def __init__(self, personLoader,person):
print("loading person ",person)
AModel.__init__(self,personLoader)
classificatorName = str(self.personLoader.classificator.name)
#load all features & keep them in memory
self.y = load('global_y_per_person' + classificatorName +'_p' + str(person))
if self.y == None:
print('[Warn] Rebuilding cache')
self.X, self.y = self.personLoader.load(person)
dump(self.X,'global_X_per_person_p' + str(person))
dump(self.y,'global_y_per_person' + classificatorName + '_p' + str(person))
else:
self.X = load('global_X_per_person_p' +str(person))
self.X = np.array(self.X)
self.y = np.array(self.y)
for index,val in enumerate(np.std(self.X,axis=0)):
if val == 0:
print('warning zero std for feature index: ', index, ' (', personLoader.featureExtractor.getFeatureNames()[index])
#manual Feature standardization
self.X = self.X - np.average(self.X,axis=0)
self.X = np.true_divide( self.X, np.std(self.X,axis=0) )
def svm_rbf_accs_gen():
# get testaccs
test_accs = []
model = PersScript("ALL", 32, 30, Classificators.ContValenceClassificator(), "../dumpedData/genScript/")
accs = load('accs_all',path=model.ddpad)[0]
for metric in accs:
test_accs.append(metric[7])
test_accs = np.array(test_accs)
sort_indices = np.array([0, 1, 2, 9, 3, 6, 10, 4, 5, 7, 11])
colors = ['b', 'b', 'b', 'b', 'r', 'r', 'r', 'g', 'g', 'g', 'g']
names = np.array(['R', 'MI', 'dC', 'LR', 'L1', 'L2', 'SVM', 'RF', 'STD', 'ANOVA', 'LDA', 'PCA'])
names = names[sort_indices]
test_accs = test_accs[sort_indices]
genPlot(test_accs,
[0 for acc in test_accs],
names,
'Accuracies of valence SVM models (cross subject)',
'model',
'test acc',
colors
)
# get testaccs
test_accs = []
model = PersScript("ALL", 32, 30, Classificators.ContArousalClassificator(), "../dumpedData/genScript/")
accs = load('accs_all', path=model.ddpad)[0]
for metric in accs:
test_accs.append(metric[7])
test_accs = np.array(test_accs)
sort_indices = np.array([0, 1, 2, 9, 3, 6, 10, 4, 5, 7, 11])
colors = ['b', 'b', 'b', 'b', 'r', 'r', 'r', 'g', 'g', 'g', 'g']
names = np.array(['R', 'MI', 'dC', 'LR', 'L1', 'L2', 'SVM', 'RF', 'STD', 'ANOVA', 'LDA', 'PCA'])
names = names[sort_indices]
test_accs = test_accs[sort_indices]
genPlot(test_accs,
[0 for acc in test_accs],
names,
'Accuracy of arousal SVM models (cross subject)',
'model',
'test acc',
colors
)
print(names)
def getAnalytics():
t0 = time.time()
feat_corr = load("valence_feat_pval")
if feat_corr == None:
feat_corr = valenceCorrelationWorker()
dump(feat_corr, "valence_feat_pval")
# here feat_corr has a list of correlations of each feature for each person => dim reduc & 3D plot
X_3D = PCA(n_components=3).fit_transform(feat_corr)
X_2D = PCA(n_components=2).fit_transform(feat_corr)
fig = plt.figure(1, figsize=(4, 3))
plt.clf()
ax = Axes3D(fig, rect=[0, 0, 0.95, 1], elev=48, azim=134)
ax.scatter(X_3D[:, 0], X_3D[:, 1], X_3D[:, 2])
plt.title("valence correlations for different persons 3D")
plt.show()
plt.clf()
plt.scatter(X_2D[:, 0], X_2D[:, 1])
plt.title("valence correlations for different persons 2D")
plt.show()
t1 = time.time()
print("valence complete, time spend: " + str(t1 - t0))
feat_corr = load("arousal_feat_pval")
if feat_corr == None:
feat_corr = arousalCorrelationWorker()
dump(feat_corr, "arousal_feat_pval")
# here feat_corr has a list of correlations of each feature for each person => dim reduc & 3D plot
X_3D = PCA(n_components=3).fit_transform(feat_corr)
X_2D = PCA(n_components=2).fit_transform(feat_corr)
fig = plt.figure(1, figsize=(4, 3))
plt.clf()
ax = Axes3D(fig, rect=[0, 0, 0.95, 1], elev=48, azim=134)
ax.scatter(X_3D[:, 0], X_3D[:, 1], X_3D[:, 2])
plt.title("arousal correlations for different persons 3D")
plt.show()
plt.clf()
plt.scatter(X_2D[:, 0], X_2D[:, 1])
plt.title("arousal correlations for different persons 2D")
plt.show()
t2 = time.time()
print("arousal complete, time spend: " + str(t2 - t1))
print("total time spend: " + str(t2 - t0))
def run(self,person, criterion):
#http://scikit-learn.org/stable/auto_examples/ensemble/plot_forest_importances.html
classificatorName = str(self.personLoader.classificator.name)
#load all features & keep them in memory
y = load('global_y_per_person' + classificatorName +'_p' + str(person))
if y == None:
print('[Warn] Rebuilding cache')
X, y = self.personLoader.load(person)
dump(X,'global_X_per_person_p' + str(person))
dump(y,'global_y_per_person' + classificatorName + '_p' + str(person))
else:
X = load('global_X_per_person_p' +str(person))
#grow forest
forest = RandomForestClassifier(
n_estimators=5000,
max_features='auto',
criterion=criterion,
n_jobs=-1,
random_state=0
)
normalize(X,copy=False)
#fit forest
forest.fit(X,y)
#get importances
importances = forest.feature_importances_
std = np.std([tree.feature_importances_ for tree in forest.estimators_], axis = 0)
indices = np.argsort(importances)[::-1]
featNames = self.personLoader.featureExtractor.getFeatureNames()
return {
'classificatorName' : classificatorName,
'featNames' : featNames,
'importances' : importances,
'std' : std,
'indices' : indices, #[ index of first, index of second] ...
