def calibration_isotonic_regression(model_name, model, prob_model,
X_calibration, y_calibration, X_train):
# 1. function that trains the calibration regressor using as input calibration data in the first instance
# 2. it then takes in the prob_out of the mdel on the test and outputs calibrated prob for further calculation of
# calibrated std
# ref: https: // arxiv.org / abs / 1807.00263
if model_name == 'Bayes_Ridge_model':
y_hat_calibration, sem_hat_calibration = model.predict(X_calibration,
return_std=True)
elif model_name == 'RF_model':
y_hat_calibration = model.predict(X_calibration)
sem_hat_calibration = np.sqrt(
fci.random_forest_error(model, X_train, X_calibration))
else:
print('Error: Not able to calculate variace!')
# y_hat, sem = model.predict(X_calibration)
prob_per_int_y_calibration, prob_y_calibration, prob_y_calibration_expected, prob = count_entries_per_interval(
y_calibration, y_hat_calibration, sem_hat_calibration)
prob_model_y_calibration = predict_prob(y_calibration, y_hat_calibration,
sem_hat_calibration)
# isotonic regression
from sklearn.isotonic import IsotonicRegression as IR
ir = IR(out_of_bounds='clip')
ir.fit(prob_model_y_calibration, prob_y_calibration)
prob_test_calibrated = ir.transform(prob_model)
return prob_test_calibrated
def __call__(self, valid_preacts, valid_labels):
ir = IR()
valid_preacts = valid_preacts.flatten()
min_valid_preact = np.min(valid_preacts)
max_valid_preact = np.max(valid_preacts)
assert len(valid_preacts) == len(valid_labels)
#sorting to be safe...I think weird results can happen when unsorted
sorted_valid_preacts, sorted_valid_labels = zip(
*sorted(zip(valid_preacts, valid_labels), key=lambda x: x[0]))
y = ir.fit_transform(sorted_valid_preacts, sorted_valid_labels)
def calibration_func(preact):
preact = np.minimum(preact, max_valid_preact)
preact = np.maximum(preact, min_valid_preact)
return ir.transform(preact.flatten())
return calibration_func
def calibration_isotonic_regression(data_calibration,
prob_model): # calibration function
y_true_calibration, y_hat_calibration, sem_hat_calibration = predict_w_DNN(
data_calibration)
prob_per_int_y_calibration, prob_y_calibration, prob_y_calibration_expected, prob = count_entries_per_interval(
y_true_calibration, y_hat_calibration, sem_hat_calibration)
prob_model_y_calibration = predict_prob(y_true_calibration,
y_hat_calibration,
sem_hat_calibration)
# isotonic regression
from sklearn.isotonic import IsotonicRegression as IR
ir = IR(out_of_bounds='clip')
ir.fit(prob_model_y_calibration, prob_y_calibration)
prob_test_calibrated = ir.transform(prob_model)
return prob_test_calibrated
def calibrate_probabilities(prob_dict,instance_label_dict):
labels = []
probabilities = []
print(len(prob_dict))
print(len(instance_label_dict))
for i in prob_dict:
labels.append(instance_label_dict[i])
probabilities.append(prob_dict[i])
ir = IR(out_of_bounds='clip')
ir.fit(probabilities,labels) #fit ir to abstract level precision and classes
p_calibrated=ir.transform(probabilities)
fig,ax = plt.subplots()
fraction_of_positives, mean_predicted_value = calibration_curve(labels, p_calibrated, n_bins=10)
ax.plot(mean_predicted_value, fraction_of_positives)
fraction_of_positives, mean_predicted_value = calibration_curve(labels, probabilities, n_bins=10)
ax.plot(mean_predicted_value, fraction_of_positives)
plt.savefig('calibration_curve_on_data.png')
return ir
def isotonic_calibration(self, xtrain, ytrain):
ir = IR(out_of_bounds='clip')
ir.fit(xtrain, ytrain)
#print ir
return ir
def __init__(self, c, device):
self.c = c
self.ir = IR(out_of_bounds='clip')
self.device = device
def calculate_probability_distribution(tree , instances , index , cal_method =None):
if cal_method == None :
return tree.distribution_for_instance(instances.get_instance(index))
elif cal_method == 'Platt' :
p_train = np.zeros(shape=(instances.num_instances,1))
y_train = np.zeros(shape=(instances.num_instances,1))
for i,instance in enumerate(instances) :
dist = tree.distribution_for_instance(instance)
p_train[i] = [ (dist[1] - 0.5)*2.0 ]
y_train[i] = [instance.get_value(instance.class_index)]
