I’m trying to run my code for Graph Convolution Network (GCN) and MLP in PyTorch with several .csv input files, but I get error below:
**
RuntimeError: The expanded size of the tensor (732) must match the existing size (731) at non-singleton dimension 0. Target sizes: [732]. Tensor sizes: [731]
**
here is my code:
import csv
import torch
import torch.nn as nn
import torch.nn.functional as F
import dgl
from sklearn.metrics import r2_score
import numpy as np
import datetime
import dgl.function as fn
# Below are the graph convolution functions:
# (where each node collects information about nearby nodes)
def gcn_message(edges):
return {'msg' : edges.src['h']}
def gcn_reduce(nodes):
return {'h' : torch.sum(nodes.mailbox['msg'], dim=1)}
# Below is the pytorch module that defines the operations at each graph convolution layer
class gcnLayer(nn.Module):
def __init__(self, in_feats, out_feats):
super(gcnLayer, self).__init__()
self.linear = nn.Linear(in_feats*2, out_feats)
def forward(self, g, inputs):
with g.local_scope():
g.ndata['h'] = inputs # inputs: POI features
print(g.ndata['h'])
g.update_all(message_func=fn.copy_u('h', 'm'), reduce_func=fn.mean('m', 'h_N'))
h_N=g.ndata['h_N']
h_total = torch.cat([inputs, h_N], dim=1) # Result (Convoluted POIs) of convolution at a layer is extracted
return self.linear(h_total) # Result is linearly transformed
# Below is the pytorch class (machine learning architectures are initiliazed as classes)
# that defines the the graph convolutional network (GCN) architecture (number of hidden layers, neurons, activation function, etc)
class gcn(torch.nn.Module):
def __init__(self, input, hidden, output):
super(gcn, self).__init__()
# Initially each row in the input has (input) number of elements.
#In other words, each node in the network has (input number of features, i.e.: number of POI types)
self.gcnInput = gcnLayer(input,hidden) # Input size is converted into hidden size
self.gcnHidden = gcnLayer(hidden,hidden) # Hidden size is converted into hidden size
self.gcnOutput = gcnLayer(hidden,output) # Hidden size is converted into desired output size
# Forward function: this function is run when we call the class
def forward(self, g, pois):
y = F.relu(self.gcnInput(g, pois)) # Result of the input layer is sent through activation function
y = F.relu(self.gcnHidden(g, y)) # Result of the hidden layer is sent through activation function
y = F.relu(self.gcnHidden(g, y)) # Result of the hidden layer is sent through activation function (Here, an arbitrary amount of hidden layers can be added)
y = self.gcnOutput(g, y) # Result of the output layer (not activated)
return y
# Below is the pytorch class that defines the the multilayer perceptron (MLP) architecture
# (number of hidden layers, neurons, activation function, etc)
class mlp(torch.nn.Module):
def __init__(self, input, hidden):
super(mlp, self).__init__() #initialize
self.classifier = nn.Sequential( # Sequential is used when combining different layers
nn.Linear(input, hidden), # Input feature matrix is converted into a matrix with shape (hidden) and linearly transformated
nn.ReLU(), # Activation function is applied
nn.Linear(hidden, hidden), # Result of previous layer is linearly transformaed
nn.ReLU(), # Activation function is applied
nn.Linear(hidden, 1)) # At the final layer, one output is given (Trip amount)
def forward(self, x):
x = self.classifier(x) # the input is sent throught the MLP architecture defined above
return x
# Below is the pytorch class that defines the the the combined deep learning architecture
class od(nn.Module):
def __init__(self, gcnInput, gcnHidden, gcnOutput, mlpHidden):
super(od, self).__init__()
self.gcn = gcn(gcnInput, gcnHidden,gcnOutput) # First: GCN
self.mlp = mlp((2*gcnoutput+1), mlpHidden) # Afterwards: MLP
def forward(self, g, pois, costs, indices, q, zoneCount):
y = self.gcn(g,pois) # First, send the input through GCN
p = torch.zeros(len(costs),2*q).cuda() # Prepare a matrix that will have the POI output at origin (size: q), POI output at destination (size: q)
count = 0
for i in range(zoneCount):
for j in range(zoneCount):
p[count][:q] = y[i][:] # POI output at origin (size: q)
p[count][q:] = y[j][:] # POI output at destination (size: q)
count +=1
p = p[indices][:] # Order the input matrix in the order of shuffled zones (or OD pairs)
costs = costs[indices][:] # Order the cost matrix in the order of shuffled zones (or OD pairs)
inputs = torch.cat((p, costs), 1).cuda() # Combine POI and cost matrices
y = self.mlp(inputs) # Last, send through MLP
return y
def train(optimizer, model, criterion, pois, costs, labels, indices, zoneCount, gcnOutput):
model.train() # Model is in the training mode (meaning gradients are calculated)
optimizer.zero_grad() # Gradients are zeroed
print(optimizer)
pred = model(g, pois, costs, indices, gcnOutput, zoneCount) # Get model output as predicted output
loss = criterion(pred, labels) # Calculate loss between prediction and label
loss.backward() # Backpropagate the gradients
optimizer.step() # (I dont fully know what happens with this code)
return loss.item() # Return loss
def test(model, pois, costs, labels, indices, zoneCount, gcnOutput):
model.eval() # Mode is in evaluation mode: no gradients are calcualted
with torch.no_grad(): # In tensorflow if tensor has a parameter "autograd:true" then, gradients are calculated. This code sets the autograd to false for all tensors below
pred = model(g, pois, costs, indices,gcnOutput, zoneCount) # Get prediction
predictions = pred.detach().cpu() # Move prediction tensor from GPU to CPU
r2 = r2_score(labels.cpu(), predictions) # Calculate R2
return r2
def data_collection(key): #Below part gets the data from the files into the program (POIS, nodes, costs, labels). If the file types are different than the ones used in this research, this part should be adjusted.
