def clusteringA(clustMeta, dir_c, filenames):
#os.mkdir(dir_c, 0777)
stats, dfn = clustering(clustMeta, filenames)
# match clusters to data
print 'Opening a file with the data on the questions'
df = pd.read_csv(filenames['input'])
print 'Matching the data on the questions with the clusters'
matchClusters(dir_c, df, stats, dfn, filenames['out'])
#TODO prediction using clusters n
dfpca = pd.read_csv(dir_c + 'pca.csv', header=None)
#print dfpca.shape
#print dfpca[0:12]
test = dfpca[0:50]
print len(test)
n_neighbors = 3
dfstats = pd.read_csv(filenames['stats'])
#dfstats = dfstats[dfstats['questions'].str.contains("questions") == False]
#print dfstats
df = pd.read_csv(filenames['clusters'])
neigh = NearestNeighbors(n_neighbors=n_neighbors)
neigh.fit(dfstats[['x','y']])
#print test
closest = neigh.kneighbors(test) #TODO: dimension mismatching
data = cp.calcAccuracy(dfstats, closest, df, n_neighbors, test)
csr.to_csv(data, dir_c + 'predictions.csv')
for datum in data:
print datum
def clusteringA(clustMeta, dir_c, filenames):
#os.mkdir(dir_c, 0777)
stats, dfn = clustering(clustMeta, filenames)
# match clusters to data
print 'Opening a file with the data on the questions'
df = pd.read_csv(filenames['input'])
print 'Matching the data on the questions with the clusters'
matchClusters(dir_c, df, stats, dfn, filenames['out'])
#TODO prediction using clusters n
dfpca = pd.read_csv(dir_c + 'pca.csv', header=None)
#print dfpca.shape
#print dfpca[0:12]
test = dfpca[0:50]
print len(test)
n_neighbors = 3
dfstats = pd.read_csv(filenames['stats'])
#dfstats = dfstats[dfstats['questions'].str.contains("questions") == False]
#print dfstats
df = pd.read_csv(filenames['clusters'])
neigh = NearestNeighbors(n_neighbors=n_neighbors)
neigh.fit(dfstats[['x', 'y']])
#print test
closest = neigh.kneighbors(test) #TODO: dimension mismatching
data = cp.calcAccuracy(dfstats, closest, df, n_neighbors, test)
csr.to_csv(data, dir_c + 'predictions.csv')
for datum in data:
print datum
def clustering(clust, filenames, saved=False):
#mergeTitle(df, filename2)
if saved:
stats = pd.read_csv(filenames['stats'])
clusters = pd.read_csv(filenames['clusters'])
else:
data, results = dp.getDataForClustering(filenames, clust)
#TODO divide data into training and testing datasets
clust['n_samples'] = len(data)
print 'total instances:', clust['n_samples']
testing_num = int(clust['n_samples'] * 0.2)
#testing_num = 1924500
results['quest_id'] = results['quest_id'][
testing_num:clust['n_samples']]
results['time_row'] = results['time_row'][
testing_num:clust['n_samples']]
print 'testing instances: ', str(testing_num) # 385981
print 'Started clustering...'
#clusters, stats = clusterData(data, clust, results, False)
clusters, stats = clusterData(data[testing_num:clust['n_samples']],
clust, results, False)
print 'Saving the clustering results...'
csr.to_csv1(stats, filenames['stats'])
clusters.to_csv(filenames['clusters'])
return stats, clusters
def clustering(clust, filenames, saved=False):
#mergeTitle(df, filename2)
if saved:
stats = pd.read_csv(filenames['stats'])
clusters = pd.read_csv(filenames['clusters'])
else:
data, results = dp.getDataForClustering(filenames, clust)
#TODO divide data into training and testing datasets
clust['n_samples'] = len(data)
print 'total instances:', clust['n_samples']
testing_num = int(clust['n_samples'] * 0.2)
#testing_num = 1924500
results['quest_id'] = results['quest_id'][testing_num:clust['n_samples']]
results['time_row'] = results['time_row'][testing_num:clust['n_samples']]
print 'testing instances: ', str(testing_num) # 385981
print 'Started clustering...'
#clusters, stats = clusterData(data, clust, results, False)
clusters, stats = clusterData(data[testing_num:clust['n_samples']], clust, results, False)
print 'Saving the clustering results...'
