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Merge pull request #432 from seoklab/feat/algo/vf2++
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feat(core/graph/vf2++): implement VF2++ algorithm
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@jnooree
jnooree authored Dec 13, 2024
2 parents 737518e + 7811f4d commit 76a232b
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Showing 7 changed files with 1,769 additions and 27 deletions.
2 changes: 1 addition & 1 deletion .clangd
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Expand Up @@ -46,7 +46,7 @@ InlayHints:
DeducedTypes: Yes
---
If:
PathMatch: "third-party/.*"
PathMatch: "(third-party|build/.*_deps)/.*"
Diagnostics:
Suppress: "*"
UnusedIncludes: None
37 changes: 37 additions & 0 deletions NOTICE.md
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Expand Up @@ -533,3 +533,40 @@ Our implementation is based on the original TM-align software (version 20220412)
notice appear in all copies or substantial portions of the Software.
It is provided "as is" without express or implied warranty.
```

### VF2++

- Project URL: <https://lemon.cs.elte.hu>
- Full license text:

```txt
Copyright (C) 2003-2012 Egervary Jeno Kombinatorikus Optimalizalasi
Kutatocsoport (Egervary Combinatorial Optimization Research Group,
EGRES).
===========================================================================
Boost Software License, Version 1.0
===========================================================================
Permission is hereby granted, free of charge, to any person or organization
obtaining a copy of the software and accompanying documentation covered by
this license (the "Software") to use, reproduce, display, distribute,
execute, and transmit the Software, and to prepare derivative works of the
Software, and to permit third-parties to whom the Software is furnished to
do so, all subject to the following:
The copyright notices in the Software and this entire statement, including
the above license grant, this restriction and the following disclaimer,
must be included in all copies of the Software, in whole or in part, and
all derivative works of the Software, unless such copies or derivative
works are solely in the form of machine-executable object code generated by
a source language processor.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE, TITLE AND NON-INFRINGEMENT. IN NO EVENT
SHALL THE COPYRIGHT HOLDERS OR ANYONE DISTRIBUTING THE SOFTWARE BE LIABLE
FOR ANY DAMAGES OR OTHER LIABILITY, WHETHER IN CONTRACT, TORT OR OTHERWISE,
ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
DEALINGS IN THE SOFTWARE.
```
64 changes: 40 additions & 24 deletions include/nuri/core/graph.h
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Expand Up @@ -1297,11 +1297,14 @@ namespace internal {
// NOLINTBEGIN(readability-identifier-naming)

template <class NT, class ET>
struct GraphTraits<Graph<NT, ET>> { };
struct GraphTraits<Graph<NT, ET>> {
constexpr static bool is_degree_constant_time = true;
};

template <class NT, class ET, bool subg_const>
struct GraphTraits<Subgraph<NT, ET, subg_const>> {
constexpr static bool is_const = subg_const;
constexpr static bool is_degree_constant_time = false;
};

template <class SGT, bool subg_const>
Expand Down Expand Up @@ -1579,11 +1582,18 @@ namespace internal {
}

private:
friend SGT;

template <class, bool>
friend class SubAdjIterator;

friend class boost::iterator_core_access;

constexpr SubAdjIterator(parent_type &subgraph, int src, int dst, int eid,
int parent_idx) noexcept
: subgraph_(&subgraph), src_(src), dst_(dst), eid_(eid),
parent_idx_(parent_idx) { }

auto parent_iter() const {
return subgraph_->parent_node(src_).begin() + parent_idx_;
}
Expand Down Expand Up @@ -2388,7 +2398,7 @@ class Subgraph {
*
* @param begin Iterator pointing to the first node to erase
* @param end Iterator pointing to the node after the last node to erase
* @note Time complexity: \f$O(V'log(E') + E')\f$ in worst case.
* @note Time complexity: \f$O(V' \log E' + E')\f$ in worst case.
*/
void erase_nodes(const_iterator begin, const_iterator end) {
std::vector<int> erased_edges;
Expand All @@ -2407,7 +2417,7 @@ class Subgraph {
*
* @param id The id of the node to erase
* @note This is a no-op if the node is not in the subgraph.
* @note Time complexity: \f$O(V'log(E') + E')\f$ in worst case.
* @note Time complexity: \f$O(V' \log E' + E')\f$ in worst case.
*/
void erase_node_of(int id) {
int idx = nodes_.find(id);
Expand All @@ -2421,7 +2431,7 @@ class Subgraph {
*
* @param node The parent node to erase
* @note This is a no-op if the node is not in the subgraph.
* @note Time complexity: \f$O(V'log(E') + E')\f$ in worst case.
* @note Time complexity: \f$O(V' \log E' + E')\f$ in worst case.
*/
void erase_node_of(typename graph_type::ConstNodeRef node) {
erase_node_of(node.id());
Expand All @@ -2433,7 +2443,7 @@ class Subgraph {
*
* @tparam UnaryPred Type of the unary predicate
* @param pred Unary predicate that returns true for nodes to erase
* @note Time complexity: \f$O(V'log(E') + E')\f$ in worst case.
* @note Time complexity: \f$O(V' \log E' + E')\f$ in worst case.
