WIP: batched graph

include/dgl/graph.h

@@ -13,6 +13,8 @@ typedef tvm::runtime::NDArray DegreeArray;
 typedef tvm::runtime::NDArray BoolArray;
 
 class Graph;
+class GraphOp;
+struct Subgraph;
 
 /*!
  * \brief Base dgl graph class.
@@ -246,7 +248,7 @@ class Graph {
    * \param vids The vertices in the subgraph.
    * \return the induced subgraph
    */
-  Graph Subgraph(IdArray vids) const;
+  Subgraph VertexSubgraph(IdArray vids) const;
 
   /*!
    * \brief Construct the induced edge subgraph of the given edges.
@@ -264,7 +266,7 @@ class Graph {
    * \param vids The edges in the subgraph.
    * \return the induced edge subgraph
    */
-  Graph EdgeSubgraph(IdArray src, IdArray dst) const;
+  Subgraph EdgeSubgraph(IdArray src, IdArray dst) const;
 
   /*!
    * \brief Return a new graph with all the edges reversed.
@@ -275,24 +277,8 @@ class Graph {
    */
   Graph Reverse() const;
 
-  // TODO
-  std::vector<Graph> Split(std::vector<IdArray> vids_array) const;
-
-  /*!
-   * \brief Merge several graphs into one graph.
-   *
-   * The new graph will include all the nodes/edges in the given graphs.
-   * Nodes/Edges will be relabled by adding the cumsum of the previous graph sizes
-   * in the given sequence order. For example, giving input [g1, g2, g3], where
-   * they have 5, 6, 7 nodes respectively. Then node#2 of g2 will become node#7
-   * in the result graph. Edge ids are re-assigned similarly.
-   *
-   * \param graphs A list of input graphs to be merged.
-   * \return the merged graph
-   */
-  static Graph Merge(std::vector<const Graph*> graphs);
-
- private:
+ protected:
+  friend class GraphOp;
   /*! \brief Internal edge list type */
   struct EdgeList {
     /*! \brief successor vertex list */
@@ -318,6 +304,22 @@ class Graph {
   uint64_t num_edges_ = 0;
 };
 
+/*! \brief Subgraph data structure */
+struct Subgraph {
+  /*! \brief The graph. */
+  Graph graph;
+  /*! 
+   * \brief The induced vertex ids.
+   * \note This is also a map from the new vertex id to the vertex id in the parent graph.
+   */
+  IdArray induced_vertices;
+  /*! 
+   * \brief The induced edge ids.
+   * \note This is also a map from the new edge id to the edge id in the parent graph.
+   */
+  IdArray induced_edges;
+};
+
 }  // namespace dgl
 
 #endif  // DGL_DGLGRAPH_H_

include/dgl/graph_op.h

+// Graph operations
+#ifndef DGL_GRAPH_OP_H_
+#define DGL_GRAPH_OP_H_
+
+#include "graph.h"
+
+namespace dgl {
+
+class GraphOp {
+ public:
+  /*!
+   * \brief Return a disjoint union of the input graphs.
+   *
+   * The new graph will include all the nodes/edges in the given graphs.
+   * Nodes/Edges will be relabled by adding the cumsum of the previous graph sizes
+   * in the given sequence order. For example, giving input [g1, g2, g3], where
+   * they have 5, 6, 7 nodes respectively. Then node#2 of g2 will become node#7
+   * in the result graph. Edge ids are re-assigned similarly.
+   *
+   * \param graphs A list of input graphs to be unioned.
+   * \return the disjoint union of the graphs
+   */
+  static Graph DisjointUnion(std::vector<const Graph*> graphs);
+
+  /*!
+   * \brief Partition the graph into several subgraphs.
+   *
+   * The graph will be partitioned by the node ids. Edges between partitions
+   * will be ignored. This requires the given number of partitions to evenly
+   * divides the number of nodes in the graph.
+   * 
+   * \param num The number of partitions.
+   * \return a list of partitioned graphs
+   */
+  static std::vector<Graph> PartitionByNum(const Graph* graph, size_t num);
+};
+
+}  // namespace dgl
+
+#endif  // DGL_GRAPH_OP_H_

python/dgl/batch.py

@@ -3,57 +3,88 @@ from __future__ import absolute_import
 
 import numpy as np
 
+from .base import ALL, is_all
+from .frame import FrameRef
 from .graph import DGLGraph
+from . import graph_index as gi
 from . import backend as F
 
