# Copyright (c) 2019 PaddlePaddle Authors. All Rights Reserved # # Licensed 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. """ Fast implementation for graph construction and sampling. """ import numpy as np cimport numpy as np cimport cython from libcpp.map cimport map from libcpp.set cimport set from libcpp.unordered_set cimport unordered_set from libcpp.unordered_map cimport unordered_map from libcpp.vector cimport vector from libc.stdlib cimport rand, RAND_MAX @cython.boundscheck(False) @cython.wraparound(False) def build_index(np.ndarray[np.int64_t, ndim=1] u, np.ndarray[np.int64_t, ndim=1] v, long long num_nodes): """Building Edge Index """ cdef long long i cdef long long h=len(u) cdef long long n_size = num_nodes cdef np.ndarray[np.int64_t, ndim=1] degree = np.zeros([n_size], dtype=np.int64) cdef np.ndarray[np.int64_t, ndim=1] count = np.zeros([n_size], dtype=np.int64) cdef np.ndarray[np.int64_t, ndim=1] _tmp_v = np.zeros([h], dtype=np.int64) cdef np.ndarray[np.int64_t, ndim=1] _tmp_u = np.zeros([h], dtype=np.int64) cdef np.ndarray[np.int64_t, ndim=1] _tmp_eid = np.zeros([h], dtype=np.int64) cdef np.ndarray[np.int64_t, ndim=1] indptr = np.zeros([n_size + 1], dtype=np.int64) with nogil: for i in xrange(h): degree[u[i]] += 1 for i in xrange(n_size): indptr[i + 1] = indptr[i] + degree[i] for i in xrange(h): _tmp_v[indptr[u[i]] + count[u[i]]] = v[i] _tmp_eid[indptr[u[i]] + count[u[i]]] = i _tmp_u[indptr[u[i]] + count[u[i]]] = u[i] count[u[i]] += 1 return degree, _tmp_v, _tmp_u, _tmp_eid, indptr @cython.boundscheck(False) @cython.wraparound(False) def slice_by_index(np.ndarray[np.int64_t, ndim=1] u, np.ndarray[np.int64_t, ndim=1] indptr, np.ndarray[np.int64_t, ndim=1] index): cdef list output = [] cdef long long i cdef long long h = len(index) cdef long long j for i in xrange(h): j = index[i] output.append(u[indptr[j]:indptr[j+1]]) return np.array(output) @cython.boundscheck(False) @cython.wraparound(False) def map_edges(np.ndarray[np.int64_t, ndim=1] eid, np.ndarray[np.int64_t, ndim=2] edges, reindex): """Mapping edges by given dictionary """ cdef unordered_map[long long, long long] m = reindex cdef long long i = 0 cdef long long h = len(eid) cdef np.ndarray[np.int64_t, ndim=2] r_edges = np.zeros([h, 2], dtype=np.int64) cdef long long j with nogil: for i in xrange(h): j = eid[i] r_edges[i, 0] = m[edges[j, 0]] r_edges[i, 1] = m[edges[j, 1]] return r_edges @cython.boundscheck(False) @cython.wraparound(False) def map_nodes(nodes, reindex): """Mapping nodes by given dictionary """ cdef np.ndarray[np.int64_t, ndim=1] t_nodes = np.array(nodes, dtype=np.int64) cdef unordered_map[long long, long long] m = reindex cdef long long i = 0 cdef long long h = len(nodes) cdef np.ndarray[np.int64_t, ndim=1] new_nodes = np.zeros([h], dtype=np.int64) cdef long long j with nogil: for i in xrange(h): j = t_nodes[i] new_nodes[i] = m[j] return new_nodes @cython.boundscheck(False) @cython.wraparound(False) def node2vec_sample(np.ndarray[np.int64_t, ndim=1] succ, np.ndarray[np.int64_t, ndim=1] prev_succ, long long prev_node, float p, float q): """Fast implement of node2vec sampling """ cdef long long i cdef succ_len = len(succ) cdef prev_succ_len = len(prev_succ) cdef vector[float] probs cdef float prob_sum = 0 cdef unordered_set[long long] prev_succ_set for i in xrange(prev_succ_len): prev_succ_set.insert(prev_succ[i]) cdef float prob for i in xrange(succ_len): if succ[i] == prev_node: prob = 1. / p elif