def testInferenceWithLocalsCPT(self):
bn = self.fill()
bn2 = self.fill2(bn)
frag = gum.BayesNetFragment(bn)
for i in bn.nodes():
frag.installNode(i)
self.assertTrue(frag.checkConsistency())
self.assertEqual(frag.size(), 6)
self.assertEqual(frag.sizeArcs(), 7)
newV5 = gum.Potential().add(frag.variable("v5")).add(
frag.variable("v2")).add(frag.variable("v3"))
newV5.fillWith(bn2.cpt("v5"))
frag.installCPT("v5", newV5)
self.assertTrue(frag.checkConsistency())
self.assertEqual(frag.size(), 6)
self.assertEqual(frag.sizeArcs(), 6)
ie2 = gum.LazyPropagation(bn2)
ie2.makeInference()
ie = gum.LazyPropagation(frag)
ie.makeInference()
for n in frag.names():
for x1, x2 in zip(
ie2.posterior(n).tolist(),
ie.posterior(n).tolist()):
self.assertAlmostEqual(x1,
x2,
delta=1e-5,
msg="For variable '{}'".format(n))
def test1(bn1):
print("=====")
print("TEST1")
print("=====")
evs = {"SAO2": 2, "CATECHOL": 1}
print("EVIDENCES {}".format(evs))
bn2, evs2 = conditionalModel(bn1, evs)
print(" - Mutilation done")
ie1 = gum.LazyPropagation(bn1)
ie1.setEvidence(evs)
ie1.makeInference()
ie2 = gum.LazyPropagation(bn2)
ie2.setEvidence(evs2)
ie2.makeInference()
print(" - Inference done")
nb_errors = 0
for n in bn1.names():
if not isAlmostEqualPot(ie1.posterior(bn1.idFromName(n)),
ie2.posterior(bn2.idFromName(n))):
nb_errors += 1
print("Error on {} : {} != {}".format(
n,
ie1.posterior(bn1.idFromName(n))[:],
ie2.posterior(bn2.idFromName(n))[:]))
else:
pass
if nb_errors > 0:
print("Errors : {}".format(nb_errors))
else:
print("No error : inference results are identical.")
def main():
bn1 = gum.loadBN("alarm.bif")
print(" - BN read")
evs = {"SAO2": 2, "CATECHOL": 1}
bn2 = mutilate(gum.BayesNet(bn1), evs)
print(" - Mutilation done")
ie1 = gum.LazyPropagation(bn1)
ie1.setEvidence(evs)
ie1.makeInference()
ie2 = gum.LazyPropagation(bn2)
ie2.setEvidence(evs)
ie2.makeInference()
print(" - Inference done")
nb_errors = 0
for n in bn1.names():
if not isAlmostEqualPot(ie1.posterior(bn1.idFromName(n)),
ie2.posterior(bn2.idFromName(n))):
nb_errors += 1
print("Error on {} : {} != {}".format(
n,
ie1.posterior(bn1.idFromName(n))[:],
ie2.posterior(bn2.idFromName(n))[:]))
else:
pass
if nb_errors > 0:
print("Errors : {}".format(nb_errors))
else:
print("No error : inference results are identical.")
