def nodeAsClf(self, term):
clf = loadClf(self.ontology[term]['name'], self.fold, self.clfName)
#clf.predict_proba = lambda *a: self.predictions[term] #HACK
#clf.__dict__['predict_proba'] = lambda *a: self.predictions[term] #HACK
class FakeClassifier:
def predict_proba(*a):
return self.predictions[term]
for a in ('X_test','y_test',):
# if a != 'predict_proba':
setattr(FakeClassifier, a, getattr(clf, a))
return FakeClassifier()
def nodeAsClf(self, term):
clf = loadClf(self.ontology[term]['name'], self.fold, self.clfName)
#clf.predict_proba = lambda *a: self.predictions[term] #HACK
#clf.__dict__['predict_proba'] = lambda *a: self.predictions[term] #HACK
class FakeClassifier:
def predict_proba(*a):
return self.predictions[term]
for a in (
'X_test',
'y_test',
):
# if a != 'predict_proba':
setattr(FakeClassifier, a, getattr(clf, a))
return FakeClassifier()
def plotRoc(term, clfName, title, clfs=None):
mean_tpr = 0.0
mean_fpr = numpy.linspace(0, 1, 100)
all_tpr = []
#plt.clf()
if clfs is None:
clfs = (loadClf(term, fold, clfName) for fold in range(NUM_FOLDS))
for i, clf in enumerate(clfs):
print("roc", clf)
#for i, (clf, X_train, y_train, X_test, y_test, X_validation, y_validation,_,_,_) in enumerate(folds):
probabs = clf.predict_proba(clf.X_test)
try:
fpr, tpr, _ = roc_curve(clf.y_test, probabs[:, 1])
except IndexError:
fpr, tpr, _ = roc_curve(clf.y_test,
probabs[:, 0],
pos_label=POSTIVE_LABEL)
mean_tpr += interp(mean_fpr, fpr, tpr)
mean_tpr[0] = 0.0
fpr = numpy.nan_to_num(fpr)
try:
roc_auc = auc(fpr, tpr)
except ValueError: # root node
roc_auc = 1.
clf.roc_auc = roc_auc
plt.plot(fpr, tpr, lw=1, label='Fold %d, AUC = %0.2f' % (i, roc_auc))
mean_tpr /= NUM_FOLDS
mean_tpr[-1] = 1.0
mean_auc = auc(mean_fpr, mean_tpr)
plt.plot(mean_fpr,
mean_tpr,
'k--',
label='Mean, AUC = %0.2f' % mean_auc,
lw=2)
plt.plot([0, 1], [0, 1], '--', color=(0.6, 0.6, 0.6))
plt.xlim([-0.05, 1.05])
plt.ylim([-0.05, 1.05])
plt.xlabel('False Positive Rate')
plt.ylabel('True Positive Rate')
plt.title('Receiver operating characteristic: ' + title)
plt.legend(loc="lower right", prop=legendprop)
def plotRoc(term, clfName, title, clfs = None):
mean_tpr = 0.0
mean_fpr = numpy.linspace(0, 1, 100)
all_tpr = []
#plt.clf()
if clfs is None:
clfs = (loadClf(term, fold, clfName) for fold in range(NUM_FOLDS))
for i,clf in enumerate(clfs):
print("roc", clf)
#for i, (clf, X_train, y_train, X_test, y_test, X_validation, y_validation,_,_,_) in enumerate(folds):
probabs = clf.predict_proba(clf.X_test)
try:
fpr, tpr, _ = roc_curve(clf.y_test, probabs[:, 1])
except IndexError:
fpr, tpr, _ = roc_curve(clf.y_test, probabs[:, 0], pos_label=POSTIVE_LABEL)
mean_tpr += interp(mean_fpr, fpr, tpr)
mean_tpr[0] = 0.0
fpr = numpy.nan_to_num(fpr)
try:
roc_auc = auc(fpr, tpr)
except ValueError: # root node
roc_auc = 1.
