def fine_tune_gradient_boosting_hyper_params(data_train_x, data_test_x, data_train_y, data_test_y):
from sklearn.ensemble import GradientBoostingRegressor
from sklearn.grid_search import RandomizedSearchCV
print "-- {} --".format("Fine-tuning Gradient Boosting Regression")
rf = GradientBoostingRegressor(
n_estimators=1000
)
param_dist = {
"learning_rate": [0.01, 0.03, 0.05, 0.07, 0.09, 0.1, 0.15, 0.2],
"max_depth": sp_randint(1, 15),
"min_samples_split": sp_randint(1, 15),
"min_samples_leaf": sp_randint(1, 15),
"subsample": [0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0],
"max_features": sp_randint(1, 15)
}
n_iter_search = 300
random_search = RandomizedSearchCV(
rf,
param_distributions=param_dist,
n_iter=n_iter_search,
n_jobs=-1,
cv=5,
verbose=1
)
start = time()
random_search.fit(data_train_x, data_train_y)
print("RandomizedSearchCV took %.2f seconds for %d candidates"
" parameter settings." % ((time() - start), n_iter_search))
report(random_search.grid_scores_)
def sk_generate_params(method, columns=None):
param_dist = {}
if 'rf' in method:
param_dist = {
"max_features": sp_unif(0.01, 1.0),
"n_estimators": sp_randint(32, 256),
"bootstrap": [True, False],
"criterion": ["gini", "entropy"],
"min_samples_split": sp_randint(2, 10),
"min_samples_leaf": sp_randint(2, 10),
"min_weight_fraction_leaf": sp_unif(0., 0.5),
"class_weight": ['balanced', 'balanced_subsample']
}
elif 'svm' in method:
param_dist = {
"C": sp_unif(0.01, 20.),
"kernel": ["linear"]
}
elif 'lr' in method:
param_dist = {
"C": sp_unif(0.01, 20.),
"penalty": ["l1", "l2"],
}
if 'bagged' in method:
_param_dist = {}
for c in columns:
for k, v in param_dist.items():
_param_dist['{}__{}'.format(c, k)] = v
_param_dist['weights'] = uniform_gen_5(0., 1.)
return _param_dist
else:
return param_dist
def getRandomForestClf(self, X, Y, param_list):
clfName = "Random_Forest"
## http://scikit-learn.org/stable/modules/generated/sklearn.ensemble.RandomForestClassifier.html
clf = rf(n_estimators=300, max_depth=None, min_samples_split=1, random_state=0, bootstrap=True, oob_score = True)
if self._gridSearchFlag == True:
log(clfName + " start searching param...")
tmpLowDepth = 8
tmpHighDepth = 30
param_dist = {
"max_depth": sp_randint(tmpLowDepth, tmpHighDepth),
"max_features": sp_randf(0,1),
"min_samples_split": sp_randint(1, 11),
"min_samples_leaf": sp_randint(1, 11),
"criterion": ["gini", "entropy"],
"n_estimators" : sp_randint(5, 12),
}
clf = self.doRandomSearch(clfName, clf, param_dist, X, Y)
else:
if not param_list is None:
clf = rf()
clf.set_params(**param_list)
clf.fit(X,Y)
return clf
def train(model_id,train_x,train_y,valid_x,valid_y,test_x):
train_x,train_y=shuffle(train_x,train_y)
random_state=random.randint(0, 1000000)
rf = RandomForestClassifier(n_jobs=8)
param_dist = {
"n_estimators":sp_randint(100,300),
"criterion": ["gini"],
#"max_depth": sp_randint(3, 10000),
#"min_samples_split": sp_randint(1, 300),
#"min_samples_leaf": sp_randint(1, 300),
"max_features": sp_randint(10, 26),
"bootstrap": [True, False],
'random_state':sp_randint(1, 1000000),
}
clf = RandomizedSearchCV(rf, param_distributions=param_dist,
n_iter=50,cv=10,scoring='roc_auc')
clf.fit(train_x, train_y)
valid_predictions = clf.predict_proba(valid_x)[:, 1]
test_predictions= clf.predict_proba(test_x)[:, 1]
loss = roc_auc_score(valid_y,valid_predictions)
print('loss:')
print(loss)
print(clf.best_estimator_)
data.saveData(valid_id,valid_predictions,"./valid_results/valid_"+str(model_id)+".csv")
data.saveData(test_id,test_predictions,"./results/results_"+str(model_id)+".csv")
def __init__(self, X: csr_matrix, Y: np.array, tune_parameters=False):
super().__init__(X, Y, tune_parameters)
if tune_parameters:
self.param_dist_random = {'max_features': sp_randint(1, self.X.shape[1]),
'n_estimators': sp_randint(1, 100)}
self.clf = BaggingClassifier(self.classifier, n_estimators=self.estimators, n_jobs=8,
max_samples=self.max_samples, max_features=self.max_features)
def train_cv():
# ---------------------- load the data
train_df = pd.read_csv("train_processed.csv",index_col="PassengerId")
Xtrain = train_df[feature_names]
ytrain = train_df["Survived"]
# ---------------------- train
loss = ['deviance', 'exponential']
learning_rate = np.logspace(-5,1)
n_estimate_dist = sp_randint(1000,4800)
max_depth_dist = sp_randint(1,10)
param_dist = dict(loss=loss,
learning_rate=learning_rate,
n_estimators=n_estimate_dist,
max_depth=max_depth_dist)
gbdt = GradientBoostingClassifier(verbose=1)
searchcv = RandomizedSearchCV(estimator=gbdt, param_distributions=param_dist,n_iter=210,verbose=1,n_jobs=-1)
print "--------------------- RandomizedSearchCV begins"
searchcv.fit(Xtrain,ytrain)
print "--------------------- RandomizedSearchCV ends"
print "best score: ",searchcv.best_score_
print "best parameters: ",searchcv.best_params_
common.dump_predictor('gbdt-cv.pkl',searchcv.best_estimator_)
print "--------------------- GBDT saved into file"
def get_random_grid_CV_params():
"""Define the Random Grid Search parameters for each model."""
logit_params = {"C": sp_expon(loc=0.001, scale=1),
"fit_intercept": [True, False],
"intercept_scaling": sp_randint(1, 5),
"warm_start": [False, True]
}
rf_params = {"min_samples_split": sp_randint(1, 50),
"min_samples_leaf": sp_randint(1, 50),
"criterion": ["gini", "entropy"],
"class_weight": ['balanced', 'balanced_subsample']
}
ada_dt_params = {"learning_rate": sp_expon(loc=0.001, scale=1.5),
"algorithm": ['SAMME.R', 'SAMME']
}
gbc_params = {"learning_rate": sp_expon(loc=0.001, scale=0.5),
"subsample": sp_uniform(loc=0.2, scale=0.8),
"max_features": [None, 'auto'],
"max_depth": sp_randint(2, 6),
}
svc_params = {"C": sp_expon(loc=0.001, scale=2),
"kernel": ['rbf', 'poly'],
"degree": sp_randint(2, 10),
"coef0": [0, 1, 2],
"shrinking": [True, False]
}
rnd_CV_param_distributions = {'Logistic': logit_params,
'RandomForest': rf_params,
'AdaBoost_DT': ada_dt_params,
'GBC': gbc_params,
'SVC': svc_params
}
return rnd_CV_param_distributions
def makeRandomCV(dataset,dbtype='CATH',
level=1,
k_iters=10,
minsamples=500,
clf = ExtraTreesClassifier(n_estimators=5,class_weight='auto')):
from scipy.stats import randint as sp_randint
dataDict = dbParser(dataset,level=level,dbtype=dbtype,minsamples=minsamples)
print dataDict
labels = dataDict['target_names']
param_dist = {"max_depth": [3, None],
"max_features": sp_randint(1, 11),
"min_samples_split": sp_randint(1, 11),
"min_samples_leaf": sp_randint(1, 11),
"bootstrap": [True, False],
"criterion": ["gini", "entropy"]}
n_iter_search = k_iters
random_search = RandomizedSearchCV(clf, param_distributions=param_dist,
n_iter=n_iter_search)
random_search.fit(dataDict['vectors'], dataDict['target_names'])
report(random_search.grid_scores_)
def best_ExtraTree(X, y):
from sklearn.grid_search import RandomizedSearchCV
from scipy.stats import randint as sp_randint
from sklearn.metrics import accuracy_score
X_train, X_test, y_train, y_test = train_test_split(X, y.ravel(),
random_state=42)
clf = ExtraTreesClassifier(max_depth=None,
bootstrap = False)
grid = {'n_estimators': sp_randint(250, 400),
'min_samples_leaf' : sp_randint(1, 12),
'max_features' : sp_randint(5, 50)}
clf_rfc = RandomizedSearchCV(clf, n_jobs=4, n_iter=10,
param_distributions=grid,
scoring='accuracy')
y_hat = clf_rfc.fit(X_train,
y_train.ravel()).predict(X_test)
print('Best Params: \n', clf_rfc.best_params_ )
print("Accuracy with Extra Forest = %4.4f" %
accuracy_score(y_test.ravel(), y_hat))
binarize_y_confustion_matrix(y_test.ravel(), y_hat)
return(clf_rfc.best_params_)
def main():
NUM_TRAIN = bw_componentrecognition.NUM_TRAIN
N_BINS = 23
N_HU_MOMENTS = 7
N_FEATURES = N_BINS + N_HU_MOMENTS
X, y = bw_componentrecognition.Data.loadTrain(NUM_TRAIN, N_BINS)
scaler = preprocessing.StandardScaler().fit(X)
X = scaler.transform(X)
clfs = [
RandomForestClassifier(n_estimators=20),
]
param_dists = [
{"max_depth": [10, 5, 3, None],
"max_features": sp_randint(1, 11),
"min_samples_split": sp_randint(1, 11),
"min_samples_leaf": sp_randint(1, 11),
"bootstrap": [True, False],
"criterion": ["gini", "entropy"]},]
for clf, param_dist in zip(clfs, param_dists):
# run randomized search
n_iter_search = 25
random_search = RandomizedSearchCV(clf, param_distributions=param_dist,
n_iter=n_iter_search)
random_search.fit(X, y)
report(random_search.grid_scores_)
def getKnnClf(self, X, Y):
clfName = "K_NN"
## http://scikit-learn.org/stable/modules/generated/sklearn.ensemble.ExtraTreesClassifier.html
clf = KNeighborsClassifier(
n_neighbors=5,
weights='uniform',
algorithm='auto',
leaf_size=30,
p=2,
metric='minkowski',
metric_params=None,
)
if self._gridSearchFlag == True:
log(clfName + " start searching param...")
