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Commit e2dca775 authored by rusty1s's avatar rusty1s
Browse files

added first version of HGT sampling

parent 3508c85b
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csrc/cpu/hg_sample_cpu.cpp deleted 100644 → 0
View file @ 3508c85b
#include "hg_sample_cpu.h"
#include <unordered_map>
#include <random>
#include "utils.h"
namespace {
void update_budget(
int64_t added_node_idx,
const node_t &added_node_type,
const c10::Dict<int64_t, torch::Tensor> &rowptr_store,
const c10::Dict<int64_t, torch::Tensor> &col_store,
const c10::Dict<int64_t, edge_t> &edge_type_idx_to_name,
std::unordered_map<node_t, std::unordered_set<int64_t>> &sampled_nodes_store,
std::unordered_map<node_t, std::unordered_map<int64_t, float>> *budget_store
) {
for (const auto &i : rowptr_store) {
const auto &edge_type_idx = i.key();
const auto &edge_type = edge_type_idx_to_name.at(edge_type_idx);
const auto &source_node_type = std::get<0>(edge_type);
const auto &dest_node_type = std::get<2>(edge_type);
// Skip processing the (rowptr, col) if the node types do not match
if (added_node_type.compare(dest_node_type) != 0) {
continue;
}
int64_t *row_ptr_raw = i.value().data_ptr<int64_t>();
int64_t *col_raw = col_store.at(edge_type_idx).data_ptr<int64_t>();
// Get the budget map and sampled_nodes for the source node type of the relation
const std::unordered_set<int64_t> &sampled_nodes = sampled_nodes_store[source_node_type];
std::unordered_map<int64_t, float> &budget = (*budget_store)[source_node_type];
int64_t row_start_idx = row_ptr_raw[added_node_idx];
int64_t row_end_idx = row_ptr_raw[added_node_idx + 1];
if (row_start_idx != row_end_idx) {
// Compute the norm of degree and update the budget for the neighbors of added_node_idx
float norm_deg = 1. / (float)(row_end_idx - row_start_idx);
for (int64_t j = row_start_idx; j < row_end_idx; j++) {
if (sampled_nodes.find(col_raw[j]) == sampled_nodes.end()) {
budget[col_raw[j]] += norm_deg;
}
}
}
}
}
// Sample n nodes according to its type budget map. The probability that node i is sampled is calculated by
// prob[i] = budget[i]^2 / l2_norm(budget)^2.
std::unordered_set<int64_t> sample_nodes(const std::unordered_map<int64_t, float> &budget, int n) {
// Compute the squared L2 norm
float norm = 0.0;
for (const auto &i : budget) {
norm += i.second * i.second;
}
// Generate n sorted random values between 0 and norm
std::vector<float> samples(n);
std::uniform_real_distribution<float> dist(0.0, norm);
std::default_random_engine gen{std::random_device{}()};
std::generate(std::begin(samples), std::end(samples), [&]{ return dist(gen); });
std::sort(samples.begin(), samples.end());
// Iterate through the budget map to compute the cumulative probability cum_prob[i] for node_i. The j-th
// sample is assigned to node_i iff cum_prob[i-1] < samples[j] < cum_prob[i]. The implementation assigns
// two iterators on budget and samples respectively, then computes the node samples in linear time by
// alternatingly incrementing the two iterators based on their values.