*/
template <class UnaryPred>
void erase_nodes_if(UnaryPred pred) {
Expand Down Expand Up @@ -2741,7 +2751,7 @@ class Subgraph {
* @param dst The destination atom
* @return An iterator to the edge if found, edge_end() otherwise.
* @note This will only find edges that are in the subgraph.
* @note Time complexity: \f$O(V'/E' log E')\f$.
* @note Time complexity: \f$O(E/V + \log E')\f$.
*/
edge_iterator find_edge(ConstNodeRef src, ConstNodeRef dst) {
return find_edge(src.id(), dst.id());
Expand All @@ -2754,7 +2764,7 @@ class Subgraph {
* @param dst The destination atom
* @return An iterator to the edge if found, edge_end() otherwise.
* @note This will only find edges that are in the subgraph.
* @note Time complexity: \f$O(V'/E' log E')\f$.
* @note Time complexity: \f$O(E/V + \log E')\f$.
*/
const_edge_iterator find_edge(ConstNodeRef src, ConstNodeRef dst) const {
return find_edge(src.id(), dst.id());
Expand All @@ -2768,7 +2778,7 @@ class Subgraph {
* @return An iterator to the edge if found, edge_end() otherwise.
* @note This will only find edges that are in the subgraph. If any of the
* nodes are not in the subgraph, returns edge_end().
* @note Time complexity: \f$O(log V' + V'/E' log E')\f$.
* @note Time complexity: \f$O(\log V' + E/V + \log E')\f$.
*/
edge_iterator find_edge(typename graph_type::ConstNodeRef src,
typename graph_type::ConstNodeRef dst) {
Expand All @@ -2787,7 +2797,7 @@ class Subgraph {
* @return An iterator to the edge if found, edge_end() otherwise.
* @note This will only find edges that are in the subgraph. If any of the
* nodes are not in the subgraph, returns edge_end().
* @note Time complexity: \f$O(log V' + V'/E' log E')\f$.
* @note Time complexity: \f$O(\log V' + E/V + \log E')\f$.
*/
const_edge_iterator find_edge(typename graph_type::ConstNodeRef src,
typename graph_type::ConstNodeRef dst) const {
Expand Down Expand Up @@ -2894,7 +2904,7 @@ class Subgraph {
* @param idx The index of the node
* @return The number of neighbors of the node that are in the subgraph
* @note The behavior is undefined if the node is not in the subgraph.
* @note Time complexity: \f$O(V/E)\f$.
* @note Time complexity: \f$O(E/V (\log V' + \log E'))\f$.
*/
int degree(int idx) const {
return std::distance(adj_cbegin(idx), adj_cend(idx));
Expand All @@ -2907,7 +2917,7 @@ class Subgraph {
* @param dst The destination atom
* @return An iterator to the adjacent node if found, adj_end(src) otherwise.
* @note This will only find edges that are in the subgraph.
* @note Time complexity: \f$O(V'/E' log E')\f$.
* @note Time complexity: \f$O(E/V + \log E')\f$.
*/
adjacency_iterator find_adjacent(ConstNodeRef src, ConstNodeRef dst) {
return find_adjacent(src.id(), dst.id());
Expand All @@ -2921,7 +2931,7 @@ class Subgraph {
* @return A const-iterator to the adjacent node if found, adj_end(src)
* otherwise.
* @note This will only find edges that are in the subgraph.
* @note Time complexity: \f$O(V'/E' log E')\f$.
* @note Time complexity: \f$O(E/V + \log E')\f$.
*/
const_adjacency_iterator find_adjacent(ConstNodeRef src,
ConstNodeRef dst) const {
Expand Down Expand Up @@ -2992,31 +3002,37 @@ class Subgraph {
}

adjacency_iterator find_adjacent(int src, int dst) {
return find_adj_helper(*this, src, dst);
return find_adj_helper<adjacency_iterator>(*this, src, dst);
}

const_adjacency_iterator find_adjacent(int src, int dst) const {
return find_adj_helper(*this, src, dst);
return find_adj_helper<const_adjacency_iterator>(*this, src, dst);
}

template <class SGT>
static auto find_adj_helper(SGT &graph, int src, int dst) {
auto ret = graph.adj_begin(src);
template <class AIT, class SGT>
static AIT find_adj_helper(SGT &graph, int src, int dst) {
auto pait = graph.parent_node(src).find_adjacent(graph.parent_node(dst));
if (pait.end())
return graph.adj_end(src);

for (; ret != graph.adj_end(src); ++ret)
if (ret->dst().id() == dst)
break;
auto eit = graph.find_edge(pait->eid());
if (eit == graph.edge_end())
return graph.adj_end(src);

return ret;
return { graph, src, dst, eit->id(),
pait - graph.parent_node(src).begin() };
}

template <class SGT>
static auto find_edge_helper(SGT &graph, int src, int dst) {
auto it = find_adj_helper(graph, src, dst);
if (it.end())
if (graph.parent_node(src).degree() > graph.parent_node(dst).degree())
std::swap(src, dst);

auto ait = graph.find_adjacent(src, dst);
if (ait.end())
return graph.edge_end();

return graph.edge_begin() + it->eid();
return graph.edge_begin() + ait->eid();
}

parent_type *parent_;
Expand Down
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