csr.to_csv1(stats, filenames['stats'])
clusters.to_csv(filenames['clusters'])
return stats, clusters
def runMinibatch(minibatch, cls_stats, classifiers, all_classes, losses1, losses2, x1, x2):
for i, (df_small, y_small) in enumerate(minibatch):
tick = time.time()
#TODO calcualte features for df_small
X_train, X_test, y_train, y_test = train_test_split(df_small, y_small.astype("int0"), test_size=0.20, random_state=0)
data = dict(
x_train=X_train,
x_test=X_test,
y_train=y_train,
y_test=y_test
)
for cls_name, cls in classifiers.items():
cls_stats[cls_name]['another_time'] += time.time() - tick
tick = time.time()
# update estimator with examples in the current mini-batch
#cls.partial_fit(data['x_train'], data['y_train'], classes=all_classes)
#print ("total number of samples for update: ", data['x_train'].shape[0])
#for i in range(0, len(data['x_train'])):
#a1 = data['x_train'].iloc[i]
#a2 = data['x_train'].iloc[i+1]
#b1 = data['y_train'][i]
#b2 = data['y_train'][i+1]
#a = [a1.as_matrix(columns=None), a2.as_matrix(columns=None)]
#b = [b1, b2]
#print (a)
#print (b)
#clf = classifiers[cls_name].fit(a, b)
#a = np.dot(cls.coef_ , data['x_train'].iloc[i+1].as_matrix(columns=None))
#print (a)
#print ("y for training: ", data['y_train'].shape[0])
if cls_name == 'DBN':
data = dataNormalise(data)
clf = DBN([data['x_train'].shape[1], 300, 2],learn_rates = 0.3,learn_rate_decays = 0.9,epochs = 10,verbose = 1)
clf.fit(data['x_train'], data['y_train'])
else:
#print (data['x_train'])
#print (data['y_train'])
clf = classifiers[cls_name].fit(data['x_train'], data['y_train'])
#clf = classifiers[cls_name].partial_fit(data['x_train'], data['y_train'], classes=[0,1])
#print ("coefficients")
#print (cls.coef_)
#print ("test point")
#print (data['x_test'])
#print (data['x_test'].iloc[1].as_matrix(columns=None))
#print ("dot product x*w")
#print (cls.coef_ * data['x_test'].iloc[1].as_matrix(columns=None) )
#print ("dot product1 x*w")
# cls.coef_ is the vector with weights of coefficients
#print ("total number of samples for testing: ", data['x_test'].shape[0])
#a1 = np.dot(cls.coef_ , data['x_test'].iloc[0].as_matrix(columns=None))
#a2 = np.dot(cls.coef_ , data['x_test'].iloc[1].as_matrix(columns=None))
#x1.append(data['x_test'].iloc[0].as_matrix(columns=None))
#x2.append(data['x_test'].iloc[1].as_matrix(columns=None))
'''
if cls_name == 'SGD':
losses1['SGD'].append(a1)
losses2['SGD'].append(a2)
elif cls_name == 'Perceptron':
losses1['Perceptron'].append(a1)
losses2['Perceptron'].append(a2)
elif cls_name == 'NB Multinomial':
losses1['NB'].append(a1)
losses2['NB'].append(a2)
elif cls_name == 'Passive-Aggressive':
losses1['PA'].append(a1)
losses2['PA'].append(a2)
'''
#print (a)
# accumulate statistics
#accStats(tick, cls, cls_stats, cls_name, data)
accStats(tick, clf, cls_stats, cls_name, data)
#print (losses)
#csr.to_csv(losses1['SGD'], 'lossesSGDx1.csv')
#csr.to_csv(losses2['SGD'], 'lossesSGDx2.csv')
#csr.to_csv(losses1['Perceptron'], 'lossesPerceptronx1.csv')
#csr.to_csv(losses2['Perceptron'], 'lossesPerceptronx2.csv')
#csr.to_csv(losses1['NB'], 'lossesNBx1.csv')
#csr.to_csv(losses2['NB'], 'lossesNBx2.csv')
#csr.to_csv(losses1['PA'], 'lossesPAx1.csv')
#csr.to_csv(losses2['PA'], 'lossesPAx2.csv')
#csr.to_csv(x1, 'x1.csv')
#csr.to_csv(x1, 'x2.csv')
for cls_name, cls in classifiers.items():
stats = []
for iter, point in enumerate(cls_stats[cls_name]['accuracy_history']):
stats.append([cls_name, iter, point[0], point[1]])
#print ([cls_name, iter, batch_size, point[0], point[1]])
csr.to_csv(stats, 'online_learning_accuracy.csv')
def clusterData(data, clust, results, to_plot):
plot_sample_size = 6000
if clust['clustering_type'] == 'kmeans':
#TODO kmeans works well even on 2.000.000 questions
kmeans = KMeans(init='k-means++', n_clusters=clust['n_clusters'], n_init=10)
kmeans.fit(data)
clust['centers'] = kmeans.cluster_centers_
results['cluster_labels'] = kmeans.labels_
if to_plot:
plot.PlotData(data, kmeans, plot_sample_size, clust['exp'])
if clust['clustering_type'] == 'spectral':
spectral = cluster.SpectralClustering(n_clusters=clust['n_clusters'],
eigen_solver='arpack',
affinity="nearest_neighbors")
spectral.fit(data)
plot.PlotData(data, spectral, plot_sample_size, clust['exp'])
if clust['clustering_type'] == 'birch':
