[Model] Fix broken CDGNN example (#111)

* pretty printer

* Conflicts:
	python/dgl/data/sbm.py

* refined line_graph implementation

* fix broken api calls

* small fix to trigger CI

* requested change

examples/pytorch/line_graph/README.md

@@ -15,5 +15,7 @@ python train.py
 
 An experiment on the Stochastic Block Model in customized settings can be run with
 ```bash
-python train.py --batch-size BATCH_SIZE --gpu GPU --n-communities N_COMMUNITIES --n-features N_FEATURES --n-graphs N_GRAPH --n-iterations N_ITERATIONS --n-layers N_LAYER --n-nodes N_NODE --model-path MODEL_PATH --radius RADIUS
+python train.py --batch-size BATCH_SIZE --gpu GPU --n-communities N_COMMUNITIES \
+                --n-features N_FEATURES --n-graphs N_GRAPH --n-iterations N_ITERATIONS \
+                --n-layers N_LAYER --n-nodes N_NODE --model-path MODEL_PATH --radius RADIUS
 ```

examples/pytorch/line_graph/gnn.py

-"""
-Supervised Community Detection with Hierarchical Graph Neural Networks
-https://arxiv.org/abs/1705.08415
-
-Deviations from paper:
-- Pm Pd
-"""
-
-
 import copy
 import itertools
 import dgl
@@ -16,59 +7,58 @@ import torch as th
 import torch.nn as nn
 import torch.nn.functional as F
 
-
 class GNNModule(nn.Module):
     def __init__(self, in_feats, out_feats, radius):
         super().__init__()
         self.out_feats = out_feats
         self.radius = radius
 
-        new_linear = lambda: nn.Linear(in_feats, out_feats * 2)
-        new_module_list = lambda: nn.ModuleList([new_linear() for i in range(radius)])
+        new_linear = lambda: nn.Linear(in_feats, out_feats)
+        new_linear_list = lambda: nn.ModuleList([new_linear() for i in range(radius)])
 
         self.theta_x, self.theta_deg, self.theta_y = \
             new_linear(), new_linear(), new_linear()
-        self.theta_list = new_module_list()
+        self.theta_list = new_linear_list()
 
         self.gamma_y, self.gamma_deg, self.gamma_x = \
             new_linear(), new_linear(), new_linear()
-        self.gamma_list = new_module_list()
+        self.gamma_list = new_linear_list()
 
         self.bn_x = nn.BatchNorm1d(out_feats)
         self.bn_y = nn.BatchNorm1d(out_feats)
 
     def aggregate(self, g, z):
         z_list = []
-        g.set_n_repr(z)
-        g.update_all(fn.copy_src(), fn.sum())
-        z_list.append(g.get_n_repr())
+        g.set_n_repr({'z' : z})
+        g.update_all(fn.copy_src(src='z', out='m'), fn.sum(msg='m', out='z'))
+        z_list.append(g.get_n_repr()['z'])
         for i in range(self.radius - 1):
             for j in range(2 ** i):
-                g.update_all(fn.copy_src(), fn.sum())
-            z_list.append(g.get_n_repr())
+                g.update_all(fn.copy_src(src='z', out='m'), fn.sum(msg='m', out='z'))
+            z_list.append(g.get_n_repr()['z'])
         return z_list
 
-    def forward(self, g, lg, x, y, deg_g, deg_lg, eid2nid):
-        xy = F.embedding(eid2nid, x)
+    def forward(self, g, lg, x, y, deg_g, deg_lg, pm_pd):
+        pmpd_x = F.embedding(pm_pd, x)
 
-        x_list = [theta(z) for theta, z in zip(self.theta_list, self.aggregate(g, x))]
+        sum_x = sum(theta(z) for theta, z in zip(self.theta_list, self.aggregate(g, x)))
 
-        g.set_e_repr(y)
-        g.update_all(fn.copy_edge(), fn.sum())
-        yx = g.get_n_repr()
+        g.set_e_repr({'y' : y})
+        g.update_all(fn.copy_edge(edge='y', out='m'), fn.sum('m', 'pmpd_y'))
+        pmpd_y = g.pop_n_repr('pmpd_y')
 
