def runLDA(X_train, X_test, y_train, y_test, comp_range):
rbf_scores = []
linear_scores = []
for n_comp in comp_range:
print("\nn_comp=%d\n"%(n_comp))
transformer = LinearDiscriminantAnalysis(solver='svd', n_components=n_comp)
transformer.fit(X_train, y_train)
X_train_proj = transformer.transform(X_train)
X_test_proj = transformer.transform(X_test)
if n_comp == 2:
np.save('X_train_proj_2d_LDA', X_train_proj)
np.save('X_test_proj_2d_LDA', X_test_proj)
score_rbf = SVMmodel.runSVM(X_train_proj, X_test_proj, y_train, y_test, SVMmodel.getBestParam('rbf'), 'rbf')
rbf_scores.append(score_rbf.mean())
score_linear = SVMmodel.runSVM(X_train_proj, X_test_proj, y_train, y_test, SVMmodel.getBestParam('linear'), 'linear')
linear_scores.append(score_linear.mean())
return rbf_scores, linear_scores
def runAE(comp_range):
rbf_scores = []
linear_scores = []
for n_comp in comp_range:
print("\nn_comp=%d\n" % (n_comp))
data_pointer = 0
X_train_proj, X_test_proj = AutoEncoder(n_comp)
if n_comp == 2:
np.save('X_train_proj_2d_AE', X_train_proj)
np.save('X_test_proj_2d_AE', X_test_proj)
score_rbf = SVMmodel.runSVM(X_train_proj, X_test_proj, y_train, y_test,
SVMmodel.getBestParam('rbf'), 'rbf')
rbf_scores.append(score_rbf.mean())
score_linear = SVMmodel.runSVM(X_train_proj, X_test_proj, y_train,
y_test, SVMmodel.getBestParam('linear'),
'linear')
linear_scores.append(score_linear.mean())
return rbf_scores, linear_scores
def runTreeBasedSelection(X_train, X_test, y_train, y_test, comp_range):
rbf_scores = []
linear_scores = []
dimension = []
for n_comp in comp_range:
print("\nn_comp=%f\n"%(n_comp))
clf = ExtraTreesClassifier(n_estimators=n_comp)
model = SelectFromModel(estimator=clf)
model.fit(X_train, y_train)
X_train_sel = model.transform(X_train)
X_test_sel = model.transform(X_test)
dimension.append(X_train_sel.shape[1])
score_rbf = SVMmodel.runSVM(X_train_sel, X_test_sel, y_train, y_test, SVMmodel.getBestParam('rbf'), 'rbf')
rbf_scores.append(score_rbf.mean())
score_linear = SVMmodel.runSVM(X_train_sel, X_test_sel, y_train, y_test, SVMmodel.getBestParam('linear'), 'linear')
linear_scores.append(score_linear.mean())
return rbf_scores, linear_scores, dimension
def runIsomap(X_train, X_test, y_train, y_test, comp_range, n_neigh):
rbf_scores = []
linear_scores = []
for n_comp in comp_range:
print("\nn_comp=%d\n" % (n_comp))
transformer = Isomap(n_neighbors=n_neigh,
n_components=n_comp,
n_jobs=8)
transformer.fit(X_train)
X_train_proj = transformer.transform(X_train)
X_test_proj = transformer.transform(X_test)
if n_comp == 2:
np.save('X_train_proj_2d_Isomap_' + str(n_neigh), X_train_proj)
np.save('X_test_proj_2d_Isomap_' + str(n_neigh), X_test_proj)
score_rbf = SVMmodel.runSVM(X_train_proj, X_test_proj, y_train, y_test,
SVMmodel.getBestParam('rbf'), 'rbf')
rbf_scores.append(score_rbf.mean())
score_linear = SVMmodel.runSVM(X_train_proj, X_test_proj, y_train,
y_test, SVMmodel.getBestParam('linear'),
'linear')
linear_scores.append(score_linear.mean())
for i, scores in enumerate([rbf_scores, linear_scores]):
if i == 0:
kernel = 'rbf'
elif i == 1:
kernel = 'linear'
else:
kernel = ''
bestIdx = np.argmax(scores)
bestNComp = comp_range[bestIdx]
bestAcc = scores[bestIdx]
with open('res_Isomap_' + kernel + '_' + str(n_neigh) + '.txt',