if key == "mb": #mb: manhattan and brooklyn case
no = 3
else:
no = 2
with open("/nodes.csv".format(key)) as f:
nodeCount = sum(1 for line in f)
print (nodeCount)
with open("/poisInfo.csv".format(key)) as f:
poiCount = sum(1 for line in f)
print(poiCount)
with open("/zones.csv".format(key)) as f:
zoneCount = sum(1 for line in f)
print(zoneCount)
pois = torch.zeros((nodeCount,poiCount)).cuda()
print(pois)
i = 0
with open('/nodes.csv'.format(key), mode='r') as rx:
r = csv.reader(rx, delimiter=',', quotechar='"', quoting=csv.QUOTE_MINIMAL)
for row in r:
print(row)
pois[i][:] = torch.FloatTensor([int(i) for i in row[no:]])
i += 1
costs = torch.zeros((zoneCount*zoneCount,1)).cuda()
labels = torch.zeros((zoneCount*zoneCount,1)).cuda()
count = 0
with open('/costsTrips.csv'.format(key), mode='r') as rx:
r = csv.reader(rx, delimiter=',', quotechar='"', quoting=csv.QUOTE_MINIMAL)
for row in r:
costs[count][0] = int(row[2])
labels[count][0] = int(row[3])
count += 1
g = dgl.DGLGraph().to(torch.device('cuda:0')) # dgl: deep graph learning library: We move POIs to the graph for graph convolution
print (nodeCount)
g.add_nodes(nodeCount) # Add nodes to the graph
print (nodeCount)
print (g.number_of_nodes)
with open('/edges.csv'.format(key), mode='r') as rx:
r = csv.reader(rx, delimiter=',', quotechar='"', quoting=csv.QUOTE_MINIMAL)
for row in r:
g.add_edge(int(row[0]), int(row[1])) # If edge exists between 2 nodes, add edge
print('We have %d nodes.' % g.number_of_nodes())
print('We have %d edges.' % g.number_of_edges())
return([g, pois, labels,costs, zoneCount, poiCount])
gcnoutput = 10
keys = ["manhattan", "brooklyn", "mb"]
count = 0
with open("costFinal.csv", mode='w', newline="") as wx:
w = csv.writer(wx, delimiter=',', quotechar='"', quoting=csv.QUOTE_MINIMAL)
w.writerow(["place", "iteration", "split", "r2"])
for key in keys:
[g, pois, labels, costs, zoneCount, poiCount] = data_collection(key)
for iteration in range(1,11): # We test each split ratio with 10 times to get the average
a = np.random.permutation(zoneCount) # randomize the zones
for i in range(1,10):
split = i/10 # Below lines split the training and test subsets
breaker = int(split * zoneCount)
train_zones = a[:breaker]
test_zones = a[breaker:]
train_indices = []
test_indices = []
for z in train_zones:
train_indices += [j for j in range(z * zoneCount, z * zoneCount + zoneCount)]
for z in test_zones:
test_indices += [j for j in range(z * zoneCount, z * zoneCount + zoneCount)]
# model parameters: gcninput, gcnhidden, gcnoutput, mlphidden
model = od(poiCount, 64, gcnoutput, 64).cuda() # construct the model
print(model)
optimizer = torch.optim.Adam(model.parameters(), lr=0.01) # optimizer: adam optimizer
print(optimizer)
criterion = torch.nn.MSELoss() # loss: mean squared error loss
print(criterion)
for epoch in range(1, 11): # Train the algorithm 500 epochs
print (epoch)
loss = train(optimizer, model, criterion, pois, costs, labels[train_indices], train_indices, zoneCount, gcnoutput)
# print(count, datetime.datetime.now() - start, key, iteration, i, epoch, loss)
count += 1
r2 = test(model, pois, costs, labels[test_indices], test_indices, zoneCount, gcnoutput) # At the end of the algorithm, test the model and get r2
w.writerow([key, iteration, i*10, r2]) # write key[manhattan,brooklyn,manhattan and brooklyn], iteration[0...9], split ratio[10%...90%], r2 to the file