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train_vs6c_dunno_Batching_timed_args_from_RUNScript.py
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train_vs6c_dunno_Batching_timed_args_from_RUNScript.py
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# -*- coding: utf-8 -*-
"""
Created on Fri Aug 31 17:13:11 2018
@author: gerasimos
"""
from __future__ import print_function
from keras.layers import Input, Dropout
from keras.models import Model
from keras.optimizers import Adam
from keras.regularizers import l2
import sys
#from kegra.layers.graph import GraphConvolution
import time
from keras.callbacks import History
import matplotlib.pyplot as plt
#from kegra.utils import *
#########################################################################################################
#from __future__ import print_function
from keras import activations, initializers, constraints
from keras import regularizers
from keras.engine import Layer
import keras.backend as K
class GraphConvolution(Layer):
"""Basic graph convolution layer as in https://arxiv.org/abs/1609.02907"""
def __init__(self, units, support=1,
activation=None,
use_bias=True,
kernel_initializer='glorot_uniform',
bias_initializer='zeros',
kernel_regularizer=None,
bias_regularizer=None,
activity_regularizer=None,
kernel_constraint=None,
bias_constraint=None,
**kwargs):
if 'input_shape' not in kwargs and 'input_dim' in kwargs:
kwargs['input_shape'] = (kwargs.pop('input_dim'),)
super(GraphConvolution, self).__init__(**kwargs)
self.units = units
self.activation = activations.get(activation)
self.use_bias = use_bias
self.kernel_initializer = initializers.get(kernel_initializer)
self.bias_initializer = initializers.get(bias_initializer)
self.kernel_regularizer = regularizers.get(kernel_regularizer)
self.bias_regularizer = regularizers.get(bias_regularizer)
self.activity_regularizer = regularizers.get(activity_regularizer)
self.kernel_constraint = constraints.get(kernel_constraint)
self.bias_constraint = constraints.get(bias_constraint)
self.supports_masking = True
self.support = support
assert support >= 1
def compute_output_shape(self, input_shapes):
features_shape = input_shapes[0]
output_shape = (features_shape[0], self.units)
return output_shape # (batch_size, output_dim)
def build(self, input_shapes):
features_shape = input_shapes[0]
assert len(features_shape) == 2
input_dim = features_shape[1]
self.kernel = self.add_weight(shape=(input_dim * self.support,
self.units),
initializer=self.kernel_initializer,
name='kernel',
regularizer=self.kernel_regularizer,
constraint=self.kernel_constraint)
if self.use_bias:
self.bias = self.add_weight(shape=(self.units,),
initializer=self.bias_initializer,
name='bias',
regularizer=self.bias_regularizer,
constraint=self.bias_constraint)
else:
self.bias = None
self.built = True
def call(self, inputs, mask=None):
features = inputs[0]
basis = inputs[1:]
supports = list()
for i in range(self.support):
supports.append(K.dot(basis[i], features))
supports = K.concatenate(supports, axis=1)
output = K.dot(supports, self.kernel)
if self.bias:
output += self.bias
return self.activation(output)
def get_config(self):
config = {'units': self.units,
'support': self.support,
'activation': activations.serialize(self.activation),
'use_bias': self.use_bias,
'kernel_initializer': initializers.serialize(
self.kernel_initializer),
'bias_initializer': initializers.serialize(
self.bias_initializer),
'kernel_regularizer': regularizers.serialize(
self.kernel_regularizer),
'bias_regularizer': regularizers.serialize(
self.bias_regularizer),
'activity_regularizer': regularizers.serialize(
self.activity_regularizer),
