From e005da830d9b0bb8ac3eb89892f1d4f1eea1905f Mon Sep 17 00:00:00 2001
From: Xuanzhao Gao <gaoxuanzhao@gmail.com>
Date: Mon, 25 Nov 2024 22:05:22 +0800
Subject: [PATCH] update xiao_2013

---
 lib/OptimalBranchingMIS/Project.toml          |   2 +
 .../src/OptimalBranchingMIS.jl                |   3 +
 .../src/algorithms/xiao2013.jl                |  45 ++---
 .../src/algorithms/xiao2013_utils.jl          |  78 --------
 lib/OptimalBranchingMIS/src/graphs.jl         |   6 +-
 lib/OptimalBranchingMIS/src/types.jl          |   2 +-
 lib/OptimalBranchingMIS/test/graphs.jl        |   1 +
 lib/OptimalBranchingMIS/test/mis.jl           | 171 ++++++++++++++++++
 lib/OptimalBranchingMIS/test/runtests.jl      |  10 +-
 9 files changed, 203 insertions(+), 115 deletions(-)
 create mode 100644 lib/OptimalBranchingMIS/test/mis.jl

diff --git a/lib/OptimalBranchingMIS/Project.toml b/lib/OptimalBranchingMIS/Project.toml
index a31af56..e3c73d9 100644
--- a/lib/OptimalBranchingMIS/Project.toml
+++ b/lib/OptimalBranchingMIS/Project.toml
@@ -4,11 +4,13 @@ authors = ["Xuanzhao Gao <gaoxuanzhao@gmail.com> and contributors"]
 version = "1.0.0-DEV"
 
 [deps]
+Combinatorics = "861a8166-3701-5b0c-9a16-15d98fcdc6aa"
 EliminateGraphs = "b3ff564c-d3b6-11e9-0ef2-9b4ae9f9cbe1"
 GenericTensorNetworks = "3521c873-ad32-4bb4-b63d-f4f178f42b49"
 OptimalBranchingCore = "c76e7b22-e1d2-40e8-b0f1-f659837787b8"
 
 [compat]
+Combinatorics = "1.0.2"
 EliminateGraphs = "0.2"
 GenericTensorNetworks = "2"
 julia = "1.6"
diff --git a/lib/OptimalBranchingMIS/src/OptimalBranchingMIS.jl b/lib/OptimalBranchingMIS/src/OptimalBranchingMIS.jl
index 0bf11b0..32af820 100644
--- a/lib/OptimalBranchingMIS/src/OptimalBranchingMIS.jl
+++ b/lib/OptimalBranchingMIS/src/OptimalBranchingMIS.jl
@@ -2,6 +2,7 @@ module OptimalBranchingMIS
 
 using OptimalBranchingCore
 using OptimalBranchingCore.BitBasis
+using Combinatorics
 using EliminateGraphs, EliminateGraphs.Graphs
 using GenericTensorNetworks
 
@@ -16,6 +17,8 @@ include("types.jl")
 include("graphs.jl")
 include("algorithms/mis1.jl")
 include("algorithms/mis2.jl")
+include("algorithms/xiao2013.jl")
+include("algorithms/xiao2013_utils.jl")
 
 include("reducer.jl")
 include("selector.jl")
diff --git a/lib/OptimalBranchingMIS/src/algorithms/xiao2013.jl b/lib/OptimalBranchingMIS/src/algorithms/xiao2013.jl
index 54e873f..e7a2767 100644
--- a/lib/OptimalBranchingMIS/src/algorithms/xiao2013.jl
+++ b/lib/OptimalBranchingMIS/src/algorithms/xiao2013.jl
@@ -1,46 +1,31 @@
-# the algorithm in Confining sets and avoiding bottleneck cases: A simple maximum independent set algorithm in degree-3 graphs
-export mis_xiao2013, count_xiao2013
+export counting_xiao2013
 
 
 """
-    mis_xiao2013(g::SimpleGraph)
+    counting_xiao2013(g::SimpleGraph)
 
-# Arguments
-- `g::SimpleGraph`: The input graph for which the maximum independent set is to be calculated.
-
-# Returns
-- `CountingMIS.mis`: The size of the MIS of a graph `g`.
-"""
-function mis_xiao2013(g::SimpleGraph)
-    gc = copy(g)    
-    return _xiao2013(gc).mis
-end
-
-
-"""
-    count_xiao2013(g::SimpleGraph)
-
-Uses the branch and bound algorithm in xiao2013 to search for the size of the MIS of a graph `g`. 
+This function counts the maximum independent set (MIS) in a given simple graph using the Xiao 2013 algorithm.
 
