def evaluate(X, y, args):
if args.task == 'regression':
if args.model == 'LR':
model = Lasso()
elif args.model == 'RF':
model = RandomForestRegressor(n_estimators=10, random_state=0)
if args.evaluate == 'mae':
r_mae = cross_val_score(model,
X,
y,
cv=5,
scoring='neg_mean_absolute_error').mean()
return r_mae
elif args.evaluate == 'mse':
r_mse = cross_val_score(model,
X,
y,
cv=5,
scoring='neg_mean_squared_error').mean()
return r_mse
elif args.evaluate == 'r2':
r_r2 = cross_val_score(model, X, y, cv=5).mean()
return r_r2
elif args.task == 'classification':
le = LabelEncoder()
y = le.fit_transform(y)
if args.model == 'RF':
model = RandomForestClassifier(n_estimators=10, random_state=0)
elif args.model == 'LR':
model = LogisticRegression(multi_class='ovr')
elif args.model == 'SVM':
model = svm.SVC()
if args.evaluate == 'f_score':
s = cross_val_score(model, X, y, scoring='f1', cv=5).mean()
elif args.evaluate == 'auc':
model = RandomForestClassifier(max_depth=10, random_state=0)
split_pos = X.shape[0] // 10
X_train, X_test = X[:9 * split_pos], X[9 * split_pos:]
y_train, y_test = y[:9 * split_pos], y[9 * split_pos:]
model.fit(X_train, y_train)
y_pred = model.predict_proba(X_test)
s = evaluate_(y_test, y_pred)
return s
class SLearner(Model):
def __init__(self, *args, **kwargs):
self.reg = None
self.l1_penalty = 0
super(SLearner, self).__init__(*args, **kwargs)
def fit(self,
x,
t,
y,
nfolds=5,
lambdas=[1e3, 1e2, 1e1, 1e0, 1e-1, 1e-2, 1e-3],
seed=282):
splits = super().get_splits(x, nfolds, seed)
#### CLASSIFICATION ####
if self.binary:
avg_bces = []
for l in lambdas:
bce_lst = []
for train_index, valid_index in splits:
x_train, x_valid = x[train_index], x[valid_index]
t_train, t_valid = t[train_index], t[valid_index]
y_train, y_valid = y[train_index], y[valid_index]
reg = LogisticRegression(C=1 / l).fit(
self.get_predictors(x_train, t_train), y_train)
log_phat_valid = reg.predict_log_proba(
self.get_predictors(x_valid, t_valid))
bce = np.mean(log_phat_valid[np.arange(len(y_valid)),
y_valid.astype('int')])
bce_lst.append(bce)
avg_bces.append(np.mean(bce_lst))
self.l1_penalty = lambdas[np.argmin(avg_bces)]
self.reg = LogisticRegression(C=1 / self.l1_penalty).fit(
self.get_predictors(x, t), y)
#### REGRESSION ####
else:
avg_rmses = []
for l in lambdas:
rmse_lst = []
for train_index, valid_index in splits:
x_train, x_valid = x[train_index], x[valid_index]
t_train, t_valid = t[train_index], t[valid_index]
y_train, y_valid = y[train_index], y[valid_index]
reg = Lasso(alpha=l).fit(
self.get_predictors(x_train, t_train), y_train)
yhat_valid = reg.predict(
self.get_predictors(x_valid, t_valid))
rmse = np.sqrt(np.mean((yhat_valid - y_valid)**2))
rmse_lst.append(rmse)
avg_rmses.append(np.mean(rmse_lst))
self.l1_penalty = lambdas[np.argmin(avg_rmses)]
self.reg = Lasso(alpha=self.l1_penalty).fit(
self.get_predictors(x, t), y)
def predict(self, x, t):
if self.reg is None:
raise Exception('SLearner not Initialized')
#### CLASSIFICATION ####
if self.binary:
return self.reg.predict_proba(self.get_predictors(x, t))[:, 1]
#### REGRESSION ####
else:
return self.reg.predict(self.get_predictors(x, t))
def get_predictors(self, x, t):
return np.hstack([x, (t - 0.5).reshape(-1, 1) * x])
def evaluate1(X, y, num_op_unary, num_op_binary, max_order, num_batch,
