from pyxvis.io.data import load_features
from pyxvis.learning.classifiers import clf_model
from pyxvis.learning.evaluation import cross_validation
# List of classifiers
ss_cl = [
'dmin', 'lda', 'qda', 'maha', 'knn3', 'knn5', 'knn7', 'knn11', 'knn15',
'bayes-naive', 'bayes-kde', 'adaboost', 'lr', 'rf', 'tree', 'svm-lin',
'svm-rbf(0.1,1)', 'svm-rbf(0.1,0.5)', 'svm-rbf(0.5,1)',
'svm-pol(0.05,0.1,2)', 'svm-pol(0.05,0.5,2)', 'svm-pol(0.05,0.5,3)',
'svm-sig(0.1,1)', 'svm-sig(0.1,0.5)', 'svm-sig(0.5,1)', 'nn(10,)',
'nn(20,)', 'nn(12,6)', 'nn(20,10,4)'
]
(X, d) = load_features('../data/G3/G3',
full=1) # load training and testing data
n = len(ss_cl)
folds = 10
acc = np.zeros((n, ))
for k in range(n):
(name, params) = clf_model(ss_cl[k]) # function name and parameters
acc[k] = cross_validation([name, params], X, d, folds=folds)
print(f'{k:3d}' + ') ' + f'{ss_cl[k]:20s}' + ': ' +
f'CV-Accuracy = {acc[k]:.4f}')
ks = np.argmax(acc)
print('-----------------------------------------------')
print('Best Classifier:')
print(f'{ks:3d}' + ') ' + f'{ss_cl[ks]:20s}' + ': ' +
f'CV-Accuracy = {acc[ks]:.4f}')
from sklearn.model_selection import train_test_split
from pyxvis.io.data import load_features
from pyxvis.io.plots import show_confusion_matrix
from pyxvis.learning.classifiers import clf_model
from pyxvis.learning.evaluation import hold_out
# load available dataset
(X0, d0) = load_features('../data/F2/F2', full=1)
# definition of training and testing data
X, Xt, d, dt = train_test_split(X0, d0, test_size=0.2, stratify=d0)
# definition of the classifier
cl_name = 'svm-rbf(0.1,1)' # generic name of the classifier
(name, params) = clf_model(cl_name) # function name and parameters
# Hold-out (train on (X,d), test on (Xt), compare with dt)
ds, acc, _ = hold_out([name, params], X, d, Xt, dt) # hold out
print(cl_name + ': ' + f'Accuracy = {acc:.4f}')
# display confusion matrix
show_confusion_matrix(dt, ds, 'Testing subset')
from pyxvis.io.data import load_features
from pyxvis.io.plots import show_confusion_matrix
from pyxvis.learning.classifiers import clf_model, define_classifier
from pyxvis.learning.classifiers import train_classifier, test_classifier
(X, d, Xt,
dt) = load_features('../data/F2/F2') # load training and testing data
# Classifier definition
ss_cl = ['dmin', 'svm-rbf(0.1,1)']
n = len(ss_cl)
for k in range(n):
(name, params) = clf_model(ss_cl[k]) # function name and parameters
clf = define_classifier([name, params]) # classifier definition
clf = train_classifier(clf, X, d) # classifier training
ds = test_classifier(clf, Xt) # classification of testing
show_confusion_matrix(dt, ds, ss_cl[k]) # display confusion matrix
import numpy as np
from pyxvis.learning.classifiers import nn_definition
from pyxvis.learning.classifiers import nn_forward_propagation, nn_backward_propagation
from pyxvis.learning.classifiers import nn_parameters_update, nn_loss_function
from pyxvis.io.plots import plot_features_y,show_confusion_matrix, plot_loss
from pyxvis.io.data import load_features
# Load training and testing data
(Xtrain,Ytrain,Xtest,Ytest) = load_features('../data/G4/G4',categorical=1)
plot_features_y(Xtrain,Ytrain,'Training Subset')
# Definitions
N = Xtrain.shape[1] # training samples
n_0 = Xtrain.shape[0] # number of inputs (X)
n_m = Ytrain.shape[0] # number of outputs (Y)
tmax = 1000 # max number of iterations