'w') as f:
for j in range(len(comp_range)):
f.write(kernel + ": n_comp = %f, acc = %f\n" %
(comp_range[j], scores[j]))
f.write(kernel + ": Best n_comp = %f\n" % (bestNComp))
f.write(kernel + ": acc = %f\n" % (bestAcc))
return rbf_scores, linear_scores
def runSelectKBest(X_train, X_test, y_train, y_test, comp_range):
rbf_scores = []
linear_scores = []
for n_comp in comp_range:
print("\nn_comp=%d\n" % (n_comp))
selector = SelectKBest(score_func=f_classif, k=n_comp)
selector.fit(X_train, y_train)
X_train_sel = selector.transform(X_train)
X_test_sel = selector.transform(X_test)
if n_comp == 2:
np.save('X_train_proj_2d_SelectKBest', X_train_sel)
np.save('X_test_proj_2d_SelectKBest', X_test_sel)
score_rbf = SVMmodel.runSVM(X_train_sel, X_test_sel, y_train, y_test,
SVMmodel.getBestParam('rbf'), 'rbf')
rbf_scores.append(score_rbf.mean())
score_linear = SVMmodel.runSVM(X_train_sel, X_test_sel, y_train,
y_test, SVMmodel.getBestParam('linear'),
'linear')
linear_scores.append(score_linear.mean())
return rbf_scores, linear_scores
def runTSNE(X_train, X_test, y_train, y_test, comp_range, ppl, m):
rbf_scores = []
linear_scores = []
for n_comp in comp_range:
print("\nn_comp=%d\n" % (n_comp))
transformer = TSNE(n_components=n_comp,
perplexity=50.0,
method=m,
n_jobs=8)
transformer.fit(X_train)
X_train_proj = transformer.fit_transform(X_train)
X_test_proj = transformer.fit_transform(X_test)
if n_comp == 2 and m == 'barnes_hut':
np.save('X_train_proj_2d_TSNE_' + str(ppl), X_train_proj)
np.save('X_test_proj_2d_TSNE_' + str(ppl), X_test_proj)
score_rbf = SVMmodel.runSVM(X_train_proj, X_test_proj, y_train, y_test,
SVMmodel.getBestParam('rbf'), 'rbf')
rbf_scores.append(score_rbf.mean())
score_linear = SVMmodel.runSVM(X_train_proj, X_test_proj, y_train,
y_test, SVMmodel.getBestParam('linear'),
'linear')
linear_scores.append(score_linear.mean())
return rbf_scores, linear_scores
def runVarianceThreshold(X_train, X_test, y_train, y_test, comp_range):
rbf_scores = []
linear_scores = []
dimension = []
for n_comp in comp_range:
print("\nn_comp=%f\n" % (n_comp))
selector = VarianceThreshold(threshold=n_comp)
selector.fit(X_train)
X_train_sel = selector.transform(X_train)
X_test_sel = selector.transform(X_test)
dimension.append(X_train_sel.shape[1])
score_rbf = SVMmodel.runSVM(X_train_sel, X_test_sel, y_train, y_test,
SVMmodel.getBestParam('rbf'), 'rbf')
rbf_scores.append(score_rbf.mean())
score_linear = SVMmodel.runSVM(X_train_sel, X_test_sel, y_train,
y_test, SVMmodel.getBestParam('linear'),
'linear')
linear_scores.append(score_linear.mean())
return rbf_scores, linear_scores, dimension
def runPCA(X_train, X_test, y_train, y_test, comp_range, Kernel):
C = SVMmodel.getBestParam(Kernel)
scores = []
for n_comp in comp_range:
print("\nn_comp=%d\n" % (n_comp))
transformer = KernelPCA(n_components=n_comp,
kernel=Kernel,
copy_X=True,
n_jobs=8)
transformer.fit(X_train)
X_train_proj = transformer.transform(X_train)
X_test_proj = transformer.transform(X_test)
if n_comp == 2:
np.save('X_train_proj_2d_' + Kernel, X_train_proj)
np.save('X_test_proj_2d_' + Kernel, X_test_proj)
score = SVMmodel.runSVM(X_train_proj, X_test_proj, y_train, y_test, C,
Kernel)
scores.append(score.mean())
print(scores)
return scores