// Find community information in each module
public static void FindCommunity(double Alfa, List <List <int> > Modules, double[,] WeightMatrix, List <ComponentStruct> VerticeMatrix, int[,] RelativeMotionMatrix,
out List <List <List <int> > > Communities, out List <double> Modularity, out List <double[, ]> SubGraphs, out List <List <ComponentStruct> > SubVerticeMs, out List <int[, ]> SubRelativeMs)
{
int NumOfModules = Modules.Count;
Communities = new List <List <List <int> > >();
Modularity = new List <double>();
SubGraphs = new List <double[, ]>();
SubVerticeMs = new List <List <ComponentStruct> >();;;
SubRelativeMs = new List <int[, ]>();
double[,] WMIntraModules;
int NumOfIteration = 5;
double CrossOverRatio = 0.4;
double MutationRatio = 0.05;
List <int> NumOfPopulation = new List <int>();
List <int> NumOfGeneration = new List <int>();
List <List <int> > SubModules;
double[] T_BestFitness;
List <int> sublist = new List <int>();
MPCCD.MPCCDSubGraph(Modules, WeightMatrix, VerticeMatrix, RelativeMotionMatrix, out WMIntraModules, out SubGraphs, out SubVerticeMs, out SubRelativeMs);
int x = 0;
for (int i = 0; i < NumOfModules; i++)
{
NumOfPopulation.Add((int)(Modules[x].Count / 2) + 1);
NumOfGeneration.Add(5 * Modules[x].Count);
x++;
}
// find the maximum modularity in each module
for (int i = 0; i < NumOfModules; i++)
{
GAModuleDiv.FindBestSolution_Multiple(SubGraphs[i], NumOfPopulation[i], NumOfGeneration[i], CrossOverRatio, MutationRatio, out SubModules, out T_BestFitness);
double XX = T_BestFitness.Max();
if (T_BestFitness.Max() > Alfa)
{
Communities.Add(SubModules.ToList());
Modularity.Add(T_BestFitness.Max());
}
else
{
SubModules.Clear();
for (int j = 0; j < Modules[i].Count; j++)
{
sublist.Add(j + 1);
}
SubModules.Add(sublist.ToList());
Communities.Add(SubModules);
Modularity.Add(T_BestFitness.Max());
sublist.Clear();
}
}
}
// Find the best module division result through multiple iterations
public static void FindBestSolution_Multiple(double[,] SymmWeightMatrix, int NumOfPopulation, int NumOfGeneration, double CrossOverRatio, double MutationRatio,
out List <List <int> > Modules, out double[] BestFitness)
{
int NumOfIteration = 5;
BestFitness = new double[NumOfGeneration];
Modules = new List <List <int> >();
for (int i = 0; i < NumOfIteration; i++)
{
double[] Fitness = new double[NumOfGeneration];
List <List <int> > Temp_Modules = new List <List <int> >();
GAModuleDiv.FindModule(NumOfPopulation, NumOfGeneration, CrossOverRatio, MutationRatio, SymmWeightMatrix, out Temp_Modules, out Fitness);
if (i > 0)
{
if (BestFitness.Max() < Fitness.Max())
{
Modules = Temp_Modules.ToList();
Array.Copy(Fitness, BestFitness, Fitness.Length);
}
}
else
{
Modules = Temp_Modules.ToList();
Array.Copy(Fitness, BestFitness, Fitness.Length);
}
/* foreach (List<int> x in Modules)
* {
* foreach (int xx in x)
* {
* Console.Write(" ");
* Console.Write(string.Join(" ", xx.ToString()));
* }
* Console.WriteLine("\n");
* }
*
* Console.WriteLine(BestFitness.Max().ToString());
* Console.WriteLine("\n");
*
*/
}
}
// find the optimal module division result
public static void FindModule(int NumOfPopulation, int NumOfGeneration, double CrossOverRatio, double MutationRatio, double[,] WeightMatrix, out List <List <int> > Modules, out double[] BestFitness)
{
int NumOfNode = WeightMatrix.GetLength(0);
Modules = new List <List <int> >();
BestFitness = new double[NumOfGeneration];
int[] BestGene = new int[NumOfNode]; // the best gene in one generation
double MaxFitness = 0;
int[] MaxGene = new int[NumOfNode]; // the max gene in one generation
int[,] InitialPop;
int[,] OldPop = new int[NumOfPopulation, NumOfNode];
int[,] NewPop = new int[NumOfPopulation, NumOfNode];
int[][] AdjacentNodes;
List <List <int> > Community = new List <List <int> >();
double[] Fitness;
double[] OldFitness = new double[NumOfPopulation];