# print("p_train ====>>>" , p_train)
# print("y_train ====>>>" , y_train)
dist = (tree.distribution_for_instance(instances.get_instance(index))[1]-0.5)*2.0
tmp = np.zeros(shape=(1,1))
tmp[0] = [dist]
print(np.sum(y_train))
if np.sum(y_train) in [len(y_train),0]:
print("all one class")
for ins in instances :
print("ins ===> " , ins)
return tree.distribution_for_instance(instances.get_instance(index))
else :
warnings.filterwarnings("ignore", category=FutureWarning)
lr = LR(solver='lbfgs')
lr.fit( p_train , np.ravel(y_train,order='C') )
return lr.predict_proba( tmp.reshape(1, -1))[0]
elif cal_method == 'Isotonic' :
p_train = np.zeros(shape=(instances.num_instances,1))
y_train = np.zeros(shape=(instances.num_instances,1))
for i,instance in enumerate(instances) :
dist = tree.distribution_for_instance(instance)
p_train[i] = [ dist[1] ]
y_train[i] = [instance.get_value(instance.class_index)]
dist = tree.distribution_for_instance(instances.get_instance(index))[1]
tmp = np.zeros(shape=(1,1))
tmp[0] = [dist]
print(np.sum(y_train))
if np.sum(y_train) in [len(y_train),0]:
print("all one class")
for ins in instances :
print("ins ===> " , ins)
return tree.distribution_for_instance(instances.get_instance(index))
else :
ir = IR( out_of_bounds = 'clip' )
ir.fit(np.ravel(p_train,order='C') , np.ravel(y_train,order='C'))
p = ir.transform( np.ravel(tmp,order='C'))[0]
return [p,1-p]
# elif cal_method == 'ProbabilityCalibrationTree' :
# pass
elif cal_method == 'ICP' :
pass
elif cal_method == 'Venn1' :
calibrPts = []
for i,instance in enumerate(instances) :
dist = tree.distribution_for_instance(instance)
score = dist[0] if dist[1] < dist[0] else dist[1]
calibrPts.append( ( (score) , instance.get_value(instance.class_index) ) )
dist = (tree.distribution_for_instance(instances.get_instance(index)))
score = dist[0] if dist[1] < dist[0] else dist[1]
tmp = [score]
p0,p1=VennABERS.ScoresToMultiProbs(calibrPts,tmp)
print("Vennnnnn =========>>>>>>>>>>>> ", p0, " , ",p1)
return [p0,p1]
pass
def calibrated(test_predictions,
oof_predictions,
flag_transform=sigmoid,
type_transform=parse_classifier_probas):
"""
Update test predictions w.r.t to calibration trained on OOF predictions
:param test_predictions:
:param oof_predictions:
:return:
"""
from sklearn.isotonic import IsotonicRegression as IR
import matplotlib.pyplot as plt
oof_predictions = oof_predictions.copy()
oof_predictions[OUTPUT_PRED_MODIFICATION_TYPE] = oof_predictions[
OUTPUT_PRED_MODIFICATION_TYPE].apply(type_transform)
oof_predictions[OUTPUT_PRED_MODIFICATION_FLAG] = oof_predictions[
OUTPUT_PRED_MODIFICATION_FLAG].apply(flag_transform)
test_predictions = test_predictions.copy()
test_predictions[OUTPUT_PRED_MODIFICATION_TYPE] = test_predictions[
OUTPUT_PRED_MODIFICATION_TYPE].apply(type_transform)
test_predictions[OUTPUT_PRED_MODIFICATION_FLAG] = test_predictions[
OUTPUT_PRED_MODIFICATION_FLAG].apply(flag_transform)
y_true = oof_predictions["true_modification_flag"].values.astype(int)
# print("Target", np.bincount(oof_predictions["true_modification_type"].values.astype(int)))
if True:
y_pred_raw = oof_predictions[OUTPUT_PRED_MODIFICATION_FLAG].values
b_auc_before = alaska_weighted_auc(y_true, y_pred_raw)
ir_flag = IR(out_of_bounds="clip", y_min=0, y_max=1)
y_pred_cal = ir_flag.fit_transform(y_pred_raw, y_true)
b_auc_after = alaska_weighted_auc(y_true, y_pred_cal)
if b_auc_after > b_auc_before:
test_predictions[
OUTPUT_PRED_MODIFICATION_FLAG] = ir_flag.transform(
test_predictions[OUTPUT_PRED_MODIFICATION_FLAG].values)
else:
# test_predictions[OUTPUT_PRED_MODIFICATION_FLAG] = ir_flag.transform(
# test_predictions[OUTPUT_PRED_MODIFICATION_FLAG].values
# )
warnings.warn(
f"Failed to train IR flag {b_auc_before} {b_auc_after}")
plt.figure()
plt.hist(y_pred_raw,
alpha=0.5,
bins=100,
label=f"non-calibrated {b_auc_after}")
plt.hist(y_pred_cal,
alpha=0.5,
bins=100,
label=f"calibrated {b_auc_before}")
plt.yscale("log")
plt.legend()
plt.show()
if True:
ir_type = IR(out_of_bounds="clip", y_min=0, y_max=1)
y_pred_raw = oof_predictions[OUTPUT_PRED_MODIFICATION_TYPE].values