alpha = 10 # learning rate
loss_eps = 0.01 # stop if loss<loss_eps
nh = [6,12] # nodes of hidden layers
n = [n_0]+nh+[n_m] # nodes of each layer
m = len(n)-1
ltrain = np.zeros([tmax,1]) # training loss
# Training
t = -1
train = 1
W,b = nn_definition(n,N) # (step 1)
while train:
t = t+1
a = nn_forward_propagation(Xtrain,W,b) # (step 2)
dW,db = nn_backward_propagation(Ytrain,a,W,b) # (step 3)
from sklearn.neural_network import MLPClassifier
from pyxvis.io.plots import plot_features2,show_confusion_matrix, plot_loss
from pyxvis.io.data import load_features
# Load training and testing data
(Xtrain,Ytrain,Xtest,Ytest) = load_features('../data/G4/G4')
plot_features2(Xtrain,Ytrain,'Training+Testing Subsets')
# Definitions
alpha = 1e-5 # learning rate
nh = (6,12) # nodes of hidden layers
tmax = 2000 # max number of iterations
solver = 'adam' # optimization approach ('lbfgs','sgd', 'adam')
# Training
net = MLPClassifier(solver=solver, alpha=alpha,hidden_layer_sizes=nh,
random_state=1,max_iter=tmax)
print(Xtrain.shape)
print(Ytrain.shape)
net.fit(Xtrain, Ytrain)
# Evaluation
Ym = net.predict(Xtrain)
show_confusion_matrix(Ym,Ytrain,'Training')
Ys = net.predict(Xtest)
show_confusion_matrix(Ys,Ytest,'Testing')
from pyxvis.learning.evaluation import best_features_classifier
dataname = 'fbdata' # prefix of npy files of training and testing data
fxnew = 1 # the features are (0) loaded or (1) extracted and saved
if fxnew:
# features to extract
fx = ['basicint', 'gabor-ri', 'lbp-ri', 'haralick-2', 'fourier', 'hog']
# feature extraction in training images
path = '../images/fishbones/'
X, d = extract_features_labels(fx, path + 'train', 'jpg')
# feature extraction in testing images
Xt, dt = extract_features_labels(fx, path + 'test', 'jpg')
# backup of extracted features
save_features(X, d, Xt, dt, dataname)
else:
X, d, Xt, dt = load_features(dataname)
X, sclean, a, b = clean_norm(X)
Xt = clean_norm_transform(Xt, sclean, a, b)
# Classifiers to evaluate
ss_cl = [
'maha', 'bayes-kde', 'svm-lin', 'svm-rbf', 'qda', 'lda', 'knn3', 'knn7',
'nn'
]
# Number of features to select
ff = [3, 5, 10, 12, 15]
# Feature selectors to evaluate
ss_fs = ['fisher', 'qda', 'svm-lin', 'svm-rbf']
from pyxvis.io.plots import show_clf_results
from pyxvis.learning.classifiers import clf_model, define_classifier
from pyxvis.learning.classifiers import train_classifier, test_classifier
# List of classifiers
ss_cl = [
'dmin', 'lda', 'qda', 'maha', 'knn3', 'knn5', 'knn7', 'knn11', 'knn15',
'bayes-naive', 'bayes-kde', 'adaboost', 'lr', 'rf', 'tree', 'svm-lin',
'svm-rbf(0.1,1)', 'svm-rbf(0.1,0.5)', 'svm-rbf(0.5,1)',
'svm-pol(0.05,0.1,2)', 'svm-pol(0.05,0.5,2)', 'svm-pol(0.05,0.5,3)',
'svm-sig(0.1,1)', 'svm-sig(0.1,0.5)', 'svm-sig(0.5,1)', 'nn(10,)',
'nn(20,)', 'nn(12,6)', 'nn(20,10,4)'
]
(X, d, Xt,
dt) = load_features('../data/G3/G3') # load training and testing data
n = len(ss_cl)
acc_train = np.zeros((n, ))
acc_test = np.zeros((n, ))
for k in range(n):
(name, params) = clf_model(ss_cl[k]) # function name and parameters
clf = define_classifier([name, params]) # classifier definition
clf = train_classifier(clf, X, d) # classifier training
d0 = test_classifier(clf, X) # classification of training
ds = test_classifier(clf, Xt) # classification of testing
acc_train[k] = accuracy_score(d, d0) # accuracy in training