std::unordered_set<int64_t> sampled_nodes;
sampled_nodes.reserve(samples.size());
auto j = samples.begin();
float cum_prob = 0.0;
for (const auto &i : budget) {
cum_prob += i.second * i.second;
// Increment iterator j until its value is greater than the current cum_prob
while (*j < cum_prob && j != samples.end()) {
sampled_nodes.insert(i.first);
j++;
}
// Terminate early after we complete the sampling
if (j == samples.end()) {
break;
}
}
return sampled_nodes;
}
} // namespace
// TODO: Add the appropriate return type
void hg_sample_cpu(
const c10::Dict<int64_t, torch::Tensor> &rowptr_store,
const c10::Dict<int64_t, torch::Tensor> &col_store,
const c10::Dict<node_t, torch::Tensor> &origin_nodes_store,
const c10::Dict<int64_t, edge_t> &edge_type_idx_to_name,
int n,
int num_layers
) {
// Verify input
for (const auto &kv : rowptr_store) {
CHECK_CPU(kv.value());
}
for (const auto &kv : col_store) {
CHECK_CPU(kv.value());
}
for (const auto &kv : origin_nodes_store) {
CHECK_CPU(kv.value());
CHECK_INPUT(kv.value().dim() == 1);
}
// Initialize various data structures for the sampling process
std::unordered_map<node_t, std::unordered_set<int64_t>> sampled_nodes_store;
for (const auto &kv : origin_nodes_store) {
const auto &node_type = kv.key();
const auto &origin_nodes = kv.value();
const int64_t *raw_origin_nodes = origin_nodes.data_ptr<int64_t>();
// Add each origin node to the sampled_nodes_store
for (int64_t i = 0; i < origin_nodes.numel(); i++) {
sampled_nodes_store[node_type].insert(raw_origin_nodes[i]);
}
}
std::unordered_map<node_t, std::unordered_map<int64_t, float>> budget_store;
for (const auto &kv : origin_nodes_store) {
const node_t &node_type = kv.key();
const auto &origin_nodes = kv.value();
const int64_t *raw_origin_nodes = origin_nodes.data_ptr<int64_t>();
// Update budget for each origin node
for (int64_t i = 0; i < origin_nodes.numel(); i++) {
update_budget(
raw_origin_nodes[i],
node_type,
rowptr_store,
col_store,
edge_type_idx_to_name,
sampled_nodes_store,
&budget_store
);
}
}
// Sampling process
for (int l = 0; l < num_layers; l++) {
for (auto &i : budget_store) {
const auto &node_type = i.first;
auto &budget = i.second;
auto &sampled_nodes = sampled_nodes_store[node_type];
// Perform sampling
std::unordered_set<int64_t> new_samples = sample_nodes(budget, n);
// Remove sampled nodes from the budget and add them to the sampled node store
for (const auto &sample : new_samples) {
sampled_nodes.insert(sample);
budget.erase(sample);
}
// Update the budget
for (const auto &sample : new_samples) {
update_budget(
sample,
node_type,
rowptr_store,
col_store,
edge_type_idx_to_name,
sampled_nodes_store,
&budget_store
);
}
}
}
// Re-index
c10::Dict<std::string, std::vector<int64_t>> type_to_n_ids;
}
csrc/cpu/hg_sample_cpu.h deleted 100644 → 0
View file @ 3508c85b
#pragma once
#include <torch/extension.h>
// Node type is a string and the edge type is a triplet of string representing
// (source_node_type, relation_type, dest_node_type).
typedef std::string node_t;
typedef std::tuple<std::string, std::string, std::string> edge_t;
// As of PyTorch 1.9.0, c10::Dict does not support tuples or complex data type as key type. We work around this
// by representing edge types using a single int64_t and a c10::Dict that maps the int64_t index to edge_t.
