def _classification_mask_report(report, mask, X, labels_dict):
report.features_correlation_matrix(mask=mask).plot()
report.features_correlation_matrix_by_class(
mask=mask, labels_dict=labels_dict).plot()
report.efficiencies(features=X.columns[1:3],
mask=mask,
labels_dict=labels_dict).plot()
report.features_pdf(mask=mask, labels_dict=labels_dict).plot()
report.learning_curve(RocAuc(), mask=mask, metric_label='roc').plot()
significance = lambda s, b: s / (numpy.sqrt(b) + 0.01)
report.metrics_vs_cut(significance, mask=mask, metric_label='sign').plot()
report.prediction_pdf(mask=mask, labels_dict=labels_dict).plot()
report.scatter([X.columns[:2], X.columns[1:3]],
mask=mask,
labels_dict=labels_dict).plot()
report.feature_importance().plot()
if labels_dict is None:
report.feature_importance_shuffling(mask=mask).plot()
report.roc(mask=mask).plot()
report.roc(mask=mask, physics_notion=False).plot()
report.efficiencies_2d(['column0', 'column1'],
0.3,
mask=mask,
labels_dict=labels_dict)
print(report.compute_metric(RocAuc()))
def test_own_classification_reports():
"""
testing clf.test_on
"""
X, y, sample_weight = generate_classification_data()
clf = SklearnClassifier(RandomForestClassifier())
clf.fit(X, y, sample_weight=sample_weight)
report = clf.test_on(X, y, sample_weight=sample_weight)
roc1 = report.compute_metric(RocAuc())
lds = LabeledDataStorage(X, y, sample_weight=sample_weight)
roc2 = clf.test_on_lds(lds=lds).compute_metric(RocAuc())
assert roc1 == roc2, 'Something wrong with test_on'
def test_gridsearch_sklearn():
metric = numpy.random.choice([OptimalAMS(), RocAuc(), LogLoss()])
scorer = ClassificationFoldingScorer(metric)
maximization = True
if isinstance(metric, LogLoss):
maximization = False
grid_param = OrderedDict({
"n_estimators": [10, 20],
"learning_rate": [0.1, 0.05],
'features': [['column0', 'column1'], ['column0', 'column1', 'column2']]
})
generator = RegressionParameterOptimizer(grid_param,
n_evaluations=4,
maximize=maximization)
grid = GridOptimalSearchCV(SklearnClassifier(clf=AdaBoostClassifier()),
generator,
scorer,
parallel_profile='threads-3')
_ = check_grid(grid, False, False, False, use_weights=True)
classifier = check_grid(grid, False, False, False, use_weights=False)
# Check parameters of best fitted classifier
assert 2 <= len(classifier.features) <= 3, 'Features were not set'
params = classifier.get_params()
for key in grid_param:
if key in params:
assert params[key] == grid.generator.best_params_[key]
else:
assert params['clf__' + key] == grid.generator.best_params_[key]
def test_gridsearch_metrics_threads(n_threads=3):
X, y, sample_weight = generate_classification_data(n_classes=2,
distance=0.7)
param_grid = OrderedDict({'reg_param': numpy.linspace(0, 1, 20)})
from itertools import cycle
optimizers = cycle([
RegressionParameterOptimizer(param_grid=param_grid,
n_evaluations=4,
start_evaluations=2),
SubgridParameterOptimizer(param_grid=param_grid, n_evaluations=4),
RandomParameterOptimizer(param_grid=param_grid, n_evaluations=4),
])
for metric in [RocAuc(), OptimalAMS(), OptimalSignificance(), log_loss]:
scorer = FoldingScorer(metric)
clf = SklearnClassifier(QDA())
grid = GridOptimalSearchCV(
estimator=clf,
params_generator=next(optimizers),
scorer=scorer,
parallel_profile='threads-{}'.format(n_threads))
grid.fit(X, y)
print(grid.params_generator.best_score_)
print(grid.params_generator.best_params_)
grid.params_generator.print_results()
def check_report_with_mask(report, mask, X):
report.roc(mask=mask).plot()
report.prediction_pdf(mask=mask).plot()
report.features_pdf(mask=mask).plot()
report.efficiencies(list(X.columns), mask=mask).plot()