acc_test[k] = accuracy_score(dt, ds) # accuracy in testing
print(f'{k:3d}' + ') ' + f'{ss_cl[k]:20s}' + ': ' +
f'Acc-Train = {acc_train[k]:.4f}' + ' ' +
f'Acc-Test = {acc_test[k]:.4f}')
Xt : matrix of testing features, one sample per row
dt : vector of testing labels
s : string with the name of the model
p : number of features to be selected
[OUTPUT] q : indices of selected features (columns)
X : new matrix of training features
Xt : new matrix of testing features
"""
from sklearn.neighbors import KNeighborsClassifier as KNN
from pyxvis.features.selection import fse_model, fsel
from pyxvis.io.data import load_features
from pyxvis.io.plots import print_confusion
# Definition of input variables
(X, d, Xt, dt) = load_features('../data/F40/F40')
s = 'lda'
p = 5
# Feature selection
(name, params) = fse_model(s)
q = fsel([name, params], X, d, p, cv=5, show=1)
print(str(len(q)) + ' from ' + str(X.shape[1]) + ' features selected.')
# New training and testing data
X = X[:, q]
Xt = Xt[:, q]
# Classification and Evaluation
clf = KNN(n_neighbors=5)
clf.fit(X, d)
"""
[INPUT] X : training features (matrix of N x p elements)
d : vector of training labels (vector of N elements)
Xt : testing features (matrix of Nt x p elements)
dt : vector of training labels (vector of Nt elements)
s : string with the name of the model
[OUTPUT] ds : classification (vector of Nt elements)
clf: trained classifier
"""
from pyxvis.io.data import load_features
from pyxvis.io.plots import print_confusion
from pyxvis.learning.classifiers import clf_model, define_classifier
from pyxvis.learning.classifiers import train_classifier, test_classifier
# Definition of input variables
(X, d, Xt, dt) = load_features('../data/G3/G3')
s = 'knn5'
# Training and Testing
(name, params) = clf_model(s) # function name and parameters
clf = define_classifier([name, params]) # classifier definition
clf = train_classifier(clf, X, d) # classifier training
ds = test_classifier(clf, Xt) # classification on testing
# Evaluation of performance
print_confusion(dt, ds)
from sklearn.metrics import precision_recall_curve, average_precision_score
from sklearn.metrics import roc_curve, roc_auc_score
from pyxvis.io.data import load_features
from pyxvis.io.plots import plot_features, plot_ROC, plot_precision_recall
from pyxvis.learning.classifiers import clf_model, define_classifier, train_classifier
(X, d, Xt, dt) = load_features('../data/F2/F2') # load train/test data
plot_features(X, d, 'F2 dataset') # plot of feature space
ss_cl = ['nn(3,)', 'nn(4,)', 'nn(8,)'] # classifiers to evaluate
curve = 1 # 0 = ROC curve, 1 = precision/recall curve
n = len(ss_cl) # number of models
for k in range(n):
cl_name = ss_cl[k]
name, params = clf_model(cl_name) # function name and parameters
clf = define_classifier([name, params]) # classifier definition
clf = train_classifier(clf, X, d) # classifier training
p = clf.predict_proba(Xt)[:, 1] # classification probabilities
if curve == 0: # ROC curve
auc = roc_auc_score(dt, p) # area under curve
fpr, tpr, _ = roc_curve(dt, p) # false and true positive rates
plot_ROC(fpr, tpr, cl_name, auc, (k, n)) # ROC curve
else: # precision/recall curve
ap = average_precision_score(dt, p) # area under curve
pr, re, _ = precision_recall_curve(dt,
p) # precision and recall values
plot_precision_recall(pr, re, cl_name, ap,