 class BatchedDGLGraph(DGLGraph):
-    def __init__(self, graph_list, node_attrs=None, edge_attrs=None, **attr):
-        super(BatchedDGLGraph, self).__init__(**attr)
-        self.graph_list = graph_list
-        self.graph_idx = {}
-        for idx, g in enumerate(self.graph_list):
-            self.graph_idx[g] = idx
-
-        self.num_nodes = [len(g) for g in self.graph_list]
-        self.num_edges = [g.size() for g in self.graph_list]
-
-        # calc index offset
-        self.node_offset = np.cumsum([0] + self.num_nodes)
-        self.edge_offset = np.cumsum([0] + self.num_edges)
-
-        # in-order add relabeled nodes
-        self.add_nodes_from(range(self.node_offset[-1]))
-
-        # in-order add relabeled edges
-        self.new_edge_list = [np.array(g.edge_list) + offset
-                        for g, offset in zip(self.graph_list, self.node_offset[:-1])]
-        self.new_edges = np.concatenate(self.new_edge_list)
-        self.add_edges_from(self.new_edges)
-
-        assert self.size() == self.edge_offset[-1]
-
-        # set new node attr
-        if node_attrs:
-            attrs = {}
-            for key in node_attrs:
-                vals = [g.pop_n_repr(key) for g in self.graph_list]
-                attrs[key] = F.pack(vals)
-            self.set_n_repr(attrs)
-        else:
-            for g in self.graph_list:
-                self._node_frame.append(g._node_frame)
-
-        # set new edge attr
-        if edge_attrs:
-            attrs = {}
-            for key in edge_attrs:
-                vals = [g.pop_e_repr(key) for g in self.graph_list]
-                attrs[key] = F.pack(vals)
-            self.set_e_repr(attrs)
-        else:
-            for g in self.graph_list:
-                self._edge_frame.append(g._edge_frame)
+    """The batched DGL graph.
+
+    The batched graph is read-only.
 
+    Parameters
+    ----------
+    graph_list : iterable
+        A list of DGLGraphs to be batched.
+    node_attrs : str or iterable
+        The node attributes to also be batched.
+    edge_attrs : str or iterable, optional
+        The edge attributes to also be batched.
+    """
+    def __init__(self, graph_list, node_attrs, edge_attrs):
+        # TODO(minjie): handle the input is again a batched graph.
+        # create batched graph index
+        batched_index = gi.disjoint_union([g._graph for g in graph_list])
+        # create batched node and edge frames
+        # NOTE: following code will materialize the columns of the input graphs.
+        batched_node_frame = FrameRef()
+        for gr in graph_list:
+            cols = {gr._node_frame[key] for key in node_attrs}
+            batched_node_frame.append(cols)
+        batched_edge_frame = FrameRef()
+        for gr in graph_list:
+            cols = {gr._edge_frame[key] for key in edge_attrs}
+            batched_edge_frame.append(cols)
+        super(BatchedDGLGraph, self).__init__(
+                graph_data=batched_index,
+                node_frame=batched_node_frame,
+                edge_frame=batched_edge_frame)
+
+        # extra members
+        self._batch_size = len(graph_list)
+        self._batch_num_nodes = [gr.number_of_nodes() for gr in graph_list]
+        self._batch_num_edges = [gr.number_of_edges() for gr in graph_list]
+
+    @property
+    def batch_size(self):
+        """Number of graphs in this batch."""
+        return self._batch_size
+
+    @property
+    def batch_num_nodes(self):
+        """Number of nodes of each graph in this batch."""
+        return self._batch_num_nodes
+
+    @property
+    def batch_num_edges(self):
+        """Number of edges of each graph in this batch."""
+        return self._batch_num_edges
+
+    # override APIs
+    def add_nodes(self, num, reprs=None):
+        """Add nodes."""
+        raise RuntimeError('Readonly graph. Mutation is not allowed.')
+
+    def add_edge(self, u, v, reprs=None):
+        """Add one edge."""
+        raise RuntimeError('Readonly graph. Mutation is not allowed.')
+
+    def add_edges(self, u, v, reprs=None):
+        """Add many edges."""
+        raise RuntimeError('Readonly graph. Mutation is not allowed.')
+
+    # new APIs
+    def __getitem__(self, idx):
+        """Slice the batch and return the batch of graphs specified by the idx."""
+        pass
+
+    def __setitem__(self, idx, val):
+        """Set the value of the slice. The graph size cannot be changed."""
+        pass
+
+    '''
     def query_new_node(self, g, u):
         idx = self.graph_idx[g]
         offset = self.node_offset[idx]
@@ -76,7 +107,12 @@ class BatchedDGLGraph(DGLGraph):
 
     def query_edge_start_offset(self):
         return self.edge_offset[:-1].copy()
+    '''
 
