/// <summary>
/// Algorithm taken from Grochow and Kellis. This is failing at the moment
/// </summary>
/// <param name="partialMap">f; Map is represented as a dictionary, with the Key as h and the Value as g</param>
/// <param name="queryGraph">G</param>
/// <param name="queryGraphEdges">G's edges. Added to speedup computation by avoiding to evaluate it frequently and needlessly</param>
/// <param name="inputGraph">H</param>
/// <param name="getInducedMappingsOnly">If true, then the querygraph must match exactly to the input subgraph. In other words, only induced subgraphs will be returned</param>
/// <returns>List of isomorphisms. Remember, Key is h, Value is g</returns>
internal static Dictionary <int[], List <Mapping> > IsomorphicExtension(Dictionary <int, int> partialMap, QueryGraph queryGraph
, Edge <int>[] queryGraphEdges, UndirectedGraph <int> inputGraph, bool getInducedMappingsOnly)
{
if (partialMap.Count == queryGraph.VertexCount)
{
#region Return base case
var function = new SortedList <int, int>(partialMap);
var result = IsMappingCorrect(function, queryGraphEdges, inputGraph, getInducedMappingsOnly);
if (result.IsCorrectMapping)
{
return(new Dictionary <int[], List <Mapping> >(1)
{
{ function.Values.ToArray(), new List <Mapping>(1)
{
new Mapping(function, result.SubgraphEdgeCount)
} }
});
}
function.Clear();
function = null;
return(null);
#endregion
}
//Remember: f(h) = g, so h is Domain and g is Range.
// In other words, Key is h and Value is g in the dictionary
// get m, most constrained neighbor
int m = GetMostConstrainedNeighbour(partialMap.Keys, queryGraph);
if (m < 0)
{
return(null);
}
var listOfIsomorphisms = new Dictionary <int[], List <Mapping> >(ModaAlgorithms.MappingNodesComparer);
var neighbourRange = ChooseNeighboursOfRange(partialMap.Values, inputGraph);
var neighborsOfM = queryGraph.GetNeighbors(m, false);
var newPartialMapCount = partialMap.Count + 1;
//foreach neighbour n of f(D)
for (int i = 0; i < neighbourRange.Count; i++)
{
//int n = neighbourRange[i];
if (false == IsNeighbourIncompatible(inputGraph, neighbourRange[i], partialMap, queryGraph, neighborsOfM))
{
//It's not; so, let f' = f on D, and f'(m) = n.
//Find all isomorphic extensions of f'.
//newPartialMap[m] = neighbourRange[i];
var newPartialMap = new Dictionary <int, int>(newPartialMapCount);
foreach (var item in partialMap)
{
newPartialMap.Add(item.Key, item.Value);
}
newPartialMap[m] = neighbourRange[i];
var subList = IsomorphicExtension(newPartialMap, queryGraph, queryGraphEdges, inputGraph, getInducedMappingsOnly);
newPartialMap.Clear();
newPartialMap = null;
if (subList != null && subList.Count > 0)
{
foreach (var item in subList)
{
if (item.Value.Count > 1)
{
queryGraph.RemoveNonApplicableMappings(item.Value, inputGraph, getInducedMappingsOnly);
}
List <Mapping> maps;
if (listOfIsomorphisms.TryGetValue(item.Key, out maps))
{
maps.AddRange(item.Value);
}
else
{
listOfIsomorphisms[item.Key] = item.Value;
}
}
subList.Clear();
}
subList = null;
}
}
neighborsOfM = null; // DO NOT Clear this variable
neighbourRange.Clear();
neighbourRange = null;
return(listOfIsomorphisms);
}
/// <summary>
/// Mapping module (aka FindSubgraphInstances in Grochow & Kellis) modified
/// The modification:
/// Instead of traversing all nodes in the query graph (H) for each node in the input graph (G),
/// we simply use just one node h in H to traverse G. This makes it much easier to parallelize
/// unlike the original algorithm, and eliminate the need for removing visited g from G.
///
/// Testing will show whether this improves, worsens or makes no difference in performance.