param_dist = {
"n_neighbors": sp_randint(4, 8),
"weights": ['uniform', 'uniform'],
"leaf_size": sp_randint(30, 60),
"algorithm": ['auto', 'auto'],
}
clf = self.doRandomSearch(clfName, clf, param_dist, X, Y)
return clf
def __init__(self, X: csr_matrix, Y: np.array, tune_parameters=False):
super().__init__(X, Y, tune_parameters)
if tune_parameters:
self.param_dist_random = {'max_depth': sp_randint(1, 100),
'min_samples_leaf': sp_randint(1, 100),
'max_features': sp_randint(1, self.X.shape[1] - 1),
'criterion': ['entropy', 'gini']}
self.clf = RandomForestClassifier(n_estimators=100, n_jobs=8)
def deploy_07(train, test):
""" Deploy 07: Ensemble modeling with two types of cross validation """
from operator import itemgetter
from scipy.stats import randint as sp_randint
from sklearn.grid_search import GridSearchCV, RandomizedSearchCV
from sklearn.ensemble import RandomForestClassifier
from sklearn.ensemble import VotingClassifier
predictors = ['PassengerId','Gender', 'AgeRange',
'Family', 'AdjFare']
# Data Munging
train, test = deploy_03_features(train, test)
train = train.fillna(0)
test = test.fillna(0)
X = train[predictors]
y = train["Survived"]
# Algorithm specs
clf = RandomForestClassifier(
n_estimators=100
)
# specify parameters and distributions to sample from
param_dist = {"max_depth": [3, None],
"max_features": sp_randint(1, 5),
"min_samples_split": sp_randint(1, 5),
"min_samples_leaf": sp_randint(1, 5),
"bootstrap": [True, False],
"criterion": ["gini", "entropy"]}
# run randomized search
n_iter_search = 20
random_search = RandomizedSearchCV(clf, param_distributions=param_dist,
n_iter=n_iter_search)
# use a full grid over all parameters
param_grid = {"max_depth": [3, None],
"max_features": [1, 3, 5],
"min_samples_split": [1, 3, 5],
"min_samples_leaf": [1, 3, 5],
"bootstrap": [True, False],
"criterion": ["gini", "entropy"]}
# run grid search
grid_search = GridSearchCV(clf, param_grid=param_grid)
# Using both with a Voting Classifier
alg = VotingClassifier(estimators=[('gr', grid_search),
('rs', random_search)], voting='soft')
# Make submission
create_submission(alg, train, test, predictors,
"results/deploy-07.csv")
def learn_and_predict_xgb(self, dataset='train'):
'''
Use xgboost to do work
'''
#predictors = ["Pclass", "Sex", "Age", "Fare", "Embarked", "FamilySize", "Titles", "FamilyId"]
predictors = self.PREDICTORS
if dataset == 'train':
param_dist = {'max_depth': sp_randint(3, 10),
'learning_rate': [0.01, 0.03, 0.1, 0.3, 1.0],
'gamma': [0, 0.1, 0.2, 0.3],
'subsample': [.1, .2, .3, .4, 0.5],
'colsample_bytree': [.4, .5],
'objective': ['binary:logistic'],
'n_estimators': sp_randint(20, 150),
}
clf = xgb.XGBClassifier()
#random_search = RandomizedSearchCV(clf, param_distributions=param_dist, n_iter=500, cv=3)
#random_search.fit(self.train_df[predictors], self.train_df['Survived'])
#report(random_search.grid_scores_)
params = {'max_depth': 6, 'learning_rate': 0.1, 'colsample_bytree': 0.5, 'n_estimators': 54, 'subsample': .3, 'gamma': 0, 'objective':'binary:logistic', 'eval_metric': 'auc'} #0.845, cv=3
bst = xgb.train(params, self.DMatrix_train)
predictions = pd.Series(bst.predict(self.DMatrix_train))
predictions[predictions >= .5] = 1
predictions[predictions < .5] = 0
predictions = [int(x) for x in predictions.tolist()]
train_model = pd.DataFrame({
'PassengerId': self.train_df['PassengerId'],
'Survived': predictions,
})
train_model.to_csv('./xgb_train.csv', index=False)
else:
params = {'max_depth': 6, 'learning_rate': 0.1, 'colsample_bytree': 0.5, 'n_estimators': 54, 'subsample': .3, 'gamma': 0, 'objective':'binary:logistic', 'eval_metric': 'auc'} #0.845, cv=3
bst = xgb.train(params, self.DMatrix_train)
#clf = xgb.XGBClassifier(params)
#clf.fit(self.train_df[predictors], self.train_df['Survived'], verbose=True)
#print(self.test_df[predictors])
predictions = pd.Series(bst.predict(self.DMatrix_test))
predictions_proba = predictions.copy()
predictions[predictions >= .5] = 1
predictions[predictions < .5] = 0
predictions = [int(x) for x in predictions.tolist()]
print(predictions)
submission = pd.DataFrame({
'PassengerId': self.test_df['PassengerId'],
'Survived': predictions
})
submission.to_csv("xgboost_845.csv", index=False)
submission_proba = pd.DataFrame({
'PassengerId': self.test_df['PassengerId'],
'Survived': predictions_proba,
})
submission_proba.to_csv("xgboost_845_soft.csv", index=False)
def build_sample(regressor, name):
# print estimator.get_params().keys() : specify parameters and distributions to sample from
param_dist = {"max_depth": [3, None],
"max_features": sp_randint(1, 11),
"min_samples_split": sp_randint(1, 11),
"min_samples_leaf": sp_randint(1, 11)}#,
#"bootstrap": [True, False],
#"criterion": ["mse", "entropy"]}
# run randomized search
n_iter_search = 20
random_search = RandomizedSearchCV(regressor, param_distributions=param_dist,
n_iter=n_iter_search)
# time...
start = time()
# repeat the CV procedure 10 times to get more precise results
n = 10
# for each iteration, randomly hold out 10% of the data as CV set
for i in range(n):
X_train, X_cv, y_train, y_cv = cross_validation.train_test_split(
sample_X, sample_y, test_size=.10, random_state=i*SEED)
# train with rand...
random_search.fit(X_train, y_train)
# train...
#regressor = regressor.fit(X_train, y_train)
# save model
#store_pkl(regressor, name + ".pkl")
# predict on train
preds = random_search.predict(X_cv)
# print
#print preds
# create DataFrame
#preds = DataFrame(preds, columns = ["prime_tot_ttc_preds"])
#print preds
#print y_cv
# mape
mape_r = mape(y_cv, preds)
# print
print "MAPE of (fold %d/%d) of %s is : %f" % (i+1 , n, name, mape_r)
# time...
print("RandomizedSearchCV took %.2f seconds for %d candidates"
" parameter settings." % ((time() - start), n_iter_search))
report(random_search.grid_scores_)
# predict on test
predict_res = random_search.predict(sample_t)
preds_on_test = DataFrame(list(zip(sample_id, predict_res)), columns = ["ID", "CODIS"])
preds_on_test['ID'].astype(int)
# save predictions
store_csv(preds_on_test, name + ".csv")
return predict_res
def build_nn(x_train, y_train, x_test, y_test, n_features):
"""
Constructing a regression neural network model from input dataframe
:param x_train: features dataframe for model training
:param y_train: target dataframe for model training
:param x_test: features dataframe for model testing
:param y_test: target dataframe for model testing
:return: None
"""
net = NeuralNet(layers=[('input', InputLayer),
('hidden0', DenseLayer),
('hidden1', DenseLayer),
('output', DenseLayer)],
input_shape=(None, x_train.shape[1]), # Number of i/p nodes = number of columns in x
hidden0_num_units=15,
hidden0_nonlinearity=lasagne.nonlinearities.softmax,
hidden1_num_units=17,
hidden1_nonlinearity=lasagne.nonlinearities.softmax,
output_num_units=1, # Number of o/p nodes = number of columns in y
output_nonlinearity=lasagne.nonlinearities.softmax,
max_epochs=100,
update_learning_rate=0.01,
regression=True,
verbose=0)
# Finding the optimal set of params for each variable in the training of the neural network
param_dist = {'hidden0_num_units':sp_randint(3, 30), 'hidden1_num_units':sp_randint(3, 30)}
clf = RandomizedSearchCV(estimator=net, param_distributions=param_dist,
n_iter=15, n_jobs=-1)
clf.fit(x_train, y_train)
y_pred = clf.predict(x_test)
# Mean absolute error regression loss
mean_abs = sklearn.metrics.mean_absolute_error(y_test, y_pred)
# Mean squared error regression loss
mean_sq = sklearn.metrics.mean_squared_error(y_test, y_pred)
# Median absolute error regression loss
median_abs = sklearn.metrics.median_absolute_error(y_test, y_pred)
# R^2 (coefficient of determination) regression score function
r2 = sklearn.metrics.r2_score(y_test, y_pred)
# Explained variance regression score function
exp_var_score = sklearn.metrics.explained_variance_score(y_test, y_pred)
with open('../trained_networks/nn_%d_data.pkl' % n_features, 'wb') as results:
pickle.dump(clf, results, pickle.HIGHEST_PROTOCOL)
pickle.dump(net, results, pickle.HIGHEST_PROTOCOL)
pickle.dump(mean_abs, results, pickle.HIGHEST_PROTOCOL)
pickle.dump(mean_sq, results, pickle.HIGHEST_PROTOCOL)
pickle.dump(median_abs, results, pickle.HIGHEST_PROTOCOL)
pickle.dump(r2, results, pickle.HIGHEST_PROTOCOL)
pickle.dump(exp_var_score, results, pickle.HIGHEST_PROTOCOL)
pickle.dump(y_pred, results, pickle.HIGHEST_PROTOCOL)
return
def best_RandomForest(self, df=pd.DataFrame(),
flag_interactions=False,
flag_clean_features=False,
impute_func=None,
fill_test_func=None):
df = self.df
if impute_func:
print('imputing data...')
df, self.df_X_realtest = self.impute_data(df,
self.df_X_realtest,
impute_func,
fill_test_func)
print('get X, y from training set')
(self.X, self.y) = self.ready_for_model_train(
df, flag_interactions=flag_interactions,
flag_clean_features=flag_clean_features)
clf = RandomForestClassifier(bootstrap=False)
grid = {'n_estimators': sp_randint(170, 350),
'min_samples_leaf': sp_randint(1, 12),
'max_features': sp_randint(2, 50),
'max_depth': sp_randint(5, 30),
'criterion': ['entropy','gini']}
clf_rfc = RandomizedSearchCV(clf, n_jobs=4,
n_iter=25, cv=6,
param_distributions=grid,
scoring='accuracy')
print('Finding the best parameters...')
clf_rfc.fit(self.X, self.y.ravel())
print('preparing X, y from test set...')