 # Arguments
-- `g::SimpleGraph`: The input graph for which the maximum independent set is to be calculated.
+- `g::SimpleGraph`: A simple graph for which the maximum independent set is to be counted.
 
 # Returns
-- `CountingMIS.count`: The number of branches generated during the entire process.
+- `CountingMIS`: An object representing the size of the maximum independent set and the count of branches.
+
 """
-function count_xiao2013(g::SimpleGraph)
-    gc = copy(g)
-    return _xiao2013(gc).count
+function counting_xiao2013(g::SimpleGraph)
+    gc = copy(g)    
+    return _xiao2013(gc)
 end
 
 
 function _xiao2013(g::SimpleGraph)
     if nv(g) == 0
-        return CountingMIS(0)
+        return MISCount(0)
     elseif nv(g) == 1
-        return CountingMIS(1)
+        return MISCount(1)
     elseif nv(g) == 2
-        return CountingMIS(2 - has_edge(g, 1, 2))
+        return MISCount(2 - has_edge(g, 1, 2))
     else
         degrees = degree(g)
         degmin = minimum(degrees)
@@ -48,11 +33,11 @@ function _xiao2013(g::SimpleGraph)
 
         if degmin == 0
             all_zero_vertices = findall(==(0), degrees)
-            return length(all_zero_vertices) + _xiao2013(remove_vertex(g, all_zero_vertices))
+            return length(all_zero_vertices) + _xiao2013(remove_vertices(g, all_zero_vertices))
         elseif degmin == 1
-            return 1 + _xiao2013(remove_vertex(g, neighbors(g, vmin) ∪ vmin))
+            return 1 + _xiao2013(remove_vertices(g, neighbors(g, vmin) ∪ vmin))
         elseif degmin == 2
-            return 1 + _xiao2013(folding(g, vmin))
+            return 1 + _xiao2013(folding(g, vmin)[1])
         end
 
         # reduction rules
diff --git a/lib/OptimalBranchingMIS/src/algorithms/xiao2013_utils.jl b/lib/OptimalBranchingMIS/src/algorithms/xiao2013_utils.jl
index 5b14488..f727d0c 100644
--- a/lib/OptimalBranchingMIS/src/algorithms/xiao2013_utils.jl
+++ b/lib/OptimalBranchingMIS/src/algorithms/xiao2013_utils.jl
@@ -1,42 +1,3 @@
-"""
-    struct CountingMIS
-
-A struct representing a counting maximum independent set (MIS), where `mis` for size of the maximum independent set and `count` for the count of branches.
-
-# Fields
-- `mis::Int`: The maximum independent set.
-- `count::Int`: The count of the maximum independent set.
-
-# Constructors
-- `CountingMIS(mis::Int)`: Constructs a CountingMIS object with the given maximum independent set and count set to 1.
-- `CountingMIS(mis::Int, count::Int)`: Constructs a CountingMIS object with the given maximum independent set and count.
-
-# Examples
-```jldoctest
-julia> CountingMIS(2, 2) + 2
-CountingMIS(4, 2)
-
-julia> CountingMIS(1, 1) + CountingMIS(2, 2)
-CountingMIS(3, 3)
-
-julia> max(CountingMIS(1, 1), CountingMIS(2, 2))
-CountingMIS(2, 3)
-```
-"""
-struct CountingMIS
-    mis::Int
-    count::Int
-    CountingMIS(mis::Int) = new(mis, 1)
-    CountingMIS(mis::Int, count::Int) = new(mis, count)
-end
-
-Base.:+(x::CountingMIS, y::Int) = CountingMIS(x.mis + y, x.count)
-Base.:+(x::Int, y::CountingMIS) = CountingMIS(x + y.mis, y.count)
-Base.:+(x::CountingMIS, y::CountingMIS) = CountingMIS(x.mis + y.mis, x.count + y.count)
-
-Base.max(x::CountingMIS, y::CountingMIS) = CountingMIS(max(x.mis, y.mis), x.count + y.count)
-Base.max(args...) = reduce(max, args)
-
 struct Path
     vertices::Vector{Int}
 end
@@ -80,45 +41,6 @@ function is_line_graph(g::SimpleGraph)
     return true
 end
 
