def main():
#getting and splitting data
print("parsing data")
patients, egm_matrix, cancer_onehot = get_data()
train_X, test_X, train_Y, test_Y = train_test_split(egm_matrix,
cancer_onehot,
test_size=0.20,
random_state=0)
#form scaled data
scaler = preprocessing.StandardScaler().fit(train_X)
print(scaler)
scaled_train_X = scaler.transform(train_X)
scaled_test_X = scaler.transform(test_X)
bagging = BaggingClassifier(DecisionTreeClassifier(max_depth=3),
max_features=20000,
max_samples=1.0,
n_estimators=11,
random_state=2)
bagging.fit(scaled_train_X, train_Y)
pred_Y = bagging.predict(scaled_test_X)
f1_score_bagging = f1_score(test_Y, pred_Y, average=None)
print("f1 score is: " + str(f1_score_bagging)
) #max_features=20000 -> f1 score is: [0.77852349 0.47619048]
mean_train_accuracy = bagging.score(scaled_train_X, train_Y)
print("mean_train_accuracy is: " + str(mean_train_accuracy))
mean_test_accuracy = bagging.score(scaled_test_X, test_Y)
print("mean_test_accuracy is: " + str(mean_test_accuracy))
print(bagging)
def main():
#getting and splitting data
print ("parsing data")
patients, egm_matrix, cancer_onehot = get_data()
train_X, test_X, train_Y, test_Y = train_test_split(egm_matrix,cancer_onehot, test_size=0.20, random_state=0)
#form scaled data
scaler = preprocessing.StandardScaler().fit(train_X)
print (scaler)
scaled_train_X = scaler.transform(train_X)
scaled_test_X = scaler.transform(test_X)
rand_forest = RandomForestClassifier(bootstrap=True, criterion='gini', n_estimators=80, max_depth=3,
max_features='auto', oob_score=True, random_state=0)
rand_forest.fit(scaled_train_X, train_Y)
pred_Y = rand_forest.predict(scaled_test_X)
rf_f1_score = f1_score(test_Y, pred_Y, average=None)
print ("rf_f1_score is: " + str(rf_f1_score))
print ("oob score is: " + str(rand_forest.oob_score_))
rf_mean_train_accuracy = rand_forest.score(scaled_train_X, train_Y)
print ("mean rf train accuracy is: " + str(rf_mean_train_accuracy))
rf_mean_test_accuracy = rand_forest.score(scaled_test_X, test_Y)
print ("mean rf test accuracy is: " + str(rf_mean_test_accuracy))
print (rand_forest)
print (len(rand_forest.feature_importances_))
feat_importance = rand_forest.feature_importances_
considered_feats = 0
total_feats = 0
total_weight = 0
max_weight = 0
for feat in feat_importance:
if feat > 0:
considered_feats += 1
total_weight += feat
max_weight = max(max_weight, feat)
total_feats += 1
print ("considered_feats is: " + str(considered_feats))
print ("total_weight is: " + str(total_weight))
print ("max weight is: " + str(max_weight))
def main():
#getting and splitting data
print ("parsing data")
patients, egm_matrix, cancer_onehot = get_data()
train_X, test_X, train_Y, test_Y = train_test_split(egm_matrix,cancer_onehot, test_size=0.20, random_state=0)
# total_train_ex = 0
# total_train_pos = 0
# for lbl in train_Y:
# total_train_ex += 1
# if lbl == 1:
# total_train_pos += 1
# print ("total_train_ex: " + str(total_train_ex) + " total_train_pos: " + str(total_train_pos))
# total_test_ex = 0
# total_test_pos = 0
# for lbl in test_Y:
# total_test_ex += 1
# if lbl == 1:
# total_test_pos += 1
# print ("total_test_ex: " + str(total_test_ex) + " total_test_pos: " + str(total_test_pos))
best_f1_score = f1_score(test_Y, test_Y, average=None)
print ("best_f1_score: " + str(best_f1_score))
print ("LR fitting")
start = timer()
max_allowed_iters = 1500
# lr = LogisticRegression(penalty='l2', solver='lbfgs', max_iter=max_allowed_iters)
# lr = LogisticRegression(solver='lbfgs', max_iter=400)
lr = LogisticRegression(solver='lbfgs', max_iter=max_allowed_iters)