X_test, y_test = self.ready_for_model_test(
self.df_X_realtest, flag_interactions)
y_hat = clf_rfc.predict(X_test)
print('Best Params: \n')
for k, v in clf_rfc.best_params_.items():
print(k, v)
print("Accuracy with Random Forest = %4.4f" %
accuracy_score(y_test, y_hat))
#binarize_y_confustion_matrix(y_test, y_hat)
return(clf_rfc.best_params_)
def randomized_search_and_grid_search_for_hyperparameter_estimation(train_data, labels):
# build a classifier
clf = RandomForestClassifier(n_estimators = 20)
# Utility function to report best scores
def report(grid_scores, n_top = 3):
top_scores = sorted(grid_scores, key = itemgetter(1), reverse = True)[:n_top]
for i, score in enumerate(top_scores):
print("Model with rank: {0}".format(i + 1))
print("Mean validation score: {0:.3f} (std: {1:.3f})".format(
score.mean_validation_score,
np.std(score.cv_validation_scores)))
print("Parameters: {0}".format(score.parameters))
print("")
# specify parameters and distributions to sample from
param_dist = {"max_depth": [3, None],
"max_features": sp_randint(1, 11),
"min_samples_split": sp_randint(1, 11),
"min_samples_leaf": sp_randint(1, 11),
"bootstrap": [True, False],
"criterion": ["gini", "entropy"]}
# run randomized search
n_iter_search = 20
random_search = RandomizedSearchCV(clf, param_distributions=param_dist,
n_iter=n_iter_search)
start = time()
random_search.fit(train_data, labels)
print("RandomizedSearchCV took %.2f seconds for %d candidates"
" parameter settings." % ((time() - start), n_iter_search))
report(random_search.grid_scores_)
# use a full grid over all parameters
param_grid = {"max_depth": [3, None],
"max_features": [1, 3, 10],
"min_samples_split": [1, 3, 10],
"min_samples_leaf": [1, 3, 10],
"bootstrap": [True, False],
"criterion": ["gini", "entropy"]}
# run grid search
grid_search = GridSearchCV(clf, param_grid=param_grid)
start = time()
grid_search.fit(train_data, labels)
print("GridSearchCV took %.2f seconds for %d candidate parameter settings."
% (time() - start, len(grid_search.grid_scores_)))
report(grid_search.grid_scores_)
def __init__(self, training_iters=1000, cv_folds=5, scoring_method="f1", n_jobs=4):
super(AdoptionPredictor, self).__init__()
self.clf = RandomForestClassifier(class_weight="balanced_subsample")
self.cv_params = {"folds": cv_folds, "scorer": scoring_method}
self.n_iter = training_iters
self.n_jobs = n_jobs
# define param search space for RandomizedSearchCV
self.param_grid = {"max_depth": [3, 5, 7, 9, None],
"n_estimators": sp_randint(10, 100),
"max_features": ["sqrt", "log2"],
"min_samples_split": sp_randint(3, 10),
"min_samples_leaf": sp_randint(1, 10),
"criterion": ["gini", "entropy"]}
def __init__(self, X: np.array, Y: np.array, tune_parameters=False):
super().__init__(X, Y, tune_parameters=False)
self.X = X.todense() # TensorFlow/Skflow doesn't support sparse matrices
output_layer = len(np.unique(Y))
if tune_parameters:
self.param_dist_random = {'learning_rate': random.random(100),
'optimizer': ['Adam'],
'hidden_units': [sp_randint(50, 500), sp_randint(50, 500)]}
self.clf = skflow.TensorFlowDNNClassifier(hidden_units=self.hidden_units,
n_classes=output_layer, steps=self.steps,
learning_rate=self.learning_rate, verbose=0,
optimizer=self.optimizer)
def RFC_Classifier(Train_DS, y, Actual_DS, grid=True):
print("***************Starting Random Forest Classifier***************")
t0 = time()
if grid:
#used for checking the best performance for the model using hyper parameters
print("Starting model fit with Grid Search")
# specify parameters and distributions to sample from
param_dist = {
"max_depth": [1, 2, 3, 4, 5, None],
"max_features": sp_randint(1, 11),
"min_samples_split": sp_randint(1, 11),
"min_samples_leaf": sp_randint(1, 11),
"bootstrap": [True, False]
}
clf = RandomForestClassifier(n_estimators=100,n_jobs=1)
# run randomized search
n_iter_search = 20
clf = RandomizedSearchCV(clf, param_distributions=param_dist,
n_iter=n_iter_search, scoring = 'log_loss')
start = time()
clf.fit(Train_DS, y)
print("RandomizedSearchCV took %.2f seconds for %d candidates"
" parameter settings." % ((time() - start), n_iter_search))
report(clf.grid_scores_)
print("Best estimator found by grid search:")
print(clf.best_estimator_)
print(clf.grid_scores_)
print(clf.best_score_)
print(clf.best_params_)
print(clf.scorer_)
else:
clf = RandomForestClassifier(n_estimators=10,n_jobs=1)
Kfold_score = Kfold_Cross_Valid(Train_DS, y, clf)
clf.fit(Train_DS, y)
#incase if it is required for stacking
pred_Train = clf.predict_proba(Train_DS)
#Predict actual model
pred_Actual = clf.predict_proba(Actual_DS)
print("Actual Model predicted")
print("***************Ending Random Forest Classifier***************")
return pred_Train, pred_Actual
def best_XGboost(self, df=pd.DataFrame(),
flag_interactions=False,
flag_clean_features=False,
impute_func=None,
fill_test_func=None):
df = self.df
if impute_func:
print('imputing data...')
df, self.df_X_realtest = self.impute_data(df,
self.df_X_realtest,
impute_func,
fill_test_func)
print('get X, y from training set')
(self.X, self.y) = self.ready_for_model_train(
df, flag_interactions=flag_interactions,
flag_clean_features=flag_clean_features)
clf = XGBClassifier()
grid = {'n_estimators': sp_randint(100, 600),
'learning_rate': [0.01, 0.03, 0.05, 0.1, 0.3, 0.5],
'max_depth': sp_randint(5, 30),
'min_child_weight': sp_randint(1, 5)}
clf_rfc = RandomizedSearchCV(clf, n_jobs=3,
n_iter=15, cv=4,
param_distributions=grid,
scoring='accuracy')
print('Finding the best parameters...')
clf_rfc.fit(self.X, self.y.ravel())
print('preparing X, y from test set...')
X_test, y_test = self.ready_for_model_test(
self.df_X_realtest, flag_interactions)
y_hat = clf_rfc.predict(X_test)
print('Best Params: \n')
for k, v in clf_rfc.best_params_.items():
print(k, v)
print("Accuracy with Random Forest = %4.4f" %
accuracy_score(y_test, y_hat))
#binarize_y_confustion_matrix(y_test, y_hat)
return(clf_rfc.best_params_)
def train(feature_names,estimators):
traindf = pd.read_csv("train_extend.csv",index_col="datetime")
parm_dist = dict(learning_rate=[0.001,0.005,0.01,0.02,0.05,0.1,0.3],
n_estimators=sp_randint(100,2000),
max_depth=sp_randint(3,6),
min_samples_leaf = range(1,10)
)
n_iter = 300
n_jobs = 6
for estimator in estimators:
best_cv_score = estimator.train(traindf,parm_dist,n_iter,n_jobs)
print "************* '%s' got best CV score: %f"%(estimator.target_column,best_cv_score)
estimator.dump()
def __init__(self, X: csr_matrix, Y: np.array, tune_parameters=False):
super().__init__(X, Y, tune_parameters)
if tune_parameters:
self.param_dist_random = {'shrinking': [True, False],
'kernel': ['linear', 'poly', 'rbf', 'sigmoid'],
'degree': sp_randint(2, 5)}
self.clf = SVC(kernel='rbf', shrinking=True)
def return_best_rf_regressor(df, target, num_trees_hyperparameter, num_trees_final_clf, num_iterations):
print "entering return best rf regressor function"
if df.shape[0] < 10000:
num_samples = df.shape[0]
else:
num_samples = int(df.shape[0]*0.7)
print "Sample dataframe"
#use
X, y, column_list_for_sampled = sample_data_frame_return_x_y_column_name(df, True, target, num_samples)
# figure out a vary this some how
"""
param_dist = {"max_depth": [5, None],
"max_features": sp_randint(1, df.shape[1]),
"min_samples_split": sp_randint(1, 15),
"min_samples_leaf": sp_randint(1, 15),
"bootstrap": [True, False],
"criterion": ["gini", "entropy"]}
"""
param_dist = {"max_depth": [5, None], "max_features": sp_randint(1, df.shape[1]), "min_samples_split": sp_randint(1, 15), "min_samples_leaf": sp_randint(1, 15), "bootstrap": [True]}
clf = RandomForestRegressor(n_estimators=num_trees_hyperparameter)
print "starting hyperparameter search"
clf_best, best_params = hyperparameter_search_random(X, y, clf, param_dist, num_iterations)
print "sample data for fitting model"
#train new classifier on the entire dataset
X, y, column_list_for_sampled = sample_data_frame_return_x_y_column_name(df, True, target, num_samples=df.shape[0])
clf_final = RandomForestRegressor(n_estimators=num_trees_final_clf, max_depth = best_params["max_depth"], min_samples_leaf = best_params["min_samples_leaf"], min_samples_split = best_params["min_samples_split"], bootstrap = best_params["bootstrap"], max_features = best_params["max_features"])
print "Fitting Random Forest Regressor"
clf_final.fit(X,y)
return clf_final, column_list_for_sampled
def grid_search(self, **kwargs):
"""Using grid search to find the best parameters."""
n_jobs = kwargs.get('n_jobs', 1)
n_iter = kwargs.get('n_iter', 5)
col2fit = kwargs.get('features')
bids_path = kwargs.get('bids_path', 'data/bids.csv')
score = kwargs.get('score')
# use a full grid over all parameters
parameters = {"max_depth": sp_randint(1, 30),
"criterion": ["gini", "entropy"],
"max_features": [1.0, 0.8, 0.6, 0.4, 0.2, 0.1],
"min_samples_leaf": sp_randint(1, 25),
"min_samples_split": sp_randint(1, 25),
"bootstrap": [True, False],
"class_weight": [None, "auto", "subsample"]}
if not self.iscleaned:
print 'Preparing the data...'
self.prepare_data(bids_path, **kwargs)
else:
print 'data frame is already cleaned...'
train_values = self.df_train[col2fit].values
target_values = self.df_train['outcome'].values
pre_dispatch = '2*n_jobs'
# Fit the grid
print 'fitting the grid with n_jobs = {}...'.format(n_jobs)
start = time()
self.set_model(**kwargs)
rf_grid = grid_search.RandomizedSearchCV(self.learner,
parameters,
n_jobs=n_jobs, verbose=2,
pre_dispatch=pre_dispatch,
scoring=score,
error_score=0,
n_iter=n_iter)
rf_grid.fit(train_values, target_values)
print('Grid search finished')
print("\n\nGridSearchCV took %.2f seconds for %d candidate parameter settings."