c_auc_before = alaska_weighted_auc(y_true, y_pred_raw)
y_pred_cal = ir_type.fit_transform(y_pred_raw, y_true)
c_auc_after = alaska_weighted_auc(y_true, y_pred_cal)
if c_auc_after > c_auc_before:
test_predictions[
OUTPUT_PRED_MODIFICATION_TYPE] = ir_type.transform(
test_predictions[OUTPUT_PRED_MODIFICATION_TYPE].values)
# plt.figure()
# plt.hist(y_pred_raw, alpha=0.5, bins=100, label=f"non-calibrated {c_auc_before}")
# plt.hist(y_pred_cal, alpha=0.5, bins=100, label=f"calibrated {c_auc_after}")
# plt.yscale("log")
# plt.legend()
# plt.show()
else:
# test_predictions[OUTPUT_PRED_MODIFICATION_TYPE] = ir_type.transform(
# test_predictions[OUTPUT_PRED_MODIFICATION_TYPE].values
# )
warnings.warn(
f"Failed to train IR on type {c_auc_before} {c_auc_after}")
# plt.figure()
# plt.hist(y_pred_raw, alpha=0.5, bins=100, label=f"non-calibrated {c_auc_before}")
# plt.hist(y_pred_cal, alpha=0.5, bins=100, label=f"calibrated {c_auc_after}")
# plt.yscale("log")
# plt.legend()
# plt.show()
results = {
"b_auc_before": b_auc_before,
"b_auc_after": b_auc_after,
"c_auc_before": c_auc_before,
"c_auc_after": c_auc_after,
}
return test_predictions, results
trainResult = runffm('../data/calibration/ffmTrain-102662.ffm',
'../data/calibration/ffm-model-102662')
p_train_all = read_csv(trainResult)['prob']
oriTrain = read_csv('../data/train.csv')
sameTrain = oriTrain[oriTrain['clickTime'] >= 190000].reset_index()
print len(sameTrain), len(p_train_all)
part_sameTrain = sameTrain[(sameTrain['clickTime'] >= 200000)
& (sameTrain['clickTime'] < 290000)]
p_train = p_train_all.loc[part_sameTrain.index]
y_train = part_sameTrain['label']
ir = IR()
ir.fit(p_train, y_train)
oriResult = read_csv(
'../data/calibration/ffm_mergeAppUser_s17_preAction_190000_no_Dist_noNum_t150_k8_l2e-05_2017-06-05-20-58-00.csv'
)
p_test = oriResult['prob']
p_calibrated = ir.transform(
p_test) # or ir.fit( p_test ), that's the same thing
oriResult['new_prob'] = Series(p_calibrated)
oriResult.to_csv('../data/calibration/calib_temp.csv', index=False)
oriResult['nozero_new_prob'] = oriResult.apply(
lambda x: x['new_prob'] if x['new_prob'] > 0 else x['prob'],
axis='columns')
def Iso(self):
IReg = IR(y_min=None, y_max=None, increasing=True, out_of_bounds='nan')
pass
def calibrate_probs(probabilities,classes):
ir = IR(out_of_bounds='clip')
ir.fit(probabilities,classes) #fit ir to abstract level precision and classes
p_calibrated=ir.transform(probabilities)
return p_calibrated
# convert to termonilogy used in all python files so far (redundant from a code perspective)
y_true = y_sample.flatten()
y_hat = m # predicted mean
return y_true, y_hat, varma
def calibration_isotonic_regression(data_calibration, prob_model): # calibration function
y_true_calibration, y_hat_calibration, sem_hat_calibration = predict_w_DNN(data_calibration)
prob_per_int_y_calibration, prob_y_calibration, prob_y_calibration_expected, prob = count_entries_per_interval(y_true_calibration, y_hat_calibration, sem_hat_calibration)
prob_model_y_calibration = predict_prob(y_true_calibration, y_hat_calibration, sem_hat_calibration)
# isotonic regression
from sklearn.isotonic import IsotonicRegression as IR
ir = IR(out_of_bounds='clip')
ir.fit(prob_model_y_calibration, prob_y_calibration)
prob_test_calibrated = ir.transform(prob_model)
return prob_test_calibrated
r2_vec = []
mape_vec = []
rmspe_vec = []
mse_vec = []
acc_zone_percentage_vec = []
beta_vec = []
rlh_vec = []
avg_calibration_vec = []
SH_vec = []
### # train/test split (in half) train_end = y.shape[0] / 2 test_start = train_end + 1 y_train = y[0:train_end] y_test = y[test_start:] p_train = p[0:train_end] p_test = p[test_start:] ### ir = IR(out_of_bounds='clip') # out_of_bounds param needs scikit-learn >= 0.15 ir.fit(p_train, y_train) p_calibrated = ir.transform(p_test) p_calibrated[np.isnan(p_calibrated)] = 0 ### acc = accuracy_score(y_test, np.round(p_test)) acc_calibrated = accuracy_score(y_test, np.round(p_calibrated)) auc = AUC(y_test, p_test) auc_calibrated = AUC(y_test, p_calibrated) ll = log_loss(y_test, p_test) ll_calibrated = log_loss(y_test, p_calibrated)