def kfold_cv(X_train, y_train,idx,k):
kf = StratifiedKFold(y_train,n_folds=k)
xx=[]
count=0
for train_index, test_index in kf:
count+=1
X_train_cv, X_test_cv = X_train[train_index,:],X_train[test_index,:]
gc.collect()
y_train_cv, y_test_cv = y_train[train_index],y_train[test_index]
y_pred=np.zeros(X_test_cv.shape[0])
m=0
for j in range(m):
clf=xgb_classifier(eta=0.05,min_child_weight=20,col=0.5,subsample=0.7,depth=7,num_round=400,seed=j*77,gamma=0.1)
y_pred+=clf.train_predict(X_train_cv,(y_train_cv),X_test_cv,y_test=(y_test_cv))
yqq=y_pred*(1.0/(j+1))
print j,llfun(y_test_cv,yqq)
#y_pred/=m;
clf=XGBClassifier(max_depth=10,colsample_bytree=0.8,learning_rate=0.02,n_estimators=500,nthread=-1)
#clf=RandomForestClassifier(n_jobs=-1,n_estimators=100,max_depth=100)
clf.fit(X_train_cv,(y_train_cv),eval_metric="logloss",eval_set=[(X_test_cv, y_test_cv)])
y_pred=clf.predict_proba(X_test_cv).T[1]
print y_pred.shape
xx.append(llfun(y_test_cv,(y_pred)))
ypred=y_pred
yreal=y_test_cv
idx=idx[test_index]
print xx[-1]#,y_pred.shape
break
print xx,'average:',np.mean(xx),'std',np.std(xx)
return ypred,yreal,idx#np.mean(xx)
def xgboostcv(max_depth,
learning_rate,
n_estimators,
gamma,
min_child_weight,
max_delta_step,
subsample,
colsample_bytree,
silent=True,
nthread=-1,
seed=1234):
clf = XGBClassifier(max_depth=int(max_depth),
learning_rate=learning_rate,
n_estimators=int(n_estimators),
silent=silent,
nthread=nthread,
gamma=gamma,
min_child_weight=min_child_weight,
max_delta_step=max_delta_step,
subsample=subsample,
colsample_bytree=colsample_bytree,
seed=seed,
objective="binary:logistic")
# Run Kfolds on the data model to stop over-fitting
X_train, X_valid, y_train, y_valid = train_test_split(train,
train_labels,
test_size=0.1,
random_state=seed)
xgb_model = clf.fit(X_train, y_train, eval_metric="auc", eval_set=[(X_valid, y_valid)], early_stopping_rounds=20)
y_pred = xgb_model.predict_proba(X_valid)[:,1]
return auc(y_valid, y_pred)
def test_predict_sklearn_pickle(self):
X,y = makeXy()
Xtest = makeXtest()
from xgboost import XGBClassifier
kwargs={}
kwargs['tree_method'] = 'gpu_hist'
kwargs['predictor'] = 'gpu_predictor'
kwargs['silent'] = 0
kwargs['objective'] = 'binary:logistic'
model = XGBClassifier(**kwargs)
model.fit(X,y)
print(model)
# pickle model
save_obj(model,"model.pkl")
# delete model
del model
# load model
model = load_obj("model.pkl")
os.remove("model.pkl")
# continue as before
print("Before model.predict")
sys.stdout.flush()
tmp = time.time()
gpu_pred = model.predict(Xtest, output_margin=True)
print(gpu_pred)
print("E non-zeroes: %d:" % (np.count_nonzero(gpu_pred)))
print("E GPU Time to predict = %g" % (time.time() - tmp))
def xgboost_classifier(self):
cls = XGBClassifier()
print 'xgboost cross validation score', cross_val_score(cls,self.x_data,self.y_data)
start_time = time.time()
cls.fit(self.x_train, self.y_train)
print 'score', cls.score(self.x_test, self.y_test)
print 'time cost', time.time() - start_time
def feature_selection(model, X_train, X_test, y_train, y_test, eval_metric='auc'):
thresholds = [thres for thres in sorted(model.feature_importances_) if thres != 0] # Use feat. with >0 importance
roc_scores = {}
for thresh in thresholds: # select features using threshold
selection = SelectFromModel(model, threshold=thresh, prefit=True)
select_X_train = selection.transform(X_train)
selection_model = XGBClassifier() # train model
selection_model.fit(select_X_train, y_train, eval_metric=eval_metric)
select_X_test = selection.transform(X_test) # eval model
y_pred = selection_model.predict(select_X_test)
roc = roc_auc_score(y_test, y_pred)
roc_scores[selection.threshold] = roc
best_thresh = max(roc_scores, key=roc_scores.get)
fs = SelectFromModel(model, threshold=best_thresh, prefit=True)
pickle_model(fs, 'feature.select')
X_train_trans_ = fs.transform(X_train)
X_test_trans_ = fs.transform(X_test)
print 'total features kept: {}'.format(X_train_trans_.shape[1])
return X_train_trans_, X_test_trans_
def train_model_xgb_meta(train_x, train_y, xgb_features):
train_ind = StratifiedShuffleSplit(train_y, random_state=1, test_size=0.2)
for train_index, test_index in train_ind:
x_train = train_x.ix[train_index, :]
y_train = train_y.ix[train_index]
x_eval = train_x.ix[test_index, :]
y_eval = train_y.ix[test_index]
#Classifier
xgb = XGBClassifier(max_depth=xgb_features['max_depth'], learning_rate=xgb_features['learning_rate'], n_estimators=int(xgb_features['n_estimators']), objective='binary:logistic',
subsample=xgb_features['subsample'], colsample_bytree=xgb_features['colsample_bytree'], min_child_weight=xgb_features['min_child_weight'])
# gives 0.458
# bag_clf = BaggingClassifier(xgb, max_samples=10, warm_start=True, verbose=10)
# x_train = pd.DataFrame(x_train, dtype=float)
# bag_clf.fit(x_train, y_train)
xgb = xgb.fit(x_train, y_train, verbose=True, eval_metric='logloss', eval_set=[(x_eval, y_eval)], early_stopping_rounds=10)
# cv_score = cross_val_score(xgb, x_train, y_train, cv=4, n_jobs=1, pre_dispatch=1, verbose=10, scoring='log_loss')
# print(cv_score)
# print(np.mean(cv_score))
# predictions = pd.Series(xgb.predict_proba(x_train, ntree_limit=xgb.best_iteration)[:, 1], name='PredictedProb')
return xgb # , predictions
def cv(X_train, y_train, features_inner):
kfold = StratifiedKFold(n_splits=5, shuffle=True)
scores_f = []
scores_p = []
scores_r = []
for train, test in kfold.split(X_train, y_train):
model = XGBClassifier()
X_train_cv = pd.DataFrame(X_train.values[train], columns=X_train.columns)
y_train_cv = pd.DataFrame(y_train.values[train], columns=["tred_cutoff"])
X_test_cv = pd.DataFrame(X_train.values[test], columns=X_train.columns)
y_test_cv = pd.DataFrame(y_train.values[test], columns=["tred_cutoff"])
model.fit(X_train_cv, y_train_cv)
y_pred = model.predict(X_test_cv)
s_f = f1_score(y_test_cv, y_pred)
s_p = precision_score(y_test_cv, y_pred)
s_r = recall_score(y_test_cv, y_pred)
print("\tscores f1", (s_f))
print("\tscores p", (s_p))
print("\tscores r", (s_r))
scores_f.append(s_f)
scores_p.append(s_p)
scores_r.append(s_r)
print("mean scores f1", np.mean(scores_f))
print("mean scores p", np.mean(scores_p))
print("mean scores r", np.mean(scores_r))
def xgboostcv(max_depth,
learning_rate,
n_estimators,
subsample,
colsample_bytree,
gamma,
min_child_weight,
silent=True,
nthread=-1,
seed=1234):
clf = XGBClassifier(max_depth=int(max_depth),
learning_rate=learning_rate,
n_estimators=int(n_estimators),
silent=silent,
nthread=nthread,
subsample=subsample,
colsample_bytree=colsample_bytree,
gamma=gamma,
min_child_weight = min_child_weight,
seed=seed,
objective="binary:logistic")
clf.fit(x0, y0, eval_metric="logloss", eval_set=[(x1, y1)],early_stopping_rounds=25)
ll = -log_loss(y1, clf.predict_proba(x1))
return ll
def XGB_model(train,y): model=XGBClassifier(n_estimators=150, learning_rate=0.01) from sklearn import cross_validation cv = cross_validation.KFold(len(train), n_folds=5,random_state=7) for traincv,testcv in cv: model.fit(train.iloc[traincv],y.iloc[traincv]) y_XGB=model.predict(test) return y_XGB
def main():
# Set seed for reproducibility
np.random.seed(0)
print("Loading data...")
