguments
---------
*bn* : a BayesNet object
*n* : an integer
The number of samples to take
Returns
-------
*sample_dict* : a dictionary, where key = rv, value = another dict
where key = instance, value = its probability value
Notes
-----
- Evidence is not currently implemented.
"""
sample_dict = {}
for var in bn.nodes():
sample_dict[var] = {}
for val in bn.values(var):
sample_dict[var][val] = 0
for i in range(n):
#if i % (n/float(10)) == 0:
# print 'Sample: ' , i
new_sample = {}
for rv in bn.nodes():
f = Factor(bn,rv)
for p in bn.parents(rv):
f.reduce_factor(p,new_sample[p])
choice_vals = bn.values(rv)
choice_probs = f.cpt
chosen_val = np.random.choice(choice_vals, p=choice_probs)
sample_dict[rv][chosen_val] += 1
new_sample[rv] = chosen_val
for rv in sample_dict:
for val in sample_dict[rv]:
sample_dict[rv][val] = int(sample_dict[rv][val]) / float(n)
return sample_dict