lr.fit(train_X, train_Y)
# print ("LR predicting")
pred_Y = lr.predict(test_X)
end = timer()
print ("logistic regression took: " + str(end - start) + " seconds")
num_iters = lr.n_iter_
print ("took " + str(num_iters[0]) + " iterations")
print ("test accuracy is: " + str(lr.score(test_X, test_Y)))
print ("train accuracy is: " + str(lr.score(train_X, train_Y)))
score_f1 = f1_score(test_Y, pred_Y, average=None)
print ("f1_score is: " + str(score_f1))
def main():
#getting and splitting data
print("parsing data")
patients, egm_matrix, cancer_onehot = get_data()
train_X, test_X, train_Y, test_Y = train_test_split(egm_matrix,
cancer_onehot,
test_size=0.20,
random_state=0)
#make y sets +/- 1
# print ("train_Y is: " + str(train_Y))
# for ind in range(train_Y):
# if train_Y[ind] == 0:
# train_Y[ind] = -1
# for ind2 in range(test_Y):
# if test_Y[ind] == 0:
# test_Y[ind] = -1
#form scaled data
scaler = preprocessing.StandardScaler().fit(train_X)
print(scaler)
scaled_train_X = scaler.transform(train_X)
scaled_test_X = scaler.transform(test_X)
ada_boost = AdaBoostClassifier(DecisionTreeClassifier(max_depth=2),
n_estimators=100,
learning_rate=1.0,
random_state=0)
ada_boost.fit(scaled_train_X, train_Y)
pred_Y = ada_boost.predict(scaled_test_X)
f1_score_adda = f1_score(test_Y, pred_Y, average=None)
print("f1 score is: " + str(f1_score_adda)
) #f1 score is: [0.63703704 0.36363636] for learning rate 1.0
mean_train_accuracy = ada_boost.score(scaled_train_X, train_Y)
print("mean_train_accuracy is: " + str(mean_train_accuracy))
mean_test_accuracy = ada_boost.score(scaled_test_X, test_Y)
print("mean_test_accuracy is: " + str(mean_test_accuracy))
print(ada_boost)
def main():
#getting and splitting data
print("parsing data")
patients, egm_matrix, cancer_onehot = get_data()
train_X, test_X, train_Y, test_Y = train_test_split(egm_matrix,
cancer_onehot,
test_size=0.20,
random_state=0)
#form scaled data
scaler = preprocessing.StandardScaler().fit(train_X)
print(scaler)
scaled_train_X = scaler.transform(train_X)
scaled_test_X = scaler.transform(test_X)
max_allowed_iters = 1500
print("SGD fitting")
start = timer()
#test sgd with l1, l2, or elasticnet
sgd = linear_model.SGDClassifier(max_iter=1000,
tol=1e-3,
penalty='l1',
shuffle=False)
sgd.fit(scaled_train_X, train_Y)
pred_Y = sgd.predict(scaled_test_X)
end = timer()
print("sgd took: " + str(end - start) + " seconds")
num_iters = sgd.n_iter_
print("took " + str(num_iters) + " iterations")
print("test accuracy is: " + str(sgd.score(scaled_test_X, test_Y)))
print("train accuracy is: " + str(sgd.score(scaled_train_X, train_Y)))
score_f1 = f1_score(test_Y, pred_Y, average=None)
print("f1_score is: " + str(score_f1))
print(sgd)
def main():
#getting and splitting data
print("parsing data")
patients, egm_matrix, cancer_onehot = get_data()
train_X, test_X, train_Y, test_Y = train_test_split(egm_matrix,
cancer_onehot,
test_size=0.20,
random_state=0)
#form scaled data
scaler = preprocessing.StandardScaler().fit(train_X)
print(scaler)
scaled_train_X = scaler.transform(train_X)
scaled_test_X = scaler.transform(test_X)
max_allowed_iters = 1500
print("SVM fitting")
start = timer()
#test sgd with l1, l2, or elasticnet
# sgd = linear_model.SGDClassifier(loss='squared_hinge', max_iter=1000, tol=1e-3,
# penalty='l1', shuffle=True)
# clf_svm = svm.SVC(C=0.5, gamma=0.2, kernel='rbf', shrinking=False)
clf_svm = svm.SVC(kernel='linear', shrinking=False)
clf_svm.fit(scaled_train_X, train_Y)