void hg_sample_cpu(
const c10::Dict<int64_t, torch::Tensor> &rowptr_store,
const c10::Dict<int64_t, torch::Tensor> &col_store,
const c10::Dict<node_t, torch::Tensor> &origin_nodes_store,
const c10::Dict<int64_t, edge_t> &edge_type_idx_to_name,
int n,
int num_layers
);
csrc/cpu/hgt_sample_cpu.cpp 0 → 100644
View file @ e2dca775
#include "hgt_sample_cpu.h"
#include <random>
edge_t split(const rel_t &rel_type) {
std::vector<std::string> result(3);
int start = 0, end = 0;
for (int i = 0; i < 3; i++) {
end = rel_type.find(delim, start);
result[i] = rel_type.substr(start, end - start);
start = end + 2;
}
return std::make_tuple(result[0], result[1], result[2]);
}
void update_budget(
std::unordered_map<node_t, std::unordered_map<int64_t, float>> *budget_dict,
const node_t &node_type, //
const std::vector<int64_t> &sampled_nodes,
const std::unordered_map<node_t, std::unordered_map<int64_t, int64_t>>
&global_to_local_node_dict,
const std::unordered_map<rel_t, edge_t> &rel_to_edge_type,
const c10::Dict<rel_t, torch::Tensor> &rowptr_dict,
const c10::Dict<rel_t, torch::Tensor> &col_dict, //
const bool remove) {
for (const auto &kv : rowptr_dict) {
const auto &rel_type = kv.key();
const auto &edge_type = rel_to_edge_type.at(rel_type);
const auto &src_node_type = std::get<0>(edge_type);
const auto &dst_node_type = std::get<2>(edge_type);
if (node_type != dst_node_type)
continue;
const auto &global_to_local_node =
global_to_local_node_dict.at(src_node_type);
const auto *rowptr_data = kv.value().data_ptr<int64_t>();
const auto *col_data = col_dict.at(rel_type).data_ptr<int64_t>();
auto &budget = (*budget_dict)[src_node_type];
for (const auto &v : sampled_nodes) {
const int64_t row_start = rowptr_data[v], row_end = rowptr_data[v + 1];
if (row_end != row_start) {
const auto inv_deg = 1.f / float(row_end - row_start);
for (int64_t j = row_start; j < row_end; j++) {
const auto w = col_data[j];
if (global_to_local_node.find(w) == global_to_local_node.end())
budget[col_data[j]] += inv_deg;
}
}
}
}
if (remove) {
auto &budget = (*budget_dict)[node_type];
for (const auto &v : sampled_nodes)
budget.erase(v);
}
}
std::unordered_set<int64_t>
sample_from(const std::unordered_map<int64_t, float> &budget,
const int64_t num_samples) {
// Compute the squared L2 norm:
auto norm = 0.f;
for (const auto &kv : budget)
norm += kv.second * kv.second;
// Generate `num_samples` sorted random values between `[0., norm)`:
std::vector<float> samples(num_samples);
std::uniform_real_distribution<float> dist(0.f, norm);
std::default_random_engine gen{std::random_device{}()};
std::generate(std::begin(samples), std::end(samples),
[&] { return dist(gen); });
std::sort(samples.begin(), samples.end());
// Iterate through the budget to compute the cumulative probability
// `cum_prob[i]` for node `i`. The j-th sample is assigned to node `i` iff
// `cum_prob[i-1] < samples[j] < cum_prob[i]`.
// The implementation assigns two iterators on budget and samples,
// respectively, and then computes the node samples in linear time by
// alternatingly incrementing the two iterators based on their values.
std::unordered_set<int64_t> output;
output.reserve(num_samples);
auto j = samples.begin();
auto cum_prob = 0.f;
for (const auto &kv : budget) {
cum_prob += kv.second * kv.second;
// Increment iterator `j` until its value is greater than `cum_prob`:
while (*j < cum_prob && j != samples.end()) {
output.insert(kv.first);
j++;
}
// Terminate early in case we have completed the sampling:
if (j == samples.end())
break;
}
return output;
}
std::tuple<c10::Dict<node_t, torch::Tensor>, c10::Dict<rel_t, torch::Tensor>,
c10::Dict<rel_t, torch::Tensor>, c10::Dict<rel_t, torch::Tensor>>
hgt_sample_cpu(const c10::Dict<rel_t, torch::Tensor> &rowptr_dict,
const c10::Dict<rel_t, torch::Tensor> &col_dict,
const c10::Dict<node_t, torch::Tensor> &input_node_dict,
const c10::Dict<node_t, std::vector<int64_t>> &num_samples_dict,
int64_t num_hops) {
// Create mapping to convert single string relations to edge type triplets:
std::unordered_map<rel_t, edge_t> rel_to_edge_type;
for (const auto &kv : rowptr_dict) {
const auto &rel_type = kv.key();
rel_to_edge_type[rel_type] = split(rel_type);
}
// Initialize various data structures for the sampling process, and add the