def testOpenBayesSiteExamples(self):
protoie = gum.LazyPropagation(self.bn)
protoie.makeInference()
proto = protoie.posterior(self.w)
ie = gum.LoopyWeightedSampling(self.bn)
ie.setVerbosity(True)
ie.setEpsilon(0.02)
ie.setMinEpsilonRate(0.001)
msg = self.iterTest(proto, ie, self.w, {})
if msg is not None:
self.fail(msg)
protoie = gum.LazyPropagation(self.bn)
protoie.makeInference()
ie.setEvidence({'s': 0, 'c': 0})
proto = protoie.posterior(self.w)
ie = gum.LoopyGibbsSampling(self.bn)
ie.setVerbosity(False)
ie.setEpsilon(0.02)
ie.setMinEpsilonRate(0.001)
msg = self.iterTest(proto, ie, self.w, {'s': 0, 'c': 0})
if msg is not None:
self.fail(msg)
def test2(bn1):
print("=====")
print("TEST2")
print("=====")
evs = {"HYPOVOLEMIA": 0, "CATECHOL": 1, "INTUBATION": 0}
bn2, evs2 = conditionalModel(bn1, evs)
# HYPOVOLEMIA has no parent
if "HYPOVOLEMIA" in evs2:
print("- HYPOVOLEMIA should not be in evs2")
try:
i = bn2.idFromName("HYPOVOLEMIA")
print("- HYPOVOLEMIA should not be in bn2")
except:
pass
# INTUBATION has no parent
if "INTUBATION" in evs2:
print("- INTUBATION should not be in evs2")
try:
i = bn2.idFromName("INTUBATION")
print("- INTUBATION should not be in bn2")
except:
pass
ie1 = gum.LazyPropagation(bn1)
ie1.setEvidence(evs)
ie1.makeInference()
ie2 = gum.LazyPropagation(bn2)
ie2.setEvidence(evs2)
ie2.makeInference()
print(" - Inference done")
nb_errors = 0
for n in bn2.names():
if not isAlmostEqualPot(ie1.posterior(bn1.idFromName(n)),
ie2.posterior(bn2.idFromName(n))):
nb_errors += 1
print("Error on {} : {} != {}".format(
n,
ie1.posterior(bn1.idFromName(n))[:],
ie2.posterior(bn2.idFromName(n))[:]))
else:
pass
if nb_errors > 0:
print("Errors : {}".format(nb_errors))
else:
print("No error : inference results are identical.")
def main():
bn = gum.loadBN("data/alarm.bif")
print("BN read")
evs = {"HR": 1, "PAP": 2}
m = Gibbs(bn, evs, verbose=True)
m.run(5e-2, 20)
print("done")
ie = gum.LazyPropagation(bn)
ie.setEvidence(evs)
ie.makeInference()
for i in bn.ids():
v, c = m.results(i)
if v is not None:
print("{} : {:3.5f}\n exact : {}\n approx : {} ({:7.5f})".
format(
bn.variable(i).name(), utils.KL(ie.posterior(i), v),
utils.compactPot(ie.posterior(i)), utils.compactPot(v),
c))
else:
print("{}: {}".format(
bn.variable(i).name(), evs[bn.variable(i).name()]))
def compareApprox(m, bn, evs):
"""
Compare results in m with a LazyPropagation on bn with evidence evs
:param m: the approximated algorithm
:param bn: the bayesian network
:param evs: the dict of evidence
:return: void
"""
ie = gum.LazyPropagation(bn)
ie.setEvidence(evs)
ie.makeInference()
res = []
for i in bn.ids():
v, c = m.results(i)
if v is not None:
res.append((bn.variable(i).name(), KL(ie.posterior(i), v),
compactPot(ie.posterior(i)), compactPot(v), c))
else:
print("{}: {}".format(
bn.variable(i).name(), evs[bn.variable(i).name()]))
for r in sorted(res, key=lambda item: item[1], reverse=True):
print(
"{} : {:3.5f}\n exact : {}\n approx : {} ({:7.5f})"
.format(*r))
def run_bn_unsup(train_corr, test_corr, structure):
""""
This method first learns a BN based on train_corr, then it propagates evidence from test_corr through it, after
which a new data set is created based on the new posteriors
:param train_corr: training-data, not in one-hot encoding form!