clf.roc_auc = roc_auc
plt.plot(fpr, tpr, lw=1, label='Fold %d, AUC = %0.2f' % (i, roc_auc))
mean_tpr /= NUM_FOLDS
mean_tpr[-1] = 1.0
mean_auc = auc(mean_fpr, mean_tpr)
plt.plot(mean_fpr, mean_tpr, 'k--',
label='Mean, AUC = %0.2f' % mean_auc, lw=2)
plt.plot([0, 1], [0, 1], '--', color=(0.6, 0.6, 0.6))
plt.xlim([-0.05, 1.05])
plt.ylim([-0.05, 1.05])
plt.xlabel('False Positive Rate')
plt.ylabel('True Positive Rate')
plt.title('Receiver operating characteristic: '+title)
plt.legend(loc="lower right", prop=legendprop)
def generateCPD(self, term): #, X_train, y_train, X_test, y_test, X_validation, y_validation, g_train, g_test, g_validation):
clf = loadClf(self.ontology[term]['name'], self.fold, self.clfName)
posTrain = sum(clf.y_train == POSTIVE_LABEL)
negTrain = sum(clf.y_train == NEGATIVE_LABEL)
totalTrain = posTrain + negTrain
children = sorted(self.ontology[term]['children'])
parents = sorted(self.ontology[term]['parents'])
labels = {l : PRIOR for l in product(*((POSTIVE_LABEL,NEGATIVE_LABEL),)*(len(children)+1))}
if children:
childNodes = [self.ontology[child]['node'][self.fold][self.clfName] for child in children]
for gene,y in zip(clf.g_train, clf.y_train):
event = []
for child in children:
event.append(POSTIVE_LABEL if gene in self.ontology.associations[child] else NEGATIVE_LABEL)
event.append(POSTIVE_LABEL if gene in self.ontology.associations[term] else NEGATIVE_LABEL)
assert (gene in self.ontology.associations[term]) == (y == POSTIVE_LABEL)
event = tuple(event)
labels[event] += 1
def countBoth(event):
return labels[event[:-1]+(POSTIVE_LABEL,)] + labels[event[:-1]+(NEGATIVE_LABEL,)]
cprior = PRIOR * (2 ** len(children))
types = [Mixture]*(len(children)-1) + [Categorical]
mixparams = [i for s in zip(childNodes, types) for i in s]
cpd = numpy.empty((2,)*(len(children)+1))
for event, counted in labels.items():
v=cpd
for b in event[:-1]:
v = v[b]
hid = event[-1]
print("Event: ", event)
if POSTIVE_LABEL not in event[:-1]: # Všichni potomci označeni "ne"
v[hid] = counted/countBoth(event)
print("Stored %d / %d" % (counted,countBoth(event)))
else:
v[hid] = {POSTIVE_LABEL: 0.99, NEGATIVE_LABEL:0.01}[hid]
print("Stored %d : %d" % (hid, v[hid]))
#print(term,"<-",",".join(children))
print(cpd)
#print(labels)
hidden = Mixture(*mixparams, cpd)
hidden.params = cpd
else: #No children
#hidden = DiscreteDistribution({'0': posTrain / totalTrain, '1': negTrain / totalTrain})
params = (posTrain / totalTrain, negTrain / totalTrain)
hidden = Categorical(params)
hidden.params = params
#print("Hidden node %s:" % term)
#print(repr(hidden))
#print([p for p in hidden.parents if isinstance(p, Stochastic)])
#print(hidden.get_moments())
conf = clf.conf + PRIOR
#posTest, negTest = numpy.sum(conf, 1)
posTest, negTest = numpy.sum(conf, 0)
#print("Confusion matrix:")
#print(conf)
try:
assert term != self.ontology.root
pos_decisions = clf.decision_function(clf.X_test[clf.y_test==POSTIVE_LABEL])
neg_decisions = clf.decision_function(clf.X_test[clf.y_test==NEGATIVE_LABEL])
means = [numpy.mean(pos_decisions)], [numpy.mean(neg_decisions)]
maxprec = 100.0
precs = [[numpy.min((1/numpy.var(pos_decisions), maxprec))]], [[numpy.min((1/numpy.var(neg_decisions), maxprec))]]
#else:
except (ValueError, AssertionError):
means = [-1.], [1.]
precs = [[1.]], [[1.]]