+def split(graph_batch, num_or_size_splits):
+    """Split the batch."""
+    # TODO(minjie): could follow torch.split syntax
+    pass
 
 def unbatch(graph_batch):
     """Unbatch the graph and return a list of subgraphs.
@@ -86,6 +122,7 @@ def unbatch(graph_batch):
     graph_batch : DGLGraph
         The batched graph.
     """
+    assert False, "disabled for now"
     graph_list = graph_batch.graph_list
     num_graphs = len(graph_list)
     # split and set node attrs
@@ -108,29 +145,36 @@ def unbatch(graph_batch):
 
     return graph_list
 
-
-# FIXME (lingfan): Do we really need the batch API?
-#                  Can't we let user call BatchedDGLGraph(graph_list) directly
-#                  and make unbatch a member function of BatchedDGLGraph
-def batch(graph_list, node_attrs=None, edge_attrs=None):
+def batch(graph_list, node_attrs=ALL, edge_attrs=ALL):
     """Batch a list of DGLGraphs into one single graph.
+
     Once batch is called, the structure of both merged graph and graphs in graph_list
-    must not bbe mutated, or unbatch's behavior will be undefined.
+    must not be mutated, or unbatch's behavior will be undefined.
 
     Parameters
     ----------
     graph_list : iterable
         A list of DGLGraphs to be batched.
-    node_attrs : str or iterable
-        A list of node attributes needed for merged graph
-        It's user's resposiblity to make sure node_attrs exists
-    edge_attrs : str or iterable
-        A list of edge attributes needed for merged graph
-        It's user's resposiblity to make sure edge_attrs exists
-
-    Return
-    ------
-    newgrh: DGLGraph
-        one single merged graph
+    node_attrs : str or iterable, optional
+        The node attributes to also be batched. Specify None to not batch any attributes.
+    edge_attrs : str or iterable, optional
+        The edge attributes to also be batched. Specify None to not batch any attributes.
+
+    Returns
+    -------
+    newgrh: BatchedDGLGraph
+        one single batched graph
     """
+    if node_attrs is None:
+        node_attrs = []
+    elif is_all(node_attrs):
+        node_attrs = graph_list[0].node_attr_schemes()
+    elif if isinstance(node_attrs, str):
+        node_attrs = [node_attrs]
+    if edge_attrs is None:
+        edge_attrs = []
+    elif is_all(edge_attrs):
+        edge_attrs = graph_list[0].edge_attr_schemes()
+    elif if isinstance(edge_attrs, str):
+        edge_attrs = [edge_attrs]
     return BatchedDGLGraph(graph_list, node_attrs, edge_attrs)

python/dgl/graph_index.py

@@ -367,6 +367,27 @@ class GraphIndex(object):
         v_array = v.todgltensor()
         return utils.toindex(_CAPI_DGLGraphOutDegrees(self._handle, v_array))
 
+    def node_subgraph(self, v):
+        """Return the induced node subgraph.
+
+        Parameters
+        ----------
+        v : utils.Index
+            The nodes.
+
+        Returns
+        -------
+        GraphIndex
+            The subgraph index.
+        utils.Index
+            The induced edge ids. This is also a map from new edge id to parent edge id.
+        """
+        v_array = v.todgltensor()
+        rst = _CAPI_DGLGraphVertexSubgraph(self._handle, v_array)
+        gi = GraphIndex(rst(0))
+        induced_edges = utils.toindex(rst(2))
+        return gi, induced_edges
+
     def adjacency_matrix(self):
         """Return the adjacency matrix representation of this graph.
 
@@ -438,9 +459,8 @@ class GraphIndex(object):
         dst = utils.toindex(dst)
         self.add_edges(src, dst)
 
-    @staticmethod
-    def merge(graphs):
-        """Merge a list of graphs into one graph.
+def disjoint_union(graphs):
+    """Return a disjoint union of the input graphs.
 
