eric-haibin-lin closed pull request #13396: add adjacency operator. URL: https://github.com/apache/incubator-mxnet/pull/13396
This is a PR merged from a forked repository. As GitHub hides the original diff on merge, it is displayed below for the sake of provenance: As this is a foreign pull request (from a fork), the diff is supplied below (as it won't show otherwise due to GitHub magic): diff --git a/src/operator/contrib/dgl_graph-inl.h b/src/operator/contrib/dgl_graph-inl.h new file mode 100644 index 00000000000..f31071b896e --- /dev/null +++ b/src/operator/contrib/dgl_graph-inl.h @@ -0,0 +1,68 @@ +/* + * Licensed to the Apache Software Foundation (ASF) under one + * or more contributor license agreements. See the NOTICE file + * distributed with this work for additional information + * regarding copyright ownership. The ASF licenses this file + * to you under the Apache License, Version 2.0 (the + * "License"); you may not use this file except in compliance + * with the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, + * software distributed under the License is distributed on an + * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY + * KIND, either express or implied. See the License for the + * specific language governing permissions and limitations + * under the License. + */ + +#ifndef MXNET_OPERATOR_CONTRIB_DGL_GRAPH_INL_H_ +#define MXNET_OPERATOR_CONTRIB_DGL_GRAPH_INL_H_ + +#include <dmlc/logging.h> +#include <dmlc/parameter.h> +#include <mxnet/operator.h> +#include <mxnet/ndarray.h> +#include <map> +#include <algorithm> +#include <vector> +#include <string> +#include <utility> +#include "../operator_common.h" +#include "../mxnet_op.h" +#include "../mshadow_op.h" +#include "../tensor/init_op.h" + +namespace mxnet { +namespace op { + +template<typename xpu> +void DGLAdjacencyForwardEx(const nnvm::NodeAttrs& attrs, + const OpContext& ctx, + const std::vector<NDArray>& inputs, + const std::vector<OpReqType>& req, + const std::vector<NDArray>& outputs) { + CHECK_EQ(inputs.size(), 1U); + CHECK_EQ(outputs.size(), 1U); + CHECK_EQ(req.size(), 1U); + CHECK_EQ(inputs[0].storage_type(), kCSRStorage); + CHECK_EQ(outputs[0].storage_type(), kCSRStorage); + CHECK_EQ(req[0], kWriteTo); + const TBlob &in_idx = inputs[0].aux_data(csr::kIdx); + const TBlob &in_indptr = inputs[0].aux_data(csr::kIndPtr); + + outputs[0].CheckAndAllocData(in_idx.shape_); + outputs[0].CheckAndAllocAuxData(csr::kIdx, in_idx.shape_); + outputs[0].CheckAndAllocAuxData(csr::kIndPtr, in_indptr.shape_); + + mshadow::Stream<xpu> *s = ctx.get_stream<xpu>(); + Fill<false>(s, outputs[0].data(), req[0], 1.0); + mxnet_op::copy(s, outputs[0].aux_data(csr::kIdx), in_idx); + mxnet_op::copy(s, outputs[0].aux_data(csr::kIndPtr), in_indptr); +} + +} // namespace op +} // namespace mxnet + +#endif // MXNET_OPERATOR_CONTRIB_DGL_GRAPH_INL_H_ diff --git a/src/operator/contrib/dgl_graph.cc b/src/operator/contrib/dgl_graph.cc index bf54ed398f9..d9bcdd4b3f1 100644 --- a/src/operator/contrib/dgl_graph.cc +++ b/src/operator/contrib/dgl_graph.cc @@ -24,13 +24,10 @@ #include <mxnet/operator_util.h> #include <dmlc/logging.h> #include <dmlc/optional.h> -#include "../operator_common.h" #include "../elemwise_op_common.h" #include "../../imperative/imperative_utils.h" #include "../subgraph_op_common.h" -#include "../mshadow_op.h" -#include "../mxnet_op.h" -#include "../tensor/init_op.h" +#include "./dgl_graph-inl.h" namespace mxnet { namespace op { @@ -459,6 +456,73 @@ The storage type of ``edge_id`` output depends on storage types of inputs .add_argument("u", "NDArray-or-Symbol", "u ndarray") .add_argument("v", "NDArray-or-Symbol", "v ndarray"); +///////////////////////// DGL Adjacency /////////////////////////// + +inline bool DGLAdjacencyShape(const nnvm::NodeAttrs& attrs, + std::vector<TShape>* in_attrs, + std::vector<TShape>* out_attrs) { + CHECK_EQ(in_attrs->size(), 1U); + CHECK_EQ(out_attrs->size(), 1U); + + SHAPE_ASSIGN_CHECK(*out_attrs, 0, in_attrs->at(0)); + SHAPE_ASSIGN_CHECK(*in_attrs, 