implement requested changes

python/dgl/backend/pytorch.py

@@ -29,8 +29,6 @@ tensor = th.tensor
 sparse_tensor = th.sparse.FloatTensor
 sum = th.sum
 max = th.max
-abs = th.abs
-all = lambda x: x.byte().all()
 stack = th.stack
 
 def astype(a, ty):
@@ -42,23 +40,6 @@ def asnumpy(a):
 def from_numpy(np_data):
     return th.from_numpy(np_data)
 
-def from_scipy_sparse(x):
-    x_coo = x.tocoo()
-    row = th.LongTensor(x_coo.row)
-    col = th.LongTensor(x_coo.col)
-    idx = th.stack([row, col])
-    dat = th.FloatTensor(x_coo.data)
-    return th.sparse.FloatTensor(idx, dat, x_coo.shape)
-
-def to_scipy_sparse(x):
-    x_cpu = x.cpu()
-    idx = x._indices()
-    row, col = idx.chunk(2, 0)
-    row = row.squeeze(0).numpy()
-    col = col.squeeze(0).numpy()
-    dat = x._values().numpy()
-    return sp.sparse.coo_matrix((dat, (row, col)), shape=x.shape)
-
 def pack(tensors, dim=0):
     return th.cat(tensors, dim)
 
@@ -71,9 +52,6 @@ def shape(x):
 def dtype(x):
     return x.dtype
 
-def item(x):
-    return x.item()
-
 unique = th.unique
 
 def gather_row(data, row_index):

python/dgl/data/sbm.py

@@ -18,10 +18,19 @@ def sbm(n_blocks, block_size, p, q, rng=None):
 
     Parameters
     ----------
-    n_blocks : number of blocks
-    block_size : block size
-    p : probability for intra-community edge
-    q : probability for inter-community edge
+    n_blocks : int
+        Number of blocks.
+    block_size : int
+        Block size.
+    p : float
+        Probability for intra-community edge.
+    q : float
+        Probability for inter-community edge.
+
+    Returns
+    -------
+    scipy sparse matrix
+        The adjacency matrix of generated graph.
     """
     n = n_blocks * block_size
     p /= n
@@ -45,17 +54,28 @@ def sbm(n_blocks, block_size, p, q, rng=None):
     return adj
 
 class SBMMixture(Dataset):
-    def __init__(self, n_graphs, n_nodes, n_communities,
-                 k=2, avg_deg=3, p='Appendix C', rng=None):
     """ Symmetric Stochastic Block Model Mixture
-        n_graphs : number of graphs
-        n_nodes : number of nodes
-        n_communities : number of communities
-        k : multiplier, optional
-        avg_deg : average degree, optional
-        p : random density generator, optional
-        rng : random number generator, optional
+    Please refer to Appendix C of "Supervised Community Detection with Hierarchical Graph Neural Networks" (https://arxiv.org/abs/1705.08415) for details.
+
+    Parameters
+    ----------
+    n_graphs : int
+        Number of graphs.
+    n_nodes : int
+        Number of nodes.
+    n_communities : int
+        Number of communities.
+    k : int, optional
+        Multiplier.
+    avg_deg : int, optional
+        Average degree.
+    p : callable or str, optional
+        Random density generator.
+    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):
         super(SBMMixture, self).__init__()
         self._n_nodes = n_nodes
         assert n_nodes % n_communities == 0

python/dgl/graph.py

@@ -3,7 +3,6 @@
 from __future__ import absolute_import
 
 import networkx as nx
-import scipy as sp
 
 import dgl
 from .base import ALL, is_all, __MSG__, __REPR__
@@ -472,7 +471,8 @@ class DGLGraph(object):
 
         Parameters
         ----------
-        a :
+        a : scipy sparse matrix
+            The graph's adjacency matrix
         """
         self.clear()
         self._graph.from_scipy_sparse_matrix(a)
@@ -1233,44 +1233,55 @@ class DGLGraph(object):
                 self._edge_frame.num_rows,
                 reduce_func)
 
-    def adjacency_matrix(self):
+    def adjacency_matrix(self, ctx=None):
         """Return the adjacency matrix representation of this graph.
 
+        Parameters
+        ----------
+        ctx : optional
+            The context of returned adjacency matrix.
+
         Returns
         -------
-        utils.CtxCachedObject
-            An object that returns tensor given context.
+        sparse_tensor
+            The adjacency matrix.
         """
-        return self._graph.adjacency_matrix()
+        return self._graph.adjacency_matrix().get(ctx)
 
-    def incidence_matrix(self, oriented=False, sorted=False):
+    def incidence_matrix(self, oriented=False, ctx=None):
         """Return the incidence matrix representation of this graph.
 
+        Parameters
+        ----------
+        oriented : bool, optional
+            Whether the returned incidence matrix is oriented.
+
+        ctx : optional
+            The context of returned incidence matrix.
+
         Returns
         -------
-        utils.CtxCachedObject
-            An object that returns tensor given context.
+        sparse_tensor
+            The incidence matrix.
         """
-        return self._graph.incidence_matrix(oriented, sorted)
+        return self._graph.incidence_matrix(oriented).get(ctx)
 
-    def line_graph(self, backtracking=True, sorted=False):
+    def line_graph(self, backtracking=True, shared=False):
         """Return the line graph of this graph.
 