'kernel_constraint': constraints.serialize(
self.kernel_constraint),
'bias_constraint': constraints.serialize(self.bias_constraint)
}
base_config = super(GraphConvolution, self).get_config()
return dict(list(base_config.items()) + list(config.items()))
##########################################################################################################
#from __future__ import print_function
import scipy.sparse as sp #import scipy.sparse
import numpy as np
from scipy.sparse.linalg.eigen.arpack import eigsh, ArpackNoConvergence
def encode_onehot(labels):
classes = set(labels)
classes_dict = {c: np.identity(len(classes))[i, :] for i, c in enumerate(classes)}
labels_onehot = np.array(list(map(classes_dict.get, labels)), dtype=np.int32)
return labels_onehot
def load_data(path="data/cora/", dataset="cora"):
"""Load citation network dataset (cora only for now)"""
print('Loading {} dataset...'.format(dataset))
idx_features_labels = np.genfromtxt("{}{}.content".format(path, dataset), dtype=np.dtype(str))
features = sp.csr_matrix(idx_features_labels[:, 1:-1], dtype=np.float32)
labels = encode_onehot(idx_features_labels[:, -1])
# build graph
idx = np.array(idx_features_labels[:, 0], dtype=np.int32)
idx_map = {j: i for i, j in enumerate(idx)}
edges_unordered = np.genfromtxt("{}{}.cites".format(path, dataset), dtype=np.int32)
edges = np.array(list(map(idx_map.get, edges_unordered.flatten())),
dtype=np.int32).reshape(edges_unordered.shape)
adj = sp.coo_matrix((np.ones(edges.shape[0]), (edges[:, 0], edges[:, 1])),
shape=(labels.shape[0], labels.shape[0]), dtype=np.float32)
# build symmetric adjacency matrix
adj = adj + adj.T.multiply(adj.T > adj) - adj.multiply(adj.T > adj)
print('Dataset has {} nodes, {} edges, {} features.'.format(adj.shape[0], edges.shape[0], features.shape[1]))
#return features.todense(), adj, labels, edges, features
return features, adj, labels, edges, features
# nodes,labels,edges,features
def normalize_adj(adj, symmetric=True):
if symmetric:
d = sp.diags(np.power(np.array(adj.sum(1)), -0.5).flatten(), 0)
a_norm = adj.dot(d).transpose().dot(d).tocsr()
else:
d = sp.diags(np.power(np.array(adj.sum(1)), -1).flatten(), 0)
a_norm = d.dot(adj).tocsr()
return a_norm
def preprocess_adj(adj, symmetric=True):
adj = adj + sp.eye(adj.shape[0])
adj = normalize_adj(adj, symmetric)
return adj
def sample_mask(idx, l):
mask = np.zeros(l)
mask[idx] = 1
return np.array(mask, dtype=np.bool)
def get_splits(y):
idx_train = range(140) # Semi-Supervised
idx_val = range(200, 500)
idx_test = range(500, 1500)
y_train = np.zeros(y.shape, dtype=np.int32)
y_val = np.zeros(y.shape, dtype=np.int32)
y_test = np.zeros(y.shape, dtype=np.int32)
y_train[idx_train] = y[idx_train]
y_val[idx_val] = y[idx_val]
y_test[idx_test] = y[idx_test]
train_mask = sample_mask(idx_train, y.shape[0])
return y_train, y_val, y_test, idx_train, idx_val, idx_test, train_mask
def categorical_crossentropy(preds, labels):
return np.mean(-np.log(np.extract(labels, preds)))
def accuracy(preds, labels):
return np.mean(np.equal(np.argmax(labels, 1), np.argmax(preds, 1)))
def evaluate_preds(preds, labels, indices):
split_loss = list()
split_acc = list()
for y_split, idx_split in zip(labels, indices):
split_loss.append(categorical_crossentropy(preds[idx_split], y_split[idx_split]))
split_acc.append(accuracy(preds[idx_split], y_split[idx_split]))
return split_loss, split_acc
def normalized_laplacian(adj, symmetric=True):
adj_normalized = normalize_adj(adj, symmetric)
laplacian = sp.eye(adj.shape[0]) - adj_normalized
return laplacian
def rescale_laplacian(laplacian):
try:
print('Calculating largest eigenvalue of normalized graph Laplacian...')
