graphmatcher 0.3.3

checksums.yaml

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+---
+SHA256:
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+  data.tar.gz: af3f0b36a377af1fee96780b87758c1be26d30eca6f51595a061dc7c3388d70b
+SHA512:
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data/lib/graphmatcher.rb

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+require 'logger'
+# require 'ruby-prof'
+
+# @query_graph & @data_graph: Arrays which are represented as an
+# array such as g=[[[1,2],[3],[3],[]],['x','y','y','z']]. g[0] is
+# adjacency array which points children of given vertex of array index,
+# -e.g. vertex 0 has 1 and 2 as children- and g[1] is labels for vertices.
+# -e.g. vertex 0 has label 'x'.
+#
+# @limit: Upper limit for number of matches. Procedure terminates after
+# reaching to an upper limit.
+# @max_allowed_time: Maximum allowed time for procedure to run.
+# @self_loops: Boolean value for representing if query is cyclic or not.
+class Graphmatcher
+  @@logger = Logger.new(STDOUT)
+  @@logger.level = Logger::FATAL
+
+  def initialize(args)
+    @query_graph = args[:query_graph].to_a
+    @data_graph = args[:data_graph].to_a
+    @limit = (args[:limit] || 1).to_i
+    @max_allowed_time = (args[:max_allowed_time] || 4.000).to_f
+    @cost_matrix = args[:cost_matrix] || nil
+    @self_loops = args[:self_loops] || false
+    validate!
+  end
+
+  # Function for generating feasible matches for query
+  # graph based on labels of vertices of data graph.
+  def label_match
+    data_labels = @data_graph[1]
+    query_labels = @query_graph[1]
+
+    feasible = query_labels.map.with_index do |ql, _index|
+      data_labels.each_index.select { |i| data_labels[i] == ql }
+    end
+
+    if @cost_matrix
+
+      feasible = assess_cost(feasible, @cost_matrix)
+
+      feasible = feasible.select { |f| f[1] }.map do |feasible_set|
+        feasible_set.sort_by { |f| f[1] }
+      end
+
+      feasible = feasible.map do |f_set|
+        f_set.map do |f|
+          f[0]
+        end
+      end
+    end
+
+    @@logger.info('Label matches(phi) are: ' + feasible.to_s)
+    feasible
+  end
+
+  # Public interface for Graphmatcher class.
+  #
+  # @matches: Array of matching indices of query graph in data graph.
+  def find_matches
+    @matches = []
+    @t0 = Time.now.to_f
+    phi = label_match
+
+    dual_iso(dual_simulation(phi), 0)
+    # @@logger.info("FINISHED matches=#{@matches}")
+    if @cost_matrix
+      # if cost matrix is available, get costs of found matches.
+
+      @matches = assess_cost(@matches, @cost_matrix)
+
+      # sort matches by sum of costs of matched resources.
+      #               MATCHES
+      # [ [[1,100],[2,10]],[[3,500],[4,800]] ]
+      #              MATCH COSTS
+      #         110              1300
+
+      # The behaviour here is important !
+      # Sum of costs vs. max of costs, depends which one is relevant.
+
+      @matches.reject! { |match_set| match_set.map { |e| e[1] }.include?(nil) }
+
+      @matches = @matches.sort_by do |match_set|
+        match_set.reduce(0) { |sum, e| sum + e[1] }
+      end
+
+    end
+    @matches
+  end
+
+  def get_resource_property(_match, property)
+    truncated_data_graph = @data_graph.truncate
+    @matches.map { |match_set| match_set.map { |match| truncated_data_graph[match[0]][2][property] } }
+  end
+
+  def get_resource_cost(costs, resource_position, query_index)
+    # costs = { resource_id => { query_index => cost } }
+    # e.g.
+    # costs = { 40 => { 0 => 5, 1 => 10 } }
+    if costs[resource_position][query_index]
+      cost = (costs[resource_position][query_index])
+      cost
+    end
+  end
+
+  def assess_cost(matches, costs)
+    # resource_graph =
+    #   [
+    #       [[],[],[],[],[],[],[]], #adj.
+    #       ['SPO2','NRF52','SPO2','NRF52','SPO2','NRF52','SPO2'], #types