-        x = self.theta_x(x) + self.theta_deg(deg_g * x) + sum(x_list) + self.theta_y(yx)
-        x = self.bn_x(x[:, :self.out_feats] + F.relu(x[:, self.out_feats:]))
+        x = self.theta_x(x) + self.theta_deg(deg_g * x) + sum_x + self.theta_y(pmpd_y)
+        n = self.out_feats // 2
+        x = th.cat([x[:, :n], F.relu(x[:, n:])], 1)
+        x = self.bn_x(x)
 
-        y_list = [gamma(z) for gamma, z in zip(self.gamma_list, self.aggregate(lg, y))]
-        lg.set_n_repr(xy)
-        lg.update_all(fn.copy_src(), fn.sum())
-        xy = lg.get_n_repr()
-        y = self.gamma_y(y) + self.gamma_deg(deg_lg * y) + sum(y_list) + self.gamma_x(xy)
-        y = self.bn_y(y[:, :self.out_feats] + F.relu(y[:, self.out_feats:]))
+        sum_y = sum(gamma(z) for gamma, z in zip(self.gamma_list, self.aggregate(lg, y)))
 
-        return x, y
+        y = self.gamma_y(y) + self.gamma_deg(deg_lg * y) + sum_y + self.gamma_x(pmpd_x)
+        y = th.cat([y[:, :n], F.relu(y[:, n:])], 1)
+        y = self.bn_y(y)
 
+        return x, y
 
 class GNN(nn.Module):
     def __init__(self, feats, radius, n_classes):
@@ -82,14 +72,8 @@ class GNN(nn.Module):
         self.module_list = nn.ModuleList([GNNModule(m, n, radius)
                                           for m, n in zip(feats[:-1], feats[1:])])
 
-    def forward(self, g, lg, deg_g, deg_lg, eid2nid):
-        def normalize(x):
-            x = x - th.mean(x, 0)
-            x = x / th.sqrt(th.mean(x * x, 0))
-            return x
-
-        x = normalize(deg_g)
-        y = normalize(deg_lg)
+    def forward(self, g, lg, deg_g, deg_lg, pm_pd):
+        x, y = deg_g, deg_lg
         for module in self.module_list:
-            x, y = module(g, lg, x, y, deg_g, deg_lg, eid2nid)
+            x, y = module(g, lg, x, y, deg_g, deg_lg, pm_pd)
         return self.linear(x)

examples/pytorch/line_graph/train.py

+"""
+Supervised Community Detection with Hierarchical Graph Neural Networks
+https://arxiv.org/abs/1705.08415
+
+Author's implementation: https://github.com/joanbruna/GNN_community
+"""
+
 from __future__ import division
+import time
 
 import argparse
 from itertools import permutations
 
-import networkx as nx
 import torch as th
 import torch.nn.functional as F
 import torch.optim as optim
 from torch.utils.data import DataLoader
 
-import dgl
 from dgl.data import SBMMixture
 import gnn
-import utils
 
 parser = argparse.ArgumentParser()
-parser.add_argument('--batch-size', type=int,
-                    help='Batch size', default=1)
-parser.add_argument('--gpu', type=int,
-                    help='GPU', default=-1)
-parser.add_argument('--n-communities', type=int,
-                    help='Number of communities', default=2)
-parser.add_argument('--n-features', type=int,
-                    help='Number of features per layer', default=2)
-parser.add_argument('--n-graphs', type=int,
-                    help='Number of graphs', default=6000)
-parser.add_argument('--n-iterations', type=int,
-                    help='Number of iterations', default=10000)
-parser.add_argument('--n-layers', type=int,
-                    help='Number of layers', default=30)
-parser.add_argument('--n-nodes', type=int,
-                    help='Number of nodes', default=1000)
-parser.add_argument('--model-path', type=str,
-                    help='Path to the checkpoint of model', default='model')
-parser.add_argument('--radius', type=int,
-                    help='Radius', default=3)
+parser.add_argument('--batch-size', type=int, help='Batch size', default=1)
+parser.add_argument('--gpu', type=int, help='GPU index', default=-1)
+parser.add_argument('--lr', type=float, help='Learning rate', default=0.001)
+parser.add_argument('--n-communities', type=int, help='Number of communities', default=2)
+parser.add_argument('--n-epochs', type=int, help='Number of epochs', default=100)
+parser.add_argument('--n-features', type=int, help='Number of features', default=16)
+parser.add_argument('--n-graphs', type=int, help='Number of graphs', default=10)
+parser.add_argument('--n-layers', type=int, help='Number of layers', default=30)
+parser.add_argument('--n-nodes', type=int, help='Number of nodes', default=10000)
+parser.add_argument('--optim', type=str, help='Optimizer', default='Adam')
+parser.add_argument('--radius', type=int, help='Radius', default=3)
+parser.add_argument('--verbose', action='store_true')
 args = parser.parse_args()
 