/// </summary>
/// <param name="queryGraph">H</param>
/// <param name="inputGraph">G</param>
/// <param name="numberOfSamples">To be decided. If not set, we use the <paramref name="inputGraph"/> size / 3</param>
private static ICollection <Mapping> Algorithm2_Modified(QueryGraph queryGraph, UndirectedGraph <int> inputGraph, int numberOfSamples, bool getInducedMappingsOnly)
{
if (numberOfSamples <= 0)
{
numberOfSamples = inputGraph.VertexCount / 3;
}
var theMappings = new Dictionary <int[], List <Mapping> >(MappingNodesComparer);
var inputGraphDegSeq = inputGraph.GetNodesSortedByDegree(numberOfSamples);
var threadName = Thread.CurrentThread.ManagedThreadId;
Console.WriteLine("Thread {0}:\tCalling Algo 2-Modified:\n", threadName);
var queryGraphEdges = queryGraph.Edges.ToArray();
var h = queryGraph.Vertices.ElementAt(0);
var f = new Dictionary <int, int>(1);
for (int i = 0; i < inputGraphDegSeq.Count; i++)
{
var g = inputGraphDegSeq[i];
if (Utils.CanSupport(queryGraph, h, inputGraph, g))
{
#region Can Support
//Remember: f(h) = g, so h is Domain and g is Range
f[h] = g;
var mappings = Utils.IsomorphicExtension(f, queryGraph, queryGraphEdges, inputGraph, getInducedMappingsOnly);
if (mappings.Count > 0)
{
foreach (var item in mappings)
{
if (item.Value.Count > 1)
{
queryGraph.RemoveNonApplicableMappings(item.Value, inputGraph, getInducedMappingsOnly);
}
//Recall: f(h) = g
List <Mapping> maps;
if (theMappings.TryGetValue(item.Key, out maps))
{
maps.AddRange(item.Value);
}
else
{
theMappings[item.Key] = item.Value;
}
}
mappings.Clear();
}
mappings = null;
#endregion
}
}
f.Clear();
f = null;
Array.Clear(queryGraphEdges, 0, queryGraphEdges.Length);
queryGraphEdges = null;
inputGraphDegSeq.Clear();
inputGraphDegSeq = null;
var toReturn = GetSet(theMappings);
theMappings = null;
Console.WriteLine("\nThread {0}:\tAlgorithm 2: All iteration tasks completed. Number of mappings found: {1}.\n", threadName, toReturn.Count);
return(toReturn);
}
/// <summary>
/// Enumeration module. NB: If either of <paramref name="allMappings"/> or <paramref name="fileName"/> is null, the other will not be.
/// </summary>
/// <param name="allMappings"></param>
/// <param name="inputGraph">G</param>
/// <param name="queryGraph">H</param>
/// <param name="expansionTree">T_k</param>
/// <param name="parentQueryGraph"></param>
/// <param name="fileName"></param>
/// <param name="parentGraphMappings">NB: This param is still used even outside this method is call. So, be careful how you set/clear its values.</param>
private static IList <Mapping> Algorithm3(Dictionary <QueryGraph, ICollection <Mapping> > allMappings, UndirectedGraph <int> inputGraph, QueryGraph queryGraph,
AdjacencyGraph <ExpansionTreeNode> expansionTree,
QueryGraph parentQueryGraph, out string newFileName, string fileName = null)
{
newFileName = null;
ICollection <Mapping> parentGraphMappings;
if (string.IsNullOrWhiteSpace(fileName))
{
if (!allMappings.TryGetValue(parentQueryGraph, out parentGraphMappings))
{
return(new Mapping[0]);
}
}
else
{
parentGraphMappings = parentQueryGraph.ReadMappingsFromFile(fileName);
}
if (parentGraphMappings.Count == 0)
{
return(new Mapping[0]);
}
var subgraphSize = queryGraph.VertexCount;
var parentQueryGraphEdges = new HashSet <Edge <int> >();
foreach (var edge in parentQueryGraph.Edges)
{
parentQueryGraphEdges.Add(edge);
}
var newEdge = GetEdgeDifference(queryGraph, parentQueryGraph, parentQueryGraphEdges);
parentQueryGraphEdges.Clear();
parentQueryGraphEdges = null;
// if it's NOT a valid edge
if (newEdge.Source == Utils.DefaultEdgeNodeVal)
{
return(new Mapping[0]);
}
var list = new List <Mapping>();
int oldCount = parentGraphMappings.Count, id = 0, queryGraphEdgeCount = queryGraph.EdgeCount;
var queryGraphEdges = queryGraph.Edges.ToArray();
var groupByGNodes = parentGraphMappings.GroupBy(x => x.Function.Values.ToArray(), MappingNodesComparer); //.ToDictionary(x => x.Key, x => x.ToArray(), MappingNodesComparer);
foreach (var set in groupByGNodes)
{
// function.value (= set of G nodes) are all same here. So build the subgraph here and pass it dowm
var subgraph = Utils.GetSubgraph(inputGraph, set.Key);
foreach (var item in set)
{
item.Id = id++;
// Remember, f(h) = g
// if (f(u), f(v)) ϵ G and meets the conditions, add to list
if (item.SubGraphEdgeCount == queryGraphEdgeCount)
{
var isMapping = Utils.IsMappingCorrect2(item.Function, subgraph, queryGraphEdges, true);
if (isMapping.IsCorrectMapping)
{
list.Add(item);
}
isMapping = null;
}
else if (item.SubGraphEdgeCount > queryGraphEdgeCount)
{
var newEdgeImage = item.GetImage(inputGraph, newEdge);
// if it's a valid edge...