# Load the data from the CSV files
training_data = pd.read_csv('/home/vipin/Videos/train.csv', header=0)
prediction_data = pd.read_csv('/home/vipin/Videos/test.csv', header=0)
training_data['countrycode']=training_data['countrycode'].apply(lambda x:ord(x))
training_data['browserid']=training_data['browserid'].apply(lambda x: myfunc (x) if np.all(pd.notnull(x)) else myfunc("unknown") )
training_data['devid']=training_data['devid'].apply(lambda x: myfunc (x) if np.all(pd.notnull(x)) else myfunc("none"))
#pd.to_csv('/home/vipin/Videos/train11.csv', sep=',', encoding='utf-8')
#exit(0)
prediction_data['countrycode']=prediction_data['countrycode'].apply(lambda x:ord(x))
prediction_data['browserid']=prediction_data['browserid'].apply(lambda x:myfunc (x) if np.all(pd.notnull(x)) else myfunc("unknown") )
prediction_data['devid']=prediction_data['devid'].apply(lambda x:myfunc (x) if np.all(pd.notnull(x)) else myfunc("none") )
features=['siteid','offerid','category','merchant','countrycode','browserid','devid']
target="click"
X = training_data[features]
x_prediction = prediction_data[features]
Y= training_data[target]
ids = prediction_data["ID"]
model = XGBClassifier()
#linear_model.LogisticRegression(n_jobs=-1)
print("Training...")
# Your model is trained on the training_data
model.fit(X, Y)
print("Predicting...")
seed =7
test_size=0.33
X_train,X_test,y_train,y_test=train_test_split(X,Y,test_size=test_size,random_state=seed)
y_prediction = model.predict_proba(x_prediction)
results = y_prediction[:, 1]
results_df = pd.DataFrame(data={'probability':results})
joined = pd.DataFrame(ids).join(results_df)
y_pred=model.predict(X_test)
accuracy=accuracy_score(y_test,y_pred)
print("Accuracy: %.2f%%" % (accuracy * 100.0))
print("Writing predictions to predictions.csv")
# Save the predictions out to a CSV file
joined.to_csv("/home/vipin/Videos/predictions.csv", index=False)
def test_xgboost():
"""Ensure that the TPOT xgboost method outputs the same as the xgboost classfier method"""
tpot_obj = TPOT()
result = tpot_obj._xgradient_boosting(training_testing_data, n_estimators=100, learning_rate=0, max_depth=3)
result = result[result['group'] == 'testing']
xgb = XGBClassifier(n_estimators=100, learning_rate=0.0001, max_depth=3, seed=42)
xgb.fit(training_features, training_classes)
assert np.array_equal(result['guess'].values, xgb.predict(testing_features))
def update_model(current_year):
print 'Creating model...\nDate: {}'.format(datetime.now().strftime('%Y-%m-%d_%H:%M:%S'))
managers = tuple(unique_managers(current_year))
sql = "select * from (select week, year, manager1_name, manager2_name, team1_points, team1_projected, team2_points, team2_projected, type \
from scoreboard_all WHERE team1_points > 0 and week<=13 \
UNION select week, year, manager2_name AS manager1_name, manager1_name as manager2_name, team2_points AS team1_points, \
team2_projected AS team1_projected, team1_points as team2_points, team1_projected AS team2_projected, type FROM scoreboard_all \
where team1_points>0 and week<=13) order by year, week, type;"
ff1 = download_data(os.path.join(os.getcwd(), 'data/fantasy_football.db'), sql)
data_features = custom_features(ff1)
data_features = data_features[(data_features.manager1_name.isin(managers)) & (data_features.manager2_name.isin(managers))]
X, y, managers, league_type = dummy_and_interaction(data_features)
# feats = X.columns.tolist()
sc = StandardScaler()
X_std = sc.fit_transform(X)
pickle_model(sc, 'standard.scaler')
# Select best features
X_train, X_test, y_train, y_test = train_test_split(X_std, y, test_size=0.25, random_state=None)
model = XGBClassifier()
model.fit(X_train, y_train)
# imports = model.feature_importances_.tolist()
# g = zip(feats, imports)
# feat_importance = sorted(g, key=lambda x: x[1], reverse=True)
# print feat_importance
X_train_trans, X_test_trans = feature_selection(model, X_train, X_test, y_train, y_test, eval_metric='auc')
# Select best params
model = XGBClassifier()
learning_rate = [0.001, 0.01, 0.1, 0.2, 0.3]
n_estimators = [50, 100, 150, 200, 250, 300]
param_grid = dict(n_estimators=n_estimators, learning_rate=learning_rate)
grid_search = GridSearchCV(model, param_grid, scoring="log_loss", cv=10, verbose=1)
result = grid_search.fit(X_train_trans, y_train)
print("Best: {0} using {1}".format(result.best_score_, result.best_params_))
print 'Best params: ', result.best_params_
best_est = result.best_estimator_
validation = best_est.predict_proba(X_train_trans)
print("Roc AUC Train: ", roc_auc_score(y_train, validation[:, 1], average='macro'))
probs = best_est.predict_proba(X_test_trans)
print("Roc AUC Validation: ", roc_auc_score(y_test, probs[:, 1], average='macro'))
pickle_model(best_est, 'fantasy.predict')
def train(imgfile='img/segmentation', modelfile='segmentation.pkl'):
filelabel = getFiles(imgfile)
row = 120
col=40
data = filter(lambda z: z is not None ,map(lambda x:Img(x[1],row,col,x[0]).imgmap,filelabel))
data = filter(lambda x:x[0] is not None,sum(data,[]))
label = np.array(map(lambda x:CHARACTER.get(x[0]),data))
feature = np.array(map(lambda x:np.array(x[1]),data))
from xgboost import XGBClassifier
xgb = XGBClassifier(objective='multi:softmax',reg_alpha=1.0,reg_lambda=0.0,subsample=0.7,n_estimators=100,learning_rate=0.3)
model = xgb.fit(feature,label,eval_set=[(feature,label)],eval_metric='mlogloss')
import pickle
fn = modelfile
with open(fn, 'w') as f: # open file with write-mode
pickle.dump(model, f)
def runner ():
m = Model()
X = m.df.drop("tred_cutoff", axis=1)
Y = m.df["tred_cutoff"]
features_inner = m.features + m.features_2
cv(X, Y, features_inner)
model = XGBClassifier()
model.fit(X, Y)
y_pred = model.predict(m.X_test)
s_f = f1_score(m.y_test, y_pred)
s_p = precision_score(m.y_test, y_pred)
s_r = recall_score(m.y_test, y_pred)
print("test f1", s_f)
print("test precision", s_p)
print("test recall", s_r)
def main():
titanic = pandas.read_csv('dataset/titanic.csv')
x_set = titanic[['pclass', 'age', 'sex']]
y_set = titanic['survived']
x_set.fillna(x_set['age'].mean(), inplace=True)
x_train, x_test, y_train, y_test = utils.prepare_train_and_test_sets(x_set, y_set)
dict_vectorizer = DictVectorizer(sparse=False)
x_train = dict_vectorizer.fit_transform(x_train.to_dict(orient='record'))
x_test = dict_vectorizer.transform(x_test.to_dict(orient='record'))
decision_tree_classifier = DecisionTreeClassifier()
utils.get_trained_result(decision_tree_classifier, x_test, x_train, y_test, y_train)
xgb_classifier = XGBClassifier()
xgb_classifier.fit(x_train, y_train)
utils.get_trained_result(xgb_classifier, x_test, x_train, y_test, y_train)
def __make_sklearn_model(self):
estimators = self.__parameters['estimators']
lrate = self.__parameters['learning_rate']
depth = self.__parameters['max_depth']
leaf_bodes = self.__parameters['max_leaf_nodes']
self.__model = SGBClassifier(n_estimators=estimators,
learning_rate=lrate,
max_depth=depth,
max_leaf_nodes=leaf_bodes,
random_state=0)
def trainXGB(data_subset):
f.write('\nTraining XGB:'+'\n')
X_train = data[data_subset]['X_train']
X_test = data[data_subset]['X_test']
y_train = data[data_subset]['y_train']
y_test = data[data_subset]['y_test']
for p in params['xgboost']:
if data_subset != 'binary' and p['objective'] == 'binary:logistic':
print("Skip using non-binary data with XGB binary:logistic objective")
continue
if data_subset == 'binary' and p['objective'] != 'binary:logistic':
print("Skip using binary data with XGB multi:* objective")
continue
header = "@ subset: {0}, params: {1}".format(data_subset, p)
f.write('\n'+header+'\n')
objective = p['objective']
max_depth = p['max_depth']
try:
n_estimators= p['n_estimators']
except KeyError as e:
n_estimators= 100
model = XGBClassifier(objective=objective, max_depth=max_depth,
n_estimators=n_estimators)
start = time.time()
model.fit(X_train, y_train)
elapsed_train = time.time() - start
y_pred = model.predict(X_test).astype(int)
elapsed_predict = time.time() - start
accuracy = accuracy_score(y_test, y_pred)
precision, recall, fscore, support = precision_recall_fscore_support(y_test, y_pred, pos_label=2, average='weighted')
print("\n{5}\nXGB with {0} objective, {6} max_depth, {7} n_estimators on data subset {1} trained in {2} seconds and predicted in {3} seconds with an accuracy of {4}\n".format(objective, data_subset, elapsed_train, elapsed_predict, accuracy, header, max_depth, n_estimators))
f.write(str(elapsed_train) + ', ' + str(elapsed_predict) + str(accuracy)+ ', ' + str(precision)+ ', ' + str(recall )+ ', ' + str(fscore )+ ', ' + str(support))
def train_model_xgb(train_x, train_y, xgb_features):
train_ind = StratifiedShuffleSplit(train_y, random_state=1, test_size=0.1)
for train_index, test_index in train_ind:
x_train = train_x.ix[train_index, :]
y_train = train_y.ix[train_index]
x_eval = train_x.ix[test_index, :]
y_eval = train_y.ix[test_index]
#Classifier
xgb = XGBClassifier(max_depth=xgb_features['max_depth'], learning_rate=xgb_features['learning_rate'], n_estimators=int(xgb_features['n_estimators']), objective='binary:logistic',
subsample=xgb_features['subsample'], colsample_bytree=xgb_features['colsample_bytree'], min_child_weight=xgb_features['min_child_weight'])
# gives 0.458
xgb = xgb.fit(x_train, y_train, verbose=True, eval_metric='logloss', eval_set=[(x_eval, y_eval)], early_stopping_rounds=10)
predictions = pd.Series(xgb.predict_proba(x_train, ntree_limit=xgb.best_iteration)[:, 1], name='PredictedProb')
return xgb, predictions
def test_predict_sklearn_pickle(self):
x, y = build_dataset()
kwargs = {'tree_method': 'gpu_hist',
'predictor': 'gpu_predictor',
'verbosity': 2,
'objective': 'binary:logistic',
'n_estimators': 10}
model = XGBClassifier(**kwargs)
model.fit(x, y)
save_pickle(model, "model.pkl")
del model
# load model
model: xgb.XGBClassifier = load_pickle("model.pkl")
os.remove("model.pkl")
gpu_pred = model.predict(x, output_margin=True)
# Switch to CPU predictor
bst = model.get_booster()
bst.set_param({'predictor': 'cpu_predictor'})
cpu_pred = model.predict(x, output_margin=True)
np.testing.assert_allclose(cpu_pred, gpu_pred, rtol=1e-5)
def get_xgb_feature_importance_plot(best_param_, experiment_,
png_folder,
png_fname,
score_threshold=0.8):