// input nodes to the final sampled output set (line 1):
std::unordered_map<node_t, std::vector<int64_t>> sampled_nodes_dict;
std::unordered_map<node_t, std::unordered_map<int64_t, int64_t>>
global_to_local_node_dict;
for (const auto &kv : input_node_dict) {
const auto &node_type = kv.key();
const auto &input_node = kv.value();
const auto *input_node_data = input_node.data_ptr<int64_t>();
auto &sampled_nodes = sampled_nodes_dict[node_type];
auto &global_to_local_node = global_to_local_node_dict[node_type];
// Add each origin node to the sampled output nodes:
for (int64_t i = 0; i < input_node.numel(); i++) {
const auto v = input_node_data[i];
sampled_nodes.push_back(v);
global_to_local_node[v] = i;
}
}
// Update budget after all input nodes have been added to the sampled output
// set (line 2-5):
std::unordered_map<node_t, std::unordered_map<int64_t, float>> budget_dict;
for (const auto &kv : sampled_nodes_dict) {
update_budget(&budget_dict, kv.first, kv.second, global_to_local_node_dict,
rel_to_edge_type, rowptr_dict, col_dict, false);
}
// Sample nodes for each node type in each layer (line 6 - 18):
for (int64_t ell = 0; ell < num_hops; ell++) {
for (auto &kv : budget_dict) {
const auto &node_type = kv.first;
auto &budget = kv.second;
const auto num_samples = num_samples_dict.at(node_type)[ell];
// Sample `num_samples` nodes of `node_type` according to the budget
// (line 9-11):
const auto samples = sample_from(budget, num_samples);
// Add sampled nodes to the sampled output set (line 13):
auto &sampled_nodes = sampled_nodes_dict[node_type];
auto &global_to_local_node = global_to_local_node_dict[node_type];
std::vector<int64_t> newly_sampled_nodes;
newly_sampled_nodes.reserve(samples.size());
for (const auto &v : samples) {
sampled_nodes.push_back(v);
newly_sampled_nodes.push_back(v);
global_to_local_node[v] = sampled_nodes.size();
}
// Add neighbors of newly sampled nodes to the bucket (line 14-15):
update_budget(&budget_dict, node_type, newly_sampled_nodes,
global_to_local_node_dict, rel_to_edge_type, rowptr_dict,
col_dict, true);
}
}
// Reconstruct the sampled adjacency matrix among the sampled nodes (line 19):
c10::Dict<rel_t, torch::Tensor> output_row_dict;
c10::Dict<rel_t, torch::Tensor> output_col_dict;
c10::Dict<rel_t, torch::Tensor> output_edge_dict;
for (const auto &kv : rowptr_dict) {
const auto &rel_type = kv.key();
const auto &edge_type = rel_to_edge_type.at(rel_type);
const auto &src_node_type = std::get<0>(edge_type);
const auto &dst_node_type = std::get<2>(edge_type);
const auto *rowptr_data = kv.value().data_ptr<int64_t>();
const auto *col_data = col_dict.at(rel_type).data_ptr<int64_t>();
const auto &sampled_dst_nodes = sampled_nodes_dict[dst_node_type];
const auto &global_to_local_src = global_to_local_node_dict[src_node_type];
std::vector<int64_t> rows, cols, edges;
for (int64_t i = 0; i < (int64_t)sampled_dst_nodes.size(); i++) {
const auto v = sampled_dst_nodes[i];
const int64_t row_start = rowptr_data[v], row_end = rowptr_data[v + 1];
for (int64_t j = row_start; j < row_end; j++) {
const auto w = col_data[j];
if (global_to_local_src.find(w) != global_to_local_src.end()) {
rows.push_back(i);
cols.push_back(global_to_local_src.at(w));
edges.push_back(j);
}
}
}
torch::Tensor out;
out = torch::from_blob((int64_t *)rows.data(), {(int64_t)rows.size()},
at::kLong);
output_row_dict.insert(rel_type, out.clone());
out = torch::from_blob((int64_t *)cols.data(), {(int64_t)cols.size()},
at::kLong);
output_col_dict.insert(rel_type, out.clone());
out = torch::from_blob((int64_t *)edges.data(), {(int64_t)edges.size()},
at::kLong);
output_edge_dict.insert(rel_type, out.clone());
}
// Generate tensor-valued output node dict (line 20):
c10::Dict<node_t, torch::Tensor> output_node_dict;
for (const auto &kv : sampled_nodes_dict) {
const auto out = torch::from_blob((int64_t *)kv.second.data(),
{(int64_t)kv.second.size()}, at::kLong);
output_node_dict.insert(kv.first, out.clone());
}
return std::make_tuple(output_node_dict, output_row_dict, output_col_dict,
output_edge_dict);
}
csrc/cpu/hgt_sample_cpu.h 0 → 100644
View file @ e2dca775
// #pragma once
// #include <torch/extension.h>
// // Node type is a string and the edge type is a triplet of string
// representing
// // (source_node_type, relation_type, dest_node_type).