     The new graph will include all the nodes/edges in the given graphs.
     Nodes/Edges will be relabled by adding the cumsum of the previous graph sizes
@@ -456,11 +476,11 @@ class GraphIndex(object):
     Returns
     -------
     GraphIndex
-            The merged graph
+        The disjoint union
     """
     inputs = c_array(GraphIndexHandle, [gr._handle for gr in graphs])
     inputs = ctypes.cast(inputs, ctypes.c_void_p)
-        handle = _CAPI_DGLGraphMerge(inputs, len(graphs))
+    handle = _CAPI_DGLDisjointUnion(inputs, len(graphs))
     return GraphIndex(handle)
 
 def create_graph_index(graph_data=None):
@@ -471,6 +491,8 @@ def create_graph_index(graph_data=None):
     graph_data : graph data, optional
         Data to initialize graph. Same as networkx's semantics.
     """
+    if isinstance(graph_data, GraphIndex):
+        return graph_data
     handle = _CAPI_DGLGraphCreate()
     gi = GraphIndex(handle)
     if graph_data is not None:

src/graph/graph.cc

 // Graph class implementation
 #include <algorithm>
+#include <unordered_map>
 #include <dgl/graph.h>
 
 namespace dgl {
@@ -345,14 +346,38 @@ DegreeArray Graph::OutDegrees(IdArray vids) const {
   return rst;
 }
 
-Graph Graph::Subgraph(IdArray vids) const {
-  LOG(FATAL) << "not implemented";
-  return *this;
+Subgraph Graph::VertexSubgraph(IdArray vids) const {
+  CHECK(IsValidIdArray(vids)) << "Invalid vertex id array.";
+  const auto len = vids->shape[0];
+  std::unordered_map<dgl_id_t, dgl_id_t> oldv2newv;
+  std::vector<dgl_id_t> edges;
+  const int64_t* vid_data = static_cast<int64_t*>(vids->data);
+  for (int64_t i = 0; i < len; ++i) {
+    oldv2newv[vid_data[i]] = i;
+  }
+  Subgraph rst;
+  rst.induced_vertices = vids;
+  rst.graph.AddVertices(len);
+  for (int64_t i = 0; i < len; ++i) {
+    const dgl_id_t oldvid = vid_data[i];
+    const dgl_id_t newvid = i;
+    for (size_t j = 0; j < adjlist_[oldvid].succ.size(); ++j) {
+      const dgl_id_t oldsucc = adjlist_[oldvid].succ[j];
+      if (oldv2newv.count(oldsucc)) {
+        const dgl_id_t newsucc = oldv2newv[oldsucc];
+        edges.push_back(adjlist_[oldvid].edge_id[j]);
+        rst.graph.AddEdge(newvid, newsucc);
+      }
+    }
+  }
+  rst.induced_edges = IdArray::Empty({static_cast<int64_t>(edges.size())}, vids->dtype, vids->ctx);
+  std::copy(edges.begin(), edges.end(), static_cast<int64_t*>(rst.induced_edges->data));
+  return rst;
 }
 
-Graph Graph::EdgeSubgraph(IdArray src, IdArray dst) const {
+Subgraph Graph::EdgeSubgraph(IdArray src, IdArray dst) const {
   LOG(FATAL) << "not implemented";
-  return *this;
+  return Subgraph();
 }
 
 Graph Graph::Reverse() const {
@@ -360,17 +385,4 @@ Graph Graph::Reverse() const {
   return *this;
 }
 
-Graph Graph::Merge(std::vector<const Graph*> graphs) {
-  Graph rst;
-  uint64_t cumsum = 0;
-  for (const Graph* gr : graphs) {
-    rst.AddVertices(gr->NumVertices());
-    for (uint64_t i = 0; i < gr->NumEdges(); ++i) {
-      rst.AddEdge(gr->all_edges_src_[i] + cumsum, gr->all_edges_dst_[i] + cumsum);
-    }
-    cumsum += gr->NumVertices();
-  }
-  return rst;
-}
-
 }  // namespace dgl

src/graph/graph_apis.cc

 #include <dgl/runtime/packed_func.h>
 #include <dgl/runtime/registry.h>
 #include <dgl/graph.h>
+#include <dgl/graph_op.h>
 
 using tvm::runtime::TVMArgs;
 using tvm::runtime::TVMArgValue;
@@ -8,17 +9,21 @@ using tvm::runtime::TVMRetValue;
 using tvm::runtime::PackedFunc;
 