# 1.
train_X, train_y = experiment_.get_train_data()
clf = XGBClassifier()
try:
del best_param_['model_type']
except:
pass
clf.set_params(**best_param_)
clf.fit(train_X, train_y)
index2feature = clf.booster().get_fscore()
fis = pd.DataFrame({'name':index2feature.keys(),
'score':index2feature.values()})
fis = fis.sort('score', ascending=False)
if len(fis.index) > 20:
score_threshold = fis['score'][fis['score'] > 0.0].quantile(score_threshold)
#where_str = 'score > %f & score > %f' % (score_threshold, 0.0)
where_str = 'score >= %f' % (score_threshold)
fis = fis.query(where_str)
# 2. plot
#gs = GridSpec(2,2)
#ax1 = plt.subplot(gs[:,0])
#ax2 = plt.subplot(gs[0,1])
#ax3 = plt.subplot(gs[1,1])
# 3.1 feature importance
sns.barplot(x = 'score', y = 'name',
data = fis,
#ax=ax1,
color="blue")
#plt.title("Feature_Importance", fontsize=10)
plt.ylabel("Feature", fontsize=10)
plt.xlabel("Feature_Importance : f-Score", fontsize=10)
"""
# 3.2 PDF
confidence_score = clf.oob_decision_function_[:,1]
sns.distplot(confidence_score, kde=False, rug=False, ax=ax2)
ax2.set_title("PDF")
# 3.3 CDF
num_bins = min(best_param_.get('n_estimators',1), 100)
counts, bin_edges = np.histogram(confidence_score, bins=num_bins, normed=True)
cdf = np.cumsum(counts)
ax3.plot(bin_edges[1:], cdf / cdf.max())
ax3.set_title("CDF")
ax3.set_xlabel("Oob_Decision_Function:Confidence_Score", fontsize=10)
"""
png_fname = os.path.join(Config.get_string('data.path'), 'graph', png_fname)
plt.tight_layout()
plt.savefig(png_fname)#, bbox_inches='tight', pad_inches=1)
plt.close()
return True
def __make_xgboost_model(self):
estimators = self.__parameters['estimators']
lrate = self.__parameters['learning_rate']
depth = self.__parameters['max_depth']
leaf_bodes = self.__parameters['max_leaf_nodes']
self.__model = XGBClassifier(nthread=4,
learning_rate=lrate,
n_estimators=estimators,
max_depth=depth,
gamma=0,
subsample=0.9,
max_leaf_nodes=leaf_bodes,
colsample_bytree=0.5)
def get_thresh(model,train,test,label_test,label_train):
if (len(test)>len(train)) or (len(label_test)>len(label_train)):
raise TypeError('Invalid train and test size')
model1 = XGBClassifier()
if type(model)!=type(XGBClassifier()):
raise TypeError('Invalid model passed')
if (pd.DataFrame(label_train).shape[1]>1) or (pd.DataFrame(label_test).shape[1]>1):
raise TypeError('Multiple columns in label, Invalid shape.')
max_score=0
thrsh=0
thresholds = np.sort(model.feature_importances_)
for thresh in thresholds:
selection = feature_selection.SelectFromModel(model, threshold=thresh,prefit=True)
select_X_train = selection.transform(train)
selection_model = XGBClassifier()
selection_model.fit(select_X_train, label_train)
select_X_test = selection.transform(test)
y_pred = selection_model.predict(select_X_test)
scr=metrics.roc_auc_score(label_test,y_pred)
if(scr>max_score):
max_score=scr
thrsh=thresh
return thrsh
def test_on_data(X, y):
x_train, x_test, y_train, y_test = train_test_split(X, y, train_size=0.5, random_state=2333)
print "train set: {}, test set: {}".format(len(x_train), len(x_test))
cls = XGBClassifier()
cls.fit(x_train, y_train)
# on test
pred = cls.predict(x_test)
print "xgb accuracy score test", accuracy_score(y_test, pred)
# on all
pred = cls.predict(X)
print "xgb accuracy score all", accuracy_score(y, pred)
# compare to gbrt in sklearn
cls = GradientBoostingClassifier()
cls.fit(x_train, y_train)
# on test
pred = cls.predict(x_test)
print "sklearn accuracy score test", accuracy_score(y_test, pred)
# on all
pred = cls.predict(X)
print "sklearn accuracy score all", accuracy_score(y, pred)
def __init__(self):
self._seed = randint(1, 9)
self._csvfile = ""
self._titles = None
self._dataset = None
self._X = None
self._y = None
self._X_original = None
self._y_original = None
self._dataset_original = None
self._model = Sequential()
self._sc = StandardScaler()
self._vnum = 0 # Number of variables
self._classifier = XGBClassifier()
self._epochs = 10
self._samplesize = 0
self._clusters = None
import numpy as np
import pandas as pd
import operator
from sklearn.linear_model import LogisticRegressionCV, LogisticRegression
from sklearn.model_selection import cross_val_predict, cross_val_score, KFold
from sklearn.pipeline import make_pipeline
from sklearn.preprocessing import Imputer, StandardScaler, MinMaxScaler, PolynomialFeatures, OneHotEncoder
from sklearn.metrics import log_loss, roc_auc_score, f1_score
from xgboost import XGBClassifier
from scipy.sparse import csr_matrix
from sklearn.decomposition import TruncatedSVD
from data_utils import *
models = {
"linear": make_pipeline(StandardScaler(), LogisticRegression()),
"xgb": XGBClassifier(n_estimators=16, learning_rate=0.5, max_depth=5)
}
def train_none_models():
X = generate_none_features("train")
y = generate_none_targets().loc[X.index] # make sure ordering is correct
for name, model in models.items():
with open("../models/none_model_{}.pkl".format(name), "wb") as f:
pkl.dump(model.fit(X, y), f)
def predict_none_models():
X = generate_none_features("test")
preds = {}
for name, model in models.items():
def __init__(self):
self.model = XGBClassifier()
self.progress = 0
def get_model(model_or_name, threads=-1, classification=False):
regression_models = {
'xgboost': (XGBRegressor(max_depth=6,
nthread=threads), 'XGBRegressor'),
'randomforest':
(RandomForestRegressor(n_estimators=100,
n_jobs=threads), 'RandomForestRegressor'),
'adaboost': (AdaBoostRegressor(), 'AdaBoostRegressor'),
'linear': (LinearRegression(), 'LinearRegression'),
'elasticnet': (ElasticNetCV(positive=True), 'ElasticNetCV'),
'lasso': (LassoCV(positive=True), 'LassoCV'),
'ridge': (Ridge(), 'Ridge'),
'xgb.1k': (XGBRegressor(max_depth=6,
n_estimators=1000,
nthread=threads), 'XGBRegressor.1K'),
'xgb.10k': (XGBRegressor(max_depth=6,
n_estimators=10000,
nthread=threads), 'XGBRegressor.10K'),
'rf.1k':
(RandomForestRegressor(n_estimators=1000,
n_jobs=threads), 'RandomForestRegressor.1K'),
'rf.10k': (RandomForestRegressor(n_estimators=10000, n_jobs=threads),
'RandomForestRegressor.10K')
}
classification_models = {
'xgboost': (XGBClassifier(nthread=threads), 'XGBClassifier'),
'randomforest':
(RandomForestClassifier(n_estimators=100,
n_jobs=threads), 'RandomForestClassifier'),
'adaboost': (AdaBoostClassifier(), 'AdaBoostClassifier'),
'logistic': (LogisticRegression(), 'LogisticRegression'),
'gaussian': (GaussianProcessClassifier(), 'GaussianProcessClassifier'),
'knn': (KNeighborsClassifier(), 'KNeighborsClassifier'),
'bayes': (GaussianNB(), 'GaussianNB'),
'svm': (SVC(), 'SVC'),
'xgb.1k': (XGBClassifier(n_estimators=1000,
nthread=threads), 'XGBClassifier.1K'),
'rf.1k':
(RandomForestClassifier(n_estimators=1000,
n_jobs=threads), 'RandomForestClassifier.1K'),
'xgb.10k': (XGBClassifier(n_estimators=10000,
nthread=threads), 'XGBClassifier.10K'),
'rf.10k': (RandomForestClassifier(n_estimators=10000, n_jobs=threads),
'RandomForestClassifier.10K')