'criterion' : criterion
}
def phyeegall_gen():
print('bullcrap alert! random forest not right here!!')
lbls = ['ALL', 'EEG', 'non-EEG']
# get testaccs
test_accs = []
for set in lbls:
model = PersScript(set, 32, 30, Classificators.ContValenceClassificator(), "../dumpedData/genScript/")
accs = load('accs_all',path=model.ddpad)[0]
test_accs.append(accs[7][7])
test_accs = np.array(test_accs)
genPlot(test_accs,
[0 for acc in test_accs],
lbls,
'Valence RF acc for different feat sets (cross subject)',
'feature Set',
'test acc',
['b', 'r', 'g']
)
print(test_accs)
# get testaccs
test_accs = []
for set in lbls:
model = PersScript(set, 32, 30, Classificators.ContArousalClassificator(), "../dumpedData/genScript/")
accs = load('accs_all', path=model.ddpad)[0]
test_accs.append(accs[7][7])
test_accs = np.array(test_accs)
genPlot(test_accs,
[0 for acc in test_accs],
lbls,
'Arousal RF acc for different feat sets (cross subject)',
'feature Set',
'test acc',
['b', 'r', 'g']
)
print(test_accs)
def run(self,criterion):
#http://scikit-learn.org/stable/auto_examples/ensemble/plot_forest_importances.html
classificatorName = str(self.personLoader.classificator.name)
featNames = np.array(self.personLoader.featureExtractor.getFeatureNames())
#load all features & keep them in memory
y = load('global_y_allpersons' + classificatorName)
if y == None:
print('[Warn] Rebuilding cache')
X, y = self.personLoader.load()
dump(X,'global_X_allpersons')
dump(y,'global_y_allpersons' + classificatorName)
else:
X = load('global_X_allpersons')
self.getIntermediateResult(criterion,X,y,'all features')
#step1
importances, std, indices = self.step1(criterion,X,y)
#step2
indices = self.step2(indices)
self.getIntermediateResult(criterion,X[:,indices],y,'80%')
#step 3 add features one by one
acc_list, best_count, best_metric = self.step3(criterion,indices,X,y,10,featNames)
return {
'classificatorName' : classificatorName,
'featNames' : self.personLoader.featureExtractor.getFeatureNames(),
'global_importances' : importances,
'global_std' : std,
'global_indices' : indices, #[ index of first, index of second] ...
'criterion' : criterion
}
def run(self):
for person in range(1, self.stopperson + 1):
# load person data
y_cont = load('cont_y_p' + str(person), path=self.ddpad)
if y_cont == None:
print('[Warn] Rebuilding cache - person ' + str(person))
personLdr = personLoader.NoTestsetLoader(self.classifier, self.featExtr)
X, y_cont = personLdr.load(person)
dump(X, 'X_p' + str(person), path=self.ddpad)
dump(y_cont, 'cont_y_p' + str(person), path=self.ddpad)
else:
X = load('X_p' + str(person), path=self.ddpad)
# manual Feature standardization
X = X - np.average(X, axis=0)
X = np.true_divide(X, np.std(X, axis=0))
self.X[person - 1] = np.array(X)
self.y_cont[person - 1] = np.array(y_cont)
y_disc = np.array(y_cont)
y_disc[y_disc <= 5] = 0
y_disc[y_disc > 5 ] = 1
self.y_disc[person - 1] = y_disc
self.results = self.getMetrics()
self.genReport()
self.accs = self.getAccs()
self.probVsDim()
self.genAccReport()
def run(self):
#create 32 classifiers
print('initialising the 32 classifiers ...')