 namespace dgl {
+
+// Graph handler type
+typedef void* GraphHandle;
+
 namespace {
-/*!\brief Convert EdgeArray structure to PackedFunc */
+// Convert EdgeArray structure to PackedFunc.
 PackedFunc ConvertEdgeArrayToPackedFunc(const Graph::EdgeArray& ea) {
   auto body = [ea] (TVMArgs args, TVMRetValue* rv) {
       int which = args[0];
       if (which == 0) {
-        *rv = ea.src;
+        *rv = std::move(ea.src);
       } else if (which == 1) {
-        *rv = ea.dst;
+        *rv = std::move(ea.dst);
       } else if (which == 2) {
-        *rv = ea.id;
+        *rv = std::move(ea.id);
       } else {
         LOG(FATAL) << "invalid choice";
       }
@@ -26,6 +31,27 @@ PackedFunc ConvertEdgeArrayToPackedFunc(const Graph::EdgeArray& ea) {
   return PackedFunc(body);
 }
 
+// Convert Subgraph structure to PackedFunc.
+PackedFunc ConvertSubgraphToPackedFunc(const Subgraph& sg) {
+  auto body = [sg] (TVMArgs args, TVMRetValue* rv) {
+      int which = args[0];
+      if (which == 0) {
+        Graph* gptr = new Graph();
+        *gptr = std::move(sg.graph);
+        GraphHandle ghandle = gptr;
+        *rv = ghandle;
+      } else if (which == 1) {
+        *rv = std::move(sg.induced_vertices);
+      } else if (which == 2) {
+        *rv = std::move(sg.induced_edges);
+      } else {
+        LOG(FATAL) << "invalid choice";
+      }
+    };
+  return PackedFunc(body);
+}
+
+// Convert the given DLTensor to a temporary DLManagedTensor that does not own memory.
 DLManagedTensor* CreateTmpDLManagedTensor(const TVMArgValue& arg) {
   const DLTensor* dl_tensor = arg;
   DLManagedTensor* ret = new DLManagedTensor();
@@ -37,9 +63,6 @@ DLManagedTensor* CreateTmpDLManagedTensor(const TVMArgValue& arg) {
 
 }  // namespace
 
-// Graph handler type
-typedef void* GraphHandle;
-
 TVM_REGISTER_GLOBAL("graph_index._CAPI_DGLGraphCreate")
 .set_body([] (TVMArgs args, TVMRetValue* rv) {
     GraphHandle ghandle = new Graph();
@@ -242,7 +265,15 @@ TVM_REGISTER_GLOBAL("graph_index._CAPI_DGLGraphOutDegrees")
     *rv = gptr->OutDegrees(vids);
   });
 
-TVM_REGISTER_GLOBAL("graph_index._CAPI_DGLGraphMerge")
+TVM_REGISTER_GLOBAL("graph_index._CAPI_DGLGraphVertexSubgraph")
+.set_body([] (TVMArgs args, TVMRetValue* rv) {
+    GraphHandle ghandle = args[0];
+    const Graph* gptr = static_cast<Graph*>(ghandle);
+    const IdArray vids = IdArray::FromDLPack(CreateTmpDLManagedTensor(args[1]));
+    *rv = ConvertSubgraphToPackedFunc(gptr->VertexSubgraph(vids));
+  });
+
+TVM_REGISTER_GLOBAL("graph_index._CAPI_DGLDisjointUnion")
 .set_body([] (TVMArgs args, TVMRetValue* rv) {
     void* list = args[0];
     GraphHandle* inhandles = static_cast<GraphHandle*>(list);
@@ -253,7 +284,7 @@ TVM_REGISTER_GLOBAL("graph_index._CAPI_DGLGraphMerge")
       graphs.push_back(gr);
     }
     Graph* gptr = new Graph();
-    *gptr = Graph::Merge(std::move(graphs));
+    *gptr = GraphOp::DisjointUnion(std::move(graphs));
     GraphHandle ghandle = gptr;
     *rv = ghandle;
   });

src/graph/graph_op.cc

+// Graph operation implementation
+#include <dgl/graph_op.h>
+
+namespace dgl {
+
+Graph GraphOp::DisjointUnion(std::vector<const Graph*> graphs) {
+  Graph rst;
+  uint64_t cumsum = 0;
+  for (const Graph* gr : graphs) {
+    rst.AddVertices(gr->NumVertices());
+    for (uint64_t i = 0; i < gr->NumEdges(); ++i) {
+      rst.AddEdge(gr->all_edges_src_[i] + cumsum, gr->all_edges_dst_[i] + cumsum);
+    }
+    cumsum += gr->NumVertices();
+  }
+  return rst;
+}
+
+}  // namespace dgl