% (time() - start, len(rf_grid.grid_scores_)))
self.grid_report(rf_grid.grid_scores_, 15)
print('\n\nBest score = {}'.format(rf_grid.best_score_))
print('Best params = {}\n\n'.format(rf_grid.best_params_))
def getExtraTressClf(self, X, Y, param_list=-1):
clfName = "Extra_Trees"
## http://scikit-learn.org/stable/modules/generated/sklearn.ensemble.ExtraTreesClassifier.html
clf = ExtraTreesClassifier(
n_estimators=10,
criterion='gini',
max_depth=None,
min_samples_split=2,
min_samples_leaf=1,
min_weight_fraction_leaf=0.0,
max_features='auto',
max_leaf_nodes=None,
bootstrap=False,
oob_score=False,
n_jobs=1,
random_state=None,
verbose=0,
warm_start=False,
class_weight=None)
if self._gridSearchFlag == True:
log(clfName + " start searching param...")
tmpLowDepth = int(len(X.columns) * 0.7)
tmpHighDepth = int(len(X.columns) )
param_dist = {
"max_depth": sp_randint(tmpLowDepth, tmpHighDepth),
"max_features": sp_randf(0,1),
"min_samples_split": sp_randint(1, 11),
"min_samples_leaf": sp_randint(1, 11),
"bootstrap": [True, True],
"criterion": ["gini", "entropy"],
"oob_score":[True, True],
"n_estimators" : sp_randint(800, 1200),
}
clf = self.doRandomSearch(clfName, clf, param_dist, X, Y)
else:
if param_list != -1:
clf = ExtraTreesClassifier(param_list)
clf.set_params(**param_list)
clf.fit(X,Y)
return clf
def evalModel(train_data, eval_data, train_labels, eval_labels, seed):
joined_data = np.concatenate((train_data, eval_data), axis=0)
joined_labels = np.concatenate((train_labels, eval_labels), axis=0)
train_mask = np.zeros(train_data.shape[0]) - 1.0
eval_mask = np.zeros(eval_data.shape[0])
joined_mask = np.concatenate((train_mask, eval_mask), axis=0)
ps = PredefinedSplit(test_fold=joined_mask)
loss = make_scorer(get_rmsle, greater_is_better=False)
train_data = sparse.csr_matrix(train_data)
eval_data = sparse.csr_matrix(eval_data)
clf = RandomForestRegressor(random_state=seed, verbose=1)
# clf.fit(train_data, train_labels)
# preds = clf.predict(eval_data)
# print(get_rmsle(eval_labels, preds))
## achieves 0.263
# specify parameters and distributions to sample from
param_dist = {
"n_estimators": sp_randint(300, 800),
"max_depth": sp_randint(10, 50),
"max_features": ["auto", "sqrt", "log2"],
"min_samples_split": sp_randint(1, 11),
"min_samples_leaf": sp_randint(1, 11),
}
# run randomized search
n_iter_search = 60
random_search = RandomizedSearchCV(
clf,
param_distributions=param_dist,
cv=ps,
scoring=loss,
n_iter=n_iter_search,
n_jobs=-1,
pre_dispatch="n_jobs",
verbose=2,
)
start = time()
random_search.fit(joined_data, joined_labels)
print(
"RandomizedSearchCV took %.2f seconds for %d candidates"
" parameter settings." % ((time() - start), n_iter_search)
)
report(random_search.grid_scores_)
def evalModel(data, labels):
loss = make_scorer(get_rmsle, greater_is_better=False)
seed1 = 42
clf = xgb.XGBRegressor(seed=seed1, silent=True)
param_dist = { "learning_rate":sp_uniform(0.01,0.1),
"n_estimators":sp_randint(50,500),
"max_depth": sp_randint(2,6),
"subsample": sp_uniform(0.5,0.4),
"max_delta_step": sp_uniform(1,2),
"min_child_weight":sp_uniform(1,6),
"colsample_bytree":sp_uniform(0.8,0.2)};
n_iter_search = 60
random_search = RandomizedSearchCV(clf, param_distributions=param_dist, cv=5, scoring=loss,
n_iter=n_iter_search,n_jobs=-1,pre_dispatch='n_jobs',verbose=2)
report(random_search.grid_scores_,n_top=5)
def createRandomSearch(clf, X, y):
param_dist = {"max_depth": [3, None], \
"max_features": sp_randint(1, 11), \
"min_samples_split": sp_randint(1, 11), \
"min_samples_leaf": sp_randint(1, 11), \
"bootstrap": [True, False], \
"criterion": ["gini", "entropy"]
}
n_iter_search = 20
random_search = RandomizedSearchCV(clf, param_distributions=param_dist, \
n_iter=n_iter_search)
start = time()
random_search.fit(X, y)
print("RandomizedSearchCV took %.2f seconds for %d candidates parameter settings." % ((time() - start), n_iter_search))
report(random_search.grid_scores_)
# Split data into train/test by year
pickups_14_15['day_of_week'] = pickups_14_15['day_of_week'].apply(str)
pickups_14_15['hour'] = pickups_14_15['hour'].apply(str)
pickups_14_15['month'] = pickups_14_15['month'].apply(str)
# Create training data (2014)
X_train = pickups_14_15[pickups_14_15['year'] == 2014]
Y_train = X_train['passenger_count']
X_train.drop(['date', 'passenger_count', 'year'], axis=1, inplace=True)
X_train = pd.get_dummies(X_train)
# Try random forest model, randomized search for optimal parameters
rf = RandomForestRegressor()
# Specify parameters and distributions to sample from
param_dist = {'n_estimators': sp_randint(1, 101),
'max_depth': [1, 2, 3, None],
'max_features': sp_randint(1, X_train.shape[1]),
'min_samples_split': sp_randint(1, 11),
'min_samples_leaf': sp_randint(1, 11),
'bootstrap': [True, False]}
# Run randomized search
# Try it on subset of training data to speed up search
sample_index = X_train.sample(50000).index
n_iter_search = 50
random_search = RandomizedSearchCV(rf, param_distributions=param_dist, n_iter=n_iter_search)
random_search.fit(X_train.ix[sample_index], Y_train.ix[sample_index])
random_search.best_params_
# Create test data (2015)
# Import data
tweets = pd.read_csv('labeled_data.csv')
grouped_tweets = tweets.groupby(['author', 'class'])['text'].apply(' '.join).reset_index()
# Train_test_split
X = grouped_tweets['text']
Y = grouped_tweets['class']
X_train, X_test, y_train, y_test = train_test_split(X, Y, test_size = .25, random_state = 0)
# Define the pipeline
tfidf = TfidfVectorizer(tokenizer = spacy_tokenizer, max_features = 5000)
rf_grid_pipe = Pipeline([('vect', tfidf),('fit', RandomForestClassifier())])
# Grid search
param_grid = {"fit__bootstrap" : [True, False],
"fit__n_estimators" : sp_randint(50, 150),
"fit__max_depth" : [10, 50, None],
"fit__max_leaf_nodes" : sp_randint(10, 50)
}
grid = RandomizedSearchCV(rf_grid_pipe, param_grid,
cv=3, n_iter=20, n_jobs=14, random_state=0)
grid.fit(X_train, y_train)
preds = grid.predict(X_test)
accuracy = accuracy_score(y_test, preds)
precision = precision_score(y_test, preds)
recall = recall_score(y_test, preds)
f1 = f1_score(y_test, preds)
# logs for comet_ml
# ElasticNet
EN_gscv_param_grid = dict(ElasticNetReg__alpha=[.1, 0.5, 1., 5., 10.],
ElasticNetReg__l1_ratio=[.05, .1, .5, .7, .9, .95])
EN_param_distro = dict(
ElasticNetReg__alpha=EN_gscv_param_grid["ElasticNetReg__alpha"],
ElasticNetReg__l1_ratio=sp_exp(scale=1))
# KNeighborsReg
KNR_gscv_param_grid = dict(KNeighborsReg__weights=['uniform', 'distance'],
KNeighborsReg__n_neighbors=[5, 10, 30, 50])
KNR_param_distro = dict(KNeighborsReg__weights=['uniform', 'distance'],
KNeighborsReg__n_neighbors=sp_randint(5, 50))
# RandomForestReg
RFR_gscv_param_grid = dict(
RandomForestReg__n_estimators=[10, 30, 50, 100, 200, 500, 1000],
RandomForestReg__criterion=['mse', 'mae'],
RandomForestReg__max_features=[None, .75, .5, 'sqrt'],
# RandomForestReg__max_features=[0.25, 'auto', 'sqrt', 'log2'],
RandomForestReg__min_samples_leaf=[1, 3, 5],
RandomForestReg__max_depth=[3, 5, 7, 10])
RFR_param_distro = RFR_gscv_param_grid
RFR_param_distro['RandomForestReg__n_estimators'] = sp_randint(
10, 500) # 100, 1000
RFR_param_distro['RandomForestReg__max_depth'] = sp_randint(3, 10)
# gskf = list(StatifiedGroupK_Fold.StratifiedGroupKfold(n_splits=5).split(X_resampled, Y_resampled, groups))
sgkf = StatifiedGroupK_Fold.StratifiedGroupKfold(n_splits=5)
params = {
'colsample_bytree': 0.9009933084016689,
'min_child_samples': 123,
'min_child_weight': 0.001,
'num_leaves': 40,
'reg_alpha': 0,
'reg_lambda': 0,
'subsample': 0.8426999443200605
}
# GRID
param_test = {
'num_leaves': sp_randint(6, 50),
'min_child_samples': sp_randint(100, 500),
'min_child_weight': [1e-5, 1e-3, 1e-2, 1e-1, 1, 1e1, 1e2, 1e3, 1e4],
'subsample': sp_uniform(loc=0.2, scale=0.8),
'colsample_bytree': sp_uniform(loc=0.4, scale=0.7),
'reg_alpha': [0, 1e-1, 1, 2, 5, 7, 10, 50, 100],
'reg_lambda': [0, 1e-1, 1, 5, 10, 20, 50, 100],
#'feval': 'auc',
}
# This parameter defines the number of HP points to be tested
n_HP_points_to_test = 100