}
neural_network_model = {
} # TODO: integrate neural network models into this framework
if isinstance(model_or_name, str):
if classification:
model_and_name = classification_models.get(model_or_name.lower())
else:
model_and_name = regression_models.get(model_or_name.lower())
if not model_and_name:
raise Exception("unrecognized model: '{}'".format(model_or_name))
else:
model, name = model_and_name
else:
model = model_or_name
name = re.search("\w+", str(model)).group(0)
return model, name
tpot_data = pd.read_csv('PATH/TO/DATA/FILE',
sep='COLUMN_SEPARATOR',
dtype=np.float64)
features = tpot_data.drop('target', axis=1)
training_features, testing_features, training_target, testing_target = \
train_test_split(features, tpot_data['target'], random_state=None)
# Average CV score on the training set was: 0.6774117647058825
exported_pipeline = make_pipeline(
StackingEstimator(estimator=ExtraTreesClassifier(bootstrap=False,
criterion="gini",
max_features=0.5,
min_samples_leaf=7,
min_samples_split=18,
n_estimators=100)),
StackingEstimator(estimator=BernoulliNB(alpha=1.0, True)),
StackingEstimator(estimator=XGBClassifier(learning_rate=0.01,
max_depth=9,
min_child_weight=20,
n_estimators=100,
nthread=1,
subsample=0.6000000000000001)),
ExtraTreesClassifier(bootstrap=True,
criterion="gini",
max_features=0.7500000000000001,
min_samples_leaf=5,
min_samples_split=10,
n_estimators=100))
exported_pipeline.fit(training_features, training_target)
results = exported_pipeline.predict(testing_features)
print(ada_score)
print(ada_cm)
print(ada_cr)
# --------------
from xgboost import XGBClassifier
from sklearn.model_selection import GridSearchCV
#Parameter list
parameters = {
'learning_rate': [0.1, 0.15, 0.2, 0.25, 0.3],
'max_depth': range(1, 3)
}
# Code starts here
xgb_model = XGBClassifier(random_state=0)
xgb_model.fit(X_train, y_train)
y_pred = xgb_model.predict(X_test)
xgb_score = accuracy_score(y_test, y_pred)
xgb_cm = confusion_matrix(y_test, y_pred)
xgb_cr = classification_report(y_test, y_pred)
print(xgb_score)
print(xgb_cm)
print(xgb_cr)
clf_model = GridSearchCV(estimator=xgb_model, param_grid=parameters)
clf_model.fit(X_train, y_train)
y_pred = clf_model.predict(X_test)
clf_score = accuracy_score(y_test, y_pred)
clf_cm = confusion_matrix(y_test, y_pred)
clf_cr = classification_report(y_test, y_pred)
print(clf_score)
d_train_X_2 = pd.concat((d_train_X_0[numeric_features], d_train_X_1), axis=1)
var_drop_1 = [
'm1_loan_sum', 'm3_loan_sum', 'm6_loan_sum', 'm12_loan_sum', 'm18_loan_sum'
]
var_drop_tz = [i for i in numeric_features if 'var_out' in i]
var_drop = var_drop_1 + var_drop_tz
d_train_X_3 = d_train_X_2.drop(var_drop, axis=1)
#XGBoost_sklearn接口
from xgboost import XGBClassifier
# 先learing_rate和n_estimators,再min_child_weight、colsample_bytree、subsample
xgc = XGBClassifier(max_depth=2, objective='binary:logistic')
model_params = {
'learning_rate': [0.05, 0.02],
'n_estimators': [300],
'colsample_bytree': [0.7],
'min_child_weight': [5],
'subsample': [0.7]
}
gs = GridSearchCV(estimator=xgc,
param_grid=model_params,
n_jobs=4,
cv=5,
verbose=1,
scoring=ks.ks_scorer)
y = dataset['legitimate'].values
# Splitting the dataset into the Training set and Test set
X_train, X_test, y_train, y_test = train_test_split(X,
y,
test_size=0.20,
random_state=0)
# Feature Scaling
sc = StandardScaler()
X_train = sc.fit_transform(X_train)
X_test = sc.transform(X_test)
# Fitting xgboost to the training Set
classifier = XGBClassifier(max_depth=20,
learning_rate=0.3,
n_estimators=150,
verbose=10)
classifier.fit(X_train, y_train)
# predict the test results
y_pred = classifier.predict(X_test)
# Makeing the confusion matrix
cm = confusion_matrix(y_test, y_pred)
print(cm)
# Applying K-Fold cross validation
accuracies = cross_val_score(estimator=classifier, X=X_train, y=y_train, cv=10)
print(accuracies.mean())
print(accuracies.std())
print('=============================================')
print('=============================================')
print(gsearch1.best_params_, gsearch1.best_score_)
print('=============================================')
print('=============================================')
print('=============================================')
param_test1 = {
'max_depth': [3, 4, 5, 6, 7],
'min_child_weight': [3, 5, 7],
'gamma': [i / 10.0 for i in range(0, 5, 2)],
'subsample': [i / 10.0 for i in range(5, 10, 2)],
'colsample_bytree': [i / 10.0 for i in range(5, 10, 2)],
'objective': ['binary:logistic']
}
model = XGBClassifier()
gsearch1 = GridSearchCV(estimator=XGBClassifier(),
param_grid=param_test1,
scoring='accuracy',
n_jobs=-1,
cv=5,
verbose=1)
gsearch1.fit(train, target)
print('=============================================')
print('=============================================')
print('=============================================')
print(gsearch1.best_params_, gsearch1.best_score_)
print('=============================================')
print('=============================================')
def cv_BDT(input, output, params, show, channel, selection, names):
# model = XGBClassifier()
cvscores = []
AUC = []
cvscores_train = []
AUC_train = []
kfold = StratifiedKFold(5, True, 3456)
for train, test in kfold.split(input, output):
model = XGBClassifier(**params)
X_train, X_test, y_train, y_test = (
input[train],
input[test],
output[train],
output[test],
)
model.fit(X_train, y_train)
y_prob = model.predict_proba(X_test)
y_pred = model.predict(X_test)
prediction = [round(value) for value in y_pred]
auc = roc_auc_score(y_test, y_prob[:, 1])
accuracy = accuracy_score(y_test, prediction)
print("Accuracy: %.2f%%; AUC = %.4f%%" % (accuracy * 100, auc))
cvscores.append(accuracy * 100)
AUC.append(auc)
y_prob = model.predict_proba(X_train)
y_pred = model.predict(X_train)
prediction = [round(value) for value in y_pred]
auc = roc_auc_score(y_train, y_prob[:, 1])
accuracy = accuracy_score(y_train, prediction)
print("Accuracy train: %.2f%%; AUC = %.4f%%" % (accuracy * 100, auc))
cvscores_train.append(accuracy * 100)
AUC_train.append(auc)
print("Accuracy test = %.2f%% (+/- %.2f%%); AUC = %.4f (+/- %.4f)" %
(np.mean(cvscores), np.std(cvscores), np.mean(AUC), np.std(AUC)))
print("Accuracy train = %.2f%% (+/- %.2f%%); AUC = %.4f (+/- %.4f)" % (
np.mean(cvscores_train),
np.std(cvscores_train),
np.mean(AUC_train),
np.std(AUC_train),
))
if show:
name = "channel_" + str(channel) + "_BDT"
name = "%s_%s" % (name, selection)
modelname = "models/%s.h5" % name
print("Save to %s" % modelname)
plotter.plot_separation(model, X_test, y_test, name, False)
plotter.plot_ROC(model, X_test, y_test, name, False)
model.get_booster().feature_names = names
mp.rc("figure", figsize=(5, 5))
plot_importance(model.get_booster(),
max_num_features=15,
importance_type="gain")
plt.subplots_adjust(left=0.3)
plt.show()
# Divide the data set into a training and testing sets, each time with a different RNG seed
training_indices, testing_indices = next(iter(StratifiedShuffleSplit(input_data['class'].values,