prev_succ_set.find(succ[i]) != prev_succ_set.end(): prob = 1. else: prob = 1. / q probs.push_back(prob) prob_sum += prob cdef float rand_num = float(rand())/RAND_MAX * prob_sum cdef long long sample_succ = 0 for i in xrange(succ_len): rand_num -= probs[i] if rand_num <= 0: sample_succ = succ[i] return sample_succ @cython.boundscheck(False) @cython.wraparound(False) def subset_choose_index(long long s_size, np.ndarray[ndim=1, dtype=np.int64_t] nid, np.ndarray[ndim=1, dtype=np.int64_t] rnd, np.ndarray[ndim=1, dtype=np.int64_t] buff_nid, long long offset): cdef long long n_size = len(nid) cdef long long i cdef long long j cdef unordered_map[long long, long long] m with nogil: for i in xrange(s_size): j = rnd[offset + i] % n_size if j >= i: buff_nid[offset + i] = nid[j] if m.find(j) == m.end() else nid[m[j]] m[j] = i if m.find(i) == m.end() else m[i] else: buff_nid[offset + i] = buff_nid[offset + j] buff_nid[offset + j] = nid[i] if m.find(i) == m.end() else nid[m[i]] @cython.boundscheck(False) @cython.wraparound(False) def subset_choose_index_eid(long long s_size, np.ndarray[ndim=1, dtype=np.int64_t] nid, np.ndarray[ndim=1, dtype=np.int64_t] eid, np.ndarray[ndim=1, dtype=np.int64_t] rnd, np.ndarray[ndim=1, dtype=np.int64_t] buff_nid, np.ndarray[ndim=1, dtype=np.int64_t] buff_eid, long long offset): cdef long long n_size = len(nid) cdef long long i cdef long long j cdef unordered_map[long long, long long] m with nogil: for i in xrange(s_size): j = rnd[offset + i] % n_size if j >= i: if m.find(j) == m.end(): buff_nid[offset + i], buff_eid[offset + i] = nid[j], eid[j] else: buff_nid[offset + i], buff_eid[offset + i] = nid[m[j]], eid[m[j]] m[j] = i if m.find(i) == m.end() else m[i] else: buff_nid[offset + i], buff_eid[offset + i] = buff_nid[offset + j], buff_eid[offset + j] if m.find(i) == m.end(): buff_nid[offset + j], buff_eid[offset + j] = nid[i], eid[i] else: buff_nid[offset + j], buff_eid[offset + j] = nid[m[i]], eid[m[i]] @cython.boundscheck(False) @cython.wraparound(False) def sample_subset(list nids, long long maxdegree, shuffle=False): cdef np.ndarray[ndim=1, dtype=np.int64_t] buff_index cdef long long buff_size, sample_size cdef long long total_buff_size = 0 cdef long long inc = 0 cdef list output = [] for inc in xrange(len(nids)): buff_size = len(nids[inc]) if buff_size > maxdegree: total_buff_size += maxdegree elif shuffle: total_buff_size += buff_size cdef np.ndarray[ndim=1, dtype=np.int64_t] buff_nid = np.zeros([total_buff_size], dtype=np.int64) cdef np.ndarray[np.int64_t, ndim=1] rnd = np.random.randint(0, np.iinfo(np.int64).max, dtype=np.int64, size=total_buff_size) cdef long long offset = 0 for inc in xrange(len(nids)): buff_size = len(nids[inc]) if not shuffle and buff_size <= maxdegree: output.append(nids[inc]) else: sample_size = buff_size if buff_size <= maxdegree else maxdegree if isinstance(nids[inc], list): tmp = np.array(nids[inc], dtype=np.int64) else: tmp = nids[inc] subset_choose_index(sample_size, tmp, rnd, buff_nid, offset) output.append(buff_nid[offset:offset+sample_size]) offset += sample_size return output @cython.boundscheck(False) @cython.wraparound(False) def sample_subset_with_eid(list nids, list eids, long long maxdegree, shuffle=False): cdef np.ndarray[ndim=1, dtype=np.int64_t] buff_index cdef long long buff_size, sample_size cdef long long total_buff_size = 0 cdef long long inc = 0 cdef list output = [] cdef list output_eid = [] for inc in xrange(len(nids)): buff_size = len(nids[inc]) if