# n_estimators is set to a "large value". The actual number of trees build will depend on early
# stopping and 5000 define only the absolute maximum
# clf = lgb.LGBMClassifier(max_depth=-1, random_state=314, silent=True, metrics='none', n_jobs=-1, n_estimators=5000, class_weight='balanced')
X_train_tfidf = tfidf_transformer.fit_transform(X_train_count)
pca = TruncatedSVD(n_components=20)
pca.fit(X_train_tfidf)
X_train_pca = pca.transform(X_train_tfidf)
# Test data transformations
X_test_count = count_vect.transform(X_test)
X_test_tfidf = tfidf_transformer.transform(X_test_count)
X_test_pca = pca.transform(X_test_tfidf)
clf = RandomForestClassifier()
parameters_rand = {
"n_estimators": sp_randint(300, 2000),
"max_depth": [3, None],
"max_features": sp_randint(1, 11),
"min_samples_split": sp_randint(2, 11),
"min_samples_leaf": sp_randint(1, 11),
"bootstrap": [True, False],
"criterion": ["gini", "entropy"]
}
# run randomized search
# Accuracy should be comparable to grid search, but runs much much faster
n_iter_search = 20
random_search = RandomizedSearchCV(clf,
param_distributions=parameters_rand,
n_iter=n_iter_search,
n_jobs=-1)
for candidate in candidates:
print("Model with rank: {0}".format(i))
print("Mean validation score: {0:.3f} (std: {1:.3f})".format(
results['mean_test_score'][candidate],
results['std_test_score'][candidate]))
print("Parameters: {0}".format(results['params'][candidate]))
print("")
# specify parameters and distributions to sample from
# param_dist = { "n_estimators": [50,100,150,200],
# "learning_rate": [0.1,0.5,1,1.5,2],
# }
param_dist = {
"max_depth": sp_randint(1, 15),
"n_estimators": [100, 150, 200, 400, 500],
"min_samples_split": sp_randint(2, 10),
"min_samples_leaf": sp_randint(1, 10)
}
# run randomized search
n_iter_search = 10
random_search = RandomizedSearchCV(clf,
param_distributions=param_dist,
n_iter=n_iter_search)
start = time()
random_search.fit(X, y)
print("RandomizedSearchCV took %.2f seconds for %d candidates"
" parameter settings." % ((time() - start), n_iter_search))
# In[2]:
n_iter = 100
k_fold = 10
# cv = kfold
# initialize the classifier
X_train, X_val, y_train, y_val, cv = load_train_and_kfold(n_folds=k_fold)
# In[4]:
model = KNeighborsClassifier()
model_name = model.__class__.__name__
param_grid = {
"n_neighbors": sp_randint(4,400),
"algorithm" : ["auto", "ball_tree", "kd_tree", "brute"],
}
# In[ ]:
search_GB = RandomizedSearchCV(model,param_grid,scoring='log_loss',n_jobs=-1,
n_iter=n_iter,cv=cv,verbose=True)
search_GB.fit(X_train,y_train.flatten())
# In[ ]:
# Utility function to report best scores
def report(grid_scores, n_top=3):
top_scores = sorted(grid_scores, key=itemgetter(1), reverse=True)[:n_top]
for i, score in enumerate(top_scores):
print("Model with rank: {0}".format(i + 1))
print("Mean validation score: {0:.3f} (std: {1:.3f})".format(
score.mean_validation_score, np.std(score.cv_validation_scores)))
print("Parameters: {0}".format(score.parameters))
print("")
# specify parameters and distributions to sample from
param_dist = {
"max_depth": [3, None],
"max_features": sp_randint(1, 30),
"min_samples_split": sp_randint(1, 11),
"min_samples_leaf": sp_randint(1, 11),
"n_estimators": sp_randint(1, X_train.shape[1]),
}
# run randomized search
n_iter_search = 20
random_search = RandomizedSearchCV(clf,
param_distributions=param_dist,
n_iter=n_iter_search)
start = time()
random_search.fit(X_train, y_train)
print(
"RandomizedSearchCV took %.2f seconds for %d candidates"
" parameter settings." % ((time() - start), n_iter_search))
print("Parameters: {0}".format(score.parameters))
print("")
print("Starting RandomizedSearchCV")
n_features = X_train.shape[1]
N_FOLDS = 10
model = xgb.XGBRegressor()
# specify parameters and distributions to sample from
param_dist = {
"objective": ["reg:linear"],
# "booster" : ["gbtree"],
# "eta": [0.1, 0.3, 0.5, 0.7],
"max_depth": sp_randint(10, 30),
"subsample": sp_uniform(0.1, 0.9),
"colsample_bytree": sp_uniform(0.1, 1.0),
"silent": [1],
"seed": [42]
}
# run randomized search
n_iter_search = 30
folds = cv.KFold(n=len(y_train),
n_folds=N_FOLDS,
shuffle=True,
random_state=42)
random_search = RandomizedSearchCV(model,
param_distributions=param_dist,
n_iter=n_iter_search,
aid_mimic.load_candidates(mimic_files['candidates'])
# aid_mimic.compute_features(features='filtered')
# aid_mimic.save_features(mimic_files['feature_values'])
aid_mimic.load_features(mimic_files['feature_values'])
aid_mimic.load_y_true(mimic_files['y_true'])
# ____________________________________________________________________________________________________________________
sample_weights = compute_sample_weight('balanced', aid_mimic.y_true)
tuning_params = [
{
'name': "Nearest Neighbors",
'predictor': make_sklearn_pipeline(KNeighborsClassifier()),
'parameters': {
'clf__n_neighbors': sp_randint(2, 20),
'clf__weights': ['uniform', 'distance'],
},
'n_iter': 1000,
'fit_params': None,
},
{
'name':
"Linear SVM",
'predictor':
make_sklearn_pipeline(
SVC(kernel="linear", class_weight='balanced', random_state=1)),
'parameters': {
'clf__C': sp_expon(),
},
'n_iter':
from scipy.stats import randint as sp_randint
from sklearn.ensemble import RandomForestClassifier
model = RandomForestClassifier()
param_dist = {
"n_estimators": [10, 20, 30, 40, 50],
"max_depth": [3, 5, 7, 9, 10, None],
"max_features": sp_randint(1, 20),
"min_samples_split": sp_randint(2, 12),
"min_samples_leaf": sp_randint(1, 12),
"bootstrap": [True, False],
"criterion": ["gini", "entropy"]
}
for i, score in enumerate(top_scores):
print("Model with rank: {0}".format(i + 1))
print("Mean validation score: {0:.3f} (std: {1:.3f})".format(
score.mean_validation_score, np.std(score.cv_validation_scores)))
print("Parameters: {0}".format(score.parameters))
print("")
#In the following randomSearchCV/GridSearchCV accept parameters values as dictionaries
#In example given below we have constructed dictionary for different parameter values
#that we want to try for randomForest model (We are setting up the grid search parameters here)
param_dist = {
"n_estimators": [10, 100, 500, 700],
"max_depth": [3, 5, None],
"max_features": sp_randint(5, 11),
"min_samples_split": sp_randint(5, 11),
"min_samples_leaf": sp_randint(5, 11),
"bootstrap": [True, False],
"criterion": ["gini", "entropy"]
}
#Total number of combinations we would get from above is 4 X 3 X 7 X 7 X 7 X 2 X 2 which would take a lot
#of time to run and hence we would need to randomly choose certain combinations from the above
#Running the randomized Search (We are randomly picking 100 combinations out of the above mentioned
#combinations)
n_iter_search = 100
#n_iter parameter of RandomizedSearchCV controls, how many parameter combination will be tried; out
#of all possible given values, we are also setting the param_distributions parameter as param_dist
#Which contains all the combinations of parameters
if best_algo == 'SVR':
algo = getattr(sklearn.svm, best_algo)(gamma='auto')
if best_algo == 'MLPRegressor':
algo = getattr(sklearn.neural_network, best_algo)()
if best_algo == 'XGBRegressor':
algo = getattr(xgboost, best_algo)()
if best_algo == 'KNeighborsRegressor':
algo = getattr(sklearn.neighbors, best_algo)()
## Begin the tune by setting hyper parameter limits per algorithm
if best_algo == 'LinearRegression':
hyperparameters = {"penalty": ["l1", "l2"], "C": sp_randint(1, 10)}
scoring_metric = make_scorer(explained_variance_score)
if best_algo == 'SGDRegressor':
hyperparameters = {
'alpha': [1e-4, 1e-3, 1e-2, 1e-1, 1e0, 1e1, 1e2, 1e3],
"learning_rate": ["constant", "optimal", "invscaling", "adaptive"]
}
scoring_metric = make_scorer(roc_auc_score)
if (best_algo
== 'RandomForestRegressor') or (best_algo == 'AdaBoostRegressor') or (
best_algo
== 'GradientBoostingRegressor') or (best_algo
== 'BaggingRegressor'):
hyperparameters = {"n_estimators": sp_randint(1, 1000)}
def report(grid_scores, n_top=3):
top_scores = sorted(grid_scores, key=itemgetter(1), reverse=True)[:n_top]
for i, score in enumerate(top_scores):