double[] NewFitness = new double[NumOfPopulation];
double[] AveFitness = new double[NumOfGeneration];
double[] Temp_NormalizeFitness = new double[NumOfPopulation];
double[] Temp_Fitness = new double[NumOfPopulation];
int SelectionFather = 0, SelectionMother = 0, CrossOverPosition = 0, MutationPosition = 0;
double Temp_sum;
int NumMax = 0;
List <int> RowOfMax = new List <int>();
// Initialize the population
GAModuleDiv.InitializePopulation(NumOfNode, NumOfPopulation, WeightMatrix, out InitialPop, out AdjacentNodes);
GAModuleDiv.FitnessCalAll(InitialPop, AdjacentNodes, WeightMatrix, out Fitness);
Array.Copy(InitialPop, OldPop, NumOfPopulation * NumOfNode);
Array.Copy(Fitness, OldFitness, Fitness.Length);
Random rnd = new Random();
//find the best solution
for (int i = 0; i < NumOfGeneration; i++)
{
Temp_sum = 0;
MaxFitness = OldFitness.Max();
AveFitness[i] = OldFitness.Sum() / NumOfPopulation;
RowOfMax.Clear();
// find the row of the max
for (int j = 0; j < NumOfPopulation; j++)
{
if (MaxFitness == OldFitness[j])
{
RowOfMax.Add(j);
}
}
for (int k = 0; k < OldPop.GetLength(1); k++)
{
MaxGene[k] = OldPop[RowOfMax[0], k];
}
// copy the best gene to the first few rows
if (i > 0)
{
if (MaxFitness > BestFitness[i - 1])
{
BestFitness[i] = MaxFitness;
Array.Copy(MaxGene, BestGene, NumOfNode);
// copy the best rows
/* for (int k = 0; k < RowOfMax.Count; k++)
* {
* for (int x = 0; x < NumOfNode; x++)
* {
* NewPop[k, x] = OldPop[RowOfMax[k], x];
* }
* }
* NumMax = RowOfMax.Count;
* */
for (int x = 0; x < NumOfNode; x++)
{
NewPop[0, x] = OldPop[RowOfMax[0], x];
}
NumMax = 1;
}
else
{
BestFitness[i] = BestFitness[i - 1];
for (int x = 0; x < NumOfNode; x++)
{
NewPop[0, x] = OldPop[RowOfMax[0], x];
}
NumMax = 1;
}
}
else
{
BestFitness[i] = MaxFitness;
Array.Copy(MaxGene, BestGene, NumOfNode);
// copy the best rows
/*for (int k = 0; k < RowOfMax.Count; k++)
* {
* for (int x = 0; x < NumOfNode; x++)
* {
* NewPop[k, x] = OldPop[RowOfMax[k], x];
* }
* }
* NumMax = RowOfMax.Count;*/
for (int x = 0; x < NumOfNode; x++)
{
NewPop[0, x] = OldPop[RowOfMax[0], x];
}
NumMax = 1;
}
// selection, normalization
double[] Temp_NormalizeFitness1 = new double[NumOfPopulation];
for (int k = 0; k < NumOfPopulation; k++)
{
Temp_NormalizeFitness1[k] = OldFitness[k] + Math.Abs(OldFitness.Min()) + 0.01;
}
for (int k = 0; k < NumOfPopulation; k++)
{
Temp_NormalizeFitness[k] = Temp_NormalizeFitness1[k] / Temp_NormalizeFitness1.Sum();
}
for (int k = 0; k < NumOfPopulation; k++)
{
Temp_sum = Temp_sum + Temp_NormalizeFitness[k];
Temp_Fitness[k] = Temp_sum;
}
for (int j = NumMax; j < NumOfPopulation; j++)
{
double Delta = rnd.NextDouble();
for (int k = 0; k < NumOfPopulation; k++)
{
if (Delta < Temp_Fitness[k])
{
for (int x = 0; x < NumOfNode; x++)
{
NewPop[j, x] = OldPop[k, x];
}
SelectionFather = k;
break;
}
}
////////////////////////check NewPop from above to find why it does not work////////////////
// crossover
SelectionMother = rnd.Next(0, NumOfPopulation);
CrossOverPosition = rnd.Next(0, NumOfNode);
double Delta2 = rnd.NextDouble();
if (Delta2 <= CrossOverRatio)
{
for (int k = 0; k < CrossOverPosition; k++)
{
NewPop[j, k] = OldPop[SelectionFather, k];
}
for (int k = CrossOverPosition; k < NumOfNode; k++)
{
NewPop[j, k] = OldPop[SelectionMother, k];
}
}
// mutation
double Delta3 = rnd.NextDouble();
MutationPosition = rnd.Next(0, NumOfNode);
if (Delta3 <= MutationRatio)
{
NewPop[j, MutationPosition] = AdjacentNodes[MutationPosition][rnd.Next(0, AdjacentNodes[MutationPosition].GetLength(0))];
}
}
GAModuleDiv.FitnessCalAll(NewPop, AdjacentNodes, WeightMatrix, out NewFitness);
Array.Copy(NewFitness, OldFitness, NumOfPopulation);
Array.Copy(NewPop, OldPop, NumOfPopulation * NumOfNode);
Array.Clear(NewPop, 0, NumOfPopulation * NumOfNode);
Array.Clear(NewFitness, 0, NumOfPopulation);
}
GAModuleDiv.TransToCommunity(NumOfNode, BestGene, out Modules);
}