stop_person = 33
if stop_person < 33:
print("[warn] not using all persons")
pool = Pool(processes=POOL_SIZE)
self.classifiers = pool.map( self.initClassifiers, range(1,stop_person) )
pool.close()
pool.join()
to_keep = {'all_orig_featureNames' : self.classifiers[0].personLoader.featureExtractor.getFeatureNames(),
'criterion': self.classifiers[0].criterion,
'classificatorName' : self.classifiers[0].personLoader.classificator.name,
'stop_person' : stop_person,
'threshold' : self.threshold
}
#step 1: variable ranking: get all importances of the different features
print('step 1: getting importances')
importances = load('importances_once')
if importances == None:
print("[warn] rebuilding importances")
pool = Pool(processes=POOL_SIZE)
importances = np.array( pool.map( self.getImportance, range(1,stop_person) ))
pool.close()
pool.join()
dump(importances, 'importances_once')
to_keep['all_importances'] = importances
avg_importances = np.average(importances[:,:,1], axis=0)
std_importances = [ np.std(importances[:,i,1]) for i in range(len(importances[0]))]
to_keep['avg_importances'] = avg_importances
to_keep['std_importances'] = std_importances
#step 2: elimintaion: remove everything below threshold, a.k.a. keep everything above the threshold
print('step 2: filtering features - threshold')
indexes_to_keep = [i for i, val in enumerate(avg_importances) if val > self.threshold]
for c in self.classifiers: c.filterFeatures(indexes_to_keep)
avg_importances = avg_importances[indexes_to_keep] #cleanup memory
to_keep['step1_featureNames'] = self.classifiers[0].personLoader.featureExtractor.getFeatureNames()
to_keep['step1_avg_importances'] = avg_importances
#sort features
indices = np.array(np.argsort(avg_importances)[::-1])
for c in self.classifiers: c.filterFeatures(indices)
#add features one by one and select smallest, lowest oob model
print('building tree')
highest_oob_score = 0
highest_index = 1
oob_scores = []
for i in range(1,len(indices)+1):
self.count = i
pool = Pool(processes=POOL_SIZE)
oob_errors = pool.map( self.getOOBErrors, range(1,stop_person) )
pool.close()
pool.join()
avg_oob = np.average(oob_errors, axis=0)
print("feat Count: " + str(i) + " - error: " + str(avg_oob))
oob_scores.append(avg_oob)
if avg_oob > highest_oob_score:
#TODO std
highest_oob_score = avg_oob
highest_index = i
to_keep['step2_oob_scores'] = oob_scores
#select smallest tree with lowest error => lowest index & lowest error
for c in self.classifiers: c.filterFeatures( [c for c in range(highest_index)] )
to_keep['step3_size'] = highest_index
to_keep['step3_oob'] = highest_oob_score
print("selected tree size:" + str(highest_index) + ' - oob: ' + str(highest_oob_score))
print('final building phase')
#restart with an empty tree and add features one by one, only keep features that decrease the error with a certain threshold
prev_oob = 0
used_features = []
used_accs = []
for i in range(highest_index):
self.count = i + 1
pool = Pool(processes=POOL_SIZE)
oob_errors = pool.map( self.getOOBErrors, range(1,stop_person) )
pool.close()
pool.join()
avg_oob = np.average(oob_errors, axis=0)
print("feat Count: " + str(i) + " - error: " + str(avg_oob))
if avg_oob - self.threshold > prev_oob or prev_oob == 0:
prev_oob = avg_oob
used_features.append(i)
used_accs = oob_errors
to_keep['step4_used_accs'] = used_accs
to_keep['step4_features'] = used_features
for c in self.classifiers: c.filterFeatures( [c for c in range(highest_index)] )
to_keep['step4_featureNames'] = self.classifiers[0].personLoader.featureExtractor.getFeatureNames()
dump(to_keep,'to_keep')
return to_keep
def getAccs(self, person):
print('gettings accs for person ' + str(person))
to_ret = load('accs_p' + str(person), path = self.ddpad)
if to_ret == None:
# load person data
# load all features & keep them in memory
y = load('cont_y_p' + str(person), path=self.ddpad)
if y == None:
print('[Warn] Rebuilding cache - person ' + str(person))
personLdr = personLoader.NoTestsetLoader(self.classifier, self.featExtr)
X, y = personLdr.load(person)
dump(X, 'X_p' + str(person), path=self.ddpad)
dump(y, 'cont_y_p' + str(person), path=self.ddpad)
else:
X = load('X_p' + str(person), path=self.ddpad)
y = np.array(y)
# manual Feature standardization
X = X - np.average(X, axis=0)
X = np.true_divide(X, np.std(X, axis=0))
#train test set
# Train / testset
X, X_test, y, y_test_cont = train_test_split(X,y,test_size=10, random_state=17)
y[y <= 5] = 0
y[y > 5] = 1
y_test = np.array(y_test_cont)
y_test[y_test <= 5] = 0
y_test[y_test > 5] = 1
to_ret = []
for model_index, model in enumerate([
#SVC(kernel='linear'),
SVC(kernel='rbf')
#KNN(n_neighbors=3),
#KNN(n_neighbors=5),
#KNN(n_neighbors=7),
#lda needs two features
#RandomForestClassifier(
# n_estimators=1000,
# max_features='auto',
# criterion='gini',
# n_jobs=-1,
#)
]):
model_to_ret = []
for metric in self.results[person-1]:
featNames = np.array(self.featExtr.getFeatureNames()) #take clean copy
#sort features
indices = np.array(np.argsort(metric)[::-1])
#take top threshold
indices = indices[:self.threshold]
#apply
X_model = np.array(X[:,indices])
X_model_test = np.array(X_test[:,indices])
featNames = featNames[indices]
best_feat, best_featNames = [], []
all_scores, all_stds = [],[]
best_score, best_std = 0, 0
for i in range(self.threshold):
to_keep = best_feat[:]
to_keep.append(i)
X_temp = np.array(X_model[:,to_keep])
# get scores
run_scores = []
for tr, te in KFold(n=len(X_temp), n_folds=5, shuffle=True, random_state=17):
model.fit(X_temp[tr], y[tr])
run_scores.append(self.accuracy(model.predict(X_temp[te]), y[te]))
new_score = np.average(run_scores)
new_std = np.std(run_scores)
all_scores.append(new_score)
all_stds.append(new_std)