if (newEdgeImage.Source != Utils.DefaultEdgeNodeVal &&
inputGraph.ContainsEdge(newEdgeImage.Source, newEdgeImage.Target))
{
list.Add(item);
}
}
}
subgraph = null;
}
Array.Clear(queryGraphEdges, 0, queryGraphEdges.Length);
queryGraphEdges = null;
var threadName = System.Threading.Thread.CurrentThread.ManagedThreadId;
// Remove mappings from the parent qGraph that are found in this qGraph
// This is because we're only interested in induced subgraphs
var theRest = parentGraphMappings.Except(list).ToList();
parentQueryGraph.RemoveNonApplicableMappings(theRest, inputGraph);
parentGraphMappings.Clear();
foreach (var item in theRest)
{
parentGraphMappings.Add(item);
}
theRest.Clear();
theRest = null;
// Now, remove duplicates
queryGraph.RemoveNonApplicableMappings(list, inputGraph);
if (!string.IsNullOrWhiteSpace(fileName) && oldCount > parentGraphMappings.Count)
{
// This means that some of the mappings from parent fit the current query graph
newFileName = parentQueryGraph.WriteMappingsToFile(parentGraphMappings);
try
{
System.IO.File.Delete(fileName);
}
catch { } // we can afford to let this fail
}
Console.WriteLine("Thread {0}:\tAlgorithm 3: All tasks completed. Number of mappings found: {1}.\n", threadName, list.Count);
return(list);
}
/// <summary>
/// Algo 1: Find subgraph frequency (mappings found are saved to disk to be retrieved later during Algo 3).
/// The value of the dictionary returned is in the form: $"{mappings.Count}#{qGraph.Label}.ser"
/// </summary>
/// <param name="inputGraph"></param>
/// <param name="qGraph">The query graph to be searched for. If not available, we use expansion trees (MODA). Otherwise, we use Grochow's (Algo 2)</param>
/// <param name="subgraphSize"></param>
/// <param name="thresholdValue">Frequency value, above which we can comsider the subgraph a "frequent subgraph"</param>
/// <returns></returns>
public static Dictionary <QueryGraph, string> Algorithm1_C(UndirectedGraph <int> inputGraph, QueryGraph qGraph, int subgraphSize, int thresholdValue)
{
// The enumeration module (Algo 3) needs the mappings generated from the previous run(s)
Dictionary <QueryGraph, string> allMappings;
int numIterations = -1;
if (inputGraph.VertexCount < 121)
{
numIterations = inputGraph.VertexCount;
}
if (qGraph == null) // Use MODA's expansion tree
{
#region Use MODA's expansion tree
var treatedNodes = new HashSet <QueryGraph>();
allMappings = new Dictionary <QueryGraph, string>(_builder.NumberOfQueryGraphs);
do
{
qGraph = GetNextNode()?.QueryGraph;
if (qGraph == null)
{
break;
}
ICollection <Mapping> mappings;
if (qGraph.EdgeCount == (subgraphSize - 1)) // i.e. if qGraph is a tree
{
if (UseModifiedGrochow)
{
// Modified Mapping module - MODA and Grockow & Kellis
mappings = Algorithm2_Modified(qGraph, inputGraph, numIterations, false);
}
else
{
var inputGraphClone = inputGraph.Clone();
mappings = Algorithm2(qGraph, inputGraphClone, numIterations, false);
inputGraphClone.Clear();
inputGraphClone = null;
}
// Because we're saving to file, we're better off doing this now
qGraph.RemoveNonApplicableMappings(mappings, inputGraph, false);
treatedNodes.Add(qGraph);
}
else
{
// Enumeration moodule - MODA
// This is part of Algo 3; but performance tweaks makes it more useful to get it here
var parentQueryGraph = GetParent(qGraph, _builder.ExpansionTree);
if (parentQueryGraph.EdgeCount == (subgraphSize - 1))
{
treatedNodes.Add(parentQueryGraph);
}
string _filename;
if (allMappings.TryGetValue(parentQueryGraph, out _filename))
{
string newFileName; // for parentQueryGraph
mappings = Algorithm3(null, inputGraph, qGraph, _builder.ExpansionTree, parentQueryGraph, out newFileName, _filename);
if (!string.IsNullOrWhiteSpace(newFileName))
{
// We change the _filename value in the dictionary since this means some of the mappings from parent fit the child
allMappings[parentQueryGraph] = newFileName;
}
}
else
{
mappings = new Mapping[0];
}
}
if (mappings.Count > thresholdValue)
{
qGraph.IsFrequentSubgraph = true;
}
// Save mappings.