birch = cluster.Birch(n_clusters=results['n_clusters'])
birch.fit(data)
results['cluster_labels'] = birch.labels_
print 'number of entries clustered', len(results['cluster_labels'])
plot.PlotData(data, birch, plot_sample_size, clust['exp'])
if clust['clustering_type'] == 'dbscan':
dbscan = cluster.DBSCAN(eps=.2)
dbscan.fit(data)
results['cluster_labels'] = dbscan.labels_
plot.PlotData(data, dbscan, plot_sample_size, clust['exp'])
if clust['clustering_type'] == 'affinity_propagation':
affinity_propagation = cluster.AffinityPropagation(damping=.9, preference=-200)
affinity_propagation.fit(data)
plot.PlotData(data, affinity_propagation, plot_sample_size, clust['exp'])
if clust['clustering_type'] == 'ward':
# connectivity matrix for structured Ward
connectivity = kneighbors_graph(data, n_neighbors=10, include_self=False)
# make connectivity symmetric
connectivity = 0.5 * (connectivity + connectivity.T)
ward = cluster.AgglomerativeClustering(n_clusters=clust['n_clusters'], linkage='ward',
connectivity=connectivity)
ward.fit(data)
results['cluster_labels'] = ward.labels_
plot.PlotData(data, ward, plot_sample_size, clust['exp'])
if clust['clustering_type'] == 'average_linkage':
# connectivity matrix for structured Ward
connectivity = kneighbors_graph(data, n_neighbors=10, include_self=False)
# make connectivity symmetric
connectivity = 0.5 * (connectivity + connectivity.T)
average_linkage = cluster.AgglomerativeClustering(
linkage="average", affinity="cityblock", n_clusters=clust['n_clusters'],
connectivity=connectivity)
average_linkage.fit(data)
results['cluster_labels'] = average_linkage.labels_
plot.PlotData(data, average_linkage, plot_sample_size, clust['exp'])
df = csr.clustDfFromRes(results)
stats = csr.clusterResults(df, clust)
return df, stats
def clusterData(data, clust, results, to_plot):
plot_sample_size = 6000
if clust['clustering_type'] == 'kmeans':
#TODO kmeans works well even on 2.000.000 questions
kmeans = KMeans(init='k-means++',
n_clusters=clust['n_clusters'],
n_init=10)
kmeans.fit(data)
clust['centers'] = kmeans.cluster_centers_
results['cluster_labels'] = kmeans.labels_
if to_plot:
plot.PlotData(data, kmeans, plot_sample_size, clust['exp'])
if clust['clustering_type'] == 'spectral':
spectral = cluster.SpectralClustering(n_clusters=clust['n_clusters'],
eigen_solver='arpack',
affinity="nearest_neighbors")
spectral.fit(data)
plot.PlotData(data, spectral, plot_sample_size, clust['exp'])
if clust['clustering_type'] == 'birch':
birch = cluster.Birch(n_clusters=results['n_clusters'])
birch.fit(data)
results['cluster_labels'] = birch.labels_
print 'number of entries clustered', len(results['cluster_labels'])
plot.PlotData(data, birch, plot_sample_size, clust['exp'])
if clust['clustering_type'] == 'dbscan':
dbscan = cluster.DBSCAN(eps=.2)
dbscan.fit(data)
results['cluster_labels'] = dbscan.labels_
plot.PlotData(data, dbscan, plot_sample_size, clust['exp'])
if clust['clustering_type'] == 'affinity_propagation':
affinity_propagation = cluster.AffinityPropagation(damping=.9,
preference=-200)
affinity_propagation.fit(data)
plot.PlotData(data, affinity_propagation, plot_sample_size,
clust['exp'])
if clust['clustering_type'] == 'ward':
# connectivity matrix for structured Ward
connectivity = kneighbors_graph(data,
n_neighbors=10,
include_self=False)
# make connectivity symmetric
connectivity = 0.5 * (connectivity + connectivity.T)
ward = cluster.AgglomerativeClustering(n_clusters=clust['n_clusters'],
linkage='ward',
connectivity=connectivity)
ward.fit(data)
results['cluster_labels'] = ward.labels_
plot.PlotData(data, ward, plot_sample_size, clust['exp'])
if clust['clustering_type'] == 'average_linkage':
# connectivity matrix for structured Ward
connectivity = kneighbors_graph(data,
n_neighbors=10,
include_self=False)
# make connectivity symmetric
connectivity = 0.5 * (connectivity + connectivity.T)
average_linkage = cluster.AgglomerativeClustering(
linkage="average",
affinity="cityblock",
n_clusters=clust['n_clusters'],
connectivity=connectivity)
average_linkage.fit(data)
results['cluster_labels'] = average_linkage.labels_
plot.PlotData(data, average_linkage, plot_sample_size, clust['exp'])
df = csr.clustDfFromRes(results)
stats = csr.clusterResults(df, clust)
return df, stats