-function remove_vertex(g, v)
-    g, vs = induced_subgraph(g, setdiff(vertices(g), v))
-    return g
-end
-
-function remove_vertices(g, vertices)
-    gc = copy(g)
-    rem_vertices!(gc, vertices)
-    return gc
-end
-
-function closed_neighbors(g::SimpleGraph, vertices::Vector{Int})
-    return open_neighbors(g, vertices) ∪ vertices
-end
-
-function open_neighbors(g::SimpleGraph, vertices::Vector{Int})
-    ov = Vector{Int}()
-    for v in vertices
-        for n in neighbors(g, v)
-            push!(ov, n)
-        end
-    end
-    return unique!(setdiff(ov, vertices))
-end
-
-function folding(g::SimpleGraph, v)
-    @assert degree(g, v) == 2
-    a, b = neighbors(g, v)
-    if !has_edge(g, a, b)
-        # apply the graph rewrite rule
-        add_vertex!(g)
-        nn = open_neighbors(g, [v, a, b])
-        for n in nn
-            add_edge!(g, nv(g), n)
-        end
-    end
-    return remove_vertex(g, [v, a, b])
-end
-
 function find_children(g::SimpleGraph, vertex_set::Vector{Int})
     u_vertices = Int[]
     
diff --git a/lib/OptimalBranchingMIS/src/graphs.jl b/lib/OptimalBranchingMIS/src/graphs.jl
index c9b2ddc..7fd31d4 100644
--- a/lib/OptimalBranchingMIS/src/graphs.jl
+++ b/lib/OptimalBranchingMIS/src/graphs.jl
@@ -34,9 +34,9 @@ function removed_vertices(vertices::Vector{Int}, g::SimpleGraph, clause::Clause{
     return unique!(rvs)
 end
 
-function remove_vertices(g::SimpleGraph, vertices::Vector{Int})
-    g_new, vmap = induced_subgraph(g, setdiff(1:nv(g), vertices))
-    return g_new
+function remove_vertices(g, v)
+    g, vs = induced_subgraph(g, setdiff(vertices(g), v))
+    return g
 end
 
 """
diff --git a/lib/OptimalBranchingMIS/src/types.jl b/lib/OptimalBranchingMIS/src/types.jl
index 505227c..e160365 100644
--- a/lib/OptimalBranchingMIS/src/types.jl
+++ b/lib/OptimalBranchingMIS/src/types.jl
@@ -14,7 +14,7 @@ Represents a Maximum Independent Set (MIS) problem.
 mutable struct MISProblem <: AbstractProblem
     g::SimpleGraph
 end
-copy(p::MISProblem) = MISProblem(copy(p.g))
+Base.copy(p::MISProblem) = MISProblem(copy(p.g))
 Base.show(io::IO, p::MISProblem) = print(io, "MISProblem($(nv(p.g)))")
 
 """
diff --git a/lib/OptimalBranchingMIS/test/graphs.jl b/lib/OptimalBranchingMIS/test/graphs.jl
index d9a2298..879e540 100644
--- a/lib/OptimalBranchingMIS/test/graphs.jl
+++ b/lib/OptimalBranchingMIS/test/graphs.jl
@@ -1,3 +1,4 @@
+using OptimalBranchingCore
 using OptimalBranchingMIS, EliminateGraphs.Graphs
 using Test
 