print("Gaussian params:", term, self.ontology[term]['name'], means, precs)
observed = Mixture(hidden, Gaussian, means, precs)
#observed = ConditionalProbabilityTable([
# ['0', '0', conf[0][0] / posTest], # if term != root else 1.],
# ['0', '1', conf[0][1] / posTest], # if term != root else 0.],
# ['1', '0', conf[1][0] / negTest], # if term != root else 0.],
# ['1', '1', conf[1][1] / negTest]], #if term != root else 1.]],
# [hidden.distribution])
#print("Observed node %s - %s:" % (term, self.ontology[term]['name']))
#print(repr(observed))
#print([p for p in observed.parents if isinstance(p, Stochastic)])
self.ontology[term]['node'][self.fold][self.clfName] = hidden
#self.ontology[term]['clf'][self.fold][self.clfName] = clf, X_validation, y_validation, g_validation
assert self.lenValidation is None or self.lenValidation == len(clf.y_validation)
self.lenValidation = len(clf.y_validation)
self.allobserved[term] = observed
self.allhidden[term] = hidden
self.extranodes.update((p for p in hidden.parents if isinstance(p, Stochastic)))
def predict(self):
#print(self.network.graph)
self.predictions = {term : numpy.empty((self.lenValidation, 2), dtype=float) for term in self.ontology.ontology}
classifiers = {
term : lambda: loadClf(self.ontology[term]['name'], self.fold, self.clfName) #self.ontology[term]['clf'][self.fold][self.clfName]
for term
in self.ontology.ontology
}
#for term, (clf,X,y,g) in classifiers.items():
# print(term, ":", repr(self.clfName), repr(clf.name), self.fold, clf.fold)
observations = {
term : clf.decision_function(clf.X_validation) if term != self.ontology.root else numpy.array([-1.]*len(clf.X_validation))
for term, clff #(clf, X, y, g)
in classifiers.items()
for clf in (clff(),)
}
#print("observations:")
#print(observations)
gt = {
term : clf().y_validation
for term, clf
in classifiers.items()}
#print("gt:")
#print(gt)
for i in range(self.lenValidation):
observation = {term : pred[i] for term, pred in observations.items()}
#print("Observation for gene %d" % i)
#print(observation)
#print(self.network.forward_backward(observation))
hidden, observed, extra = self.getCopy()
#print(hidden)
#print(observed)
#print(observation)
#for term, node in hidden.items():
# print(i, term, node.get_moments()[0])
for k,v in observation.items():
observed[k].observe((v,))
# print("%s observes %s" % (k, v))
allv = (*hidden.values(), *observed.values(), *extra)
#print([(x, [p for p in x.parents if isinstance(p, Stochastic)]) for x in [*hidden.values(), *observed.values()]])
Q = VB(*allv)
Q.update(*allv, tol=1e-7, repeat=1000, verbose=True)
#print("---")
for term, node in hidden.items():
#print(i, term, node.get_moments()[0])
self.predictions[term][i,:] = node.get_moments()[0]
#print("predictions:")
#print(self.predictions)
for term in observations:
compare = numpy.empty((len(gt[term]),4), dtype=float)
compare[:,0] = gt[term]
compare[:,1] = observations[term]
compare[:,2] = self.predictions[term][:,1]
compare[:,3] = numpy.round(self.predictions[term][:,1])
print(term, self.ontology[term]['name'])
print(compare)
def generateCPD(
self, term
): #, X_train, y_train, X_test, y_test, X_validation, y_validation, g_train, g_test, g_validation):
clf = loadClf(self.ontology[term]['name'], self.fold, self.clfName)
posTrain = sum(clf.y_train == POSTIVE_LABEL)
negTrain = sum(clf.y_train == NEGATIVE_LABEL)
totalTrain = posTrain + negTrain
children = sorted(self.ontology[term]['children'])
parents = sorted(self.ontology[term]['parents'])
labels = {
l: PRIOR
for l in product(*((POSTIVE_LABEL, NEGATIVE_LABEL), ) *
(len(children) + 1))
}
if children:
childNodes = [
self.ontology[child]['node'][self.fold][self.clfName]
for child in children
]
for gene, y in zip(clf.g_train, clf.y_train):
event = []
for child in children:
event.append(POSTIVE_LABEL if gene in self.ontology.
associations[child] else NEGATIVE_LABEL)
event.append(POSTIVE_LABEL if gene in self.ontology.
associations[term] else NEGATIVE_LABEL)
assert (gene in self.ontology.associations[term]) == (
y == POSTIVE_LABEL)
event = tuple(event)
labels[event] += 1
def countBoth(event):
return labels[event[:-1] +
(POSTIVE_LABEL, )] + labels[event[:-1] +
(NEGATIVE_LABEL, )]
cprior = PRIOR * (2**len(children))
types = [Mixture] * (len(children) - 1) + [Categorical]
mixparams = [i for s in zip(childNodes, types) for i in s]
cpd = numpy.empty((2, ) * (len(children) + 1))
for event, counted in labels.items():
v = cpd
for b in event[:-1]:
v = v[b]
hid = event[-1]
print("Event: ", event)
if POSTIVE_LABEL not in event[:
-1]: # Všichni potomci označeni "ne"
v[hid] = counted / countBoth(event)
print("Stored %d / %d" % (counted, countBoth(event)))
else:
v[hid] = {POSTIVE_LABEL: 0.99, NEGATIVE_LABEL: 0.01}[hid]
print("Stored %d : %d" % (hid, v[hid]))
#print(term,"<-",",".join(children))
print(cpd)
#print(labels)
hidden = Mixture(*mixparams, cpd)
hidden.params = cpd
else: #No children
#hidden = DiscreteDistribution({'0': posTrain / totalTrain, '1': negTrain / totalTrain})
params = (posTrain / totalTrain, negTrain / totalTrain)
hidden = Categorical(params)
hidden.params = params
#print("Hidden node %s:" % term)
#print(repr(hidden))
#print([p for p in hidden.parents if isinstance(p, Stochastic)])
#print(hidden.get_moments())
conf = clf.conf + PRIOR
#posTest, negTest = numpy.sum(conf, 1)
posTest, negTest = numpy.sum(conf, 0)
#print("Confusion matrix:")
#print(conf)
try:
assert term != self.ontology.root
pos_decisions = clf.decision_function(
clf.X_test[clf.y_test == POSTIVE_LABEL])
neg_decisions = clf.decision_function(
clf.X_test[clf.y_test == NEGATIVE_LABEL])
means = [numpy.mean(pos_decisions)], [numpy.mean(neg_decisions)]
maxprec = 100.0
precs = [[numpy.min((1 / numpy.var(pos_decisions), maxprec))]
], [[numpy.min((1 / numpy.var(neg_decisions), maxprec))]]
#else:
except (ValueError, AssertionError):
means = [-1.], [1.]