largest_eigval = eigsh(laplacian, 1, which='LM', return_eigenvectors=False)[0]
except ArpackNoConvergence:
print('Eigenvalue calculation did not converge! Using largest_eigval=2 instead.')
largest_eigval = 2
scaled_laplacian = (2. / largest_eigval) * laplacian - sp.eye(laplacian.shape[0])
return scaled_laplacian
def chebyshev_polynomial(X, k):
"""Calculate Chebyshev polynomials up to order k. Return a list of sparse matrices."""
print("Calculating Chebyshev polynomials up to order {}...".format(k))
T_k = list()
T_k.append(sp.eye(X.shape[0]).tocsr())
T_k.append(X)
def chebyshev_recurrence(T_k_minus_one, T_k_minus_two, X):
X_ = sp.csr_matrix(X, copy=True)
return 2 * X_.dot(T_k_minus_one) - T_k_minus_two
for i in range(2, k+1):
T_k.append(chebyshev_recurrence(T_k[-1], T_k[-2], X))
return T_k
def sparse_to_tuple(sparse_mx):
if not sp.isspmatrix_coo(sparse_mx):
sparse_mx = sparse_mx.tocoo()
coords = np.vstack((sparse_mx.row, sparse_mx.col)).transpose()
values = sparse_mx.data
shape = sparse_mx.shape
return coords, values, shape
###############################################################################
###############################################################################
with open('results_CORA_NODESno_EDGESno_FEATURESno_LABELSno_LOADt_TRAINt_TESTt_COST_ACCURACY_DataSize_BatchNo_IterNo_LayersNo.txt', 'a') as output_file:
#with open('results_CORA_NODESno_EDGESno_FEATURESno_LABELSno_LOADt_TRAINt_TESTt_BatchSize_COST_ACCURACY.txt', 'a') as output_file:
# Define parameters
DATASET = 'cora'
path="data/cora/"
dataset="cora"
FILTER = 'localpool' # 'chebyshev' # print('{}'.format(FILTER))
MAX_DEGREE = 2 # maximum polynomial degree
SYM_NORM = True # symmetric (True) vs. left-only (False) normalization
NB_EPOCH = 20 #1000 # 200
PATIENCE = 10 #1000 # early stopping patience
print("Number of arguments: ", len(sys.argv))
print("The arguments are: " , str(sys.argv))
# arg2= 600 # sys.argv[1]
SampleNum = int(float(sys.argv[1])) # 7 #10 # This is the OVERLAP # print("SampleNum={}".format(SampleNum))
#index_no_of_file=int(float(arg1))
data_size=int(float(sys.argv[2]))
##########################################################################
# Get data
#X, A, y, edges, features = load_data(dataset=DATASET)
# features.todense(), adj, labels, edges, features
X0, A0, y0, edges, features0 = load_data(dataset=DATASET)
y_train0, y_val0, y_test0, idx_train0, idx_val0, idx_test0, train_mask0 = get_splits(y0)
X, A, y, features, y_train, y_val, y_test, idx_train, idx_val, idx_test, train_mask = X0, A0, y0, features0, y_train0, y_val0, y_test0, idx_train0, idx_val0, idx_test0, train_mask0
X = X.todense()
X /= X.sum(1).reshape(-1, 1)
graph0 = [X, preprocess_adj(A, SYM_NORM)]
# Gerasimos mini batching: We need to chop the ADJacency matrix & the X INPUT matrix
k = data_size # 50 # 30 # This is the size of the data piece # batch