:param test_corr: test-data that is being updated, in one-hot encoding form
:param structure: structure of the data (how many categories each attribute has)
"""
structure_0 = [0] + structure
# Learn the BN based on train_corr
learner = gum.BNLearner(train_corr)
learner.useScoreBDeu()
bn = learner.learnBN()
# Create a placeholder for the net_data
new_data = np.zeros(test_corr.shape)
for i in range(test_corr.shape[0]):
dp = test_corr[i, :] # fix an observation
evs = {}
k = 0
for n in bn.nodes(
): # Convert the evidence to a dictionary structure needed for propagation
evs[n] = dp[sum(structure_0[:k + 1]):sum(structure_0[:k + 2])]
k += 1
ie = gum.LazyPropagation(bn)
ie.setEvidence(evs) # set the evidence
pst = [ie.posterior(n).toarray() for n in bn.nodes()
] # Extract the posteriors and store them in new_data
new_data[i, :] = list(itertools.chain.from_iterable(pst))
ie.eraseAllEvidence()
return new_data
def compil(bn, targets, evs):
"""This function uses all the predefined functions above to fill the compiler array with instructions to get the targets of a bn according to evidences"""
ie = gum.LazyPropagation(bn)
jt = ie.junctionTree()
#hardToSoftEvidences(bn, evs)
absorp = [] #the list for the absorption
diffu = [] #the list for the diffusion
cliquesTar = {
} #the dictionnary which contains the couples {target:clique}
r = mainClique(bn, jt, targets)
n = r
targetmp1 = list(targets) #for parcours (this list is changed)
deleteTarMainCliq(bn, jt, targetmp1, r)
targetmp2 = list(targetmp1) #for inference (this list is not changed)
parcours(bn, jt, targetmp1, n, r, absorp, diffu, cliquesTar)
#Creation and initialization of potentials
creationPotentialsAbsorp(bn, jt, absorp)
initPotentialsAbsorp(bn, jt, absorp)
evsPotentials(bn, jt, evs, absorp)
creaIniPotentialsDiffu(bn, jt, diffu, cliquesTar, targets, absorp)
#Absorption and diffusion
inference(bn, jt, absorp, diffu, targets, targetmp2, cliquesTar)
#Computing targets
output(bn, jt, targets, absorp, diffu, cliquesTar)
return compilator.getTab()
def testWithDifferentVariables(self):
protoie = gum.LazyPropagation(self.bn)
protoie.addEvidence('r', 1)
protoie.addEvidence('w', 0)
protoie.makeInference()
proto = protoie.posterior(self.s)
ie = gum.LoopyWeightedSampling(self.bn)
ie.setVerbosity(False)
ie.setEpsilon(0.1)
ie.setMinEpsilonRate(0.01)
msg = self.iterTest(proto, ie, self.s, {'r': [0, 1], 'w': (1, 0)})
if msg is not None:
self.fail(msg)
ie2 = gum.LoopyGibbsSampling(self.bn)
ie2.setVerbosity(False)
ie2.setEpsilon(0.1)
ie2.setMinEpsilonRate(0.01)
ie2.setEvidence({'r': 1, 'w': 0})
ie2.makeInference()
msg = self.iterTest(proto, ie2, self.s, {'r': 1, 'w': 0})
if msg is not None:
self.fail(msg)
ie3 = gum.LoopyMonteCarloSampling(self.bn)
ie3.setVerbosity(False)
ie3.setEpsilon(0.1)
ie3.setMinEpsilonRate(0.01)
msg = self.iterTest(proto, ie3, self.s, {'r': [0, 1], 'w': (1, 0)})
if msg is not None:
self.fail(msg)
def getInformationGraph(bn,
evs=None,
size=None,
cmap=_INFOcmap,
withMinMax=False):
"""
Create a dot representation of the information graph for this BN
Parameters
----------
bn: gum.BayesNet
the BN
evs : Dict[str,str|int|List[float]]
map of evidence
size: str|int
size of the graph
cmap: matplotlib.colors.Colormap
color map
withMinMax: bool
min and max in the return values ?