# better?
if new_score - new_std > best_score - best_std:
best_score = new_score
best_std = new_std
best_feat = to_keep
best_featNames.append(featNames[i])
#get test score
if model_index == 0:
test_model = SVC(kernel='rbf', probability=True)
test_model.fit(X_model[:,best_feat], y)
X_model_test = np.array(X_model_test[:,best_feat])
test_pred = test_model.predict(X_model_test)
test_prob = test_model.predict_proba(X_model_test)
test_acc = self.accuracy(test_model.predict(X_model_test), y_test)
else:
test_model = RandomForestClassifier(
n_estimators=2000,
max_features='auto',
criterion='gini',
n_jobs=-1
)
test_model.fit(X_model[:, best_feat], y)
X_model_test = np.array(X_model_test[:, best_feat])
test_pred = test_model.predict(X_model_test)
test_prob = test_model.predict_proba(X_model_test)
test_acc = self.accuracy(test_model.predict(X_model_test), y_test)
model_to_ret.append([best_feat, best_featNames, best_score, best_std, all_scores, all_stds, indices, test_acc, test_pred, test_prob, y_test, y_test_cont])
to_ret.append(model_to_ret)
dump(to_ret, 'accs_p' + str(person), path = self.ddpad)
return to_ret
def getAccs(self):
pool = Pool(processes=POOL_SIZE)
results = pool.map(self.top30Accs, range(1,self.stop_person))
pool.close()
pool.join()
return results
if __name__ == '__main__':
stop_person = 33
if stop_person < 33:
print('[warn] not using all persons!')
# lda
lda_results = load('results_valence_lda')
if lda_results == None:
print('[warn] rebuilding valence lda results cache')
pool = Pool(processes=POOL_SIZE)
lda_results = pool.map(ldaRankings, range(1, stop_person))
pool.close()
pool.join()
dump(lda_results, 'results_valence_lda')
lda_results = np.array(lda_results)
train_accs = np.array(lda_results[:, 0])
test_accs = np.array(lda_results[:, 1])
genLDAReport(train_accs, test_accs)
results = load('results_valence')
if results == None:
def RFPerson(person):
print("person: " + str(person))
# load X , y
# load all features & keep them in memory
featExtr = getFeatures()
featureNames = np.array(featExtr.getFeatureNames())
y_cont = load("cont_y_p" + str(person))
if y_cont == None:
print("[Warn] Rebuilding cache - person " + str(person))
X, y_cont = personLoader.NoTestsetLoader(
classificator=Classificators.ContValenceClassificator(), featExtractor=featExtr
).load(person)
dump(X, "X_p" + str(person))
dump(y_cont, "cont_y_p" + str(person))
else:
X = load("X_p" + str(person))
y_disc = np.array(y_cont)
y_disc[y_disc <= 5] = 0
y_disc[y_disc > 5] = 1
# manual Feature standardization
X = X - np.average(X, axis=0)
X = np.true_divide(X, np.std(X, axis=0))
# step 1 determine importances using RF forest
indices_step1, featureNames_step1 = step1(X, y_disc, featureNames)
featureNames = np.array(featureNames_step1)
indices = np.array(indices_step1)
# filter features (X) based on the results from step 1
X = X[:, indices]
# step 2 - interpretation
featCount_inter, score_inter, std_inter = step2_interpretation(X, y_disc, featureNames)
indices_inter = indices[:featCount_inter]
featureNames_inter = featureNames[indices_inter]
# step 2 - prediction
indices_pred, score_pred, std_pred = step2_prediction(X, y_disc, featureNames)
featureNames_pred = featureNames[indices_pred]
print(
"["
+ str(person)
+ "interpretation - score: "
+ str(score_inter)
+ "("
+ str(std_inter)
+ ")prediction - score: "
+ str(score_pred)
+ " - "
+ str(std_pred)
)
to_ret = [
[featCount_inter, score_inter, std_inter, featureNames_inter],
[len(indices_pred), score_pred, std_pred, featureNames_pred],
]
dump(to_ret, "rf_P" + str(person))
return to_ret
def getAccs(self):
to_ret = load('accs_all', path=self.ddpad)
if to_ret == None:
# Train / testset
X, X_test, y, y_test_cont = train_test_split(self.X, self.y_cont,test_size=8, random_state=17)
X = np.array(X)
X_test = np.array(X_test)
y = np.array(y)
y_test_cont = np.array(y_test_cont)
y[y <= 5] = 0
y[y > 5] = 1
y_test = np.array(y_test_cont)
y_test[y_test <= 5] = 0
y_test[y_test > 5] = 1
to_ret = []
model = SVC(kernel='rbf', probability=True)
for mindex, metric in enumerate(self.results):
print('model' + str(0) + ' - metric' + str(mindex))
featNames = np.array(self.featExtr.getFeatureNames()) #take clean copy
#sort features
indices = np.array(np.argsort(metric)[::-1])
#take top threshold
indices = indices[:self.threshold]
#old struct
if mindex == 0:
X, y = self.fixStructure(X, y)
junk, y_test_cont = self.fixStructure(np.array(X_test), y_test_cont)
X_test, y_test = self.fixStructure(X_test, y_test)
#Filter features
X_model = np.array(X[:,indices])
featNames = featNames[indices]
best_feat, best_featNames = [], []
all_scores, all_stds = [],[]
best_score, best_std = 0, 0
for i in range(self.threshold):
to_keep = best_feat[:]
to_keep.append(i)
X_temp = np.array(X_model[:,to_keep])
# get scores
run_scores = []
X_temp, y = self.reverseFixStructure(X_temp, y)
for tr, te in KFold(n=len(X_temp), n_folds=5, shuffle=True, random_state=17):
X_t, y_t = self.fixStructure(X_temp[tr], y[tr])
X_te, y_te = self.fixStructure(X_temp[te], y[te])
model.fit(X_t, y_t)
run_scores.append(self.accuracy(model.predict(X_te), y_te))
X_temp, y = self.fixStructure(X_temp, y)
new_score = np.average(run_scores)
new_std = np.std(run_scores)
all_scores.append(new_score)
all_stds.append(new_std)