+    #       ['img_x','img_y','img_z','img_t','img_z','img_q','img_z'], #images
+    #       ['12','52','25','61','74','95','11']            #resource_id
+    #   ]
+
+    # request_graph =
+    #   [
+    #       [[],[]],
+    #       ['NRF52','NRF52'],
+    #       ['img_y','img_z'],
+    #       ['NODE_A','HUB_A']
+    #   ]
+
+    # costs = {
+    #   52 => {0 => 0, 1 => 50} , #y
+    #   61 => {0 => 30, 1 => 70} , #t
+    #   95 => {0 => 40, 1 => 55} , #q
+    # }
+
+    # matches = [
+    #   [[1],[2]],[[1],[4]],[[1],[6]],
+    #   [[3],[2]],[[3],[4]],[[3],[6]],
+    #   [[5],[2]],[[5],[4]],[[5],[6]]
+    # ]
+
+    matches.map do |match_set| # [ [1],[2] ]
+      match_set.flatten.map.with_index do |match, query_index| # 1
+        [match, get_resource_cost(costs, match, query_index).to_f]
+      end
+    end
+  end
+
+  # INFO: Function that uses parameter phi -which is generated by label_match-
+  # to determine which matches of data have expected relations in query graph.
+  # phi = ...
+  def dual_simulation(phi)
+    # One directional adjacency array for data graph and query graphs.
+    data_children = @data_graph[0]
+    query_children = @query_graph[0]
+    # @@logger.info("Data children: #{data_children.to_s}")
+    # @@logger.info("Query children: #{query_children.to_s}")
+    changed = true
+    while changed
+      changed = false
+      return nil if (Time.now.to_f - @t0) > @max_allowed_time
+
+      # children = query_edges
+      # q_index = query_vertex_index
+      query_children.each_with_index do |children, q_index|
+        # query_child = query_edge_target
+        children.each do |query_child|
+          # Create a temporary phi object.
+          temp_phi = []
+          # Loop over candidates of each vertex in data graph.
+          to_delete = []
+
+          phi[q_index].map do |child| # loop 3
+            # @@logger.debug("u=#{q_index}, u_c=#{query_child}, child=#{child}")
+
+            # Find intersection of children of 'child' in data graph and
+            # candidates of 'query child' in data graph.
+            phi_intersection = data_children[child] & phi[query_child]
+            # @@logger.debug("datachildren[child]=#{data_children[child]}")
+            # @@logger.debug("phi[query_child]=#{phi[query_child]}")
+            # @@logger.debug("Intersection=#{phi_intersection}")
+            if phi_intersection.nil? || phi_intersection.empty?
+              to_delete.push(child)
+              return phi if phi[q_index].empty?
+
+              changed = true
+            end
+            temp_phi |= phi_intersection
+          end
+
+          unless to_delete.empty?
+            to_delete.each do |td|
+              phi[q_index].delete(td)
+            end
+          end
+          return phi if temp_phi.flatten.empty?
+
+          changed = true if temp_phi.size < phi[query_child].size
+          if @self_loops && query_child == q_index
+            phi[query_child] &= temp_phi
+          else
+            # @@logger.debug("phi=#{phi} and phi[#{query_child}]=#{temp_phi}")
+            phi[query_child] = temp_phi
+          end
+        end
+      end
+    end
+    @@logger.info("Returning phi=#{phi}")
+    phi
+  end
+
+  # INFO: Function call to collect matches from phi object.
+  # phi = ...
+  # depth = ...
+  # matches = ...
+  def dual_iso(phi, depth)
+    if depth == @query_graph[0].length
+      unless phi.nil? || phi.empty?
+        @matches <<
+          if phi.include?([]) # Unable to match this vertex in graph.
+            [nil]
+          else
+            phi
+          end
+      end
+    elsif !(phi.nil? || phi.empty?)
+      phi[depth].sort_by { |value| @cost_matrix ? (@cost_matrix[value][depth] || Float::INFINITY) : next }.each do |value|
+        next if contains(phi, depth, value)
+