buff_size > maxdegree: total_buff_size += maxdegree elif shuffle: total_buff_size += buff_size cdef np.ndarray[ndim=1, dtype=np.int64_t] buff_nid = np.zeros([total_buff_size], dtype=np.int64) cdef np.ndarray[ndim=1, dtype=np.int64_t] buff_eid = np.zeros([total_buff_size], dtype=np.int64) cdef np.ndarray[np.int64_t, ndim=1] rnd = np.random.randint(0, np.iinfo(np.int64).max, dtype=np.int64, size=total_buff_size) cdef long long offset = 0 for inc in xrange(len(nids)): buff_size = len(nids[inc]) if not shuffle and buff_size <= maxdegree: output.append(nids[inc]) output_eid.append(eids[inc]) else: sample_size = buff_size if buff_size <= maxdegree else maxdegree if isinstance(nids[inc], list): tmp = np.array(nids[inc], dtype=np.int64) tmp_eids = np.array(eids[inc], dtype=np.int64) else: tmp = nids[inc] tmp_eids = eids[inc] subset_choose_index_eid(sample_size, tmp, tmp_eids, rnd, buff_nid, buff_eid, offset) output.append(buff_nid[offset:offset+sample_size]) output_eid.append(buff_eid[offset:offset+sample_size]) offset += sample_size return output, output_eid @cython.boundscheck(False) @cython.wraparound(False) def skip_gram_gen_pair(vector[long long] walk, long win_size=5): cdef vector[long long] src cdef vector[long long] dst cdef long long l = len(walk) cdef long long real_win_size, left, right, i cdef np.ndarray[np.int64_t, ndim=1] rnd = np.random.randint(1, win_size+1, dtype=np.int64, size=l) with nogil: for i in xrange(l): real_win_size = rnd[i] left = i - real_win_size if left < 0: left = 0 right = i + real_win_size if right >= l: right = l - 1 for j in xrange(left, right+1): if walk[i] == walk[j]: continue src.push_back(walk[i]) dst.push_back(walk[j]) return src, dst @cython.boundscheck(False) @cython.wraparound(False) def alias_sample_build_table(np.ndarray[np.float64_t, ndim=1] probs): cdef long long l = len(probs) cdef np.ndarray[np.float64_t, ndim=1] alias = probs * l cdef np.ndarray[np.int64_t, ndim=1] events = np.zeros(l, dtype=np.int64) cdef vector[long long] larger_num, smaller_num cdef long long i, s_i, l_i with nogil: for i in xrange(l): if alias[i] > 1: larger_num.push_back(i) elif alias[i] < 1: smaller_num.push_back(i) while smaller_num.size() > 0 and larger_num.size() > 0: s_i = smaller_num.back() l_i = larger_num.back() smaller_num.pop_back() events[s_i] = l_i alias[l_i] -= (1 - alias[s_i]) if alias[l_i] <= 1: larger_num.pop_back() if alias[l_i] < 1: smaller_num.push_back(l_i) return alias, events @cython.boundscheck(False) @cython.wraparound(False) def extract_edges_from_nodes( np.ndarray[np.int64_t, ndim=1] adj_indptr, np.ndarray[np.int64_t, ndim=1] sorted_v, np.ndarray[np.int64_t, ndim=1] sorted_eid, vector[long long] sampled_nodes, ): """ Extract all eids of given sampled_nodes for the origin graph. ret_edge_index: edge ids between sampled_nodes. Refers: https://github.com/GraphSAINT/GraphSAINT """ cdef long long i, v, j cdef long long num_v_orig, num_v_sub cdef long long start_neigh, end_neigh cdef vector[int] _arr_bit cdef vector[long long] ret_edge_index num_v_orig = adj_indptr.size-1 _arr_bit = vector[int](num_v_orig,-1) num_v_sub = sampled_nodes.size() i = 0 with nogil: while i < num_v_sub: _arr_bit[sampled_nodes[i]] = i i = i + 1 i = 0 while i < num_v_sub: v = sampled_nodes[i] start_neigh = adj_indptr[v] end_neigh = adj_indptr[v+1] j = start_neigh while j < end_neigh: if _arr_bit[sorted_v[j]] > -1: ret_edge_index.push_back(sorted_eid[j]) j = j + 1 i = i + 1 return ret_edge_index