# better?
if new_score - new_std > best_score - best_std:
best_score = new_score
best_std = new_std
best_feat = to_keep
best_featNames.append(featNames[i])
#get test score => old struct :D
model.fit(X_model[:,best_feat], y)
X_model_test = np.array(X_test[:, best_feat])
test_pred = model.predict(X_model_test)
test_prob = model.predict_proba(X_model_test)
test_acc = self.accuracy(test_pred, y_test)
to_ret.append([best_feat, best_featNames, best_score, best_std, all_scores, all_stds, indices, test_acc, test_pred, test_prob, y_test,
y_test_cont])
X, y = self.reverseFixStructure(X, y)
X_test, y_test = self.reverseFixStructure(X_test, y_test)
dump(to_ret, 'accs_all', path = self.ddpad)
return to_ret
def getMetrics(self):
metrics = load("all_metrics", path=self.ddpad)
if metrics == None:
X, y_cont = self.fixStructure(self.X, self.y_cont)
y_disc = np.array(y_cont)
y_disc[y_disc <= 5] = 0
y_disc[y_disc > 5] = 1
metrics = []
#pearson
corr = []
for index in range(len(X[0])):
corr.append( pearsonr(X[:, index], y_cont)[0] )
metrics.append(corr)
#Mut inf
#dcorr
mi = []
dcorr = []
for feature in np.transpose(X):
# normalized mutual information
c_xy = np.histogram2d(feature, y_cont, 2)[0]
entX = entropy(feature, y_cont)
entY = entropy(feature, y_cont)
nMutInf = mutual_info_score(None, None, contingency=c_xy) / float(np.sqrt(entX * entY))
mi.append(nMutInf)
# Distance Correlation
dc, dr, dvx, dvy = self.dcov_all(feature, y_cont)
dcorr.append(dr)
metrics.append(mi)
metrics.append(dcorr)
#Linear Regression
lr = LinearRegression(n_jobs=-1)
lr.fit(X, y_cont)
metrics.append(lr.coef_)
#Lasso Regression
alphas = [0.03, 0.1, 0.3, 1, 3, 10]
best_alpha = 0.01
best_acc = 0
for train_index, test_index in KFold(len(y_cont), n_folds=5):
X_train, X_test = X[train_index], X[test_index]
y_train, y_test = y_cont[train_index], y_cont[test_index]
lasso = Lasso(alpha=best_alpha)
lasso.fit(X_train, y_train)
pred = lasso.predict(X_test)
best_acc += self.accuracy(pred, y_cont)
best_acc /= float(5)
for alpha in alphas:
acc = 0
for train_index, test_index in KFold(len(y_cont), n_folds=5):
X_train, X_test = X[train_index], X[test_index]
y_train, y_test = y_cont[train_index], y_cont[test_index]
lasso = Lasso(alpha=alpha)
lasso.fit(X_train, y_train)
pred = lasso.predict(X_test)
acc += self.accuracy(pred, y_test)
acc /= float(5)
if acc > best_acc:
best_acc = acc
best_alpha = alpha
lasso = Lasso(alpha=best_alpha)
lasso.fit(X, y_cont)
metrics.append(lasso.coef_)
#Ridge Regression
alphas = [0.03, 0.1, 0.3, 1, 3, 10]
best_alpha = 0.01
best_acc = 0
for train_index, test_index in KFold(len(y_cont), n_folds=5):
X_train, X_test = X[train_index], X[test_index]
y_train, y_test = y_cont[train_index], y_cont[test_index]
ridge = Ridge(alpha=best_alpha)
ridge.fit(X_train, y_train)
pred = ridge.predict(X_test)
best_acc += self.accuracy(pred, y_test)
best_acc /= float(5)
for alpha in alphas:
acc = 0
for train_index, test_index in KFold(len(y_cont), n_folds=5):
X_train, X_test = X[train_index], X[test_index]
y_train, y_test = y_cont[train_index], y_cont[test_index]
ridge = Ridge(alpha=alpha)
ridge.fit(X_train, y_train)
pred = lasso.predict(X_test)
acc += self.accuracy(pred, y_test)
acc /= float(5)
if acc > best_acc:
best_acc = acc
best_alpha = alpha
ridge = Ridge(alpha=best_alpha)
ridge.fit(X, y_cont)
metrics.append(ridge.coef_)
#SVM
clf = SVC(kernel='linear')
clf.fit(X, y_disc)
svm_weights = (clf.coef_ ** 2).sum(axis=0)
svm_weights /= float(svm_weights.max())
metrics.append(svm_weights)
#Random Forests
#rf importances
#grow forest
importances = []
for run in range(self.runs):
forest = RandomForestClassifier(
n_estimators=2000,
max_features='auto',
criterion='gini',
n_jobs=-1,
)
forest.fit(X, y_disc)
importances.append(forest.feature_importances_)
# stds.append( np.std([tree.feature_importances_ for tree in forest.estimators_], axis = 0) )
metrics.append(np.average(importances, axis=0))
metrics.append(np.std(importances, axis=0))
X, y_disc = self.reverseFixStructure(X, y_disc)
forest.fit(X,y_disc)
importances, stds = forest.getImportance()
metrics.append(importances)
metrics.append(stds)
X, y_disc = self.fixStructure(X,y_disc)
#ANOVA
anova = SelectKBest(f_regression, k=self.threshold)
anova.fit(X,y_disc)
selected_features = anova.get_support()
metrics.append(selected_features)
#Linear Discriminant Analysis
lda = LinearDiscriminantAnalysis(n_components=1)
lda.fit(X,y_disc)
metrics.append(lda.coef_[0])
#Principal Component Analysis
pca = PCA(n_components=1)
pca.fit(X)
metrics.append(pca.components_[0])
#absolute values