 dev = th.device('cpu') if args.gpu < 0 else th.device('cuda:%d' % args.gpu)
+K = args.n_communities
+
+training_dataset = SBMMixture(args.n_graphs, args.n_nodes, K)
+training_loader = DataLoader(training_dataset, args.batch_size,
+                             collate_fn=training_dataset.collate_fn, drop_last=True)
+
+ones = th.ones(args.n_nodes // K)
+y_list = [th.cat([x * ones for x in p]).long().to(dev) for p in permutations(range(K))]
+
+feats = [1] + [args.n_features] * args.n_layers + [K]
+model = gnn.GNN(feats, args.radius, K).to(dev)
+optimizer = getattr(optim, args.optim)(model.parameters(), lr=args.lr)
+
+def compute_overlap(z_list):
+    ybar_list = [th.max(z, 1)[1] for z in z_list]
+    overlap_list = []
+    for y_bar in ybar_list:
+        accuracy = max(th.sum(y_bar == y).item() for y in y_list) / args.n_nodes
+        overlap = (accuracy - 1 / K) / (1 - 1 / K)
+        overlap_list.append(overlap)
+    return sum(overlap_list) / len(overlap_list)
+
+def step(i, j, g, lg, deg_g, deg_lg, pm_pd):
+    """ One step of training. """
+    t0 = time.time()
+    z = model(g, lg, deg_g, deg_lg, pm_pd)
+    t_forward = time.time() - t0
 
-dataset = SBMMixture(args.n_graphs, args.n_nodes, args.n_communities)
-loader = utils.cycle(DataLoader(dataset, args.batch_size,
-                     shuffle=True, collate_fn=dataset.collate_fn, drop_last=True))
-
-ones = th.ones(args.n_nodes // args.n_communities)
-y_list = [th.cat([th.cat([x * ones for x in p])] * args.batch_size).long().to(dev)
-      for p in permutations(range(args.n_communities))]
-
-feats = [1] + [args.n_features] * args.n_layers + [args.n_communities]
-model = gnn.GNN(feats, args.radius, args.n_communities).to(dev)
-opt = optim.Adamax(model.parameters(), lr=0.04)
-
-for i in range(args.n_iterations):
-    g, lg, deg_g, deg_lg, eid2nid = next(loader)
-    deg_g = deg_g.to(dev)
-    deg_lg = deg_lg.to(dev)
-    eid2nid = eid2nid.to(dev)
-    y_bar = model(g, lg, deg_g, deg_lg, eid2nid)
-    loss = min(F.cross_entropy(y_bar, y) for y in y_list)
-    opt.zero_grad()
+    z_list = th.chunk(z, args.batch_size, 0)
+    loss = sum(min(F.cross_entropy(z, y) for y in y_list) for z in z_list) / args.batch_size
+    overlap = compute_overlap(z_list)
+
+    optimizer.zero_grad()
+    t0 = time.time()
     loss.backward()
-    opt.step()
+    t_backward = time.time() - t0
+    optimizer.step()
+
+    return loss, overlap, t_forward, t_backward
+
+def test():
+    p_list =[6, 5.5, 5, 4.5, 1.5, 1, 0.5, 0]
+    q_list =[0, 0.5, 1, 1.5, 4.5, 5, 5.5, 6]
+    N = 1
+    overlap_list = []
+    for p, q in zip(p_list, q_list):
+        dataset = SBMMixture(N, args.n_nodes, K, pq=[[p, q]] * N)
+        loader = DataLoader(dataset, N, collate_fn=dataset.collate_fn)
+        g, lg, deg_g, deg_lg, pm_pd = next(iter(loader))
+        deg_g = deg_g.to(dev)
+        deg_lg = deg_lg.to(dev)
+        pm_pd = pm_pd.to(dev)
+        z = model(g, lg, deg_g, deg_lg, pm_pd)
+        overlap_list.append(compute_overlap(th.chunk(z, N, 0)))
+    return overlap_list
+
+n_iterations = args.n_graphs // args.batch_size
+for i in range(args.n_epochs):
+    total_loss, total_overlap, s_forward, s_backward = 0, 0, 0, 0
+    for j, [g, lg, deg_g, deg_lg, pm_pd] in enumerate(training_loader):
+        deg_g = deg_g.to(dev)
+        deg_lg = deg_lg.to(dev)
+        pm_pd = pm_pd.to(dev)
+        loss, overlap, t_forward, t_backward = step(i, j, g, lg, deg_g, deg_lg, pm_pd)
+
+        total_loss += loss
+        total_overlap += overlap
+        s_forward += t_forward
+        s_backward += t_backward
+
+        epoch = '0' * (len(str(args.n_epochs)) - len(str(i)))
+        iteration = '0' * (len(str(n_iterations)) - len(str(j)))
+        if args.verbose:
+            print('[epoch %s%d iteration %s%d]loss %.3f | overlap %.3f'
+                  % (epoch, i, iteration, j, loss, overlap))
 