nodescount = np.shape(A0)[0] # This is N number of nodes/rows/columns # dim1 = dim[0]
featurescount = np.shape(X0)[1]
labelscount = np.shape(y0)[1]
def batchin2(adj,featureMatr,train_mask,y_train,y_val,y_test,a,b,c):
# A, X, train_mask, val_mask, test_mask
# newy_train = [[0 for x in range(k)] for y in range(labelscount)]
#def batchin2(adj,featureMatr,train_mask,**val_mask,test_mask**,y_train,y_val,y_test,a,b,c):
newadj = np.zeros((k,k)) # sp.coo_matrix((k,k), dtype=np.float32)
#idx_features_labels = np.genfromtxt("{}{}.content".format(path, dataset), dtype=np.dtype(str))
newfeatureMatr = sp.csr_matrix((k,featurescount), dtype=np.float32) # np.zeros((k,featurescount))
newy_train = np.zeros((k,labelscount))
newy_val = np.zeros((k,labelscount))
newy_test = np.zeros((k,labelscount))
newtrain_mask = np.zeros(k) # Matrix = [[0 for x in range(w)] for y in range(h)]
#newval_mask = np.zeros(k)
#newtest_mask = np.zeros(k)
##a=np.random.choice(range(nodescount), k, replace=False) # np.random.randint(0,)
# WE CONSTRUCTED THE matrices' INDICES TO BE SELECTED
# a = np.random.choice(range(1000), 10, replace=False)
# adj = np.zeros((1000,1000))
##b = np.arange(featurescount) # construct array range() up to featurescount
##c = np.arange(labelscount) # construct array range() up to labelscount
# IN EACH MATRIX GO SELECT THE ROWS as indices
newadj = adj[a[:,np.newaxis],a]
newfeatureMatr = featureMatr[a[:,np.newaxis],b]
newtrain_mask = train_mask[a]
#newval_mask = val_mask[a]
#newtest_mask = test_mask[a]
newy_train = y_train[a[:,np.newaxis],c]
newy_val = y_val[a[:,np.newaxis],c]
newy_test = y_test[a[:,np.newaxis],c]
adj = newadj
featureMatr = newfeatureMatr
y_train = newy_train
y_val = newy_val
y_test = newy_test
train_mask = newtrain_mask # val_mask = newval_mask
# test_mask = newtest_mask
################################################################################
featureMatr = featureMatr.todense()
# Normalize X
featureMatr /= featureMatr.sum(1).reshape(-1, 1)
# Some preprocessing
if FILTER == 'localpool':
""" Local pooling filters (see 'renormalization trick' in Kipf & Welling, arXiv 2016) """
#print('Using local pooling filters...')
A_ = preprocess_adj(adj, SYM_NORM)
support = 1
graph = [featureMatr, A_]
G = [Input(shape=(None, None), batch_shape=(None, None), sparse=True)]
elif FILTER == 'chebyshev':
""" Chebyshev polynomial basis filters (Defferard et al., NIPS 2016) """
print('Using Chebyshev polynomial basis filters...')
L = normalized_laplacian(adj, SYM_NORM)
L_scaled = rescale_laplacian(L)
T_k = chebyshev_polynomial(L_scaled, MAX_DEGREE)
support = MAX_DEGREE + 1
graph = [featureMatr]+T_k
G = [Input(shape=(None, None), batch_shape=(None, None), sparse=True) for _ in range(support)]
else:
raise Exception('Invalid filter type.')