+        Parameters
+        ----------
+        backtracking : bool, optional
+            Whether the returned line graph is backtracking.
+
+        shared : bool, optional
+            Whether the returned line graph shares representations with `self`.
+
         Returns
         -------
         DGLGraph
             The line graph of this graph.
         """
-        return DGLGraph(self._graph.line_graph(backtracking, sorted))
-
-def _get_repr(attr_dict):
-    if len(attr_dict) == 1 and __REPR__ in attr_dict:
-        return attr_dict[__REPR__]
-    else:
-        return attr_dict
-
-def _set_repr(attr_dict, attr):
-    if utils.is_dict_like(attr):
-        attr_dict.update(attr)
-    else:
-        attr_dict[__REPR__] = attr
+        graph_data = self._graph.line_graph(backtracking)
+        node_frame = self._edge_frame if shared else None
+        return DGLGraph(graph_data, node_frame)

python/dgl/graph_index.py

@@ -408,26 +408,22 @@ class GraphIndex(object):
             self._cache['adj'] = utils.CtxCachedObject(lambda ctx: F.to_context(mat, ctx))
         return self._cache['adj']
 
-    def incidence_matrix(self, oriented=False, sorted=False):
+    def incidence_matrix(self, oriented=False):
         """Return the incidence matrix representation of this graph.
         
         Parameters
         ----------
         oriented : bool, optional (default=False)
           Whether the returned incidence matrix is oriented.
-        sorted : bool, optional (default=False)
-          If true, nodes in L(G) are sorted as pairs.
-          If False, nodes in L(G) are ordered by their edge id's in G.
 
         Returns
         -------
         utils.CtxCachedObject
             An object that returns tensor given context.
         """
-        key = ('oriented ' if oriented else '') + \
-                ('sorted ' if sorted else '') + 'incidence matrix'
+        key = ('oriented ' if oriented else '') + 'incidence matrix'
         if not key in self._cache:
-            src, dst, _ = self.edges(sorted=sorted)
+            src, dst, _ = self.edges(sorted=False)
             src = src.tousertensor()
             dst = dst.tousertensor()
             m = self.number_of_edges()
@@ -519,7 +515,7 @@ class GraphIndex(object):
         dst = utils.toindex(adj_coo.col)
         self.add_edges(src, dst)
 
-    def line_graph(self, backtracking=True, sorted=False):
+    def line_graph(self, backtracking=True):
         """Return the line graph of this graph.
 
         Parameters
@@ -527,9 +523,6 @@ class GraphIndex(object):
         backtracking : bool, optional (default=False)
           Whether (i, j) ~ (j, i) in L(G).
           (i, j) ~ (j, i) is the behavior of networkx.line_graph.
-        sorted : bool, optional (default=False)
-          If true, nodes in L(G) are sorted as pairs.
-          If False, nodes in L(G) are ordered by their edge id's in G.
 
         Returns
         -------

src/graph/graph_op.cc

 // Graph operation implementation
 #include <dgl/graph_op.h>
 #include <algorithm>
-#include <stdio.h>
 
 namespace dgl {
 

tests/pytorch/test_line_graph.py

@@ -9,20 +9,18 @@ def check_eq(a, b):
     return a.shape == b.shape and np.allclose(a.numpy(), b.numpy())
 
 def test_line_graph():
-    # FIXME
-    return
-    """
     N = 5
     G = dgl.DGLGraph(nx.star_graph(N))
-    G.set_e_repr(th.randn((2*N, D)))
+    G.set_e_repr(th.randn((2 * N, D)))
     n_edges = G.number_of_edges()
-    L = dgl.line_graph(G)
-    assert L.number_of_nodes() == 2*N
+    L = G.line_graph(shared=True)
+    assert L.number_of_nodes() == 2 * N
+    L.set_n_repr(th.randn((2 * N, D)))
     # update node features on line graph should reflect to edge features on
     # original graph.
     u = [0, 0, 2, 3]
     v = [1, 2, 0, 0]
-    eid = G.get_edge_id(u, v)
+    eid = G.edge_ids(u, v)
     L.set_n_repr(th.zeros((4, D)), eid)
     assert check_eq(G.get_e_repr(u, v), th.zeros((4, D)))
 
@@ -31,23 +29,18 @@ def test_line_graph():
     data = th.randn(n_edges, D)
     L.set_n_repr({'w': data})
     assert check_eq(G.get_e_repr()['w'], data)
-    """
 
 def test_no_backtracking():
-    # FIXME
-    return
-    """
     N = 5
     G = dgl.DGLGraph(nx.star_graph(N))
-    G.set_e_repr(th.randn((2*N, D)))
-    L = dgl.line_graph(G, no_backtracking=True)
-    assert L.number_of_nodes() == 2*N
+    G.set_e_repr(th.randn((2 * N, D)))
+    L = G.line_graph(backtracking=False)
+    assert L.number_of_nodes() == 2 * N
     for i in range(1, N):
-        e1 = G.get_edge_id(0, i)
-        e2 = G.get_edge_id(i, 0)
+        e1 = G.edge_id(0, i)
+        e2 = G.edge_id(i, 0)
         assert not L.has_edge(e1, e2)
         assert not L.has_edge(e2, e1)
-    """
 
 if __name__ == '__main__':
     test_line_graph()