print("Model with rank: {0}".format(i + 1))
print("Mean validation score: {0:.3f} (std: {1:.3f})".format(
score.mean_validation_score, np.std(score.cv_validation_scores)))
print("Parameters: {0}".format(score.parameters))
print("")
xgbnew = XGBRegressor()
# specify parameters and distributions to sample from
one_to_left = st.beta(10, 1)
from_zero_positive = st.expon(0, 50)
param_dist = {
"n_estimators": sp_randint(80, 120),
"max_depth": sp_randint(2, 15),
"learning_rate": st.uniform(0.05, 0.1),
"gamma": st.uniform(0, 10),
'reg_alpha': from_zero_positive,
"min_child_weight": from_zero_positive,
}
# run randomized search
n_iter_search = 20
random_search = RandomizedSearchCV(xgbnew,
param_distributions=param_dist,
n_iter=n_iter_search)
start = time()
random_search.fit(x_train2num, y_train2num)
def test(self):
im_ratio = [10, 100, 200]
sep_condition = [1, 4, 8]
params_dict1 = {
'test__max_depth': [None],
'test__max_features': sp_randint(1,
3), #Number of features per bag
'test__min_samples_split':
sp_randint(2, 100), #Min number of samples in a leaf node split
'test__min_samples_leaf':
sp_randint(1, 100), #Min number of samples in a leaf node
'test__bootstrap':
[True, False], #Sample \mathbf{x}x with/without replacement
'test__n_estimators': [1, 2, 5, 10, 50, 75, 100, 250, 500,
1000], #Number of trees in the forest
"test__n_jobs": [-1],
"test__class_weight": ["balanced", "balanced_subsample"]
}
params_dict2 = {
'test__n_estimators': [1, 2, 5, 10, 50, 75, 100, 250, 500],
"test__n_jobs": [-1],
"test__replacement": [True, False]
}
params_dict3 = {
'test__n_estimators': [1, 2, 5, 10, 50, 75, 100],
"test__algorithm": ["SAMME", "SAMME.R"],
"test__replacement": [True, False]
}
params_dict4 = {
'test__n_estimators': [1, 2, 5, 10, 50, 75, 100, 250, 500, 1000],
"test__n_jobs": [-1],
"test__replacement": [True, False],
"test__base_estimator": [
SVC(C=1.0,
cache_size=200,
class_weight="balanced",
coef0=0.0,
decision_function_shape='ovr',
degree=3,
gamma='auto',
kernel='rbf',
max_iter=-1,
probability=False,
random_state=None,
shrinking=True,
tol=0.001,
verbose=False)
],
"test__max_samples":
sp_unif(0, 1),
"test__max_features":
sp_unif(0, 1)
}
ensembler = [("BalancedRandomForestClassifier",
BalancedRandomForestClassifier, params_dict1),
("EasyEnsembleClassifier", EasyEnsembleClassifier,
params_dict2),
("RUSBoostClassifier", RUSBoostClassifier, params_dict3),
("BalancedBaggingClassifier", BalancedBaggingClassifier,
params_dict4)]
# with open("Ensembler.txt", "a") as f:
# f.write("Strategy\timbalanced_ratio\tclass_separability\tk_J1\tu_J1\tcv_score\tcv_gms\treplace_score\treplace_gms\n")
for classifier in ensembler:
for sep in sep_condition:
for ratio in im_ratio:
X_train, Y_train, X_test, Y_test = self.load_data(
ratio=ratio, sep=sep)
batch = len(X_train)
for i in range(1):
self.classifier = classifier[1]
self.params_dict = classifier[2]
self.X_train, self.Y_train, self.X_test, self.Y_test = X_train[
i], Y_train[i], X_test[i], Y_test[i]
k_J1, u_J1 = self.J1_estimate(self.X_train,
self.Y_train,
self.X_test, self.Y_test)
f1_cv, g_cv, f1_rp, g_rp = self.phase2(
self.X_train, self.Y_train)
with open("Ensembler.txt", "a") as f:
f.write(
"{}\t{}\t{}\t{:.2f}\t{:.2f}\t{:.4f}\t{:.4f}\t{:.4f}\t{:.4f}\n"
.format(classifier[0], ratio, sep, k_J1, u_J1,
f1_cv, g_cv, f1_rp, g_rp))
print("TRAIN:", train_index, "TEST:", test_index)
doc_train = doc_data[train_index]
doc_test = doc_data[test_index]
X_train, y_train = utils.convert_docs_to_lines(doc_train)
X_test, y_test = utils.convert_docs_to_lines(doc_test)
argument_sets += [(X_train, X_test, y_train, y_test)]
text_clf = Pipeline([('vect', CountVectorizer()),
('tfidf', TfidfTransformer()),
('pca', TruncatedSVD(n_components=20)),
('clf', RandomForestClassifier(n_jobs=-1))])
param_distributions = {
"vect__ngram_range": [(1, 3)],
"pca__n_components": sp_randint(20, 400),
"clf__n_estimators": sp_randint(100, 2000),
"clf__max_features": sp_randint(1, 8),
"clf__min_samples_leaf": sp_randint(1, 6),
# "clf__class_weight": [
# {0: 1, 1: 1.5, 2: 1.75},
# {0: 1, 1: 2, 2: 3},
# {0: 1, 1: 3, 2: 5},
# ],
"clf__criterion": ["entropy", "gini"]
}
n_iter_search = 10
random_search = RandomizedSearchCV(text_clf,
param_distributions=param_distributions,
n_iter=n_iter_search,
trainData = df.ix[:, :-1].values
trainLabels = df.ix[:, -1].values
dataset = "output/fungi/googlenetwithcontrol-test.csv"
# Loading dataset
df = pd.read_csv(dataset)
testData = df.ix[:, :-1].values
testLabels = df.ix[:, -1].values
#================================================================================================================
print("MultiLayer Perceptron")
#================================================================================================================
from sklearn.neural_network import MLPClassifier
clf = MLPClassifier(random_state=84)
n_iter_search = 20
param_dist = {
'activation': ['identity', 'logistic', 'tanh', 'relu'],
'solver': ['lbgfs', 'sgd', 'adam'],
'alpha': sp_randint(0.0001, 1),
'learning_rate': ['constant', 'invscaling', 'adaptive'],
'momentum': [0.9, 0.95, 0.99]
}
model = RandomizedSearchCV(clf,
param_distributions=param_dist,
n_iter=n_iter_search)
model.fit(trainData, trainLabels)
predictionsMLP = model.predict(testData)
print(classification_report(testLabels, predictionsMLP))
print(accuracy_score(testLabels, predictionsMLP))
x_train, x_test, y_train, y_test = train_test_split(x,
y,
random_state=42,
test_size=0.3)
print(x_train.shape, x_test.shape)
# RandomSearch
from sklearn.model_selection import RandomizedSearchCV
from scipy.stats import randint as sp_randint # Statistikpaket -> für zufällige WErte aus Intervall für RandomSearch
# Liste der Möglichen Parameter mit
# sp_randint(1,15) -> Zufällige Zahl zwischen 1 und 15. Intervall sollte jedoch gut überlegt werden
# "weights": ["uniform", "distance"] -> Zufälliger Auswahl zwischen uniform und Distance
# "p": [1, 2] -> Zufälliger Auswahl zwischen p = 1 oder 2
param_dist = {
"n_neighbors": sp_randint(1, 15),
"weights": ["uniform", "distance"],
"p": [1, 2]
}
n_iter_search = 20 # Es sollen 20 Modelle erstellt werden
neigh = KNeighborsClassifier()
clf = RandomizedSearchCV(
neigh, param_distributions=param_dist, n_iter=n_iter_search, cv=3
) # CV (Crossvalidation). Bei kleinen Datensätzen CV~ 3. Bei großen Datensätzen (mehrere 1000) CV = 5...10
clf.fit(x_train, y_train)
for key in clf.cv_results_.keys(
): # Listet Attribute auf die Aufgerufen werden können
print(key)
bestParams = []
cv = StratifiedShuffleSplit(n_splits=10, test_size=0.6, random_state=0)
for grp in all_train_data:
print 'Working on group : %s' % (grp)
# get some data
X = all_train_data[grp]['features'].values.astype(np.float32)
y = all_train_data[grp]['labels'].astype(np.int16)
# build a classifier
clf = RandomForestClassifier()
# specify parameters and distributions to sample from
param_dist = {
"n_estimators": sp_randint(1, 1000),
"max_depth": sp_randint(3, 303),
"max_features": sp_randint(1, 350),
"min_samples_split": sp_randint(2, 350),
"min_samples_leaf": sp_randint(1, 350),
"bootstrap": [True, False],
"criterion": ["gini", "entropy"]
}
# run randomized search
n_iter_search = 5000
random_search = RandomizedSearchCV(clf,
scoring='neg_log_loss',
param_distributions=param_dist,
n_iter=n_iter_search,
cv=cv,
# Hence, the default parameters are:
# * criterion (default=‘mse’). The function to measure the quality of a split.
# * splitter (default=‘best’). The strategy used to choose the split at each node.
# * min_samples_leaf (default=1). The minimum number of samples required to be at a leaf node.
# * min_weight_fraction_leaf (default=0.). The minimum weighted fraction of the sum total of weights (of all the input samples) required to be at a leaf node.
# * random_state (default=None). The random number generator is the RandomState instance used by np.random.
# * max_leaf_nodes (default=None). Unlimited number of nodes.
# * min_impurity_decrease (default=0.). A node will be split if this split induces a decrease of the impurity greater than or equal to 0.