"""featureMatr = preprocess_features(featureMatr)
if FLAGS.model == 'gcn':
support = [preprocess_adj(adj)]
num_supports = 1
model_func = GCN
elif FLAGS.model == 'gcn_cheby':
support = chebyshev_polynomials(adj, FLAGS.max_degree)
num_supports = 1 + FLAGS.max_degree
model_func = GCN
elif FLAGS.model == 'dense':
support = [preprocess_adj(adj)] # Not used
num_supports = 1
model_func = MLP
else:
raise ValueError('Invalid argument for model: ' + str(FLAGS.model))"""
return adj,featureMatr,train_mask,y_train,y_val,y_test,support,graph,G
#return support,features,train_mask,val_mask,test_mask,y_train,y_val,y_test,num_supports,model_func
#selectInd = # np.random.randint(0,)
t20 = time.time()
##################### CALL ME NOW: BATCH THE INITIAL INPUT #####################
a=np.random.choice(range(nodescount), k, replace=False) # np.random.randint(0,)
# WE CONSTRUCTED THE matrices' INDICES TO BE SELECTED
# a = np.random.choice(range(1000), 10, replace=False)
# adj = np.zeros((1000,1000))
b=np.arange(featurescount) # construct array range() up to featurescount
c=np.arange(labelscount)
################################################################################
A,X,train_mask,y_train,y_val,y_test,support,graph,G = batchin2(A0,X0,train_mask0,y_train0,y_val0,y_test0,a,b,c)
################################################################################
t21 = time.time()
#print('I have just batched the loaded data for the first time and this lasted for {} seconds'.format(t21-t20))
print('I will build the layers now')
################### GERASIMOS 's BATCHING 1 ENDS HERE #####################
#print('Dataset has {} nodes, {} edges, {} features, {} labels, '.format(A.shape[0],edges.shape[0],features.shape[1],y.shape[1]),file=output_file,end='')
print('{} nodes, {} edges, {} features, {} labels, '.format(A0.shape[0],edges.shape[0],features0.shape[1],y.shape[1]),file=output_file,end='')
X_in = Input(shape=(X.shape[1],))
# Define model architecture
# NOTE: We pass arguments for graph convolutional layers as a list of tensors.
# This is somewhat hacky, more elegant options would require rewriting the Layer base class.
LayersNum = 2
H = Dropout(0.5)(X_in)
H = GraphConvolution(16, support, activation='relu', kernel_regularizer=l2(5e-4))([H]+G)
#########################################################################################
#H = Dropout(0.5)(H)
#H = GraphConvolution(500, support, activation='relu', kernel_regularizer=l2(5e-4))([H]+G)
###############################################################################
#H = Dropout(0.5)(H)
#H = GraphConvolution(500, support, activation='relu', kernel_regularizer=l2(5e-4))([H]+G)
###############################################################################
#H = Dropout(0.5)(H)
#H = GraphConvolution(16, support, activation='relu', kernel_regularizer=l2(5e-4))([H]+G)
###############################################################################
#H = Dropout(0.5)(H)
#H = GraphConvolution(16, support, activation='relu', kernel_regularizer=l2(5e-4))([H]+G)
#########################################################################################
H = Dropout(0.5)(H)
Y = GraphConvolution(y.shape[1], support, activation='softmax')([H]+G)
# Compile model
model = Model(inputs=[X_in]+G, outputs=Y)
# model.summary()
model.compile(loss='categorical_crossentropy', optimizer=Adam(lr=0.01))
model.summary()
# Helper variables for main training loop
wait = 0
preds = None
best_val_loss = 99999
##############################################################################
##############################################################################
# Prepare batch indices
t3 = time.time()
print('I am the train.py archive and I am starting to train at {}'.format(t3))
#print('I am the train.py archive and I am starting to train at {}'.format(t3), file=output_file)
TotSampNu = SampleNum*int((nodescount-1) / k + 1 ) # iteratNo = 50*int(nodescount / k + 1 ) # N / k
apothekeA = []
apothekeB = []
apothekeC = []
for index in range(TotSampNu):
#apotheke.append(batchin(adj0,features0,train_mask0,val_mask0,test_mask0,y_train0,y_val0,y_test0))