n_iter=1,
train_size=0.75,
test_size=0.25,
random_state=dataset_repeat)))
training_features = input_data.loc[training_indices].drop('class', axis=1).values
training_classes = input_data.loc[training_indices, 'class'].values
testing_features = input_data.loc[testing_indices].drop('class', axis=1).values
testing_classes = input_data.loc[testing_indices, 'class'].values
# Create and fit the model on the training data
try:
clf = XGBClassifier(learning_rate=learning_rate, n_estimators=n_estimators, max_depth=max_depth)
clf.fit(training_features, training_classes)
testing_score = clf.score(testing_features, testing_classes)
except:
continue
param_string = ''
param_string += 'learning_rate={},'.format(learning_rate)
param_string += 'n_estimators={},'.format(n_estimators)
param_string += 'max_depth={}'.format(max_depth)
out_text = '\t'.join([dataset.split('/')[-1][:-7],
'XGBClassifier',
param_string,
str(testing_score)])
#XXX[1,i]=minmax[1]
minmax=band.ComputeStatistics(1)
XXX[0,i]=minmax[2]
XXX[1,i]=minmax[3]
return XXX
Xtrain,Ytrain=gen_training(4000)
XXX=gen_scale(sel)
joblib.dump(XXX, path+'Mosquito-Modeling/Climate/data/XXX.pkl')
for i in range(Xtrain.shape[1]):
# Xtrain[:,i]=(Xtrain[:,i]-XXX[0,i])/(XXX[1,i]-XXX[0,i])
Xtrain[:,i]=(Xtrain[:,i]-XXX[0,i])/XXX[1,i]
# define the cross validation
from sklearn.model_selection import KFold
from sklearn.model_selection import cross_val_score
forest=XGBClassifier(learning_rate=0.01,max_depth=9,n_estimators=700)
kfold=KFold(n_splits=10)
scores = cross_val_score(forest, Xtrain, Ytrain, cv=kfold)
print(scores)
print('Accuracy: %.2f%% (%.2f%%)' % (scores.mean()*100,scores.std()*100))
clf = svm.SVC(kernel='rbf', C=1000)
scores = cross_val_score(clf, Xtrain, Ytrain, cv=kfold)
print(scores)
print('Accuracy: %.2f%% (%.2f%%)' % (scores.mean()*100,scores.std()*100))
clf = svm.SVC(kernel='rbf', C=1000, probability=True)
clf.fit(Xtrain, Ytrain)
joblib.dump(clf,path+'Mosquito-Modeling/Climate/data/clf.pkl')
def hyperopt_xgb_score(params):
clf = XGBClassifier(**params)
current_score = cross_val_score(clf, X, y, cv=3).mean()
print(current_score, params)
return -current_score
print("Shape of data after applying PCA: ", X.shape)
# In[11]:
from sklearn.model_selection import KFold
from sklearn.metrics import accuracy_score
kf = KFold(n_splits=3)
kf.get_n_splits(X)
print(kf)
finalaccuracy=[]
for train_index, test_index in kf.split(X):
X_train, X_test = X[train_index], X[test_index]
y_train, y_test = y[train_index], y[test_index]
xgmodel = XGBClassifier()
xgmodel.fit(X_train, y_train)
y_pred = xgmodel.predict(X_test)
predictions = [round(value) for value in y_pred]
accuracy = accuracy_score(y_test, predictions)
print(accuracy*100.0)
finalaccuracy.append(accuracy*100.0)
print("Accuracy: ", sum(finalaccuracy)/float(len(finalaccuracy)))
# In[12]:
from sklearn.ensemble import AdaBoostClassifier
finalaccuracy=[]
for train_index, test_index in kf.split(X):
X[:, 1] = labelencoder_X_1.fit_transform(X[:, 1])
labelencoder_X_2 = LabelEncoder()
X[:, 2] = labelencoder_X_2.fit_transform(X[:, 2])
onehotencoder = OneHotEncoder(categorical_features=[1])
X = onehotencoder.fit_transform(X).toarray()
X = X[:, 1:]
# Splitting the dataset into the Training set and Test set
from sklearn.model_selection import train_test_split
X_train, X_test, y_train, y_test = train_test_split(X,
y,
test_size=0.2,
random_state=0)
# Fitting XGBoost to the Training set
from xgboost import XGBClassifier
classifier = XGBClassifier()
classifier.fit(X_train, y_train)
# Predicting the Test set results
y_pred = classifier.predict(X_test)
# Making the Confusion Matrix
from sklearn.metrics import confusion_matrix
cm = confusion_matrix(y_test, y_pred)
# Applying k-Fold Cross Validation
from sklearn.model_selection import cross_val_score
accuracies = cross_val_score(estimator=classifier, X=X_train, y=y_train, cv=10)
accuracies.mean()
accuracies.std()
digits = datasets.load_digits()
x = digits.data
y = digits.target
x_train, x_test, y_train, y_test = train_test_split(x, y, test_size=.2)
# A parameter grid for XGBoost
params = {
"min_child_weight": [1, 5, 10],
"gamma": [0.5, 1, 1.5, 2, 5],
"subsample": [0.6, 0.8, 1.0],
"colsample_bytree": [0.6, 0.8, 1.0],
"max_depth": [3, 4, 5],
}
xgb = XGBClassifier(
learning_rate=0.02,
n_estimators=50,
objective="binary:logistic",
silent=True,
nthread=1,
)
digit_search = TuneSearchCV(xgb,
param_distributions=params,
n_iter=3,
use_gpu=True)
digit_search.fit(x_train, y_train)
print(digit_search.best_params_)
print(digit_search.cv_results_)
def objective(space):
### MODEL SELECTION
if model_name == "lr":
# logistic regression
from sklearn.linear_model import LogisticRegression
model = LogisticRegression(**space)
elif model_name == "rf":
# print("Setting model as RandomForestClassifier")
from sklearn.ensemble import RandomForestClassifier
model = RandomForestClassifier(**space, n_jobs=-1)
if verbose:
print("Hyperparameters: ", space)
elif model_name == "xgb":
# print("Setting model as XGBClassifier")
from xgboost import XGBClassifier
model = XGBClassifier(**space,
objective="binary:logistic",
nthread=-1)
if verbose:
print("Hyperparameters: ", space)
elif model_name == "dt":
# print("Setting model as DecisionTreeClassifier")
from sklearn.tree import DecisionTreeClassifier
model = DecisionTreeClassifier(**space)
if verbose:
print("Hyperparameters: ", space)
elif model_name == "catboost":
# print("Setting model as CatBoost")
from catboost import CatBoostClassifier
model = CatBoostClassifier(**space)
if verbose:
print("Hyperparameters: ", space)
elif model_name == "extratrees":
# print("Setting model as CatBoost")
from sklearn.ensemble import ExtraTreesClassifier
model = ExtraTreesClassifier(**space, n_jobs=-1)
if verbose:
print("Hyperparameters: ", space)
elif model_name == "svc":
from sklearn.svm import SVC
model = SVC(**space)
if verbose:
print("Hyperparameters: ", space)
elif model_name == "ann":
# print("Setting model as ANN")
from sklearn import neural_network
model = neural_network.MLPClassifier(**space)
if verbose:
print("Hyperparameters: ", space)
elif model_name == "lgb":
import lightgbm as lgb
model = lgb.LGBMClassifier(**space, n_jobs=-1, random_state=42)
if verbose:
print("Hyperparameters: ", space)
elif model_name == "knn":
from sklearn.neighbors import KNeighborsClassifier
model = KNeighborsClassifier(**space)
if verbose:
print("Hyperparameters: ", space)
else:
# print("ERRO: Especifique um nome valido para model_name: rf, xgb, dt ou catboost")
raise Exception(
"Invalid model_name - Please specify one of the supported model_name: rf, xgb, ann, dt, svc, lgr, knn or catboost"
)
score = cross_val_score(model,
x_train,
y_train,
cv=3,
scoring=scoring,
verbose=False,
n_jobs=-1).mean()
score = 1 - score ## ajusta para a funcao de minimizacao.