pred_Y = clf_svm.predict(scaled_test_X)
end = timer()
print("sgd took: " + str(end - start) + " seconds")
# num_iters = clf_svm.n_iter_
# print ("took " + str(num_iters) + " iterations")
print("test accuracy is: " + str(clf_svm.score(scaled_test_X, test_Y)))
print("train accuracy is: " + str(clf_svm.score(scaled_train_X, train_Y)))
print("pred_Y is: " + str(pred_Y))
score_f1 = f1_score(test_Y, pred_Y, average=None)
print("f1_score is: " + str(score_f1))
print(clf_svm)
def main():
#getting and splitting data
print("parsing data")
patients, egm_matrix, cancer_onehot = get_data()
train_X, test_X, train_Y, test_Y = train_test_split(egm_matrix,
cancer_onehot,
test_size=0.20,
random_state=0)
#form scaled data
scaler = preprocessing.StandardScaler().fit(train_X)
print(scaler)
scaled_train_X = scaler.transform(train_X)
scaled_test_X = scaler.transform(test_X)
max_allowed_iters = 1500
print("SGD fitting")
#test sgd with l1, l2, or elasticnet
alpha_values = [
0.0001, 0.005, 0.02, 0.03, 0.04, 0.05, 0.07, 0.08, 0.09, 0.1
] #0.07 is best
f1_l1_scores = []
f1_elasticnet_scores = []
f1_l2_scores = []
for alpha_val in alpha_values:
sgd_elasticnet = linear_model.SGDClassifier(max_iter=1000,
tol=1e-3,
penalty='elasticnet',
alpha=alpha_val,
shuffle=False)
sgd_elasticnet.fit(scaled_train_X, train_Y)
pred_elasticnet_Y = sgd_elasticnet.predict(scaled_test_X)
score_elasticnet_f1 = f1_score(test_Y, pred_elasticnet_Y)
print("f1_score is: " + str(score_elasticnet_f1) + "for alpha: " +
str(alpha_val))
f1_elasticnet_scores.append(score_elasticnet_f1)
sgd_l1 = linear_model.SGDClassifier(max_iter=1000,
tol=1e-3,
penalty='l1',
alpha=alpha_val,
shuffle=False)
sgd_l1.fit(scaled_train_X, train_Y)
pred_l1_Y = sgd_l1.predict(scaled_test_X)
score_l1_f1 = f1_score(test_Y, pred_l1_Y)
f1_l1_scores.append(score_l1_f1)
sgd_l2 = sgd_l1 = linear_model.SGDClassifier(max_iter=1000,
tol=1e-3,
penalty='l2',
alpha=alpha_val,
shuffle=False)
sgd_l2.fit(scaled_train_X, train_Y)
pred_l2_f1 = sgd_l2.predict(scaled_test_X)
score_l2_f1 = f1_score(test_Y, pred_l2_f1)
f1_l2_scores.append(score_l2_f1)
plt.plot(alpha_values, f1_elasticnet_scores, 'ro-', alpha_values,
f1_l1_scores, 'g^-', alpha_values, f1_l2_scores, 'b2-')
plt.ylabel('f1 score')
plt.xlabel("regularization alpha values")
plt.title("F1 scores for SGD Classifier with Regularization")
plt.show()
def main():
#load_BioAge1HO()
#getting and splitting data
print("parsing data...")
patients, X, y = get_data()
print("done.")
#form test and train set
num_ex, num_features = X.shape
train_X_arr = []
train_Y_arr = []
test_X_arr = []
test_Y_arr = []
num_neg_test_ex = 64
num_pos_test_ex = 42
for ind in range(num_ex):
lbl = y[ind]
if num_pos_test_ex > 0 and lbl == 1:
test_Y_arr.append(1)
test_X_arr.append(X[ind])
num_pos_test_ex -= 1
elif num_neg_test_ex > 0 and lbl == 0:
test_Y_arr.append(0)
test_X_arr.append(X[ind])
num_neg_test_ex -= 1
else:
train_Y_arr.append(lbl)
train_X_arr.append(X[ind])
train_X = np.array(train_X_arr)
train_Y = np.array(train_Y_arr)
test_X = np.array(test_X_arr)
test_Y = np.array(test_Y_arr)
#random forests
# n_estimators_arr = [50, 75, 90, 95, 100, 105, 110,115]
# evaluate_hyperparams(n_estimators_arr, random_forest_classifier,
# train_X, train_Y, "Random Forests", "Number of trees per forest")
# rf_clf = random_forest_classifier(100)
# run_on_test_data(rf_clf, train_X, train_Y, test_X, test_Y, 'random forest test')
#sgd w/ l2 regularization
alphas = [0.0001, 0.001, 0.01, 0.1, 0.7, 1, 5]