+        # keys are indices 0...n, values are possible values for that index
+        phicopy = phi.map(&:clone)
+        # @@logger.info("phicopy=#{phicopy},depth=#{depth},value=#{value}")
+        phicopy[depth] = [value]
+        if @matches.length >= @limit
+          @@logger.info("FINISHED matches=#{@matches}")
+          return @matches
+        end
+        dual_iso(dual_simulation(phicopy), depth + 1)
+      end
+    end
+  end
+
+  # INFO: Checks if vertex J is contained in any of previous matches.
+  # TODO: Change with find method.
+  def contains(phi, depth, vertex_j)
+    false if depth <= 0
+    (0..depth - 1).each do |i|
+      # @@logger.info("phi[#{i}]=#{phi[i]},depth=#{depth},vertex_j=#{vertex_j}")
+      return true if phi[i].include?(vertex_j)
+    end
+    false
+  end
+
+  # EXPERIMENTAL
+  # INFO: Produce a GraphViz-compliant directed graph syntax.
+  # INFO: Needs dot/graphviz tools installed as a dependency.
+  # TODO: Unable to handle multiple results, color each result different.
+  # Indices are IDs, labels are labels adjencency array is outgoing edges.
+  def dot_graph(data, subgraph = nil, prefix = '')
+    output = ['digraph {']
+    data.transpose.each_with_index do |node, id|
+      output <<
+        ["#{id} [label=\"#{node[1]}##{id}\"]",
+         "#{id}->{#{node[0].join(' ')}}"].join("\n")
+    end
+    if subgraph
+      subgraph.each_with_index do |node, _id|
+        output << "#{node} [fontcolor=\"Red\"]"
+      end
+    end
+    output << '}'
+    tstamp = Time.new.to_i.to_s
+    File.write("#{prefix}#{tstamp}.dot", output.join("\n"))
+    dot_produce = ['dot', '-Tpng', "#{prefix}#{tstamp}.dot",
+                   '-o', "#{prefix}#{tstamp}.png"].join(' ')
+    `#{dot_produce}`
+  end
+
+  def validate!
+    unless @query_graph.is_a?(Array) && @data_graph.is_a?(Array)
+      raise ArgumentError,
+            'Type mismatch for graphs in initialization !'
+    end
+    unless @limit.is_a?(Numeric) && @max_allowed_time.is_a?(Numeric)
+      raise ArgumentError,
+            'Type mismatch for limit or timeout value in initialization !'
+    end
+    unless @query_graph.length >= 2 && @data_graph.length >= 2
+      raise ArgumentError,
+            'Input graphs must have at least two dimensions !'
+    end
+    unless @query_graph.map(&:length).uniq.size == 1 &&
+           @data_graph.map(&:length).uniq.size == 1
+      raise ArgumentError,
+            'Input graphs\' adjencency and label arrays must be sized equal !'
+    end
+  end
+end

metadata

@@ -0,0 +1,115 @@
+--- !ruby/object:Gem::Specification
+name: graphmatcher
+version: !ruby/object:Gem::Version
+  version: 0.3.3
+platform: ruby
+authors:
+- Emre Unlu
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2020-10-21 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.10'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.10'
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.0'
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 3.5.0
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 3.5.0
+- !ruby/object:Gem::Dependency
+  name: ruby-prof
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.16.2
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.16.2
+- !ruby/object:Gem::Dependency
+  name: rspec-prof
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.0.7
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.0.7
+description: An effective subgraph matching gem based on DualIso algorithm of M. Saltz
+  et al.
+email:
+- emre@eunlu.com
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- lib/graphmatcher.rb
+homepage: https://github.com/forvelin/graphmatcher
+licenses:
+- MIT
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubygems_version: 3.1.2
+signing_key: 
+specification_version: 4
+summary: Subgraph matching based on DualIso algorithm.
+test_files: []