var fileName = qGraph.WriteMappingsToFile(mappings);
if (mappings.Count > 0)
{
mappings.Clear();
}
allMappings.Add(qGraph, fileName);
// Check for complete-ness; if complete, break
if (qGraph.IsComplete(subgraphSize))
{
qGraph = null;
break;
}
qGraph = null;
}while (true);
#endregion
}
else
{
ICollection <Mapping> mappings;
if (UseModifiedGrochow)
{
// Modified Mapping module - MODA and Grockow & Kellis
mappings = Algorithm2_Modified(qGraph, inputGraph, numIterations, true);
}
else
{
mappings = Algorithm2(qGraph, inputGraph, numIterations, true);
}
qGraph.RemoveNonApplicableMappings(mappings, inputGraph);
var fileName = $"{mappings.Count}#{qGraph.Identifier}.ser";
System.IO.File.WriteAllText(fileName, Extensions.CompressString(Newtonsoft.Json.JsonConvert.SerializeObject(mappings)));
if (mappings.Count > 0)
{
mappings.Clear();
}
allMappings = new Dictionary <QueryGraph, string>(1)
{
{ qGraph, fileName }
};
}
return(allMappings);
}
/// <summary>
/// Algo 1: Find subgraph frequency (mappings help in memory)
/// </summary>
/// <param name="inputGraph"></param>
/// <param name="qGraph">The query graph to be searched for. If not available, we use expansion trees (MODA). Otherwise, we use Grochow's (Algo 2)</param>
/// <param name="subgraphSize"></param>
/// <param name="thresholdValue">Frequency value, above which we can comsider the subgraph a "frequent subgraph"</param>
/// <returns></returns>
public static Dictionary <QueryGraph, ICollection <Mapping> > Algorithm1(UndirectedGraph <int> inputGraph, QueryGraph qGraph, int subgraphSize = -1, int thresholdValue = 0)
{
// The enumeration module (Algo 3) needs the mappings generated from the previous run(s)
Dictionary <QueryGraph, ICollection <Mapping> > allMappings;
int numIterations = -1;
if (inputGraph.VertexCount < 121)
{
numIterations = inputGraph.VertexCount;
}
if (qGraph == null) // Use MODA's expansion tree
{
#region Use MODA's expansion tree
var treatedNodes = new HashSet <QueryGraph>();
allMappings = new Dictionary <QueryGraph, ICollection <Mapping> >(_builder.NumberOfQueryGraphs);
do
{
qGraph = GetNextNode()?.QueryGraph;
if (qGraph == null)
{
break;
}
ICollection <Mapping> mappings;
if (qGraph.IsTree(subgraphSize))
{
if (UseModifiedGrochow)
{
// Modified Mapping module - MODA and Grockow & Kellis
mappings = Algorithm2_Modified(qGraph, inputGraph, numIterations, false);
}
else
{
// Mapping module - MODA and Grockow & Kellis.
var inputGraphClone = inputGraph.Clone();
mappings = Algorithm2(qGraph, inputGraphClone, numIterations, false);
inputGraphClone.Clear();
inputGraphClone = null;
}
}
else
{
// Enumeration moodule - MODA
// This is part of Algo 3; but performance tweaks makes it more useful to get it here
var parentQueryGraph = GetParent(qGraph, _builder.ExpansionTree);
if (parentQueryGraph.IsTree(subgraphSize))
{
treatedNodes.Add(parentQueryGraph);
}
string file;
mappings = Algorithm3(allMappings, inputGraph, qGraph, _builder.ExpansionTree, parentQueryGraph, out file);
}
if (mappings != null && mappings.Count > thresholdValue)
{
qGraph.IsFrequentSubgraph = true;
}
// Save mappings. Do we need to save to disk? Maybe not!