Returns
-------
dot.Dot | Tuple[dot.Dot,float,float]
graph as a dot representation and if asked, min_information_value, max_information_value
"""
if size is None:
size = gum.config["notebook", "default_graph_size"]
if evs is None:
evs = {}
ie = gum.LazyPropagation(bn)
ie.setEvidence(evs)
ie.makeInference()
idEvs = {bn.idFromName(name) for name in evs}
nodevals = {
bn.variable(n).name(): ie.H(n)
for n in bn.nodes() if not n in idEvs
}
arcvals = {(x, y): ie.I(x, y) for x, y in bn.arcs()}
gr = BN2dot(bn,
size,
nodeColor=_normalizeVals(nodevals, hilightExtrema=False),
arcWidth=arcvals,
cmapNode=cmap,
cmapArc=cmap,
showMsg=nodevals)
mi = min(nodevals.values())
ma = max(nodevals.values())
if withMinMax:
return gr, mi, ma
else:
return gr
def testJointMutualInformation(self):
bn = gum.fastBN("A->B->C->D;A->E->D;F->B;C->H;")
ie = gum.LazyPropagation(bn)
ie.makeInference()
with self.assertRaises(gum.InvalidArgument):
ie.jointMutualInformation([0])
self.assertAlmostEqual(ie.I(0, 1), ie.jointMutualInformation([0, 1]))
self.assertAlmostEqual(ie.I("A", "B"), ie.jointMutualInformation(["A", "B"]))
ie = gum.LazyPropagation(bn)
ie.addJointTarget({1, 4, 3})
ie.addAllTargets()
ie.makeInference()
byHandJMI = 0
byHandJMI -= ie.jointPosterior({1, 3, 4}).entropy()
byHandJMI += ie.jointPosterior({1, 4}).entropy() + ie.jointPosterior({1, 3}).entropy() + ie.jointPosterior(
{4, 3}).entropy()
byHandJMI -= ie.posterior(1).entropy() + ie.posterior(4).entropy() + ie.posterior(3).entropy()
ie2 = gum.LazyPropagation(bn)
JMI = ie2.jointMutualInformation({1, 3, 4})
self.assertAlmostEqual(JMI, byHandJMI)
ie = gum.LazyPropagation(bn)
ie.addJointTarget({0, 1, 2, 3})
ie.addAllTargets()
ie.makeInference()
byHandJMI = 0
byHandJMI -= ie.jointPosterior({0, 1, 2, 3}).entropy()
byHandJMI += ie.jointPosterior({0, 1, 2}).entropy() + ie.jointPosterior({0, 1, 3}).entropy() + ie.jointPosterior(
{0, 2, 3}).entropy() + ie.jointPosterior({1, 2, 3}).entropy()
byHandJMI -= ie.jointPosterior({0, 1}).entropy() + ie.jointPosterior({0, 2}).entropy() + ie.jointPosterior(
{0, 3}).entropy() + ie.jointPosterior({1, 2}).entropy() + ie.jointPosterior(
{1, 3}).entropy() + ie.jointPosterior({2, 3}).entropy()
byHandJMI += ie.posterior(0).entropy() + ie.posterior(1).entropy() + ie.posterior(2).entropy() + ie.posterior(
3).entropy()
ie2 = gum.LazyPropagation(bn)
JMI = ie2.jointMutualInformation({0, 1, 2, 3})
self.assertAlmostEqual(JMI, byHandJMI)
def plotFollowUnrolled(lovars, dbn, T, evs, vars_title=None):
"""
plot the dynamic evolution of a list of vars with a dBN
:param lovars: list of variables to follow
:param dbn: the unrolled dbn
:param T: the time range
:param evs: observations
:param vars_title: string for default or a dictionary with the variable name as key and the respective title as value.