metrics = np.absolute(np.array(metrics))
dump(metrics, 'all_metrics', path=self.ddpad)
return np.array(metrics)
def top30Accs(self,person):
FOLDS = 5
# take averages
avg_results = [[0] * len(self.results[0, 0])] * len(self.results[0])
for result in self.results:
for i in range(len(result)): # each feature
for j in range(len(result[i])):
avg_results[i][j] += result[i][j]
avg_results = np.array(avg_results)
avg_results = np.true_divide(avg_results, float(len(self.results)))
acc_train_no_features = []
acc_test_no_features = []
#for person in range(1, len(results) + 1):
print('working on person ' + str(person))
# load all features & keep them in memory
y_cont = load('cont_y_p' + str(person))
X = load('X_p' + str(person))
X = np.array(X)
y_cont = np.array(y_cont)
y_disc = y_cont
y_disc[y_disc <= 5] = 0
y_disc[y_disc > 5] = 1
for index, val in enumerate(np.std(X, axis=0)):
if val == 0:
print('warning zero std for feature index: ', index, ' (', personLoader.featureExtractor.getFeatureNames()[index])
# manual Feature standardization
X = X - np.average(X, axis=0)
X = np.true_divide(X, np.std(X, axis=0))
pers_train_accs = []
pers_test_accs = []
for metric in range(len(avg_results[0])): #for each metric
# sort features
indices = np.array(np.argsort(avg_results[:, metric])[::-1])
# get first 30 indexes
features_to_keep = indices[:30]
X_filtered = X[:, features_to_keep]
model_train_accs = []
model_test_accs = []
for i in range(1, len(features_to_keep) + 1): #for each feat count
print('[' + str(person) + '] - metric: ' + str(metric) + '-' + str(i))
X_temp = X_filtered[:, :i]
train_acc, test_acc = 0, 0
for train_index, test_index in KFold(len(y_disc), n_folds=FOLDS, random_state=19, shuffle=True):
X_train, X_test = X_temp[train_index], X_temp[test_index]
y_train, y_test = y_disc[train_index], y_disc[test_index]
'''
clf = RandomForestClassifier(
n_estimators=2000,
max_features='auto',
criterion='gini',
n_jobs=-1,
)
clf.fit(X_train, y_train)
'''
clf = svm.SVC()
clf.fit(X_train, y_train)
train_acc += accuracy(clf.predict(X_train), y_train) / float(FOLDS)
test_acc += accuracy(clf.predict(X_test) , y_test ) / float(FOLDS)
model_train_accs.append(train_acc)
model_test_accs.append(test_acc)
pers_train_accs.append(model_train_accs)
pers_test_accs.append(model_test_accs)
acc_train_no_features.append(pers_train_accs)
acc_test_no_features.append(pers_test_accs)
return [acc_train_no_features, acc_test_no_features]
def ldaRankings(person):
FOLDS = 5
# load all features & keep them in memory
y_cont = load('cont_y_p' + str(person))
if y_cont == None:
print('[Warn] Rebuilding cache - person ' + str(person))
classificator = Classificators.ContValenceClassificator()
featExtr = getFeatures()
personLdr = personLoader.NoTestsetLoader(classificator, featExtr)
X, y_cont = personLdr.load(person)
dump(X, 'X_p' + str(person))
dump(y_cont, 'cont_y_p' + str(person))
else:
X = load('X_p' + str(person))
X = np.array(X)
y_cont = np.array(y_cont)
y_disc = y_cont
y_disc[y_disc <= 5] = 0
y_disc[y_disc > 5] = 1
for index, val in enumerate(np.std(X, axis=0)):
if val == 0:
print('warning zero std for feature index: ', index, ' (', personLoader.featureExtractor.getFeatureNames()[index])
# manual Feature standardization
X = X - np.average(X, axis=0)
X = np.true_divide(X, np.std(X, axis=0))
feat_test_error = []
feat_train_error = []
X_temp = X[:, [0, 1, 2, 3, 4, 5, 6, 7, 8, 9]] #phy only
feat_test_error.append(0)
feat_train_error.append(0)
for train_index, test_index in KFold(len(y_disc), n_folds=FOLDS, random_state=17, shuffle=True):
X_train, X_test = X_temp[train_index], X_temp[test_index]
y_train, y_test = y_disc[train_index], y_disc[test_index]
clf = LDA(shrinkage='auto', solver='lsqr')
clf.fit(X_train, y_train)
feat_train_error[0] += accuracy(clf.predict(X_train), y_train) / float(FOLDS)
feat_test_error[0] += accuracy(clf.predict(X_test) , y_test ) / float(FOLDS)
print("train: " + str(feat_train_error[0]) + " test: " + str(feat_test_error[0]))
for feat_index in range(10,30):#len(X[0,:])):
index = feat_index - 9
X_temp = X[:, [0,1,2,3,4,5,6,7,8,9,feat_index]]
feat_test_error.append(0)
feat_train_error.append(0)
for train_index, test_index in KFold(len(y_disc), n_folds=FOLDS, random_state=17, shuffle=True):
X_train, X_test = X_temp[train_index], X_temp[test_index]
y_train, y_test = y_disc[train_index], y_disc[test_index]
clf = LDA(shrinkage='auto',solver='lsqr')
clf.fit(X_train, y_train)
feat_train_error[index] += accuracy(clf.predict(X_train), y_train) / float(FOLDS)
feat_test_error[index] += accuracy(clf.predict(X_test) , y_test ) / float(FOLDS)