diff --git a/lib/OptimalBranchingMIS/test/mis.jl b/lib/OptimalBranchingMIS/test/mis.jl
new file mode 100644
index 0000000..f669a5c
--- /dev/null
+++ b/lib/OptimalBranchingMIS/test/mis.jl
@@ -0,0 +1,171 @@
+using EliminateGraphs, EliminateGraphs.Graphs
+using Test
+
+using OptimalBranchingMIS: find_children, unconfined_vertices, is_line_graph, first_twin, twin_filter!, short_funnel_filter!, desk_filter!, effective_vertex, all_three_funnel, all_four_funnel, rho, optimal_four_cycle, optimal_vertex, has_fine_structure, count_o_path, closed_neighbors, is_complete_graph
+
+function graph_from_edges(edges)
+    return SimpleGraph(Graphs.SimpleEdge.(edges))
+end
+
+@testset "find_children" begin
+    g = graph_from_edges([(1,2),(2,3), (1,4), (2,5), (3,5)])
+    @test find_children(g, [1]) == [2, 4]
+    @test find_children(g, [1,2,3]) == [4]
+end
+
+@testset "line graph" begin
+    edges = [(1,2),(1,4),(1,5),(2,3),(2,4),(2,5),(3,4),(3,5)]
+    example_g = SimpleGraph(Graphs.SimpleEdge.(edges))
+    @test is_lg = is_line_graph(example_g) == true
+
+    edges = [(1,2),(1,4),(1,5),(2,3),(2,4),(2,5),(3,4),(3,5),(4,5)]
+    example_g = SimpleGraph(Graphs.SimpleEdge.(edges))
+    @test is_lg = is_line_graph(example_g) == false
+end
+
+
+@testset "confined set and unconfined vertices" begin
+    # via dominated rule
+    g = graph_from_edges([(1,2),(1,3),(1, 4), (2, 3), (2, 4), (2, 6), (3, 5), (4, 5)])
+    @test unconfined_vertices(g) == [2]
+    
+    # via roof
+    g = graph_from_edges([(1, 2), (1, 5), (1, 6), (2, 5), (2, 3), (4, 5), (3, 4), (3, 7), (4, 7)])
+    @test in(1, unconfined_vertices(g))
+end
+
+
+@testset "twin" begin
+    # xiao2013 fig.2(a)
+    edges = [(1, 3), (1, 4), (1, 5), (2, 3), (2, 4), (2, 5), (4, 5), (3, 6), (3, 7), (4, 8), (5, 9), (5, 10)]
+    example_g = SimpleGraph(Graphs.SimpleEdge.(edges))
+    @test first_twin(example_g) == (1, 2)
+    @test twin_filter!(example_g)
+    @test ne(example_g) == 0
+    @test nv(example_g) == 5
+
+    #xiao2013 fig.2(b)
+    edges = [(1, 3), (1, 4), (1, 5), (2, 3), (2, 4), (2, 5), (3, 6), (3, 7), (4, 8), (5, 9), (5, 10)]
+    example_g = SimpleGraph(Graphs.SimpleEdge.(edges))
+    @test first_twin(example_g) == (1, 2)
+    @test twin_filter!(example_g)
+    @test ne(example_g) == 5
+    @test nv(example_g) == 6
+end
+
+
+
+@testset "short funnel" begin
+    edges = [(1, 2), (1, 4), (1, 5), (2, 3), (2, 6), (3, 6), (4, 6)]
+    example_g = SimpleGraph(Graphs.SimpleEdge.(edges))
+    @test short_funnel_filter!(example_g)
+    @test example_g == SimpleGraph{Int64}(5, [[2, 3, 4], [1, 3], [1, 2, 4], [1, 3]])
+
+    # xiao2013 fig.2(c)
+    edges = [(1, 2), (1, 3), (1, 4), (2, 5), (2, 6), (3, 4), (3, 7), (4, 5), (4, 8), (5, 10), (6, 9)]
+    example_g = SimpleGraph(Graphs.SimpleEdge.(edges))
+    @test short_funnel_filter!(example_g)
+    @test nv(example_g) == 8
+    @test ne(example_g) == 9
+end
+
+
+@testset "desk" begin
+    edges = [(1, 2), (1, 4), (1, 8), (2, 3), (2, 7), (3, 8), (5, 7), (6, 8), (7, 8)]
+    example_g = SimpleGraph(Graphs.SimpleEdge.(edges))
+    @test desk_filter!(example_g)
+    @test example_g == SimpleGraph{Int64}(4, [[2, 4], [1, 3], [2, 4], [1, 3]])
+
+    #xiao2013 fig.2(d)
+    edges = [(1, 2), (1, 4), (1, 5), (2, 3), (2, 6), (3, 4), (3, 5), (3, 7), (4, 8), (5, 9), (6, 10), (7, 11), (8, 12)]
+    example_g = SimpleGraph(Graphs.SimpleEdge.(edges))
+    @test desk_filter!(example_g)
+    @test nv(example_g) == 8
+    @test ne(example_g) == 8
+end
+
+
+@testset "effective vertex" begin