"""
ie = gum.LazyPropagation(dbn)
ie.setEvidence(evs)
ie.makeInference()
x = np.arange(T)
for var in lovars:
v0 = dbn.variableFromName(var + "0")
lpots = []
for i in range(v0.domainSize()):
serie = []
for t in range(T):
serie.append(ie.posterior(dbn.idFromName(var + str(t)))[i])
lpots.append(serie)
_, ax = plt.subplots()
plt.xlim(left=0, right=T - 1)
plt.ylim(top=1, bottom=0)
ax.xaxis.grid()
# Setting a customized title
if vars_title is None:
plt.title(f"Following variable {var}", fontsize=20)
elif len(vars_title) != 0:
plt.title(vars_title[var], fontsize=20)
else:
raise TypeError("Incorrect format of the plots title dictionary")
plt.xlabel('time')
stack = ax.stackplot(x, lpots)
proxy_rects = [
Rectangle((0, 0), 1, 1, fc=pc.get_facecolor()[0]) for pc in stack
]
labels = [v0.label(i) for i in range(v0.domainSize())]
plt.legend(proxy_rects,
labels,
loc='center left',
bbox_to_anchor=(1, 0.5),
ncol=1,
fancybox=True,
shadow=True)
plt.show()
def testEvidenceJointImpact(self):
bn = gum.fastBN("A->B->C->D;A->E->D;F->B;C->H;")
ie = gum.LazyPropagation(bn)
res = ie.evidenceJointImpact(["D", "E"], ["A", "B", "C", "F"])
joint = bn.cpt("A") * bn.cpt("B") * bn.cpt("C") * bn.cpt("D") * bn.cpt("E") * bn.cpt("F") * bn.cpt("H")
pADCE = joint.margSumIn(["A", "C", "D", "E"])
pAC = pADCE.margSumOut(["D", "E"])
self.assertEqual(res, pADCE / pAC)
def testMutilateBN2(self):
bn = gum.fastBN("P2->N<-P1;A->E2<-N->E1")
bn2, ev2 = gum.mutilateBN(bn,
intervention={},
observation={
'A': ["1"],
"N": [1, 1]
})
ie = gum.LazyPropagation(bn)
ie.setEvidence(ev2)
ie.makeInference()
ie2 = gum.LazyPropagation(bn2)
ie2.setEvidence(ev2)
ie2.makeInference()
for n in bn2.names():
self.assertEquals(
ie.posterior(n).tolist(),
ie2.posterior(n).tolist())
def predict_learner_knowledge_states_from_learner_traces(
self, learner_traces):
knowledge_components = self.associated_learner_pool.get_knowledge_components(
)
bn = unroll_2tbn(self.bn, len(learner_traces) + 1)
# Setup the soft evidences in the BNow
evidences = {}
for i, trace in enumerate(learner_traces):
evaluated_kc = trace.get_kc()
success = trace.get_success()
exercise = trace.get_exercise()
guess, slip = self.associated_learner_pool.get_guess(
exercise), self.associated_learner_pool.get_slip(exercise)
learn, forget = self.associated_learner_pool.get_learn(
evaluated_kc), self.associated_learner_pool.get_forget(
evaluated_kc)
bn.add(
gum.LabelizedVariable(f"exercise({exercise.id}){i}",
f"exercise({exercise.id}){i}", 2))
bn.addArc(f"({evaluated_kc.id}){i}", f"exercise({exercise.id}){i}")
bn.cpt(f"exercise({exercise.id}){i}")[{
f"({evaluated_kc.id}){i}": 0
}] = [1 - guess, guess]
bn.cpt(f"exercise({exercise.id}){i}")[{
f"({evaluated_kc.id}){i}": 1
}] = [slip, 1 - slip]
evidences[f"exercise({exercise.id}){i}"] = int(success)
bn.cpt(f"(Z[({evaluated_kc.id})0->({evaluated_kc.id})t]){i+1}")[{
f"({evaluated_kc.id}){i}":
0
}] = [1 - learn, learn]
bn.cpt(f"(Z[({evaluated_kc.id})0->({evaluated_kc.id})t]){i+1}")[{
f"({evaluated_kc.id}){i}":
1
}] = [forget, 1 - forget]
"""
evidences[f"({evaluated_kc.id}){i}"] = [guess, 1 - guess] if success else [
