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gxn's Issues

Higher order Rhop is not implemented

Hi,

In equation (2) page 4 https://arxiv.org/pdf/2010.01804.pdf it is mentioned that we can vary R parameter to consider higher order neighboring systems. However, in the code l didn't find where do you use Rhop parametrer. The following functions are parameterized with R which is not used. How can l incorporate R ? I have missed something ?

Thank you for your consideration and for this nice work !

In the function IndexSelect()

GXN/ops.py

Line 249 in cb01e49

class IndexSelect(nn.Module):

and in the Discriminator()

GXN/ops.py

Line 120 in cb01e49

class Discriminator(nn.Module):

Capture d’écran 2020-12-21 à 16 47 14

Low accuracy

Hi:
I use your published code for this paper without any change, why can't I reproduce some dataset result, such as PROTEINS, MUTAG. There occurs overfitting question in training these datasets.

Does your model have true test dataset?

I think your code actually reports the validation result right? More specifically, in here

for epoch in range(cmd_args.num_epochs):
        random.shuffle(train_idxes)
        classifier.train()
        avg_loss = loop_dataset(train_graphs, classifier, mi_loss, train_idxes, epoch, optimizer=optimizer, device=device)
        avg_loss[4] = 0.0
        print('\033[92maverage training of epoch %d: clsloss: %.5f miloss: %.5f loss %.5f acc %.5f auc %.5f\033[0m'
              % (epoch, avg_loss[0], avg_loss[1], avg_loss[2], avg_loss[3], avg_loss[4])) # noqa

        classifier.eval()
        test_loss = loop_dataset(test_graphs, classifier, mi_loss, list(range(len(test_graphs))), epoch, device=device)
        test_loss[4] = 0.0
        print('\033[93maverage test of epoch %d: clsloss: %.5f miloss: %.5f loss %.5f acc %.5f auc %.5f\033[0m'
              % (epoch, test_loss[0], test_loss[1], test_loss[2], test_loss[3], test_loss[4])) # noqa

        with open(logfile, 'a+') as log:
            log.write('test of epoch %d: clsloss: %.5f miloss: %.5f loss %.5f acc %.5f auc %.5f'
                      % (epoch, test_loss[0], test_loss[1], test_loss[2], test_loss[3], test_loss[4]) + '\n')

        if test_loss[3] > max_acc:
            max_acc = test_loss[3]
            fname = './checkpoint_%s/time_%s/FOLD%s/model_epoch%s.pt' % (cmd_args.data, first_timstr, foldidx, str(epoch))
            torch.save(classifier.state_dict(), fname)

with open('./result_%s/result_%s/acc_result_%s_%s.txt' % (cmd_args.data, first_timstr, cmd_args.data, first_timstr), 'a+') as f:
        f.write('\n')
        f.write('Fold index: ' + str(foldidx) + '\t')
        f.write(str(max_acc) + '\n')

Problem in loss computation

Hi, in your paper you say 'In the loss function L, α decays from 2 to 0 during training, where the VIPool needs fast convergence for vertex selection'. However, in your code, the α actually decays from 2 to 1, see here.

Problem in class IndexSelect

Hi, your GXN work is interesting and I'm trying to implement it using DGL. However, I find something strange in your code.
Specifically, in your paper, the criterion function for VIPool involves two function values: T_w(\mathbf{x}_v, \mathbf{y}_{\mathcal{N}_v}) and T_w(\mathbf{x}_v, \mathbf{y}_{\mathcal{N}_u}), where T_w(\mathbf{x}_v, \mathbf{y}_{\mathcal{N}_u}) = \mathcal{S}_w(\mathcal{E}_w(\mathbf{x}_v), \mathcal{P}_w(\mathbf{y}_{\mathcal{N}_u})). And as described in your paper, \mathcal{E} is MLP, \mathcal{P} is some Message-Passing layer.

However, in your code, it seems like you implement these in the form of T_w(\mathbf{y}_{\mathcal{N}_v}, \mathbf{x}_v) and T_w(\mathbf{y}_{\mathcal{N}_u}, \mathbf{x}_v). More specifically, in the class IndexSelect of your code:

class IndexSelect(nn.Module):

    def __init__(self, k, n_h, act,  R=1):
        super().__init__()
        self.k = k
        self.R = R
        self.sigm = nn.Sigmoid()
        self.fc = MLP(n_h, n_h, act)
        self.disc = Discriminator(n_h)
        self.gcn1 = GCN(n_h, n_h)

    def forward(self, seq1, seq2, A, samp_bias1=None, samp_bias2=None):
        h_1 = self.fc(seq1)
        h_2 = self.fc(seq2)
        h_n1 = self.gcn1(A, h_1)

        X = self.sigm(h_n1)
        ret, ret_true = self.disc(X, h_1, h_2, samp_bias1, samp_bias2)
        scores = self.sigm(ret_true).squeeze()
        num_nodes = A.shape[0]
        values, idx = torch.topk(scores, int(num_nodes))
        values1, idx1 = values[:int(self.k*num_nodes)], idx[:int(self.k*num_nodes)]
        values0, idx0 = values[int(self.k*num_nodes):], idx[int(self.k*num_nodes):]

        return ret, values1, idx1, idx0, h_n1

Looks like only X is the output of GCN, while h_1 and h_2 (In my understanding, they represent for \mathcal{P}_w(\mathbf{y}_{\mathcal{N}_v}) and \mathcal{P}_w(\mathbf{y}_{\mathcal{N}_u}) respectively) are output of MLP. If we follow the setting in your paper, shouldn't h_1 and h_2 be the output of GCN?

Baseline

Hi,

Your work is really impressive! I have a question about baseline methods. Do you implement them by yourself or use the public code? To my knowledge, different baseline methods use different GCN module. If you implement them by yourself, could you please share your implementation? Thanks!

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