print("train: " + str(feat_train_error[index]) + " test: " + str(feat_test_error[index]))
return [feat_test_error, feat_train_error]
def getPersonRankings(person):
#load all features & keep them in memory
y_cont = load('cont_y_p' + str(person))
if y_cont == None:
print('[Warn] Rebuilding cache - person ' + str(person))
classificator = Classificators.ContValenceClassificator()
featExtr = getFeatures()
personLdr = personLoader.NoTestsetLoader(classificator, featExtr)
X, y_cont = personLdr.load(person)
dump(X,'X_p' + str(person))
dump(y_cont,'cont_y_p' + str(person))
else:
X = load('X_p' +str(person))
X = np.array(X)
y_cont = np.array(y_cont)
y_disc = y_cont
y_disc[ y_disc <= 5 ] = 0
y_disc[ y_disc > 5 ] = 1
for index,val in enumerate(np.std(X,axis=0)):
if val == 0:
print('warning zero std for feature index: ', index, ' (', personLoader.featureExtractor.getFeatureNames()[index])
#manual Feature standardization
X = X - np.average(X,axis=0)
X = np.true_divide(X, np.std(X,axis=0) )
#statistical tests
#get pearson
corr = []
for index in range(len(X[0])):
corr.append( pearsonr(X[:, index], y_cont) )
#model based:
#normal regression
lr = LinearRegression(n_jobs=-1)
lr.fit(X, y_cont)
lr_scores = lr.coef_
#l1 regression
alphas = [0.03,0.1,0.3,1,3,10]
best_alpha = 0.01
best_acc = 0
for train_index, test_index in KFold(len(y_cont), n_folds=5):
X_train, X_test = X[train_index], X[test_index]
y_train, y_test = y_cont[train_index], y_cont[test_index]
lasso = Lasso(alpha=best_alpha)
lasso.fit(X_train,y_train)
pred = lasso.predict(X_test)
best_acc += accuracy(pred,y_cont)
best_acc /= float(5)
for alpha in alphas:
acc = 0
for train_index, test_index in KFold(len(y_cont), n_folds=5):
X_train, X_test = X[train_index], X[test_index]
y_train, y_test = y_cont[train_index], y_cont[test_index]
lasso = Lasso(alpha=alpha)
lasso.fit(X_train,y_train)
pred = lasso.predict(X_test)
acc += accuracy(pred,y_test)
acc /= float(5)
if acc > best_acc:
best_acc = acc
best_alpha = alpha
lasso = Lasso(alpha=best_alpha)
lasso.fit(X, y_cont)
l1_scores = lasso.coef_
#l2 regression
alphas = [0.03,0.1,0.3,1,3,10]
best_alpha = 0.01
best_acc = 0
for train_index, test_index in KFold(len(y_cont), n_folds=5):
X_train, X_test = X[train_index], X[test_index]
y_train, y_test = y_cont[train_index], y_cont[test_index]
ridge = Ridge(alpha=best_alpha)
ridge.fit(X_train,y_train)
pred = ridge.predict(X_test)
best_acc += accuracy(pred,y_test)
best_acc /= float(5)
for alpha in alphas:
acc = 0
for train_index, test_index in KFold(len(y_cont), n_folds=5):
X_train, X_test = X[train_index], X[test_index]
y_train, y_test = y_cont[train_index], y_cont[test_index]
ridge = Ridge(alpha=alpha)
ridge.fit(X_train,y_train)
pred = lasso.predict(X_test)
acc += accuracy(pred,y_test)
acc /= float(5)
if acc > best_acc:
best_acc = acc
best_alpha = alpha
ridge = Ridge(alpha=best_alpha)
ridge.fit(X, y_cont)
l2_scores = ridge.coef_
#svm coefficients
clf = svm.SVC(kernel='linear')
clf.fit(X, y_disc)
svm_weights = (clf.coef_ ** 2).sum(axis=0)
svm_weights /= float(svm_weights.max())
#rf importances
#grow forest
forest = RandomForestClassifier(
n_estimators=3000,
max_features='auto',
criterion='gini',
n_jobs=-1,
)
forest.fit(X,y_disc)
#get importances
importances = forest.feature_importances_
#std = np.std([tree.feature_importances_ for tree in forest.estimators_], axis = 0)
# pca coef
pca = PCA(n_components=1)
pca.fit(X)
pca_coef = pca.components_[0]
# [pearson_r, mutual inf, max inf, dist, l1 coef, l2 coef, svm coef, rf importances, coord search]
#featExtr = getFeatures()
#featnames = featExtr.getFeatureNames()
pers_results = []
for corr, lr_scores, l1_scores, l2_scores, svm_weights, importances, pca_coef in zip(corr, lr_scores, l1_scores, l2_scores, svm_weights, importances, pca_coef):
pers_results.append([np.abs(corr[0]), np.abs(lr_scores), np.abs(l1_scores), np.abs(l2_scores), np.abs(svm_weights), np.abs(importances), np.abs(pca_coef)])
return pers_results#, featExtr.featureExtrs
# run model
results = model.run()
return results
def arousalWorker(criterion,treecount,threshold):
featExtr = getFeatures()
# create classificator
classificator = Classificators.ArousalClassificator()
# create personloader
personLdr = personLoader.NoTestsetLoader(classificator, featExtr)
# run model
model = models.RFModel(personLoader=personLdr, criterion=criterion, treeCount=treecount, threshold=threshold)
return results
if __name__ == '__main__':
treeCount = 2000
threshold = 0.002
reporter = reporters.HTMLRFModelReporter()
results = load('to_keep')