optimizer, lr, epochs, evaluate, task, dataset, model, alpha,
lr_value, RL_model, reg, controller, num_random_sample, lambd,
multiprocessing, package):
if task == 'regression':
if model == 'LR':
model = Lasso()
elif model == 'RF':
model = RandomForestRegressor(n_estimators=10, random_state=0)
if evaluate == 'mae':
r_mae = cross_val_score(model,
X,
y,
cv=5,
scoring='neg_mean_absolute_error').mean()
return r_mae
elif evaluate == 'mse':
r_mse = cross_val_score(model,
X,
y,
cv=5,
scoring='neg_mean_squared_error').mean()
return r_mse
elif evaluate == 'r2':
r_r2 = cross_val_score(model, X, y, cv=5).mean()
return r_r2
elif evaluate == 'rae':
#print_file("rae")
y_mean = statistics.mean(y)
X1 = X.copy()
y1 = y.copy()
r_rae = 0
Num = len(X.index)
Seg = int(Num / 5)
for i in range(5):
if (i == 0):
X_test = X1[i * Seg:Seg]
X_train = X1[Seg:]
y_test = y1[i * Seg:Seg]
y_train = y1[Seg:]
elif (i == 4):
X_test = X1[i * Seg:]
X_train = X1[:i * Seg]
y_test = y1[i * Seg:]
y_train = y1[:i * Seg]
else:
X_test = X1[i * Seg:(i + 1) * Seg]
y_test = y1[i * Seg:(i + 1) * Seg]
X_train = X1[:i * Seg]
y_train = y1[:i * Seg]
X_train2 = X1[(i + 1) * Seg:]
y_train2 = y1[(i + 1) * Seg:]
X_train = X_train.append(X_train2)
y_train = y_train.append(y_train2)
model.fit(X_train, y_train)
y_pred = model.predict(X_test)
diff1 = y_pred - y_test
diff2 = y_mean - y_test
diff1_sum = 0
for i in diff1:
diff1_sum = diff1_sum + abs(i)
diff2_sum = 0
for i in diff2:
diff2_sum = diff2_sum + abs(i)
r_rae = 1 - (diff1_sum / diff2_sum) + r_rae
return (r_rae / 5)
elif task == 'classification':
le = LabelEncoder()
y = le.fit_transform(y)
if model == 'RF':
model = RandomForestClassifier(n_estimators=10, random_state=0)
elif model == 'LR':
model = LogisticRegression(multi_class='ovr')
elif model == 'SVM':
model = svm.SVC()
if evaluate == 'f_score':
s = cross_val_score(model, X, y, scoring='f1', cv=5).mean()
elif evaluate == 'auc':
model = RandomForestClassifier(max_depth=10, random_state=0)
split_pos = X.shape[0] // 10
X_train, X_test = X[:9 * split_pos], X[9 * split_pos:]
y_train, y_test = y[:9 * split_pos], y[9 * split_pos:]
model.fit(X_train, y_train)
y_pred = model.predict_proba(X_test)
s = evaluate_(y_test, y_pred)
return s
y = get_locations_train()
X = df.copy()
X, y, cl = shuffle(X, y, cl)
dftest = pd.read_csv("test.bottleneck.{}.csv".format(architecture), index_col=0)
dftest.head()
p = []
pt = []
cv = StratifiedKFold(8)
for i, (train, test) in enumerate(cv.split(X, y, cl)):
print(np.unique(y[train]))
print(X.iloc[train].shape, y[train].shape)
model = Lasso(C=C).fit(X.iloc[train], y[train])
print(log_loss(y[test], model.predict_proba(X.iloc[test]), labels=[0, 1, 2, 3, 4, 5, 6, 7]))
p.append((y[test], model.predict_proba(X.iloc[test])))
pt.append(model.predict_proba(dftest))
model = Lasso(C=C).fit(X, y)
p = model.predict_proba(dftest.values)
sub = pd.read_csv("sample_submission_stg1.csv", index_col=0)
samp = sub.copy()
print(samp.mean(axis=0))
sub.loc[dftest.index, :] = p
print(sub.mean(axis=0))
sub.to_csv("sub.lr{:.5f}.bottleneck_{}.csv.gz".format(C, architecture), compression="gzip")
print(sub.head())
def regularize_by_l1(X_train,
X_test,
y_train,
y_test,
all_features,
N_k,
task,
N_repeat,
seed_no=0):