return score
def opt_BDT(input, output, params, show, names):
model = XGBClassifier(**params)
xgb_param = model.get_xgb_params()
cvscores = []
AUC = []
X_train, X_test, y_train, y_test = train_test_split(input,
output,
test_size=0.2,
random_state=42)
matrix_train = xgb.DMatrix(X_train, label=y_train)
cvresult = xgb.cv(
xgb_param,
matrix_train,
num_boost_round=model.get_params()["n_estimators"],
nfold=5,
metrics="auc",
early_stopping_rounds=30,
verbose_eval=True,
)
model.set_params(n_estimators=cvresult.shape[0])
model.fit(X_train, y_train, eval_metric="auc")
y_prob = model.predict_proba(X_test)
y_pred = model.predict(X_test)
prediction = [round(value) for value in y_pred]
auc = roc_auc_score(y_test, y_prob[:, 1])
accuracy = accuracy_score(y_test, prediction)
print("Accuracy: %.2f%%; AUC = %.4f%" % (accuracy * 100, auc))
if show:
name = "channel_" + str(channel) + "_BDT"
name = "%s_%s" % (name, selection)
modelname = "models/%s.h5" % name
print("Save to %s" % modelname)
plotter.plot_separation(model, X_test, y_test, name, False)
plotter.plot_ROC(model, X_test, y_test, name, False)
model.get_booster().feature_names = names
mp.rc("figure", figsize=(5, 5))
plot_importance(model.get_booster())
plt.subplots_adjust(left=0.3)
plt.show()
from xgboost import XGBClassifier
X_train_no_last_crop = X_train_no_last_crop.reset_index()
X_train_no_last_crop = X_train_no_last_crop.iloc[:, 1:]
# Search for best xgb params.
# A parameter grid for XGBoost
#params = {
# 'min_child_weight': [1, 5, 10],
# 'gamma': [0.5, 1, 1.5, 2, 5],
# 'subsample': [0.6, 0.8, 1.0],
# 'colsample_bytree': [0.6, 0.8, 1.0],
# 'max_depth': [3, 4, 5]
# }
# Define classifier.
XGB_clf = XGBClassifier(learning_rate=0.02, n_estimators=200, silent=True,
objective="multi:softmax", scoring="roc_auc")
## Create grid search.
#folds = 3
#param_comb = 5
#
#skf = StratifiedKFold(n_splits=folds, shuffle = True, random_state = 1001)
#
#random_search = RandomizedSearchCV(XGB_clf, param_distributions=params, n_iter=param_comb, scoring='roc_auc',
# n_jobs=4, cv=skf.split(X_train_no_last_crop,y_train),
# verbose=3, random_state=1001 )
# Here we go
#random_search.fit(X_train_no_last_crop, y_train)
# Print the best estimator.
class classifier:
def __init__(self):
self.model = XGBClassifier()
self.progress = 0
def para_tuning(
self,
X,
y,
para,
grid,
seed=0,
verbose=False
): # verbose = 1 for tuning log, verbose = 2 for plotting, verbose = 3 for both
# determine which to parameter to tune this time
if para == '':
return None
elif para == 'learning_rate':
param_grid = dict(learning_rate=grid) # [0,0.1]
elif para == 'max_depth':
param_grid = dict(max_depth=grid) # int
elif para == 'min_child_weight':
param_grid = dict(min_child_weight=grid) # [0,1]
elif para == 'gamma':
param_grid = dict(gamma=grid) # [0,1]
elif para == 'max_delta_step':
param_grid = dict(max_delta_step=grid) # int
elif para == 'colsample_bytree':
param_grid = dict(colsample_bytree=grid) # [0,1]
elif para == 'reg_alpha':
param_grid = dict(reg_alpha=grid) # [0,1]
elif para == 'reg_lambda':
param_grid = dict(reg_lambda=grid) # [0,1]
else:
print('WRONG PARAMETER.')
return None
kfold = StratifiedKFold(n_splits=8, shuffle=True, random_state=seed)
grid_search = GridSearchCV(self.model,
param_grid,
scoring='accuracy',
n_jobs=-1,
cv=kfold)
grid_result = grid_search.fit(X, y)
# summarize results
means = grid_result.cv_results_['mean_test_score']
stds = grid_result.cv_results_['std_test_score']
params = grid_result.cv_results_['params']
if verbose == 1 or verbose == 3:
for mean, stdev, param in zip(means, stds, params):
print('{:.4f} ({:.4f}) WITH: {} = {}'.format(
mean, stdev, para,
list(param.values())[0]))
print('-' * 63)
self.progress += 1
progress = int(self.progress / 7 * 100)
progress_bar = int(self.progress / 7 * 58)
print('\r' + '█' * progress_bar + ' ' * (58 - progress_bar) +
' {:>3}%'.format(progress),
end='')
if verbose == 2 or verbose == 3:
# plot
plt.close()
plt.figure(figsize=(20, 10))
plt.errorbar(grid, means, yerr=stds)
plt.title('XGBoost {} Tuning'.format(para))
plt.xlabel(para)
plt.ylabel('accuracy')
plt.show()
return list(grid_result.best_params_.values())[0]
def tune(self, X, y, verbose=False, seed=0):
self.model.seed = seed
# fit model no training data
print('-' * 63)
print('AUTO TUNING ON TRAINING DATASET.')
self.model.n_estimators = 1024
self.model.subsample = 0.6
self.model.learning_rate = 0.01
self.model.max_depth = self.para_tuning(X, y, 'max_depth',
[2, 4, 6, 8], seed, verbose)
self.model.min_child_weight = self.para_tuning(X, y,
'min_child_weight',
[4, 8, 12, 16], seed,
verbose)
self.model.gamma = self.para_tuning(
X, y, 'gamma', [0, 0.1, 0.2, 0.4, 0.8, 1.6, 3.2, 6.4, 12.8], seed,
verbose)
self.model.max_delta_step = self.para_tuning(X, y, 'max_delta_step',
[0, 1, 2, 4], seed,
verbose)
self.model.colsample_bytree = self.para_tuning(X, y,
'colsample_bytree',
[0.5, 0.6, 0.7], seed,
verbose)
self.model.reg_alpha = self.para_tuning(X, y, 'reg_alpha',
[0, 0.001, 0.01, 0.1, 10, 100],
seed, verbose)
self.model.reg_lambda = self.para_tuning(
X, y, 'reg_lambda', [0, 0.001, 0.01, 0.1, 10, 100], seed, verbose)
self.model.learning_rate /= 2
sleep(3)
print('\rAUTO TUNING FINISHED.' + ' ' * 42)
print('-' * 63)
if input('MODEL REVIEWING? (Y/N) ') == 'Y':
print(self.model)
def train(self, data, early_stopping_rounds=None, verbose=True, seed=0):
X_train, y_train = data.train[0], data.train[1]
X_test, y_test = data.test[0], data.test[1]
# tune paramters using trainging dataset
self.tune(X_train, y_train, seed=seed)
print('-' * 63)
# train the model with optimized parameters
print('MODEL TRAINING.')
metric = ['error', 'logloss', 'auc']
# self.model.min_child_weight = 4
self.model.fit(X_train,
y_train,
eval_metric=metric,
eval_set=[(X_train, y_train), (X_test, y_test)],
early_stopping_rounds=early_stopping_rounds,
verbose=False)
# make predictions for train data
y_pred = self.model.predict(X_train)
predictions = [round(value) for value in y_pred]
# evaluate predictions
accuracy = accuracy_score(y_train, predictions)
print('TRAINING FINISHED.')
print('ACCURACY TRAINING: {:.2f}%'.format(accuracy * 100))
# make predictions for test data
y_pred = self.model.predict(X_test)
predictions = [round(value) for value in y_pred]
# evaluate predictions
accuracy = accuracy_score(y_test, predictions)
print('ACCURACY TESTING: {:.2f}%'.format(accuracy * 100))
if verbose is True:
try:
# plot boosting results
results = self.model.evals_result()
epochs = len(results['validation_0'][metric[0]])
x_axis = range(0, epochs)
plt.style.use('ggplot')
plt.rcParams['font.size'] = 8
plt.figure(figsize=(20, 10))
i = 0
for m in metric:
ax = plt.subplot2grid((len(metric), 2), (i, 0))
i += 1
ax.plot(x_axis, results['validation_0'][m], label='Train')
ax.plot(x_axis, results['validation_1'][m], label='Test')
ax.legend()
ax.set_ylabel(m)
# plot feature importances
features = data.features
mapFeat = dict(
zip(['f' + str(i) for i in range(len(features))],
features))
imp = pd.Series(self.model.booster().get_fscore())
imp.index = imp.reset_index()['index'].map(mapFeat)
ax = plt.subplot2grid((len(metric), 2), (0, 1),
rowspan=len(metric))
imp.sort_values().plot(kind='barh')
ax.set_ylabel('importance')
plt.show()
except:
print('PLOTTING ERROR.')