# * min_impurity_split (default=1e-7). Threshold for early stopping in tree growth.
# In[10]:
from scipy.stats import randint as sp_randint
param_grid = {
'max_depth': sp_randint(2, 20),
'min_samples_split': sp_randint(2, 20)
}
from sklearn.model_selection import RandomizedSearchCV
rgt_grid = RandomizedSearchCV(rgt,
param_grid,
scoring='neg_mean_squared_error',
cv=tr_val_partition,
n_jobs=1,
verbose=1)
rgt_grid.fit(X_train_minmax, y_train)
y_test_pred_rgt_G = rgt_grid.predict(X_test_minmax)
class initialConfig:
## The following parameters correspond to the machine learning
## part of the framework.
# This parameter refers to the number of outer folds that
# are being used in order for the k-fold cross-validation
# to take place.
kfold_parameter = 5
kfold_inner_parameter = 4
# Number of parallel jobs to be initiated:
# -1: use all processors
# int: no of processors to use
n_jobs = -1
test_dataset = './datasets/dataset-string-similarity_original_1k.csv'
# test_dataset = './datasets/dataset-string-similarity_latin_EU_NA_1k.txt'
# test_dataset = './datasets/dataset-string-similarity-100.csv'
# the classification method used: basic, basic_sorted, lgm
classification_method = 'lgm'
# This parameter contains a list of the various classifiers
# the results of which will be compared in the experiments.
# classifiers = ['SVM', 'Decision Tree', 'Random Forest', 'AdaBoost',
# 'Naive Bayes', 'MLP', 'Gaussian Process', 'Extra Trees']
# Search Method to use for best hyperparameters: randomized, grid, hyperband - not yet implemented!!!
hyperparams_search_method = 'randomized'
# These are the parameters that constitute the search space for GridSearchCV
# in our experiments.
SVM_hyperparameters = [
{'kernel': ['rbf'], 'gamma': [1e-3, 1e-4],
'C': [0.001, 0.01, 0.1, 1, 10, 100, 1000], 'max_iter': [300]},
{'kernel': ['poly'], 'degree': [1, 2, 3, 4], 'gamma': ['scale'],
'C': [0.001, 0.01, 0.1, 1, 10, 100, 1000], 'max_iter': [300]},
{'kernel': ['linear'], 'C': [0.001, 0.01, 0.1, 1, 10, 100, 1000], 'gamma': ['scale'], 'max_iter': [300]}
]
DecisionTree_hyperparameters = {
'max_depth': [i for i in range(1, 33)],
'min_samples_split': list(np.linspace(0.1, 1, 10)),
'min_samples_leaf': list(np.linspace(0.1, 0.5, 5)),
'max_features': [i for i in range(1, 10)]
}
RandomForest_hyperparameters = {
'bootstrap': [True, False],
'max_depth': [10, 20, 30, 40, 50, 60, 100, None],
'criterion': ['gini', 'entropy'],
'max_features': ['log2', 'sqrt'], # auto is equal to sqrt
'min_samples_leaf': [1, 2, 4],
'min_samples_split': [2, 5, 10],
"n_estimators": [250, 500, 1000]
}
XGBoost_hyperparameters = {
"n_estimators": [500, 1000, 3000],
# 'max_depth': [10, 20, 30, 40, 50, 60, 70, 80, 90, 100, None],
# hyperparameters to avoid overfitting
'eta': list(np.linspace(0.01, 0.2, 10)), # 'learning_rate'
'gamma': [0, 1, 5],
'subsample': [0.8, 0.9, 1],
'colsample_bytree': list(np.linspace(0.3, 1, 8)),
'min_child_weight': [1, 5, 10],
}
MLP_hyperparameters = {
'learning_rate_init': [0.0001, 0.0005, 0.001, 0.005, 0.01, 0.05, 0.1],
'max_iter': [300, 500, 1000],
'solver': ['sgd', 'adam']
}
# These are the parameters that constitute the search space for RandomizedSearchCV
# in our experiments.
SVM_hyperparameters_dist = {
'C': expon(scale=100), 'gamma': expon(scale=.1), 'kernel': ['rbf'], 'class_weight': ['balanced', None]
}
DecisionTree_hyperparameters_dist = {
'max_depth': sp_randint(10, 100),
'min_samples_split': list(np.linspace(0.1, 1, 50)),
'min_samples_leaf': list(np.linspace(0.1, 0.5, 25)),
'max_features': sp_randint(1, 11),
}
RandomForest_hyperparameters_dist = {
'bootstrap': [True, False],
'max_depth': [10, 20, 30, 40, 50, 60, 100, None],
'criterion': ['gini', 'entropy'],
'max_features': ['sqrt', 'log2'], # sp_randint(1, 11)
'min_samples_leaf': sp_randint(1, 5),
'min_samples_split': sp_randint(2, 11),
"n_estimators": sp_randint(250, 1000),
}
XGBoost_hyperparameters_dist = {
"n_estimators": sp_randint(500, 4000),
# 'max_depth': [10, 20, 30, 40, 50, 60, 70, 80, 90, 100, None],
# hyperparameters to avoid overfitting
'eta': expon(loc=0.01, scale=0.1), # 'learning_rate'
'gamma': [0, 1, 5],
'subsample': truncnorm(0.7, 1),
'colsample_bytree': truncnorm(0, 1),
'min_child_weight': [1, 5, 10],
}
MLP_hyperparameters_dist = {
'learning_rate_init': expon(loc=0.0001, scale=0.1),
'max_iter': [300, 500, 1000],
'solver': ['sgd', 'adam']
}
max_iter = 250
import psycopg2 as pg
from scipy.stats import randint as sp_randint
from scipy.stats import uniform as sp_uniform
from sqlalchemy import create_engine
ALERT_AGENT_THRESHOLD = .15
LOCK_ACCOUNT_THRESHOLD = .3
connection = pg.connect(
host='localhost',
port=54320,
dbname='ht_db',
user='******'
)
engine = create_engine('postgresql://*****:*****@127.0.0.1:54320/ht_db')
data_path = '../data'
model_path = 'artifacts'
schema_path = '../misc/schemas.yaml'
# LGBM RandomSearch parameters
param_test = {'num_leaves': sp_randint(6, 50),
'subsample': sp_uniform(loc=0.2, scale=0.8),
'colsample_bytree': sp_uniform(loc=0.4, scale=0.6),
'reg_alpha': [0, 1e-1, 1, 2, 5, 7, 10, 50, 100],
'reg_lambda': [0, 1e-1, 1, 5, 10, 20, 50, 100],
'min_data_in_leaf': sp_randint(100, 3000),
'max_bin': sp_randint(150, 400),
'scale_pos_weight': sp_randint(2, 90)}
def ModelFit():
global best_model
#contruct hyperparameter grid
param_dist = {"max_depth": [3, 10, 20, 70, None],
"max_features": [2, 10, 41, 80, 'sqrt'],
"min_samples_split": sp_randint(2, 11),
"min_samples_leaf": sp_randint(1, 11),
#"bootstrap": [True, False],
"criterion": ["gini", "entropy"],
"n_estimators": [100, 300, 500, 800, 1000]}
pprint(param_dist)
#define random forest classifier function
rf = RandomForestClassifier(random_state = 120)
#search across 1000 randomized combinations in the above grid
estimator = RandomizedSearchCV(estimator = rf, param_distributions = param_dist, n_iter = 1000, cv = 10, verbose = 10, random_state = 12, scoring = 'roc_auc', n_jobs = -1)
#fit the model
grid_result = estimator.fit(X_train, y_train)
#find and define best estimator based on grid search
best_model = grid_result.best_estimator_
print('\nbest_model:\n', best_model)
#predict y based on test data
y_pred = grid_result.predict(X_test)
#accuracy score
print('accuracy score:', accuracy_score(y_test, y_pred))
#confusion matrix
tn, fp, fn, tp = confusion_matrix(y_test, y_pred).ravel()
print(tn,fp,fn,tp)
#classification report
print('\nclassification report:\n',classification_report(y_test, y_pred))
#AUC and ROC curve
y_pred_prob = grid_result.predict_proba(X_test)[:,1]
auc = roc_auc_score(y_test, y_pred_prob)
print('auc:', auc)
false_positive, true_positive, _ = roc_curve(y_test, y_pred_prob)
font = {'fontname':'Helvetica'}
plt.figure()
plt.plot([0, 1], [0, 1], 'k--')
plt.plot(false_positive, true_positive, color='black')
plt.xlabel('False positive rate', **font)
plt.ylabel('True positive rate', **font)
plt.savefig('feces_roc.png', dpi=300)
plt.show()
# Save the model as a pickle in a file
joblib.dump(grid_result, 'campy_rf_feces.pkl')
#determine best features
feature_importances = grid_result.best_estimator_.feature_importances_
column_names=list(feces)
del column_names[-0]
importance = pd.DataFrame(feature_importances, index=column_names, columns=["Importance"])
sort_importance = importance.sort_values(by=['Importance'], ascending = False)
sort_column_names = sort_importance.index.values.tolist()
mult = 100/(sort_importance['Importance'].iloc[0])
sort_imp_mult = sort_importance * mult
top_imp = sort_imp_mult['Importance'].iloc[0:15].tolist()
top_column_names = sort_column_names[0:15]
top_column_names = ['AvgMaxGustSpeed1.6',
'AvgAverageHumidity1.7',
'AverageHumidityTwoDayBefore',
'AvgMaxGustSpeed1.3',
'AvgMaxGustSpeed1.5',
'AvgMinTemperature1.7',
'AvgMaxWindSpeed1.7',
'AvgMinHumidity1.4',
'AvgMaxHumidity1.3',
'AvgPrecipitation1.4',
'MaxGustSpeedOneDayBefore',
'AvgMaxGustSpeedS1.2',
'AvgMaxWindSpeed1.4',
'AvgAverageHumidity1.3',
'MaxGustSpeedTwoDayBefore']
plt.rcParams.update(plt.rcParamsDefault)
y_ticks = np.arange(0, len(top_column_names))
fig, ax = plt.subplots()
ax.barh(y_ticks, top_imp, color = "dimgray")
ax.set_yticklabels(top_column_names, **font)
ax.set_yticks(y_ticks)
plt.xlabel('Relative Importance', **font)
fig.tight_layout()
plt.gca().invert_yaxis()
plt.savefig('feces_var.png', dpi=300)
plt.show()
return
y,
scoring=self.scoring,
cv=self.cv).mean()
print("Model with rank: {0}".format(i))
print("Pred score: {0}".format(pred[idx]))
print("Mean validation score: {0:.3f}".format(score_mean))
print("Parameters: {0}".format(param))
print("")
if __name__ == '__main__':
# get some data
digits = load_digits()
X, y = digits.data, digits.target
clf = RandomForestClassifier(n_estimators=20)
param_dist = {
"max_depth": sp_randint(1, 11),
"max_features": sp_randint(1, 11),
"min_samples_split": sp_randint(2, 11),
"min_samples_leaf": sp_randint(1, 11),