-    placeholder = '0' * (len(str(args.n_iterations)) - len(str(i)))
-    print('[iteration %s%d]loss %f' % (placeholder, i, loss))
+    epoch = '0' * (len(str(args.n_epochs)) - len(str(i)))
+    loss = total_loss / (j + 1)
+    overlap = total_overlap / (j + 1)
+    t_forward = s_forward / (j + 1)
+    t_backward = s_backward / (j + 1)
+    print('[epoch %s%d]loss %.3f | overlap %.3f | forward time %.3fs | backward time %.3fs'
+          % (epoch, i, loss, overlap, t_forward, t_backward))
 
-th.save(model.state_dict(), args.model_path)
+    overlap_list = test()
+    overlap_str = ' - '.join(['%.3f' % overlap for overlap in overlap_list])
+    print('[epoch %s%d]overlap: %s' % (epoch, i, overlap_str))

examples/pytorch/line_graph/utils.py

-def cycle(loader):
-    while True:
-        for x in loader:
-            yield x

python/dgl/data/sbm.py

 import math
 import os
 import pickle
+import random
 
 import numpy as np
 import numpy.random as npr
@@ -68,48 +69,56 @@ class SBMMixture:
         Multiplier.
     avg_deg : int, optional
         Average degree.
-    p : callable or str, optional
-        Random density generator.
+    pq : list of pair of nonnegative float or str, optional
+        Random densities.
     rng : numpy.random.RandomState, optional
         Random number generator.
     """
     def __init__(self, n_graphs, n_nodes, n_communities,
-                 k=2, avg_deg=3, p='Appendix C', rng=None):
+                 k=2, avg_deg=3, pq='Appendix C', rng=None):
         self._n_nodes = n_nodes
         assert n_nodes % n_communities == 0
         block_size = n_nodes // n_communities
-        if type(p) is str:
-            p = {'Appendix C' : self._appendix_c}[p]
         self._k = k
         self._avg_deg = avg_deg
         self._gs = [DGLGraph() for i in range(n_graphs)]
-        adjs = [sbm(n_communities, block_size, *p()) for i in range(n_graphs)]
+        if type(pq) is list:
+            assert len(pq) == n_graphs
+        elif type(pq) is str:
+            generator = {'Appendix C' : self._appendix_c}[pq]
+            pq = [generator() for i in range(n_graphs)]
+        else:
+            raise RuntimeError()
+        adjs = [sbm(n_communities, block_size, *x) for x in pq]
         for g, adj in zip(self._gs, adjs):
             g.from_scipy_sparse_matrix(adj)
-        self._lgs = [g.line_graph() for g in self._gs]
+        self._lgs = [g.line_graph(backtracking=False) for g in self._gs]
         in_degrees = lambda g: g.in_degrees(Index(F.arange(g.number_of_nodes(),
-                        dtype=F.int64))).unsqueeze(1).float()
+                                            dtype=F.int64))).unsqueeze(1).float()
         self._g_degs = [in_degrees(g) for g in self._gs]
         self._lg_degs = [in_degrees(lg) for lg in self._lgs]
-        self._eid2nids = list(zip(*[g.edges(sorted=True) for g in self._gs]))[0]
+        self._pm_pds = list(zip(*[g.edges() for g in self._gs]))[0]
 