from sklearn.metrics import classification_report, confusion_matrix, accuracy_score
print(classification_report(y_test, y_pred_svc))
print(confusion_matrix(y_test, y_pred_svc))
from sklearn.linear_model import LogisticRegression
# Building pipeline
text_clf_lr = Pipeline([('tfidf', TfidfVectorizer()),
('clf', LogisticRegression())])
# Fitting and generating predictions
text_clf_lr.fit(X_train, y_train)
y_pred_lr = text_clf_lr.predict(X_test)
print(classification_report(y_test, y_pred_lr))
print(confusion_matrix(y_test, y_pred_lr))
from xgboost import XGBClassifier
# Building pipeline
text_clf_xgb = Pipeline([('tfidf', TfidfVectorizer()),
('clf', XGBClassifier())])
# Fitting and generating predictions
text_clf_xgb.fit(X_train, y_train)
y_pred_xgb = text_clf_xgb.predict(X_test)
print(classification_report(y_test, y_pred_xgb))
print(confusion_matrix(y_test, y_pred_xgb))
from sklearn.ensemble import RandomForestClassifier
# Building pipeline
text_clf_rf = Pipeline([('tfidf', TfidfVectorizer()),
('clf', RandomForestClassifier())])
# Fitting and generating predictions
text_clf_rf.fit(X_train, y_train)
y_pred_rf = text_clf_rf.predict(X_test)
print(classification_report(y_test, y_pred_rf))
print(confusion_matrix(y_test, y_pred_rf))
model_performance = [
def print_results(dataset, set1, set2):
X_set1, y_set1 = prepare_full_dataset(
dataset.loc[dataset['patient_ID'].isin(set1)])
X_set2, y_set2 = prepare_full_dataset(
dataset.loc[dataset['patient_ID'].isin(set2)])
# X_set1 = np.random.rand(*X_set1.shape)
# X_set2 = np.random.rand(*X_set2.shape)
X_set1_wf = add_one_features(X_set1, 0)
X_set2_wf = add_one_features(X_set2, 1)
X_genes_wf = np.concatenate([X_set1_wf, X_set2_wf])
y_all = np.concatenate([y_set1, y_set2])
kf = RepeatedStratifiedKFold(n_splits=5, n_repeats=10)
print_order = [
"genes", "genes_set", "genes_biased", "genes_double", "study"
]
max_len_order = max(map(len, print_order))
rez = defaultdict(list)
for i, (train_index, test_index) in enumerate(kf.split(X_genes_wf, y_all)):
X_genes_wf_train, X_genes_wf_test = X_genes_wf[
train_index], X_genes_wf[test_index]
y_train, y_test = y_all[train_index], y_all[test_index]
print("before balanced")
print_count_two_sets(X_genes_wf_train[:, 0], y_train)
print_count_two_sets(X_genes_wf_test[:, 0], y_test)
# print("counter before balance", Counter(X_genes_wf_train[:,0]), Counter(X_genes_wf_test[:,0]), Counter(y_train), Counter(y_test))
X_genes_wf_train, y_train = random_upsample_balance(
X_genes_wf_train, y_train)
X_genes_wf_test, y_test = random_upsample_balance(
X_genes_wf_test, y_test)
# print("counter after balance", Counter(X_genes_wf_train[:,0]), Counter(X_genes_wf_test[:,0]), Counter(y_train), Counter(y_test))
print("after balanced")
print_count_two_sets(X_genes_wf_train[:, 0], y_train)
print_count_two_sets(X_genes_wf_test[:, 0], y_test)
X_genes_train = X_genes_wf_train[:, 1:]
X_genes_test = X_genes_wf_test[:, 1:]
Xs_train = X_genes_wf_train[:, :1]
Xs_test = X_genes_wf_test[:, :1]
rez["genes"].append(
calc_results_simple(X_genes_train, X_genes_test, y_train, y_test,
XGBClassifier()))
rez["genes_set"].append(
calc_results_simple(X_genes_wf_train, X_genes_wf_test, y_train,
y_test, XGBClassifier()))
rez["genes_biased"].append(
calc_results_simple(X_genes_wf_train, X_genes_wf_test, y_train,
y_test, BiasedXgboost()))
rez["genes_double"].append(
calc_results_simple(X_genes_wf_train, X_genes_wf_test, y_train,
y_test, DoubleXgboost()))
rez["study"].append(
calc_results_simple(Xs_train, Xs_test, y_train, y_test,
XGBClassifier()))
for order in print_order:
print(order, " " * (max_len_order - len(order)), ": ",
list_to_4g_str(rez[order][-1]))
print("")
for order in print_order:
print("==> ", order, " " * (max_len_order - len(order)), ": ",
list2d_to_4g_str_pm(rez[order]))
for col in numeric_cols:
plt.subplot(int(np.ceil(len(numeric_cols)/3)),3,nplot)
sns.distplot(zeros[col],hist=False,label='Misses')
sns.distplot(ones[col],hist=False,label='Hits')
nplot+=1
plt.legend()
plt.tight_layout()
plt.show()
# %% Modelling
###############################################
estimator = XGBClassifier()
# estimator = LogisticRegression()
param_grid={
'max_depth':[3,5,12],
'n_estimators':[50,100,200],
'objective':['binary:logistic']
}
# param_grid={}
clf = GridSearchCV(estimator,param_grid,scoring='precision',cv=2,verbose=2,n_jobs=-1)
clf.fit(X_train,y_train)
preds_proba = clf.predict_proba(X_test)[:,1]
threshold = 0.35
# preds = clf.predict(X_test)
lparams['bagging_freq'] = 6
#lparams['early_stopping_round'] = 20
cparams['n_estimators'] = 120
cparams['max_depth'] = 3
#cparams['l2_leaf_reg'] = 0.001
if use_gpu:
xparams['tree_method'] = 'gpu_hist'
xparams['predictor'] = 'gpu_predictor'
xparams['objective'] = 'gpu:binary:logistic'
n_jobs = 1
else:
xparams['objective'] = 'binary:logistic'
lparams['objective'] = 'binary'
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]
cv = []
biter = []
for fold, (itr, icv) in enumerate(skf):
print "------ Fold %d -----------\n" % (fold + 1)
X_train = train_processed.iloc[itr]
X_valid = train_processed.iloc[icv]
Y_train = target[itr]
Y_valid = target[icv]
gbm = XGBClassifier(max_depth=8,
learning_rate=0.01,
n_estimators=10000,
subsample=0.9,
colsample_bytree=0.45,
objective="binary:logistic",
silent=False,
min_child_weight=1,
nthread=-1)
gbm.fit(X_train,
Y_train,
eval_metric="logloss",
eval_set=[(X_train, Y_train), (X_valid, Y_valid)],
early_stopping_rounds=200,
verbose=20)
ll = gbm.best_score
best_iter = gbm.best_iteration
cv.append(ll)
crossval_splits = 5
accuracy = numpy.zeros(crossval_splits)
sensitivity = numpy.zeros(crossval_splits)
specificity = numpy.zeros(crossval_splits)
cont = 0
skf = StratifiedKFold(n_splits=crossval_splits, shuffle=True, random_state=123)
skf.get_n_splits(data, labels)
for train_index, test_index in skf.split(data, labels):
train_data, test_data = data[train_index], data[test_index]
train_labels, test_labels = labels[train_index], labels[test_index]
#XGB Classifier
model = XGBClassifier(use_label_encoder=False,
booster='gbtree',
random_state=123)
model.fit(train_data, train_labels)
#Compute scores
pred = model.predict(test_data)
predictions = [round(value) for value in pred]
predictions = numpy.asarray(predictions)
ConfussionMatrix = numpy.zeros((no_classes, no_classes))
for i in range(pred.shape[0]):
ConfussionMatrix[test_labels[i], predictions[i]] += 1.0
for i in range(no_classes):
accuracy[cont] += ConfussionMatrix[i, i]
accuracy[cont] /= ConfussionMatrix.sum()
print('accuracy: ' + str(accuracy[cont]))
auc = roc_auc_score(y_actual, y_pred)
accuracy = accuracy_score(y_actual, (y_pred > thresh))
recall = recall_score(y_actual, (y_pred > thresh))
precision = precision_score(y_actual, (y_pred > thresh))
specificity = calc_specificity(y_actual, y_pred, thresh)
print('AUC:%.3f' % auc)
print('accuracy:%.3f' % accuracy)
print('recall:%.3f' % recall)
print('precision:%.3f' % precision)
print('specificity:%.3f' % specificity)
print('prevalence:%.3f' % rate(y_actual))
print(' ')
return auc, accuracy, recall, precision, specificity
from xgboost import XGBClassifier
import xgboost as xgb
xgbc = XGBClassifier()
xgbc.fit(X_train_tf, y_train)
y_train_preds = xgbc.predict_proba(X_train_tf)[:, 1]
y_valid_preds = xgbc.predict_proba(X_valid_tf)[:, 1]
print('Xtreme Gradient Boosting Classifier ')
print('Training: ')
xgbc_train_auc, xgbc_train_accuracy, xgbc_train_recall, xgbc_train_precision, xgbc_train_specificity = print_report(
y_train, y_train_preds, thresh)
print('Validation: ')
xgbc_valid_auc, xgbc_valid_accuracy, xgbc_valid_recall, xgbc_valid_precision, xgbc_valid_specificity = print_report(
y_valid, y_valid_preds, thresh)