0, out_attrs->at(0)); + return out_attrs->at(0).ndim() != 0U && out_attrs->at(0).Size() != 0U; +} + +inline bool DGLAdjacencyType(const nnvm::NodeAttrs& attrs, + std::vector<int>* in_attrs, + std::vector<int>* out_attrs) { + CHECK_EQ(in_attrs->size(), 1U); + CHECK_EQ(out_attrs->size(), 1U); + CHECK_EQ(in_attrs->at(0), mshadow::kInt64); + TYPE_ASSIGN_CHECK(*out_attrs, 0, mshadow::kFloat32); + return out_attrs->at(0) != -1; +} + +inline bool DGLAdjacencyStorageType(const nnvm::NodeAttrs& attrs, + const int dev_mask, + DispatchMode* dispatch_mode, + std::vector<int>* in_attrs, + std::vector<int>* out_attrs) { + CHECK_EQ(in_attrs->size(), 1U) << "Only works for 2d arrays"; + CHECK_EQ(out_attrs->size(), 1U); + int& out_stype = out_attrs->at(0); + bool dispatched = storage_type_assign(&out_stype, kCSRStorage, + dispatch_mode, DispatchMode::kFComputeEx); + if (!dispatched) { + LOG(ERROR) << "Cannot dispatch output storage type: " << common::stype_string(out_stype) + << ". dgl_adjacency only works for csr matrices"; + } + return dispatched; +} + +NNVM_REGISTER_OP(_contrib_dgl_adjacency) +.describe(R"code(This operator converts a CSR matrix whose values are edge Ids +to an adjacency matrix whose values are ones. The output CSR matrix always has +the data value of float32. +Example:: + + x = [[ 1, 0, 0 ], + [ 0, 2, 0 ], + [ 0, 0, 3 ]] + dgl_adjacency(x) = + [[ 1, 0, 0 ], + [ 0, 1, 0 ], + [ 0, 0, 1 ]] + +)code" ADD_FILELINE) +.set_num_inputs(1) +.set_num_outputs(1) +.set_attr<nnvm::FListInputNames>("FListInputNames", + [](const NodeAttrs& attrs) { + return std::vector<std::string>{"data"}; + }) +.set_attr<nnvm::FInferShape>("FInferShape", DGLAdjacencyShape) +.set_attr<nnvm::FInferType>("FInferType", DGLAdjacencyType) +.set_attr<FInferStorageType>("FInferStorageType", DGLAdjacencyStorageType) +.set_attr<FComputeEx>("FComputeEx<cpu>", DGLAdjacencyForwardEx<cpu>) +.add_argument("data", "NDArray-or-Symbol", "Input ndarray"); + } // namespace op } // namespace mxnet diff --git a/src/operator/contrib/dgl_graph.cu b/src/operator/contrib/dgl_graph.cu new file mode 100644 index 00000000000..336e9d4f802 --- /dev/null +++ b/src/operator/contrib/dgl_graph.cu @@ -0,0 +1,29 @@ +/* + * Licensed to the Apache Software Foundation (ASF) under one + * or more contributor license agreements. See the NOTICE file + * distributed with this work for additional information + * regarding copyright ownership. The ASF licenses this file + * to you under the Apache License, Version 2.0 (the + * "License"); you may not use this file except in compliance + * with the License. You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, + * software distributed under the License is distributed on an + * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY + * KIND, either express or implied. See the License for the + * specific language governing permissions and limitations + * under the License. + */ + +#include "dgl_graph-inl.h" + +namespace mxnet { +namespace op { + +NNVM_REGISTER_OP(_contrib_dgl_adjacency) +.set_attr<FComputeEx>("FComputeEx<gpu>", DGLAdjacencyForwardEx<gpu>); + +} // namespace op +} // namespace mxnet diff --git a/tests/python/unittest/test_dgl_graph.py b/tests/python/unittest/test_dgl_graph.py index 774f811a0d1..1d758b939b2 100644 --- a/tests/python/unittest/test_dgl_graph.py +++ b/tests/python/unittest/test_dgl_graph.py @@ -75,6 +75,15 @@ def test_subgraph(): v2 = vertices[subv2] assert sp_g[v1, v2] == sp_subg[subv1, subv2] +def test_adjacency(): + sp_g, g = generate_graph(100) + adj = mx.nd.contrib.dgl_adjacency(g) + assert adj.dtype == np.float32 + assert adj.shape == g.shape + assert_array_equal(adj.indptr, g.indptr) + assert_array_equal(adj.indices, g.indices) + assert_array_equal(adj.data, mx.nd.ones(shape=g.indices.shape)) + if __name__ == "__main__": import nose nose.runmodule() ---------------------------------------------------------------- This is an automated message from the Apache Git Service. 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