     def __len__(self):
         return len(self._gs)
 
     def __getitem__(self, idx):
         return self._gs[idx], self._lgs[idx], \
-                self._g_degs[idx], self._lg_degs[idx], self._eid2nids[idx]
+                self._g_degs[idx], self._lg_degs[idx], self._pm_pds[idx]
 
     def _appendix_c(self):
         q = npr.uniform(0, self._avg_deg - math.sqrt(self._avg_deg))
         p = self._k * self._avg_deg - q
-        return p, q
+        if random.random() < 0.5:
+            return p, q
+        else:
+            return q, p
 
     def collate_fn(self, x):
-        g, lg, deg_g, deg_lg, eid2nid = zip(*x)
+        g, lg, deg_g, deg_lg, pm_pd = zip(*x)
         g_batch = batch(g)
         lg_batch = batch(lg)
         degg_batch = F.pack(deg_g)
         deglg_batch = F.pack(deg_lg)
-        eid2nid_batch = F.pack([x + i * self._n_nodes for i, x in enumerate(eid2nid)])
-        return g_batch, lg_batch, degg_batch, deglg_batch, eid2nid_batch
+        pm_pd_batch = F.pack([x + i * self._n_nodes for i, x in enumerate(pm_pd)])
+        return g_batch, lg_batch, degg_batch, deglg_batch, pm_pd_batch

src/graph/graph_op.cc

@@ -15,44 +15,18 @@ inline bool IsValidIdArray(const IdArray& arr) {
 }  // namespace
 
 Graph GraphOp::LineGraph(const Graph* g, bool backtracking) {
-  typedef std::pair<dgl_id_t, dgl_id_t> entry;
-  typedef std::map<dgl_id_t, std::vector<entry>> csm;  // Compressed Sparse Matrix
-
-  csm adj;
-  std::vector<entry> vec;
-  for (size_t i = 0; i != g->all_edges_src_.size(); ++i) {
-    auto u = g->all_edges_src_[i];
-    auto v = g->all_edges_dst_[i];
-    auto ret = adj.insert(csm::value_type(u, vec));
-    (ret.first)->second.push_back(std::make_pair(v, i));
-  }
-
-  std::vector<dgl_id_t> lg_src, lg_dst;
-  for (size_t i = 0; i != g->all_edges_src_.size(); ++i) {
-    auto u = g->all_edges_src_[i];
-    auto v = g->all_edges_dst_[i];
-    auto j = adj.find(v);
-    if (j != adj.end()) {
-      for (size_t k = 0; k != j->second.size(); ++k) {
-        if (backtracking || (!backtracking && j->second[k].first != u)) {
-          lg_src.push_back(i);
-          lg_dst.push_back(j->second[k].second);
-        }
+  Graph lg;
+  lg.AddVertices(g->NumEdges());
+  for (size_t i = 0; i < g->all_edges_src_.size(); ++i) {
+    const auto u = g->all_edges_src_[i];
+    const auto v = g->all_edges_dst_[i];
+    for (size_t j = 0; j < g->adjlist_[v].succ.size(); ++j) {
+      if (backtracking || (!backtracking && g->adjlist_[v].succ[j] != u)) {
+        lg.AddEdge(i, g->adjlist_[v].edge_id[j]);
       }
     }
   }
 
-  const int64_t len = lg_src.size();
-  IdArray src = IdArray::Empty({len}, DLDataType{kDLInt, 64, 1}, DLContext{kDLCPU, 0});
-  IdArray dst = IdArray::Empty({len}, DLDataType{kDLInt, 64, 1}, DLContext{kDLCPU, 0});
-  int64_t* src_ptr = static_cast<int64_t*>(src->data);
-  int64_t* dst_ptr = static_cast<int64_t*>(dst->data);
-  std::copy(lg_src.begin(), lg_src.end(), src_ptr);
-  std::copy(lg_dst.begin(), lg_dst.end(), dst_ptr);
-
-  Graph lg;
-  lg.AddVertices(g->NumEdges());
-  lg.AddEdges(src, dst);
   return lg;
 }