report.features_correlation_matrix(mask=mask).plot()
report.feature_importance().plot()
report.scatter([(X.columns[0], X.columns[2])], mask=mask).plot()
report.learning_curve(RocAuc(), mask=mask).plot()
report.metrics_vs_cut(significance, mask=mask).plot()
def check_classification_learning_curve_masks(report, n_classes):
"""testing predict_only_mask option"""
for mask in [None, "column0 > 0", "column0 > -0.5"]:
if n_classes == 2:
loss = RocAuc()
else:
loss = log_loss
lc1 = report.learning_curve(loss,
mask=mask,
predict_only_masked=True,
steps=3)
lc2 = report.learning_curve(loss,
mask=mask,
predict_only_masked=False,
steps=3)
assert lc1.functions == lc2.functions
def test_gridsearch_threads(n_threads=3):
scorer = FoldingScorer(numpy.random.choice([OptimalAMS(), RocAuc()]))
grid_param = OrderedDict({
"n_estimators": [10, 20],
"learning_rate": [0.1, 0.05],
'features': [['column0', 'column1'], ['column0', 'column1', 'column2']]
})
generator = RegressionParameterOptimizer(grid_param, n_evaluations=4)
base = SklearnClassifier(clf=AdaBoostClassifier())
grid = GridOptimalSearchCV(base,
generator,
scorer,
parallel_profile='threads-{}'.format(n_threads))
X, y, sample_weight = generate_classification_data()
grid.fit(X, y, sample_weight=sample_weight)
def test_gridsearch_on_tmva():
metric = numpy.random.choice([OptimalAMS(), RocAuc()])
scorer = FoldingScorer(metric)
grid_param = OrderedDict({"MaxDepth": [4, 5], "NTrees": [10, 20]})
generator = SubgridParameterOptimizer(grid_param)
try:
from rep.estimators import TMVAClassifier
grid = GridOptimalSearchCV(
TMVAClassifier(features=['column0', 'column1']), generator, scorer)
classifier = check_grid(grid, False, False, False)
# checking parameters
assert len(classifier.features) == 2
params = classifier.get_params()
for key in grid_param:
assert params[key] == grid.generator.best_params_[key]
except ImportError:
pass
def test_gridsearch_on_tmva():
metric = numpy.random.choice([OptimalAMS(), RocAuc()])
scorer = FoldingScorer(metric)
grid_param = OrderedDict({"MaxDepth": [4, 5], "NTrees": [10, 20]})
generator = SubgridParameterOptimizer(n_evaluations=5,
param_grid=grid_param)
try:
from rep.estimators import TMVAClassifier
base_tmva = TMVAClassifier(
factory_options="Silent=True:V=False:DrawProgressBar=False",
features=['column0', 'column1'],
method='kBDT')
grid = GridOptimalSearchCV(base_tmva, generator, scorer)
classifier = check_grid(grid, False, False, False)
# checking parameters
assert len(classifier.features) == 2
params = classifier.get_params()
for key in grid_param:
assert params[key] == grid.generator.best_params_[key]
except ImportError:
pass
def clf_mayou(data1, data2, n_folds=3, n_base_clf=5):
"""DEVELOPEMENT, WIP. Test a setup of clf involving bagging and stacking."""
# import raredecay.analysis.ml_analysis as ml_ana
# import pandas as pd
import copy
from rep.estimators import SklearnClassifier, XGBoostClassifier
from rep.metaml.folding import FoldingClassifier
from sklearn.ensemble import GradientBoostingClassifier, RandomForestClassifier
from sklearn.ensemble import BaggingClassifier # , VotingClassifier, AdaBoostClassifier
from rep.estimators.theanets import TheanetsClassifier
from sklearn.linear_model import LogisticRegression
from rep.metaml.cache import CacheClassifier
from rep.report.metrics import RocAuc
import rep.metaml.cache
from rep.metaml._cache import CacheHelper
rep.metaml.cache.cache_helper = CacheHelper('/home/mayou/cache', 100000)
# data1.make_folds(n_folds)
# data2.make_folds(n_folds)
output = {}
# for i in range(n_folds):
xgb_clf = XGBoostClassifier(n_estimators=350,