apothekeA.append(np.random.choice(range(nodescount), k, replace=False)) # np.random.randint(0,)
# WE CONSTRUCTED THE matrices' INDICES TO BE SELECTED
# a = np.random.choice(range(1000), 10, replace=False)
# adj = np.zeros((1000,1000))
apothekeB.append(np.arange(featurescount)) # construct array range() up to featurescount
apothekeC.append(np.arange(labelscount)) # construct array range() up to labelscount
###########################################################################
# Fit
history = History()
with open('Time_Measurements_results_CORA_NODESno_EDGESno_FEATURESno_LABELSno_LOADt_TRAINt_TESTt_COST_ACCURACY_DataSize_BatchNo_IterNo_LayersNo.txt', 'a') as output_file2:
print('{} nodes, {} edges, {} features, {} labels, '.format(A0.shape[0],edges.shape[0],features0.shape[1],y.shape[1]),file=output_file2,end='')
print("SampleSize={}, BatchSize={}, SamplesNo={}, LayersNo={}\n".format(k,1,TotSampNu,LayersNum), file=output_file2,end='')
t9 = time.time()
for epoch in range(1, NB_EPOCH+1):
# Log wall-clock time
t = time.time()
for i in range(TotSampNu):
#################### CALL ME AGAIN: BATCH THE INITIAL INPUT ####################
#support, features, train_mask, val_mask, test_mask, y_train, y_val, y_test, num_supports, model_func = batchin(adj0,features0,train_mask0,val_mask0,test_mask0,y_train0,y_val0,y_test0)
#support, features, train_mask, val_mask, test_mask, y_train, y_val, y_test, num_supports, model_func = apotheke
t20 = time.time()
################################################################################
A,X,train_mask,y_train,y_val,y_test,support,graph,G = batchin2(A0,X0,train_mask0,y_train0,y_val0,y_test0,apothekeA[i],apothekeB[i],apothekeC[i])
#X = X.todense()
################################################################################
t21 = time.time()
print('Piece selected out of the loaded data for the {}'.format(i)+' time: {} sec. '.format(t21-t20), file=output_file2, end='')
#print('I have just selected a piece out of the loaded data for the the {}'.format(TotSampNu)+' time and this lasted for {} seconds'.format(t21-t20))
################### GERASIMOS 's BATCHING i ENDS HERE #####################
################################################################################
# Single training iteration (we mask nodes without labels for loss calculation)
t22 = time.time()
model.fit(graph, y_train, sample_weight=train_mask, batch_size=A.shape[0], epochs=1, shuffle=False, verbose=0, callbacks=[history])
t23 = time.time()
print('Model fitting: {} sec. \n'.format(t23-t22), file=output_file2, end='')
#print('I have just performed a model fitting with this sample and this lasted for {} seconds\n'.format(t23-t22))
# Predict on full dataset
preds = model.predict(graph0, batch_size=A0.shape[0])
# Train / validation scores
train_val_loss, train_val_acc = evaluate_preds(preds, [y_train0, y_val0],
[idx_train0, idx_val0])
print("Epoch: {:04d}".format(epoch),
"train_loss= {:.4f}".format(train_val_loss[0]),
"train_acc= {:.4f}".format(train_val_acc[0]),
"val_loss= {:.4f}".format(train_val_loss[1]),
"val_acc= {:.4f}".format(train_val_acc[1]),
"time= {:.4f}".format(time.time() - t))
print("Epoch: {:04d}".format(epoch),
"time= {:.4f}\n".format(time.time() - t), file=output_file2, end='')
# Early stopping
if train_val_loss[1] < best_val_loss:
best_val_loss = train_val_loss[1]
wait = 0
else:
if wait >= PATIENCE:
print('Epoch {}: early stopping'.format(epoch))
break
wait += 1
t10 = time.time()
# Testing
preds = model.predict(graph0, batch_size=A0.shape[0])
test_loss, test_acc = evaluate_preds(preds, [y_test0], [idx_test])
print("Test set results:",
"loss= {:.4f}".format(test_loss[0]),
"accuracy= {:.4f}".format(test_acc[0]))
print("loss= {:.4f}".format(test_loss[0]),"accuracy= {:.4f}, TrainT={:.4f}, SampleSize={}, BatchSize={}, Overlap={}, SamplesNo={}, LayersNo={}\n".format(test_acc[0],t10-t9,k,1,SampleNum, TotSampNu,LayersNum), file=output_file,end='')
print(history.history)
# summarize history for accuracy
#plt.plot(history.history['acc'])
#plt.plot(history.history['val_acc'])