1 - slip, slip]
"""
# Setup the inference
ie = gum.LazyPropagation(bn)
ie.setEvidence(evidences)
ie.makeInference()
knowledge_states = {}
for kc in knowledge_components:
knowledge_states[f"{kc.id}"] = ie.posterior(
bn.idFromName(f"({kc.id}){len(evidences.keys())}"))[1]
return knowledge_states
def testRelevantReasonning(self):
# an inference for all the bn with an hard evidence and an inference for
# the right fragment with a local CPT should be the same
bn = self.fill()
inf_complete = gum.LazyPropagation(bn)
inf_complete.setEvidence({"v3": 1})
inf_complete.makeInference()
p = inf_complete.posterior("v6")
frag = gum.BayesNetFragment(bn)
frag.installAscendants("v6")
marg = gum.Potential().add(frag.variable("v3"))
marg.fillWith([0, 1])
frag.installMarginal("v3", marg)
self.assertEqual(frag.size(), 3)
self.assertEqual(frag.sizeArcs(), 1)
inf_frag = gum.LazyPropagation(frag)
inf_frag.makeInference()
for x1, x2 in zip(
inf_complete.posterior("v6").tolist(),
inf_frag.posterior("v6").tolist()):
self.assertAlmostEqual(x1, x2, delta=1e-5)
def main():
bn = gum.loadBN("alarm.bif")
ie = gum.LazyPropagation(bn)
ie.makeInference()
m = ParallelMonteCarlo(bn)
m.run(1e-2, 300, verbose=True)
print("done")
for i in bn.ids():
print("{}: {}".format(
bn.variable(i).name(),
int(100000 * utils.KL(ie.posterior(i), m.posterior(i))) / 1000))
def main():
bn = gum.loadBN("alarm.bif")
ie = gum.LazyPropagation(bn)
ie.makeInference()
m = MonteCarlo(bn)
m.run(1e-2, 300, verbose=True)
print("done")
for i in bn.ids():
ev, ec, hv, hc = m.everything(i)
print("{}: {} ({}) =!= {} ({})".format(
bn.variable(i).name(), ev, ec, hv, hc))
def testEvidenceImpactWithNodeId(self):
bn = gum.loadBN(self.agrumSrcDir('asia.bif'), [],
verbose=False) # verbose=False : don't want to see the warnings
ie = gum.LazyPropagation(bn)
self.assertEqual(len(ie.BN().arcs()),8)
with self.assertRaises(gum.InvalidArgument):
res = ie.evidenceImpact(0, [0, 1, 2])
res = ie.evidenceImpact(0, [1, 2])
self.assertEqual(res.nbrDim(), 2) # 2 indep 0 given 1
self.assertEqual(res.extract({"tuberculosis?": 0}), gum.getPosterior(bn, target=0, evs={1: 0}))
self.assertEqual(res.extract({"tuberculosis?": 1}), gum.getPosterior(bn, target=0, evs={1: 1}))
def testOr(self):
bn = gum.BayesNet()
c1, c2 = [bn.add(gum.LabelizedVariable(item, item, 2)) for item in ['C1', 'C2']]
a = bn.addOR(gum.LabelizedVariable('a', 'a', 2))
bn.addArc(c1, a)
bn.addArc(c2, a)
for i in range(2):
bn.cpt(c1)[:] = [i, 1 - i]
for j in range(2):
bn.cpt(c2)[:] = [j, 1 - j]
ie = gum.LazyPropagation(bn)
ie.makeInference()
if i * j == 0:
self.assertEqual(ie.posterior(a)[:][0], 0.0)
self.assertEqual(ie.posterior(a)[:][1], 1.0)
else:
self.assertEqual(ie.posterior(a)[:][0], 1.0)
self.assertEqual(ie.posterior(a)[:][1], 0.0)
def testEvidenceImpactWithName(self):
bn = gum.loadBN(self.agrumSrcDir('asia.bif'), [],
verbose=False) # verbose=False : don't want to see the warnings
ie = gum.LazyPropagation(bn)
with self.assertRaises(gum.InvalidArgument):
res = ie.evidenceImpact("visit_to_Asia?", ["visit_to_Asia?", "tuberculosis?", "tuberculos_or_cancer?"])
