Fixing tensor dimension matching error (with 1 unit difference)

sh.nejadshamsi: <p>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:</p>
<p>**</p>
<blockquote>
<p>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]</p>
</blockquote>
<p>**</p>
<p>here is my code:</p>
<pre><code class="lang-auto">

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
</code></pre>

sh.nejadshamsi: <p>Please delete this post…</p>