"bootstrap": [True, False],
"criterion": ["gini", "entropy"]
}
rpt = RPTune(clf,
param_distributions=param_dist,
n_iter='auto',
n_jobs=-1,
random_state=42,
scoring='accuracy')
rpt.fit(X, y)
file.close()
CLASSIFIER_MAPPING = {
# clf - classifier
# prep - according prepare data method
# dist - specify parameters and distributions to sample from
# grid - use a full grid over all parameters
'perceptron': {
'clf': linear_model.Perceptron,
'prep': prepare_two_class_data,
'dist': {
'penalty': [None, 'l2', 'l1', 'elasticnet'],
'alpha': [0.0001, 0.001, 0.01, 0.1, 1],
'fit_intercept': [True, False],
'n_iter': sp_randint(1, 20),
'shuffle': [True, False],
'verbose': sp_randint(1, 5),
'eta0': [1.0, 1.5, 2.0],
'random_state': [0, None],
'class_weight': ['balanced', None],
'warm_start': [True, False]
},
'grid': {
'penalty': [None, 'l2', 'l1', 'elasticnet'],
'alpha': [0.0001, 0.0003, 0.0005, 0.0007, 0.0008, 0.0009],
'fit_intercept': [True, False],
'n_iter': [5, 10, 20, 30],
'shuffle': [True, False],
'verbose': [0, 2, 4],
'eta0': [1.0, 1.5, 2.0],
def report(results, n_top=3):
for i in range(1, n_top + 1):
candidates = np.flatnonzero(results['rank_test_score'] == i)
for candidate in candidates:
print("Model with rank: {0}".format(i))
print("Mean validation score: {0:.3f} (std: {1:.3f})".format(
results['mean_test_score'][candidate],
results['std_test_score'][candidate]))
print("Parameters: {0}".format(results['params'][candidate]))
print("")
# specify parameters and distributions to sample from
param_dist = {
"svm__C": [0.001, 0.01, 0.1, 1, 10, 100, 1000],
"xgb__max_depth": sp_randint(3, 25),
"xgb__min_child_weight": sp_randint(1, 7),
"xgb__subsample": [0.6, 0.7, 0.8, 0.9, 1.0],
"xgb__reg_lambda": [0.01, 0.1, 1.0],
"xgb__reg_alpha": [0, 0.1, 0.5, 1.0],
"rf__n_estimators": [10, 50, 100, 150, 200, 300, 500],
"rf__max_depth": [5, 8, 15, 25, 30, None],
"rf__max_features": sp_randint(1, 11),
"rf__min_samples_split": sp_randint(2, 100),
"rf__min_samples_leaf": sp_randint(1, 11),
"rf__bootstrap": [True, False],
"rf__criterion": ["gini", "entropy"]
}
# run randomized search
n_iter_search = 10000
#switch between motions and particle sets for RandomizedSearchCV
test_motions = False
if test_motions:
model = model_m
X_train = X_train_m
y_train = y_train_m
print("RandomizedSearchCV testing the Motions dataset")
else:
model = model_p
X_train = X_train_p
y_train = y_train_p
print("RandomizedSearchCV testing the Particles dataset")
# specify parameters and distributions to sample from
param_dist = {"min_samples_leaf": sp_randint(5, 3000),
"max_leaf_nodes": sp_randint(5, 300),
"max_depth": sp_randint(3, 100),
"criterion": ['gini', 'entropy']
}
#https://scikit-learn.org/stable/auto_examples/model_selection/plot_randomized_search.html#sphx-glr-auto-examples-model-selection-plot-randomized-search-py
n_iter_search = 1000
random_search = RandomizedSearchCV(model, param_distributions = param_dist, n_iter=n_iter_search, cv = 5, scoring='accuracy', verbose=10)
random_search.fit(X_train, y_train)
report(random_search.cv_results_)
#scores = random_search.cv_results_['mean_test_score']
grid_cv = False
if grid_cv:
def finding_parameter():
"""
Finding parameter for machine learning model
:return: parameter for traditional machine learning algorithm
"""
def report(results, n_top=3):
for i in range(1, n_top + 1):
candidates = np.flatnonzero(results['rank_test_score'] == i)
for candidate in candidates:
print("Model with rank: {0}".format(i))
print("Mean validation score: {0:.3f} (std: {1:.3f})".format(
results['mean_test_score'][candidate],
results['std_test_score'][candidate]))
print("Parameters: {0}".format(results['params'][candidate]))
print("")
df = pd.read_csv(args.raw_data)
df_train_input_sc, df_train_target, df_test_input_sc, df_test_target = lib.clear_data(df, args)
if args.algo == 'decisiontree':
clf = tree.DecisionTreeClassifier()
param_dist = {"max_depth": [3, 4, 5, 6, 7, 8, 9, 10],
"max_features": sp_randint(1, 11),
"min_samples_split": sp_randint(2, 11),
"min_samples_leaf": [0.05, 0.1, 1],
"criterion": ["gini", "entropy"],
"splitter": ["best", "random"],
"class_weight": ["balanced", None]
}
if args.algo == 'randomforest':
print("Finding parameter for random forest")
# build a classifier
clf = RandomForestClassifier(n_estimators=1000)
param_dist = {"max_depth": [3, 4, 5, 6, 7, 8, 9, 10],
"max_features": sp_randint(1, 11),
"min_samples_split": sp_randint(2, 11),
"bootstrap": [True, False],
"criterion": ["gini", "entropy"]}
# Utility function to report best scores
if args.algo == "logisticregression":
print("Finding parameter for logisticregression")
clf = LogisticRegression()
param_dist = {
"penalty": ["l1", "l2"],
"tol": [0.00001, 0.0001, 0.001, 0.01, 0.1, 1],
"C": [0.05, 0.1],
"fit_intercept": [True, False],
"intercept_scaling": [0.01, 0.1, 1],
"max_iter": [10, 100, 1000]
}
# specify parameters and distributions to sample from
# run randomized search
n_iter_search = 10000
random_search = RandomizedSearchCV(clf, param_distributions=param_dist,
n_iter=n_iter_search, cv=5, iid=False)
start = time()
random_search.fit(df_train_input_sc, df_train_target)
print("RandomizedSearchCV took %.2f seconds for %d candidates"
" parameter settings." % ((time() - start), n_iter_search))
report(random_search.cv_results_)
xgbm = XGBClassifier(**xparams)
lgbm = LGBMClassifier(**lparams)
cgbm = CatBoostClassifier(**cparams)
rdf = RandomForestClassifier()
classifiers = [rdf, xgbm, lgbm]
classifiers = [xgbm, lgbm, cgbm]
classifiers = [xgbm, lgbm]
lr = LogisticRegression(C=0.1)
grid = StackingClassifier(classifiers=classifiers,
use_probas=True,
average_probas=False,
meta_classifier=lr)
n_estimators = [100, 300]
n_estimators = sp_randint(250, 500)
max_depth = [2, 3]
subsample = [0.5, 0.7]
subsample = sp_rec(0.3, 0.8)
C = [0.01, 0.2]
C = sp_rec(0.01, 0.2)
learning_rate = [0.1, 0.4]
learning_rate = sp_rec(0.1, 0.4)
reg_lambda = [2, 6]
reg_lambda = sp_randint(2, 10)
reg_alpha = [0.1, 0.3]
reg_alpha = sp_rec(0.1, 0.8)
gamma = sp_rec(0.1, 0.8)
feature_fraction = sp_rec(0.3, 0.8)
bagging_fraction = sp_rec(0.3, 0.8)
bagging_freq = sp_randint(3, 8)
def tune_xgb_params_randomized(estimator_cls,
folds: Union[KFold, StratifiedKFold],
label: np.ndarray,
metric_sklearn: str,
n_jobs: int,
params: dict,
train: np.ndarray,
n_iter: int = 20,
verbosity_level: int = 10,
**kwargs):
"""
:param estimator_cls:
The class type of the estimator to instantiate - either an XGBClassifier or an XGBRegressor.
:param folds:
A KFold or StratifiedKFold object to cross validate the parameters.
:param label:
An array-like containing the labels of the classification or regression problem.
:param metric_sklearn:
The evaluation metric to be passed to scikit-learn's GridSearchCV - see
http://scikit-learn.org/stable/modules/model_evaluation.html
for the options this can take - e.g. 'neg_mean_squared_error' for RMSE.
:param n_jobs:
The number of jobs to run simultaneously.
:param params:
A dictionary of XGB parameters.
:param train:
An array-like containing the training input samples.
:param n_iter:
An optional parameter to control the number of parameter settings that are sampled.
:param n_jobs:
An optional parameter to control the amount of parallel jobs - defaults to the amount of CPUs available.
:param verbosity_level:
An optional parameter to control the verbosity of the grid searching - defaults to the most verbose option.
:param kwargs:
Parameter distributions may be controlled through keyword arguments - e.g. to sample uniformly between 0.5 and 0.7 for
colsample_bytree, supply colsample_bytree_loc=0.5 and colsample_bytree_scale=0.2.
:return:
A dictionary of tuned parameters and a list of the parameters found at each step with their respective scores.
"""
params_copy = clean_params_for_sk(params)
param_distributions = {
'colsample_bytree':
uniform(kwargs.get('colsample_bytree_loc', 0.2),
kwargs.get('colsample_bytree_scale', 0.8)),
'gamma':
uniform(kwargs.get('gamma_loc', 0), kwargs.get('gamma_scale', 0.9)),
'max_depth':
sp_randint(kwargs.get('max_depth_low', 2),
kwargs.get('max_depth_high', 11)),
'min_child_weight':
sp_randint(kwargs.get('min_child_weight_low', 1),
kwargs.get('min_child_weight_high', 11)),
'reg_alpha':
halfnorm(kwargs.get('reg_alpha_loc', 0),
kwargs.get('reg_alpha_scale', 5)),
'reg_lambda':
halfnorm(kwargs.get('reg_alpha_loc', 0),
kwargs.get('reg_alpha_scale', 5)),
'subsample':
uniform(kwargs.get('subsample_loc', 0.2),
kwargs.get('subsample_scale', 0.8))
}
rand_search = RandomizedSearchCV(cv=folds.split(train, label),
estimator=estimator_cls(**params_copy),
n_iter=n_iter,
n_jobs=n_jobs,
param_distributions=param_distributions,
scoring=metric_sklearn,
verbose=verbosity_level)
rand_search.fit(train, label)
return rand_search.best_params_, [(rand_search.best_params_,
rand_search.best_score_)]