with self.assertRaises(gum.NotFound):
res = ie.evidenceImpact("visit_to_Asia?", ["toto", "tuberculosis?", "tuberculos_or_cancer?"])
res = ie.evidenceImpact("visit_to_Asia?", ["tuberculosis?", "tuberculos_or_cancer?"])
self.assertEqual(res.nbrDim(), 2) # 2 indep 0 given 1
self.assertEqual(res.extract({"tuberculosis?": 0}),
gum.getPosterior(bn, target="visit_to_Asia?", evs={"tuberculosis?": 0}))
self.assertEqual(res.extract({"tuberculosis?": 1}),
gum.getPosterior(bn, target="visit_to_Asia?", evs={"tuberculosis?": 1}))
def build_save_BN(self, dGraphNodes, dGraphEdges, randomCPTs):
dGraphEdges = [(str(A), str(B)) for (A, B) in dGraphEdges]
bn = gum.BayesNet(self.name)
[
bn.add(gum.LabelizedVariable(str(var), str(var), 2))
for var in dGraphNodes
]
for edge in dGraphEdges:
bn.addArc(edge[0], edge[1])
if randomCPTs:
# For generate all CPTs
bn.generateCPTs()
# To graph and save BN
gumGraph.dotize(bn, self.path + self.name, 'pdf')
gum.saveBN(bn, self.path + self.name + '.bifxml')
self.generator = gum.BNDatabaseGenerator(bn)
self.ie = gum.LazyPropagation(bn)
self.bn = bn
self.structure = [dGraphNodes, dGraphEdges]
def WikipediaExample(self):
protoie = gum.LazyPropagation(self.bn2)
protoie.makeInference()
proto = protoie.posterior('w2')
ie = gum.LoopyWeightedSampling(self.bn2)
ie.setVerbosity(False)
ie.setEpsilon(0.01)
ie.setMinEpsilonRate(0.001)
msg = self.iterTest(proto, ie, 'w2', {})
if msg is not None:
self.fail(msg)
ie2 = gum.LoopyMonteCarloSampling(self.bn2)
ie2.setVerbosity(False)
ie2.setEpsilon(0.01)
ie2.setMinEpsilonRate(0.001)
msg = self.iterTest(proto, ie2, 'w2', {})
if msg is not None:
self.fail(msg)
def __init__(self, bn, truth_values):
self.truth_values = truth_values
self.scenario_nodes = []
try:
bn.variable('constraint')
try:
bn.variable('aux')
except:
print("No aux node found, restructuring network into Fenton 2016 style")
self.restructure_bn_fenton(bn)
except:
#print("No constraint-aux construction implemented yet. Doing that now.")
self.implement_aux_constraint_structure(bn)
self.bn = bn
self.casemodel = case_model.CaseModel([({}, 1)])
ie = gum.LazyPropagation(bn)
self.ie = ie
self.global_evidence_dict = {'constraint': truth_values[0]}
ie.setEvidence(self.global_evidence_dict)
self.create_first_cases()
def testDictOfSequences(self):
protoie = gum.LazyPropagation(self.bn)
protoie.addEvidence('s', 1)
protoie.addEvidence('w', 0)
protoie.makeInference()
proto = protoie.posterior(self.r)
ie = gum.LoopyImportanceSampling(self.bn)
ie.setVerbosity(False)
ie.setEpsilon(0.05)
ie.setMinEpsilonRate(0.001)
msg = self.iterTest(proto, ie, self.r, {'s': [0, 1], 'w': (1, 0)})
if msg is not None:
self.fail(msg)
ie = gum.LoopyImportanceSampling(self.bn)
ie.setVerbosity(False)
ie.setEpsilon(0.05)
ie.setMinEpsilonRate(0.001)
msg = self.iterTest(proto, ie, self.r, ({'s': 1, 'w': 0}))
if msg is not None:
self.fail(msg)