# evaluate_hyperparams(alphas, sgd_classifier, train_X, train_Y
# "SGD w/ L2 regularization", "alpha values")
#bagging
max_features_arr = [17000, 18500, 20000, 20500, 21000, 21100, 21200, 22000]
# evaluate_hyperparams(max_features_arr, bagging_classifier, train_X, train_Y,
# "Bagging", "Maximum Features for Estimator")
# bagging_clf = bagging_classifier(21000)
# run_on_test_data(bagging_clf, train_X, train_Y, test_X, test_Y, 'bagging test')
#adaboost
learn_rates = [0.2, 0.4, 0.5, 0.7, 0.9, 1.0]
# evaluate_hyperparams(learn_rates, adaBoost_classifier, train_X, train_Y,
# "AdaBoost", "Learning Rate")
#sigmoid
# sigmoid_penalty_terms = [0.2, 0.4, 0.5, 0.7, 0.75, 0.85, 1.0]
# evaluate_hyperparams(sigmoid_penalty_terms, svm_classifier, train_X, train_Y,
# "Sigmoid Kernel", "Penalty term")
sigmoid_coef0_arr = [0.0, 0.2, 0.25, 0.3, 0.4, 0.5, 0.7]
# evaluate_hyperparams(sigmoid_coef0_arr, svm_classifier, train_X, train_Y,
# "Sigmoid Kernel", "Constant value")
# sigmoid_clf = svm_classifier(0.0)
# run_on_test_data(sigmoid_clf, train_X, train_Y, test_X, test_Y, 'sigmoid kernel test')
#polynomial
degrees = [1,2,3,4]
# evaluate_hyperparams(degrees, svm_classifier, train_X, train_Y,
# "Polynomial Kernel", "Degree of Polynomial")
# poly_svm = svm_classifier(1)
# run_on_test_data(poly_svm, train_X, train_Y, test_X, test_Y, 'poly test')
#rbf svm
rbf_gamma_arr = [0.1, 0.2, 0.4, 0.55, 0.6, 0.75, 0.8, 0.85, 0.9]
# rbf_penalty_terms = [0.2, 0.4, 0.5, 0.7, 0.75, 0.85]
# evaluate_hyperparams(rbf_gamma_arr, svm_classifier, train_X, train_Y,
# "RBF kernel", 'Gamma values')
# rbf_clf = svm_classifier()
# run_on_test_data(rbf_clf, train_X, )
#PCA
# retained_variance = [0.5, 0.6, 0.75, 0.85, 0.95]
num_components = [75, 80, 85, 90, 95, 100, 110, 115, 120, 125, 130, 135, 140]
# evaluate_hyperparams(num_components, PCA_classifier, train_X, train_Y,
# "PCA", "Number of Components Retained")
# pca_clf = PCA_classifier(110)
# run_on_test_data(pca_clf, train_X, train_Y, test_X, test_Y, 'pca test')
#decision trees
max_depths = [1,2,3,4,5,6]
# max_features = ['auto', 'sqrt', None]
# evaluate_hyperparams(max_depths, tree_classifier, train_X, train_Y,
# "Decision Tree", "Maximum Depth")
# dt_clf = tree_classifier(4)
# run_on_test_data(dt_clf, train_X, train_Y, test_X, test_Y, "decision tree test")
# lr_model = LR_classifier()
# lr_results = test_model(lr_model, train_X, train_Y)
# print ("lr results:")
# print ("avg_train_acc: " + str(lr_results[0]))
# print ("avg_test_acc: " + str(lr_results[1]))
# print ("avg_prec: " + str(lr_results[2]))
# print ("avg_recall: " + str(lr_results[3]))
# print ("f1_score: " + str(lr_results[4]))
#lr train/test
# test_model = LogisticRegression(solver='lbfgs', max_iter=MAX_ITERS)
test_model = LR_classifier()
test_model.fit(train_X, train_Y)
test_pred = test_model.predict(test_X)
train_pred = test_model.predict(train_X)
train_acc = accuracy_score(train_Y, train_pred)
test_acc = accuracy_score(test_Y, test_pred)
prec_score = precision_score(test_Y, test_pred)
rec_score = recall_score(test_Y, test_pred)
lr_f1_score = f1_score(test_Y, test_pred)
print ("1's in train_pred: " + str(train_pred.tolist().count(1)))
print ("1's in test_pred: " + str(test_pred.tolist().count(1)))
print ("test_acc: " + str(test_acc))
print ("train_acc: " + str(train_acc))
print ("prec_score: " + str(prec_score))
print ("rec_score: " + str(rec_score))
print ("f1_score: " + str(lr_f1_score))
lr_conf_matrix = confusion_matrix(test_Y, test_pred)
print ("lr confusion matrix is: " + str(lr_conf_matrix))