eta=0.1,
max_depth=4,
nthreads=3)
xgb_folded = FoldingClassifier(base_estimator=xgb_clf,
stratified=True,
parallel_profile='threads-2')
xgb_bagged = BaggingClassifier(base_estimator=xgb_folded,
n_estimators=n_base_clf,
bootstrap=False)
xgb_bagged = SklearnClassifier(xgb_bagged)
xgb_big_stacker = copy.deepcopy(xgb_bagged)
xgb_bagged = CacheClassifier(name='xgb_bagged1', clf=xgb_bagged)
xgb_single = XGBoostClassifier(n_estimators=350,
eta=0.1,
max_depth=4,
nthreads=3)
xgb_single = FoldingClassifier(base_estimator=xgb_single,
stratified=True,
n_folds=10,
parallel_profile='threads-2')
xgb_single = CacheClassifier(name='xgb_singled1', clf=xgb_single)
rdf_clf = SklearnClassifier(
RandomForestClassifier(n_estimators=300, n_jobs=3))
rdf_folded = FoldingClassifier(base_estimator=rdf_clf,
stratified=True,
parallel_profile='threads-2')
rdf_bagged = BaggingClassifier(base_estimator=rdf_folded,
n_estimators=n_base_clf,
bootstrap=False)
rdf_bagged = SklearnClassifier(rdf_bagged)
rdf_bagged = CacheClassifier(name='rdf_bagged1', clf=rdf_bagged)
gb_clf = SklearnClassifier(GradientBoostingClassifier(n_estimators=50))
gb_folded = FoldingClassifier(base_estimator=gb_clf,
stratified=True,
parallel_profile='threads-6')
gb_bagged = BaggingClassifier(base_estimator=gb_folded,
n_estimators=n_base_clf,
bootstrap=False,
n_jobs=5)
gb_bagged = SklearnClassifier(gb_bagged)
gb_bagged = CacheClassifier(name='gb_bagged1', clf=gb_bagged)
nn_clf = TheanetsClassifier(layers=[300, 300],
hidden_dropout=0.03,
trainers=[{
'optimize': 'adagrad',
'patience': 5,
'learning_rate': 0.2,
'min_improvement': 0.1,
'momentum': 0.4,
'nesterov': True,
'loss': 'xe'
}])
nn_folded = FoldingClassifier(base_estimator=nn_clf,
stratified=True,
parallel_profile=None) # 'threads-6')
nn_bagged = BaggingClassifier(base_estimator=nn_folded,
n_estimators=n_base_clf,
bootstrap=False,
n_jobs=1)
nn_bagged = CacheClassifier(name='nn_bagged1', clf=nn_bagged)
nn_single_clf = TheanetsClassifier(layers=[300, 300, 300],
hidden_dropout=0.03,
trainers=[{
'optimize': 'adagrad',
'patience': 5,
'learning_rate': 0.2,
'min_improvement': 0.1,
'momentum': 0.4,
'nesterov': True,
'loss': 'xe'
}])
nn_single = FoldingClassifier(base_estimator=nn_single_clf,
n_folds=3,
stratified=True)
nn_single = CacheClassifier(name='nn_single1', clf=nn_single)
logit_stacker = SklearnClassifier(
LogisticRegression(penalty='l2', solver='sag'))
logit_stacker = FoldingClassifier(base_estimator=logit_stacker,
n_folds=n_folds,
stratified=True,
parallel_profile='threads-6')
logit_stacker = CacheClassifier(name='logit_stacker1', clf=logit_stacker)
xgb_stacker = XGBoostClassifier(n_estimators=400,
eta=0.1,
max_depth=4,
nthreads=8)
# HACK
xgb_stacker = xgb_big_stacker
xgb_stacker = FoldingClassifier(base_estimator=xgb_stacker,
n_folds=n_folds,
random_state=42,
stratified=True,
parallel_profile='threads-6')
xgb_stacker = CacheClassifier(name='xgb_stacker1', clf=xgb_stacker)
# train1, test1 = data1.get_fold(i)
# train2, test2 = data1.get_fold(i)
#
# t_data, t_targets, t_weights =
data, targets, weights = data1.make_dataset(data2, weights_ratio=1)
# xgb_bagged.fit(data, targets, weights)
# xgb_report = xgb_bagged.test_on(data, targets, weights)
# xgb_report.roc(physics_notion=True).plot(new_plot=True, title="ROC AUC xgb_base classifier")
# output['xgb_base'] = "roc auc:" + str(xgb_report.compute_metric(metric=RocAuc()))
# xgb_proba = xgb_report.prediction['clf'][:, 1]
# del xgb_bagged, xgb_folded, xgb_clf, xgb_report
#
# xgb_single.fit(data, targets, weights)
# xgb_report = xgb_single.test_on(data, targets, weights)
# xgb_report.roc(physics_notion=True).plot(new_plot=True, title="ROC AUC xgb_single classifier")
# output['xgb_single'] = "roc auc:" + str(xgb_report.compute_metric(metric=RocAuc()))
# xgb_proba = xgb_report.prediction['clf'][:, 1]
# del xgb_single, xgb_report
nn_single.fit(data, targets, weights)