def testDictOfLabels(self):
protoie = gum.LazyPropagation(self.bn)
protoie.addEvidence('s', 0)
protoie.addEvidence('w', 1)
protoie.makeInference()
proto = protoie.posterior(self.r)
ie = gum.LoopyGibbsSampling(self.bn)
ie.setVerbosity(False)
ie.setEpsilon(0.05)
ie.setMinEpsilonRate(0.001)
msg = self.iterTest(proto, ie, self.r, {'s': 0, 'w': 1})
if msg is not None:
self.fail(msg)
ie = gum.LoopyGibbsSampling(self.bn)
ie.setVerbosity(False)
ie.setEpsilon(0.05)
ie.setMinEpsilonRate(0.001)
msg = self.iterTest(proto, ie, self.r, {'s': 'no', 'w': 'yes'})
if msg is not None:
self.fail(msg)
def eval(self, contextual_bn: "pyAgrum.BayesNet") -> "pyAgrum.Potential":
if self._verbose:
print(f"EVAL ${self.fastToLatex(defaultdict(int))}$ in context",
flush=True)
ie = pyAgrum.LazyPropagation(contextual_bn)
if len(self.varNames) > 1:
svars = set(self.varNames)
ie.addJointTarget(svars)
ie.makeInference()
res = ie.jointPosterior(svars)
else:
for name in self.varNames:
break # take the first and only one name in varNames
ie.makeInference()
res = ie.posterior(name)
if self._verbose:
print(
f"END OF EVAL ${self.fastToLatex(defaultdict(int))}$ : {res}",
flush=True)
return res
def eval(self, contextual_bn: "pyAgrum.BayesNet") -> "pyAgrum.Potential":
if self._verbose:
print(f"EVAL ${self.fastToLatex(defaultdict(int))} in context",
flush=True)
ie = pyAgrum.LazyPropagation(contextual_bn)
p = None
# simple case : we just need a CPT from the BN
if len(self.vars) == 1:
for x in self.vars:
break # we keep the first one and only one
ix = contextual_bn.idFromName(x)
if {
contextual_bn.variable(i).name()
for i in contextual_bn.parents(ix)
} == self.knw:
p = contextual_bn.cpt(ix)
if p is None:
if len(self.knw) == 0:
ie.addJointTarget(self.vars)
ie.makeInference()
p = ie.jointPosterior(self.vars)
else:
ie.addJointTarget(self.vars | self.knw)
ie.makeInference()
p = ie.jointPosterior(self.vars
| self.knw) / ie.jointPosterior(self.knw)
#
# res = p.extract({k: v for k, v in context.todict().items() if k in self.vars + self.knw})
if self._verbose:
print(f"END OF EVAL ${self.fastToLatex(defaultdict(int))}$ : {p}",
flush=True)
return p
def setUp(self):
self.bn = gum.BayesNet()
self.c, self.r = \
[self.bn.add(gum.LabelizedVariable(name, name, 2))
for name in 'c r'.split()]
self.s, self.w = \
[self.bn.add(gum.LabelizedVariable(name, name, 0).addLabel('no').addLabel('yes'))
for name in 's w'.split()]
for link in [(self.c, self.s), (self.c, self.r), (self.s, self.w),
(self.r, self.w)]:
self.bn.addArc(*link)
self.bn.cpt(self.c)[:] = [0.5, 0.5]
self.bn.cpt(self.s)[:] = [[0.5, 0.5], [0.9, 0.1]]
self.bn.cpt(self.r)[:] = [[0.8, 0.2], [0.2, 0.8]]
self.bn.cpt(self.w)[0, 0, :] = [1, 0]
self.bn.cpt(self.w)[0, 1, :] = [0.1, 0.9]
self.bn.cpt(self.w)[1, 0, :] = [0.1, 0.9]
self.bn.cpt(self.w)[1, 1, :] = [0.01, 0.99]
self.ie = gum.LazyPropagation(self.bn)
self.jt = self.ie.junctionTree()