// typedef std::string node_t;
// typedef std::tuple<std::string, std::string, std::string> edge_t;
// // As of PyTorch 1.9.0, c10::Dict does not support tuples or complex data
// type as key type. We work around this
// // by representing edge types using a single int64_t and a c10::Dict that
// maps the int64_t index to edge_t. void hg_sample_cpu( const
// c10::Dict<int64_t, torch::Tensor> &rowptr_store, const c10::Dict<int64_t,
// torch::Tensor> &col_store, const c10::Dict<node_t, torch::Tensor>
// &origin_nodes_store, const c10::Dict<int64_t, edge_t>
// &edge_type_idx_to_name, int n, int num_layers
// );
//
#pragma once
#include <torch/extension.h>
typedef std::string node_t;
typedef std::string rel_t;
typedef std::tuple<std::string, std::string, std::string> edge_t;
const std::string delim = "__";
std::tuple<c10::Dict<node_t, torch::Tensor>, c10::Dict<rel_t, torch::Tensor>,
c10::Dict<rel_t, torch::Tensor>, c10::Dict<rel_t, torch::Tensor>>
hgt_sample_cpu(const c10::Dict<rel_t, torch::Tensor> &rowptr_dict,
const c10::Dict<rel_t, torch::Tensor> &col_dict,
const c10::Dict<node_t, torch::Tensor> &input_node_dict,
const c10::Dict<node_t, std::vector<int64_t>> &num_samples_dict,
int64_t num_hops);
csrc/hgt_sample.cpp 0 → 100644
View file @ e2dca775
#include <Python.h>
#include <torch/script.h>
#include "cpu/hgt_sample_cpu.h"
#ifdef _WIN32
#ifdef WITH_CUDA
PyMODINIT_FUNC PyInit__hgt_sample_cuda(void) { return NULL; }
#else
PyMODINIT_FUNC PyInit__hgt_sample_cpu(void) { return NULL; }
#endif
#endif
std::tuple<c10::Dict<node_t, torch::Tensor>, c10::Dict<rel_t, torch::Tensor>,
c10::Dict<rel_t, torch::Tensor>, c10::Dict<rel_t, torch::Tensor>>
hgt_sample(const c10::Dict<std::string, torch::Tensor> &rowptr_dict,
const c10::Dict<std::string, torch::Tensor> &col_dict,
const c10::Dict<std::string, torch::Tensor> &input_node_dict,
const c10::Dict<std::string, std::vector<int64_t>> &num_samples_dict,
const int64_t num_hops) {
return hgt_sample_cpu(rowptr_dict, col_dict, input_node_dict,
num_samples_dict, num_hops);
}
static auto registry =
torch::RegisterOperators().op("torch_sparse::hgt_sample", &hgt_sample);
torch_sparse/__init__.py
View file @ e2dca775
...@@ -9,7 +9,7 @@ suffix = 'cuda' if torch.cuda.is_available() else 'cpu' ...@@ -9,7 +9,7 @@ suffix = 'cuda' if torch.cuda.is_available() else 'cpu'
for library in [ for library in [
'_version', '_convert', '_diag', '_spmm', '_spspmm', '_metis', '_rw', '_version', '_convert', '_diag', '_spmm', '_spspmm', '_metis', '_rw',
'_saint', '_sample', '_ego_sample', '_relabel' '_saint', '_sample', '_ego_sample', '_hgt_sample', '_relabel'
]: ]:
torch.ops.load_library(importlib.machinery.PathFinder().find_spec( torch.ops.load_library(importlib.machinery.PathFinder().find_spec(
f'{library}_{suffix}', [osp.dirname(__file__)]).origin) f'{library}_{suffix}', [osp.dirname(__file__)]).origin)
......
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