nn_report = nn_single.test_on(data, targets, weights)
nn_report.roc(physics_notion=True).plot(
new_plot=True, title="ROC AUC nn_single classifier")
output['nn_single'] = "roc auc:" + str(
nn_report.compute_metric(metric=RocAuc()))
# nn_proba = nn_report.prediction['clf'][:, 1]
del nn_single, nn_report
# rdf_bagged.fit(data, targets, weights)
# rdf_report = rdf_bagged.test_on(data, targets, weights)
# rdf_report.roc(physics_notion=True).plot(new_plot=True, title="ROC AUC rdf_base classifier")
# output['rdf_base'] = "roc auc:" + str(rdf_report.compute_metric(metric=RocAuc()))
# rdf_proba = rdf_report.prediction['clf'][:, 1]
# del rdf_bagged, rdf_clf, rdf_folded, rdf_report
# gb_bagged.fit(data, targets, weights)
# gb_report = gb_bagged.test_on(data, targets, weights)
# gb_report.roc(physics_notion=True).plot(new_plot=True, title="ROC AUC gb_base classifier")
# output['gb_base'] = "roc auc:" + str(gb_report.compute_metric(metric=RocAuc()))
# gb_proba = gb_report.prediction['clf'][:, 1]
# del gb_bagged, gb_clf, gb_folded, gb_report
# nn_bagged.fit(data, targets, weights)
# nn_report = nn_bagged.test_on(data, targets, weights)
# nn_report.roc(physics_notion=True).plot(new_plot=True, title="ROC AUC nn_base classifier")
# output['nn_base'] = "roc auc:" + str(nn_report.compute_metric(metric=RocAuc()))
# nn_proba = nn_report.prediction['clf'][:, 1]
# del nn_bagged, nn_clf, nn_folded, nn_report
#
# base_predict = pd.DataFrame({'xgb': xgb_proba,
# #'rdf': rdf_proba,
# #'gb': gb_proba,
# 'nn': nn_proba
# })
#
#
# xgb_stacker.fit(base_predict, targets, weights)
# xgb_report = xgb_stacker.test_on(base_predict, targets, weights)
# xgb_report.roc(physics_notion=True).plot(new_plot=True,
# title="ROC AUC xgb_stacked classifier")
# output['stacker_xgb'] = "roc auc:" + str(xgb_report.compute_metric(metric=RocAuc()))
# del xgb_stacker, xgb_report
#
# logit_stacker.fit(base_predict, targets, weights)
# logit_report = logit_stacker.test_on(base_predict, targets, weights)
# logit_report.roc(physics_notion=True).plot(new_plot=True,
# title="ROC AUC logit_stacked classifier")
# output['stacker_logit'] = "roc auc:" + str(logit_report.compute_metric(metric=RocAuc()))
# del logit_stacker, logit_report
print output
data = data.drop('g', axis=1)
import numpy
import numexpr
import pandas
from rep import utils
from sklearn.ensemble import GradientBoostingClassifier
from rep.report.metrics import RocAuc
from rep.metaml import GridOptimalSearchCV, FoldingScorer, RandomParameterOptimizer
from rep.estimators import SklearnClassifier, TMVAClassifier, XGBoostRegressor
# define grid parameters
grid_param = {}
grid_param['learning_rate'] = [0.2, 0.1, 0.05, 0.02, 0.01]
grid_param['max_depth'] = [2, 3, 4, 5]
# use random hyperparameter optimization algorithm
generator = RandomParameterOptimizer(grid_param)
# define folding scorer
scorer = FoldingScorer(RocAuc(), folds=3, fold_checks=3)
estimator = SklearnClassifier(GradientBoostingClassifier(n_estimators=30))
#grid_finder = GridOptimalSearchCV(estimator, generator, scorer)
#% time grid_finder.fit(data, labels)
grid_finder = GridOptimalSearchCV(estimator,
generator,
scorer,
parallel_profile="default")
print "start grid search"
grid_finder.fit(data, labels)
grid_finder.params_generator.print_results()
assert 10 == grid_finder.params_generator.n_evaluations, "oops"