precs = [[1.]], [[1.]]
print("Gaussian params:", term, self.ontology[term]['name'], means,
precs)
observed = Mixture(hidden, Gaussian, means, precs)
#observed = ConditionalProbabilityTable([
# ['0', '0', conf[0][0] / posTest], # if term != root else 1.],
# ['0', '1', conf[0][1] / posTest], # if term != root else 0.],
# ['1', '0', conf[1][0] / negTest], # if term != root else 0.],
# ['1', '1', conf[1][1] / negTest]], #if term != root else 1.]],
# [hidden.distribution])
#print("Observed node %s - %s:" % (term, self.ontology[term]['name']))
#print(repr(observed))
#print([p for p in observed.parents if isinstance(p, Stochastic)])
self.ontology[term]['node'][self.fold][self.clfName] = hidden
#self.ontology[term]['clf'][self.fold][self.clfName] = clf, X_validation, y_validation, g_validation
assert self.lenValidation is None or self.lenValidation == len(
clf.y_validation)
self.lenValidation = len(clf.y_validation)
self.allobserved[term] = observed
self.allhidden[term] = hidden
self.extranodes.update(
(p for p in hidden.parents if isinstance(p, Stochastic)))
def predict(self):
#print(self.network.graph)
self.predictions = {
term: numpy.empty((self.lenValidation, 2), dtype=float)
for term in self.ontology.ontology
}
classifiers = {
term: lambda:
loadClf(self.ontology[term]['name'], self.fold, self.clfName
) #self.ontology[term]['clf'][self.fold][self.clfName]
for term in self.ontology.ontology
}
#for term, (clf,X,y,g) in classifiers.items():
# print(term, ":", repr(self.clfName), repr(clf.name), self.fold, clf.fold)
observations = {
term: clf.decision_function(clf.X_validation) if
term != self.ontology.root else numpy.array([-1.] *
len(clf.X_validation))
for term, clff #(clf, X, y, g)
in classifiers.items() for clf in (clff(), )
}
#print("observations:")
#print(observations)
gt = {term: clf().y_validation for term, clf in classifiers.items()}
#print("gt:")
#print(gt)
for i in range(self.lenValidation):
observation = {
term: pred[i]
for term, pred in observations.items()
}
#print("Observation for gene %d" % i)
#print(observation)
#print(self.network.forward_backward(observation))
hidden, observed, extra = self.getCopy()
#print(hidden)
#print(observed)
#print(observation)
#for term, node in hidden.items():
# print(i, term, node.get_moments()[0])
for k, v in observation.items():
observed[k].observe((v, ))
# print("%s observes %s" % (k, v))
allv = (*hidden.values(), *observed.values(), *extra)
#print([(x, [p for p in x.parents if isinstance(p, Stochastic)]) for x in [*hidden.values(), *observed.values()]])
Q = VB(*allv)
Q.update(*allv, tol=1e-7, repeat=1000, verbose=True)
#print("---")
for term, node in hidden.items():
#print(i, term, node.get_moments()[0])
self.predictions[term][i, :] = node.get_moments()[0]
#print("predictions:")
#print(self.predictions)
for term in observations:
compare = numpy.empty((len(gt[term]), 4), dtype=float)
compare[:, 0] = gt[term]
compare[:, 1] = observations[term]
compare[:, 2] = self.predictions[term][:, 1]
compare[:, 3] = numpy.round(self.predictions[term][:, 1])
print(term, self.ontology[term]['name'])
print(compare)