if results == None:
results = valenceWorker('gini',treeCount,threshold)
print("[warn] rebuilding cache")
dump(results,'to_keep')
reporter.genReport(results)
def runPers(self,person):
#load person data
pers_results = load('pers_res_p' + str(person), path=self.ddpad)
if pers_results == None:
pers_results = []
# load all features & keep them in memory
y_cont = load('cont_y_p' + str(person), path=self.ddpad)
if y_cont == None:
print('[Warn] Rebuilding cache - person ' + str(person))
personLdr = personLoader.NoTestsetLoader(self.classifier, self.featExtr)
X, y_cont = personLdr.load(person)
dump(X, 'X_p' + str(person), path=self.ddpad)
dump(y_cont, 'cont_y_p' + str(person), path=self.ddpad)
else:
X = load('X_p' + str(person), path=self.ddpad)
y_disc = np.array(y_cont)
y_disc[y_disc <= 5] = 0
y_disc[y_disc > 5] = 1
# manual Feature standardization
X = X - np.average(X, axis=0)
X = np.true_divide(X, np.std(X, axis=0))
#pearson
corr = []
for index in range(len(X[0])):
corr.append( pearsonr(X[:, index], y_cont)[0] )
pers_results.append(corr)
#Mut inf
#dcorr
mi = []
dcorr = []
for feature in np.transpose(X):
# normalized mutual information
c_xy = np.histogram2d(feature, y_cont, 2)[0]
entX = entropy(feature, y_cont)
entY = entropy(feature, y_cont)
nMutInf = mutual_info_score(None, None, contingency=c_xy) / float(np.sqrt(entX * entY))
mi.append(nMutInf)
# Distance Correlation
dc, dr, dvx, dvy = self.dcov_all(feature, y_cont)
dcorr.append(dr)
pers_results.append(mi)
pers_results.append(dcorr)
#Linear Regression
lr = LinearRegression(n_jobs=-1)
lr.fit(X, y_cont)
pers_results.append(lr.coef_)
#Lasso Regression
alphas = [0.03, 0.1, 0.3, 1, 3, 10]
best_alpha = 0.01
best_acc = 0
for train_index, test_index in KFold(len(y_cont), n_folds=5):
X_train, X_test = X[train_index], X[test_index]
y_train, y_test = y_cont[train_index], y_cont[test_index]
lasso = Lasso(alpha=best_alpha)
lasso.fit(X_train, y_train)
pred = lasso.predict(X_test)
best_acc += self.accuracy(pred, y_cont)
best_acc /= float(5)
for alpha in alphas:
acc = 0
for train_index, test_index in KFold(len(y_cont), n_folds=5):
X_train, X_test = X[train_index], X[test_index]
y_train, y_test = y_cont[train_index], y_cont[test_index]
lasso = Lasso(alpha=alpha)
lasso.fit(X_train, y_train)
pred = lasso.predict(X_test)
acc += self.accuracy(pred, y_test)
acc /= float(5)
if acc > best_acc:
best_acc = acc
best_alpha = alpha
lasso = Lasso(alpha=best_alpha)
lasso.fit(X, y_cont)
pers_results.append(lasso.coef_)
#Ridge Regression
alphas = [0.03, 0.1, 0.3, 1, 3, 10]
best_alpha = 0.01
best_acc = 0
for train_index, test_index in KFold(len(y_cont), n_folds=5):
X_train, X_test = X[train_index], X[test_index]
y_train, y_test = y_cont[train_index], y_cont[test_index]
ridge = Ridge(alpha=best_alpha)
ridge.fit(X_train, y_train)
pred = ridge.predict(X_test)
best_acc += self.accuracy(pred, y_test)
best_acc /= float(5)
for alpha in alphas:
acc = 0
for train_index, test_index in KFold(len(y_cont), n_folds=5):
X_train, X_test = X[train_index], X[test_index]
y_train, y_test = y_cont[train_index], y_cont[test_index]
ridge = Ridge(alpha=alpha)
ridge.fit(X_train, y_train)
pred = lasso.predict(X_test)
acc += self.accuracy(pred, y_test)
acc /= float(5)
if acc > best_acc:
best_acc = acc
best_alpha = alpha
ridge = Ridge(alpha=best_alpha)
ridge.fit(X, y_cont)
pers_results.append(ridge.coef_)
#SVM
clf = SVC(kernel='linear')
clf.fit(X, y_disc)
svm_weights = (clf.coef_ ** 2).sum(axis=0)
svm_weights /= float(svm_weights.max())
pers_results.append(svm_weights)
#Random Forests
#rf importances
#grow forestµ
importances = []
for run in range(self.runs):
forest = RandomForestClassifier(
n_estimators=2000,
max_features='auto',
criterion='gini',
n_jobs=-1,
)
forest.fit(X,y_disc)
importances.append(forest.feature_importances_)
#stds.append( np.std([tree.feature_importances_ for tree in forest.estimators_], axis = 0) )
pers_results.append(np.average(importances, axis=0))
pers_results.append(np.std(importances, axis=0))
#ANOVA
anova = SelectKBest(f_regression, k=self.threshold)
anova.fit(X,y_disc)
selected_features = anova.get_support()
pers_results.append(selected_features)
#Linear Discriminant Analysis
lda = LinearDiscriminantAnalysis(n_components=1)
lda.fit(X,y_disc)
pers_results.append(lda.coef_[0])
#Principal Component Analysis
pca = PCA(n_components=1)
pca.fit(X)
pers_results.append(pca.components_[0])
#absolute values
pers_results = np.absolute(np.array(pers_results))
dump(pers_results, 'pers_res_p' + str(person), path=self.ddpad)
return np.array(pers_results)