model.fit(X_train, Y_train) from sklearn.ensemble import RandomForestRegressor model = RandomForestRegressor(n_estimators=300, random_state=0) model.fit(X_train, Y_train) from sklearn.tree import DecisionTreeRegressor model = DecisionTreeRegressor(random_state=0) model.fit(X_train, Y_train) from sklearn.svm import SVR model = SVR(kernel='rbf') model.fit(X_train, Y_train) from xgboost import XGBClassifier model = XGBClassifier() model.fit(X_train, Y_train) from sklearn.neighbors import KNeighborsRegressor model = KNeighborsRegressor(n_neighbors=5, metric='manhattan') model.fit(X_train, Y_train) from sklearn.linear_model import Lasso model = Lasso() model.fit(x_train, y_train) from sklearn.linear_model import Ridge model = Ridge() model.fit(x_train, y_train) from sklearn.linear_model import ElasticNet
X=ohe.fit_transform(X).toarray() X = X[:,1:] #%% #verilerin egitim ve test icin bolunmesi from sklearn.model_selection import train_test_split x_train, x_test,y_train,y_test = train_test_split(X,Y,test_size=0.33, random_state=0) #%% #verilerin olceklenmesi """ FEATURE SCALING UYGULAMAYA GEREK KALMIYOR SANIRIM """ #%% """ XGBoost """ from xgboost import XGBClassifier classifier = XGBClassifier() classifier.fit(x_train, y_train) # Sonuçta bu bir classifier. XGBoostta bir classification alg. demekki. y_pred = classifier.predict(x_test) from sklearn.metrics import confusion_matrix cm = confusion_matrix(y_pred,y_test) print(cm)
print('We have %d classes and %d models TOTAL so in resulting arrays \
we expect to see %d columns.' % (n_classes, len(models_1) + len(models_2),
n_classes * (len(models_1) + len(models_2))))
# Create empty arrays
S_train_all = np.zeros((X_train.shape[0], 0))
S_test_all = np.zeros((X_test.shape[0], 0))
# Load results
for name in sorted(glob('*.npy')):
print('Loading: %s' % name)
S = np.load(name)
S_train_all = np.c_[S_train_all, S[0]]
S_test_all = np.c_[S_test_all, S[1]]
print('\nS_train_all shape:', S_train_all.shape)
print('S_test_all shape: ', S_test_all.shape)
# Initialize 2nd level model
model = XGBClassifier(random_state=0, n_jobs=-1, learning_rate=0.1,
n_estimators=100, max_depth=3)
# Fit 2nd level model
model = model.fit(S_train_all, y_train)
# Predict
y_pred = model.predict_proba(S_test_all)
# Final prediction score
print('Final prediction score: %.8f' % log_loss(y_test, y_pred))
def fit_xgboost(params, X, y):
clf = XGBClassifier(**params)
clf.fit(X, y)
return clf
_ = death_preds.actual.value_counts().plot.bar(
ax=ax[0], rot=0,
color=(sns.color_palette()[0],
sns.color_palette()[2])).set(xticklabels=["Alive", "Deceased"])
_ = death_preds.actual.value_counts().plot.pie(labels = ("Alive", "Deceased"), autopct = "%.2f%%", label = "", fontsize = 13., ax = ax[1],\
colors = (sns.color_palette()[0], sns.color_palette()[2]), wedgeprops = {"linewidth": 1.5, "edgecolor": "#F7F7F7"}), ax[1].texts[1].set_color("#F7F7F7"), ax[1].texts[3].set_color("#F7F7F7")
X = death_preds[death_preds.actual == 0].sample(350, random_state=62).append(
death_preds[death_preds.actual == 1].sample(
350, random_state=62)).copy(deep=True).astype(np.float64)
Y = X.actual.values
tX = death_preds[~death_preds.index.isin(X.index)].copy(deep=True).astype(
np.float64)
tY = tX.actual.values
X.drop(["SNo", "actual", "DateoFdeath"], 1, inplace=True)
tX.drop(["SNo", "actual", "DateoFdeath"], 1, inplace=True)
clf_xgb = XGBC(subsample=.8, colsample_bytree=.8, seed=14,
max_depth=3).fit(X, Y)
preds_xgb = clf_xgb.predict_proba(tX)
ax = pd.DataFrame(list(clf_xgb.get_booster().get_fscore().items())).set_index(0)\
.sort_values(1).plot.barh(figsize = (12, 8))
_ = ax.set(frame_on=False,
ylim=(0, len(clf_xgb.get_booster().get_fscore())),
xticklabels="",
xlabel="",
ylabel=""), ax.legend("")
_ = plt.title("XGB Feature Importance", fontsize=18.)
logreg = LogisticRegression(random_state=14).fit(X, Y)
preds_lr = logreg.predict_proba(tX)
df = pd.DataFrame(list(zip(tX.columns, logreg.coef_[0])))
df = df.reindex(df[1].abs().sort_values().index).set_index(0)
ax = df.plot.barh(width=.6, legend="", figsize=(12, 9))
# plot decision tree
from numpy import loadtxt
from xgboost import XGBClassifier
from xgboost import plot_tree
from matplotlib import pyplot
# load data
dataset = loadtxt('pima-indians-diabetes.csv', delimiter=",")
# split data into X and y
X = dataset[:,0:8]
y = dataset[:,8]
# fit model no training data
model = XGBClassifier()
model.fit(X, y)
# plot single tree
plot_tree(model)
pyplot.show()
skf = StratifiedKFold(np.array(train["TARGET"]), n_folds = 10, shuffle = True, random_state = 14)
cv = []
biter = []
for fold, (itr, icv) in enumerate(skf):
print "------ Fold %d -----------\n" %(fold+1)
trainingSet = train.iloc[itr]
validationSet = train.iloc[icv]
gbm = XGBClassifier(max_depth=4,
learning_rate = 0.01,
n_estimators=3000,
subsample=0.8,
colsample_bytree=0.5,
objective="binary:logistic",
silent = False,
min_child_weight=5,
nthread=-1)
gbm.fit(trainingSet[feature_names], np.array(trainingSet["TARGET"]),
eval_metric="auc",
eval_set=[(trainingSet[feature_names], np.array(trainingSet["TARGET"])), (validationSet[feature_names], np.array(validationSet["TARGET"]))],
early_stopping_rounds=200,verbose=20)
ll = gbm.best_score
best_iter = gbm.best_iteration
cv.append(ll)
biter.append(best_iter)
print "---auc : %0.6f\n" %ll
#df_null_check.to_excel('Data/Null check.xlsx', index=False)
_ = StandardScaler().fit_transform(X_test)
X_test = pd.DataFrame(_, columns=X_test.columns)
X_train = X_train.round(3)
y_train = y_train.round(3)
#X_train.to_excel(r'Linh Tinh/Linh tinh.xlsx', index = False)
# rfecv.fit(X_train, y_train)
# df_new = rfecv.fit_transform(X_train,y_train)
# print("Best Features:", rfecv.get_support)
# print("Optimal number of features : %d" % rfecv.n_features_)
print("Start Feature Selection")
clf_feature_selection = XGBClassifier(colsample_bytree=0.5,
gamma=0.1,
learning_rate=0.15,
max_depth=20,
min_child_weight=5,
n_estimators=400)
clf = XGBClassifier()
rfecv = RFECV(estimator=clf_feature_selection,
step=1,
cv=StratifiedKFold(2),
scoring='roc_auc')
params = {
"learning_rate": [0.05, 0.15, 0.3],
"max_depth": [5, 10, 20, 30, 50, 70],
"min_child_weight": [5, 10, 20, 50, 100],
"gamma": [0.0, 0.1, 0.2, 0.4, 0.5],
"colsample_bytree": [0.2, 0.3, 0.5, 0.7],
"n_estimators": [100, 200, 400, 500, 600]
target = df['TARGET']
del df['TARGET']
# del df['ID']
id = df_test['ID']
# del df_test['ID']
pca = PCA(n_components=250)
train_pcaed = pca.fit_transform(df, target)
random_forest = RandomForestClassifier(n_estimators=30, max_depth=5, max_features=20)
random_forest.fit(train_pcaed, target)
forested = random_forest.predict_proba(train_pcaed)
# pipe = Pipeline(steps=[('pca', pca), ('random_forest', random_forest)])
m2_xgb = XGBClassifier(n_estimators=110, nthread=1, max_depth=4)
m2_xgb.fit(train_pcaed, target)
m2_xgbed = m2_xgb.predict_proba(train_pcaed)
logistic_regression = LogisticRegression(penalty='l1')
logistic_regression.fit(train_pcaed, target)
logistic_regressioned = logistic_regression.predict_proba(train_pcaed)
combined = np.concatenate([forested, m2_xgbed, logistic_regressioned], axis=1)
log_reg = LogisticRegression()
log_reg.fit(combined, target)
scores = cross_validation.cross_val_score(log_reg, combined, target,
cv=5, scoring='roc_auc')
# split into training and test
from sklearn.model_selection import train_test_split
validation_size = 0.2
seed = 0
X_train, X_test, y_train, y_test = train_test_split(X, y, test_size = validation_size, random_state = seed)
# create instance of algorithm
from xgboost import XGBClassifier
model = XGBClassifier()
# fit algorithm to the training set (not required if using parameter tuning)
model.fit(X_train, y_train)
# predict
y_predicted = model.predict(X_test)