## 0. Input arguments:
# X_train: array that contains training feature data
# X_test: array that contains testing feature data
# y_train: array that contains traning response data
# y_test: array that contains testing response data
# all_features: names of all features (column names of X_train)
# N_k: number of folds to split into
# task: type of supervised learning task: 'regression' or 'classification'
# N_repeat: number of independent cross-validation runs, each run will generate one performance score
# seed_no: seed number to be used in the first run, 'seed_start + 1' will be used for the second run, ...
## 1. Perform regularized classification/regression based on the specified task
# regression
if task == 'regression':
# split data into K folds
kf = KFold(n_splits=N_k, random_state=seed_no, shuffle=True)
# find the optimal alpha (regularization factor) using K-fold cross validation on training data
cv_regressor = LassoCV(cv=kf, random_state=seed_no)
cv_regressor.fit(X_train, y_train)
best_alpha = cv_regressor.alpha_
# fit lasso regression using the optimal alpha
final_learner = Lasso(alpha=best_alpha)
final_learner.fit(X_train, y_train)
# obtain selected features by fitted lasso regression model (features with coefficients > 0)
select_features = all_features[(final_learner.coef_ != 0).flatten()]
N_select = len(select_features)
# perform K-fold cross validation to obtain the training performance of fitted lasso regression model
train_metric = []
for i in range(0, N_repeat):
cv_kf = KFold(n_splits=N_k, random_state=i + 1, shuffle=True)
r2 = cross_val_score(final_learner,
X_train,
y_train,
cv=cv_kf,
scoring='r2')
mse = cross_val_score(final_learner,
X_train,
y_train,
cv=cv_kf,
scoring='neg_mean_squared_error')
train_metric.append({'r2': np.mean(r2), 'mse': np.mean(mse)})
train_metric_df = pd.DataFrame(train_metric)
# implement fitted lasso regression model on the testing set and obtain the testing performance
y_pred = final_learner.predict(X_test)
test_r2 = r2_score(y_test, y_pred)
test_mse = mean_squared_error(y_test, y_pred)
test_metric = {'r2': test_r2, 'test_mse': test_mse}
# classification
if task == 'classification':
# straitified split for classification tasks
kf = StratifiedKFold(n_splits=N_k, random_state=seed_no, shuffle=True)
# find the optimal C (regularization factor) using K-fold cross validation on training data
cv_classifier = LogisticRegressionCV(penalty='l1',
solver='liblinear',
cv=kf,
random_state=seed_no)
cv_classifier.fit(X_train, y_train)
best_c = float(cv_classifier.C_)
# fit logistic regression using the optimal C
final_learner = LogisticRegression(penalty='l1',
solver='liblinear',
C=best_c,
random_state=seed_no)
final_learner.fit(X_train, y_train)
# obtain selected features by fitted logistic regression model (features with coefficients > 0)
select_features = all_features[(final_learner.coef_ != 0).flatten()]
N_select = len(select_features)
# perform K-fold cross validation to obtain the training performance of fitted logistic regression model
train_metric = []
for i in range(0, N_repeat):
cv_kf = StratifiedKFold(n_splits=N_k,
random_state=i + 1,
shuffle=True)
auc = cross_val_score(final_learner,
X_train,
y_train,
cv=cv_kf,
scoring='roc_auc')
bac = cross_val_score(final_learner,
X_train,
y_train,
cv=cv_kf,
scoring='balanced_accuracy')
f1 = cross_val_score(final_learner,
X_train,
y_train,
cv=cv_kf,
scoring='f1')
train_metric.append({
'auc': np.mean(auc),
'bac': np.mean(bac),
'f1': np.mean(f1)
})
train_metric_df = pd.DataFrame(train_metric)
# compare with testing response data, compute metrics
y_pred_prob = final_learner.predict_proba(X_test)[:, 1]
y_pred = final_learner.predict(X_test)
test_auc = roc_auc_score(y_test, y_pred_prob)
test_bac = balanced_accuracy_score(y_test, y_pred)
test_f1 = f1_score(y_test, y_pred)
test_metric = {'auc': test_auc, 'bac': test_bac, 'f1': test_f1}
return final_learner, select_features, train_metric_df, test_metric
X_train_scale,
y_train,
cv=5,
scoring=['accuracy', 'roc_auc'],
return_train_score=True)
print('Cross Validation Results')
print('Train accuracy CV: %.4f' % scores['train_accuracy'].mean())
print('Test accuracy CV: %.4f' % scores['test_accuracy'].mean())
print('Test AUC: %.4f' % scores['test_roc_auc'].mean())
# In[408]:
clf = grid_search.best_estimator_
clf.fit(X_train_scale, y_train)
y_pred_prob = clf.predict_proba(X_test_scale)[:, 1]
y_pred = clf.predict(X_test_scale)
print('Training accuracy: %.2f%%' % (clf.score(X_train_scale, y_train) * 100))
print('Test accuracy: %.2f%%' % (clf.score(X_test_scale, y_test) * 100))
print('AUC: %.2f%%' % (metrics.roc_auc_score(y_test, y_pred_prob) * 100))
print(confusion_matrix(y_test, y_pred))
print(classification_report(y_test, y_pred))
fpr_log, tpr_log, _ = roc_curve(y_test, y_pred_prob)
# In[409]:
coefs = pd.DataFrame(clf_gridsearch.coef_[0],
index=X_train.columns,