allMappings.Add(qGraph, mappings);
// Do not call mappings.Clear()
mappings = null;
// Check for complete-ness; if complete, break
if (qGraph.IsComplete(subgraphSize))
{
qGraph = null;
break;
}
qGraph = null;
}while (true);
if (treatedNodes.Count > 0)
{
foreach (var mapping in allMappings)
{
if (mapping.Key.IsTree(subgraphSize) && !treatedNodes.Contains(mapping.Key))
{
mapping.Key.RemoveNonApplicableMappings(mapping.Value, inputGraph);
}
}
treatedNodes.Clear();
}
treatedNodes = null;
#endregion
}
else
{
ICollection <Mapping> mappings;
if (UseModifiedGrochow)
{
// Modified Mapping module - MODA and Grockow & Kellis
mappings = Algorithm2_Modified(qGraph, inputGraph, numIterations, true);
// mappings = ModaAlgorithm2Parallelized.Algorithm2_Modified(qGraph, inputGraph, numIterations);
}
else
{
mappings = Algorithm2(qGraph, inputGraph, numIterations, true);
}
qGraph.RemoveNonApplicableMappings(mappings, inputGraph);
allMappings = new Dictionary <QueryGraph, ICollection <Mapping> >(1)
{
{ qGraph, mappings }
};
// Do not call mappings.Clear()
mappings = null;
}
return(allMappings);
}
/// <summary>
/// Mapping module; aka FindSubgraphInstances in Grochow & Kellis
/// </summary>
/// <param name="queryGraph">H</param>
/// <param name="inputGraphClone">G</param>
/// <param name="numberOfSamples">To be decided. If not set, we use the <paramref name="inputGraphClone"/> size / 3</param>
internal static ICollection <Mapping> Algorithm2(QueryGraph queryGraph, UndirectedGraph <int> inputGraphClone, int numberOfSamples, bool getInducedMappingsOnly)
{
if (numberOfSamples <= 0)
{
numberOfSamples = inputGraphClone.VertexCount / 3;
}
// Do we need this clone? Can't we just remove the node directly from the graph?
// We do need it.
var theMappings = new Dictionary <int[], List <Mapping> >(MappingNodesComparer);
var inputGraphDegSeq = inputGraphClone.GetNodesSortedByDegree(numberOfSamples);
var queryGraphVertices = queryGraph.Vertices.ToArray();
var queryGraphEdges = queryGraph.Edges.ToArray();
var subgraphSize = queryGraphVertices.Length;
var threadName = System.Threading.Thread.CurrentThread.ManagedThreadId;
Console.WriteLine("Thread {0}:\tCallingu Algo 2:\n", threadName);
for (int i = 0; i < inputGraphDegSeq.Count; i++)
{
var g = inputGraphDegSeq[i];
for (int j = 0; j < subgraphSize; j++)
{
var h = queryGraphVertices[j];
if (Utils.CanSupport(queryGraph, h, inputGraphClone, g))
{
#region Can Support
//Remember: f(h) = g, so h is Domain and g is Range
var f = new Dictionary <int, int>(1);
f[h] = g;
var mappings = Utils.IsomorphicExtension(f, queryGraph, queryGraphEdges, inputGraphClone, getInducedMappingsOnly);
f.Clear();
f = null;
if (mappings.Count > 0)
{
foreach (var item in mappings)
{
if (item.Value.Count > 1)
{
queryGraph.RemoveNonApplicableMappings(item.Value, inputGraphClone, getInducedMappingsOnly);
}
//Recall: f(h) = g
List <Mapping> maps;
if (theMappings.TryGetValue(item.Key, out maps))
{
maps.AddRange(item.Value);
}
else
{
theMappings[item.Key] = item.Value;
}
}
mappings.Clear();
}
mappings = null;
#endregion
}
}
//Remove g
inputGraphClone.RemoveVertex(g);
if (inputGraphClone.EdgeCount == 0)
{
break;
}
}
Array.Clear(queryGraphEdges, 0, queryGraphEdges.Length);
queryGraphEdges = null;
Array.Clear(queryGraphVertices, 0, subgraphSize);
queryGraphVertices = null;
inputGraphDegSeq.Clear();
inputGraphDegSeq = null;
var toReturn = GetSet(theMappings);
theMappings = null;
Console.WriteLine("Thread {0}:\tAlgorithm 2: All tasks completed. Number of mappings found: {1}.", threadName, toReturn.Count);
return(toReturn);
}