+    function is_effective_vertex(g::SimpleGraph, a::Int, S_a::Vector{Int})
+        g_copy = copy(g)
+        rem_vertices!(g_copy, closed_neighbors(g, S_a))
+        degree(g,a) == 3 && all(degree(g,n) == 3 for n in neighbors(g,a)) && rho(g) - rho(g_copy) >= 20
+    end
+
+    g = random_regular_graph(1000, 3)
+    a, S_a = effective_vertex(g)
+    @test is_effective_vertex(g, a, S_a)
+end
+
+@testset "funnel" begin
+    function is_n_funnel(g::SimpleGraph, n::Int, a::Int, b::Int)
+        degree(g,a) == n && is_complete_graph(g, setdiff(neighbors(g,a), [b]))
+    end
+
+    edges = [(1, 2), (1, 3), (1, 4), (3, 4)]
+    g = SimpleGraph(Graphs.SimpleEdge.(edges))
+    three_funnels = all_three_funnel(g)
+    @test three_funnels == [(1, 2)]
+    @test is_n_funnel(g, 3, 1, 2)
+
+    edges = [(1, 2), (1, 3), (1, 4), (1, 5), (3, 4), (3, 5), (4, 5)]
+    g = SimpleGraph(Graphs.SimpleEdge.(edges))
+    four_funnels = all_four_funnel(g)
+    @test four_funnels == [(1, 2)]
+    @test is_n_funnel(g, 4, 1, 2)
+end
+
+@testset "o_path" begin
+    edges = [(1, 2), (2, 3), (3, 4), (1, 5), (1, 6), (3, 7)]
+    example_g = SimpleGraph(Graphs.SimpleEdge.(edges))
+    o_path_num = count_o_path(example_g)
+    @test o_path_num == 1
+
+    edges = [(1, 2), (2, 3), (3, 4), (1, 5), (1, 6), (4, 7),(4, 8)]
+    example_g = SimpleGraph(Graphs.SimpleEdge.(edges))
+    o_path_num = count_o_path(example_g)
+    @test o_path_num == 0
+end
+
+@testset "fine_structure" begin
+    edges = [(1, 2), (2, 3), (3, 4), (1, 5), (1, 6), (3, 7)]
+    example_g = SimpleGraph(Graphs.SimpleEdge.(edges))
+    @test has_fine_structure(example_g) == true
+
+    edges = [(1, 2), (1, 3), (1, 4), (2, 3), (2, 7), (3, 8), (4, 5), (4, 6)]
+    example_g = SimpleGraph(Graphs.SimpleEdge.(edges))
+    @test has_fine_structure(example_g) == true
+
+    edges = [(1, 2), (2, 3), (3, 4), (1, 5), (1, 6), (4, 7),(4, 8)]
+    example_g = SimpleGraph(Graphs.SimpleEdge.(edges))
+    @test has_fine_structure(example_g) == false
+end
+
+@testset "four_cycle" begin
+    edges = [(1, 2), (2, 3), (3, 4), (4, 1), (1, 5)]
+    example_g = SimpleGraph(Graphs.SimpleEdge.(edges))
+    opt_quad = optimal_four_cycle(example_g)
+    @test opt_quad == [1, 2, 3, 4]
+
+    edges = [(1, 2), (2, 3), (3, 4), (4, 1), (3, 5), (4, 6), (5, 6), (1, 7)]
+    example_g = SimpleGraph(Graphs.SimpleEdge.(edges))
+    opt_quad = optimal_four_cycle(example_g)
+    @test opt_quad == [1, 2, 3, 4]
+end
+
+@testset "optimal vertex" begin
+    edges = [(1, 2), (2, 6), (1, 3), (3, 7), (1, 4), (4, 8), (1, 5), (5, 9)]
+    example_g = SimpleGraph(Graphs.SimpleEdge.(edges))
+    v = optimal_vertex(example_g)
+    @test v == 1
+end
+
+@testset "xiao2013" begin
+    for seed in 10:2:100
+        g = random_regular_graph(seed, 3)
+        eg = EliminateGraph(g)
+        mis_size_standard = mis2(eg)
+        mis_size = counting_xiao2013(g).mis_size
+        @test mis_size_standard == mis_size
+    end
+end
\ No newline at end of file
diff --git a/lib/OptimalBranchingMIS/test/runtests.jl b/lib/OptimalBranchingMIS/test/runtests.jl
index 144ee49..58c3b2a 100644
--- a/lib/OptimalBranchingMIS/test/runtests.jl
+++ b/lib/OptimalBranchingMIS/test/runtests.jl
@@ -1,10 +1,14 @@
 using OptimalBranchingMIS
 using Test
 
-@testset "branch" begin
-    include("branch.jl")
-end
+# @testset "branch" begin
+#     include("branch.jl")
+# end
 
 @testset "graphs" begin
     include("graphs.jl")
 end
+
+@testset "mis" begin
+    include("mis.jl")
+end