public void SetCentroidsAsMeansHighDimensionality()
{
foreach (Cluster Clust in clusters)
{
Clust.SetCentroidAsMean(true);
}
}
public void SetCentroidsAsMeans()
{
foreach (Cluster Clust in clusters)
{
Clust.SetCentroidAsMean();
}
}
/**
* ART 2A algorithm, inputs: examples and input parameters given by an user
* How exactly it is working can be found at www.fi.muni.cz/~xhudik/art/drafts
* \param sample set if input examples (Eks)
* \param par all input parameters set by an user or default
**/
public void art2A(List<Math.DynamicVector<float>> sample, in_param param, Clust results)
{
// prototype with highest score
Math.DynamicVector<float> P;
// list of all prototypes
List<Math.DynamicVector<float>> prot;
// the best representation of the prototypes of the whole history
List<Math.DynamicVector<float>> prot_best;
// sequences of samples Ek from which prototype has been created
// it is possible to reconstruct a prototype from the sequence
// defined in art_common.h
List<List<int>> prot_seq;
// the best representation of the prototypes of the whole history
List<List<int>> prot_seq_best;
// list of prototypes which were used already
List<Math.DynamicVector<float>> used;
used = new List<Math.DynamicVector<float>>();
prot = new List<Math.DynamicVector<float>>();
prot_seq = new List<List<int>>();
prot_best = new List<Math.DynamicVector<float>>();
prot_seq_best = new List<List<int>>();
float fluctuation = 100.0f;
// the lowest error of the whole history
// it is initialized as some impossible number(higher than 100% can't be), to avoid problems with first iteration
float fluctuation_best = 120.0f;
// how many times it run throughout the samples
int pass = 0;
// how many Ek's has been reassign to other cluster (prototype) in a previous pass (run)
List<bool> changed;
int i, j;
changed = new List<bool>();
for( i = 0; i < sample.Count; i++ )
{
changed.Add(true);
}
// do cycle while error is higher than the parameter -e or a number of passes is lower than the parameter -E
while((pass<param.pass)&&(fluctuation>param.error))
{
int number_changed;
// nullifying changed values
for( i = 0; i < sample.Count; i++ )
{
changed[i] = false;
}
// cycle for instances
for( i = 0; i < sample.Count; i++ )
{
// zeroing 'used' prototypes
used.Clear();
do
{
float score;
float alphaSum;
// find the best prototype for current Ek
P = bestPrototype2A(sample[i],prot,used);
// if there is no best prototype
if( P.array.Length == 0 )
{
int prototypeIndex;
//check if the instance is not included already in some other prototype
prototypeIndex = Common.instanceInSequence(prot_seq,i);
if( prototypeIndex != -1 )
{
//if so, remove it (recreate prototype--without the instance)
removeInstance(sample, i, prot, prototypeIndex, prot_seq, param.beta, param.vigilance);
}
createPrototype(sample, i, prot, prot_seq, param.vigilance);
changed[i] = true;
break;
}
// add P among 'used'
used.Add(P);
//count similarity between P and Ek (it is called "score") and alpha*sum_i Eki
score = countScore(P, sample[i]);
alphaSum = 0.0f;
for( j = 0; j < sample[i].array.Length; j++ )
{
alphaSum += param.alpha*sample[i][j];
}
// if similarity is sufficient -- sample[i] is member of the P
if( score >= alphaSum )
{
if( score >= param.vigilance )
{
int prot_index;
int Pindex;
// if the example Ek is already included in some prototype -- find it
prot_index = Common.instanceInSequence(prot_seq,i);
if( prot_index != -1 )
{
// test if the found prototype is not actual one (P) in that case try - go for another Ek
if( prot[prot_index] == P )
{
break;
}
else
{
// re-build prototype - without the sample
removeInstance(sample,i,prot,prot_index,prot_seq,param.beta,param.vigilance);
}
}
// find an index of P in prototypes
Pindex = Common.findItem(prot, P, true);
// add instance to the current prototype
addInstance(sample[i],prot[Pindex],param.beta);
prot_seq[Pindex].Add(i);
changed[i]=true;
break;
}
// try other best P
else
{
continue;
}
} //score=>alphaSize
else
{
int prot_index;
// if prototype is not enough similar to the example(sample[i]) then create a new prototype
// check if the instance is not already in some other prototype
prot_index=Common.instanceInSequence(prot_seq,i);
if( prot_index != -1 )
{
// if so, remove it (recreate prototype--without the instance)
removeInstance(sample,i,prot,prot_index,prot_seq,param.beta,param.vigilance);
}
createPrototype(sample,i,prot, prot_seq,param.vigilance);
changed[i] = true;
break;
}
}
while( prot.Count != sample.Count );
} // for sample
//count statistics for this pass
number_changed=0;
for( j = 0; j < changed.Count; j++ )
{
if( changed[j] )
{
number_changed++;
}
}
fluctuation = ((float)number_changed/sample.Count)*100;
pass++;
//cout << "Pass: "******", fluctuation: " << fluctuation << "%" << ", clusters: " << prot.size() << endl;
//test if this iteration has not lower error
if(fluctuation < fluctuation_best){
//if it is so - assign the new best results
prot_best = prot;
prot_seq_best = prot_seq;
fluctuation_best = fluctuation;
}
} // while
// create results
results.proto = prot_best;
results.proto_seq = prot_seq_best;
results.fluctuation = fluctuation_best;
}
public override void IterateOnce()
{
double AlphaI = 0;
double AlphaJ = 0;
double Beta = 0;
double Gamma = 0;
int Winner;
if (!stopped)
{
if (clusters.Count > 1)
{
DenseMatrix InterimMatrix = new DenseMatrix(currentDistanceMatrix.RowCount);
currentDistanceMatrix.CopyTo(InterimMatrix);
Cluster[] InterimClusters = new Cluster[clusters.Count];
Parallel.For(0, clusters.Count, i => {
InterimClusters[i] = (Cluster)clusters[i].Clone();
});
List <Cluster> InterimClusterList = InterimClusters.ToList <Cluster>();
Tuple <int, int, double> CurrentMinimumDistance = new Tuple <int, int, double>(0, 0, 0);
Parallel.ForEach <Tuple <int, int, double> >(currentDistanceMatrix.EnumerateIndexed(), CurrentTuple =>
{
if (CurrentTuple.Item3 == nextDistance)
{
CurrentMinimumDistance = CurrentTuple;
}
});
switch (style)
//this loops initialises coefficient values for the lance williams algorithm - this is within the iterate once method
//as some styles require iterative recalculation
{
case HACDistanceStyle.Centroid:
AlphaI = calculateMeanAlpha(clusters[CurrentMinimumDistance.Item1], clusters[CurrentMinimumDistance.Item2]);
AlphaJ = calculateMeanAlpha(clusters[CurrentMinimumDistance.Item2], clusters[CurrentMinimumDistance.Item1]);
Beta = calculateCentroidBeta(clusters[CurrentMinimumDistance.Item1], clusters[CurrentMinimumDistance.Item2]);
Gamma = 0;
break;
case HACDistanceStyle.CLink:
AlphaI = 0.5;
AlphaJ = 0.5;
Beta = 0;
Gamma = 0.5;
break;
case HACDistanceStyle.MeanDist:
AlphaI = calculateMeanAlpha(clusters[CurrentMinimumDistance.Item1], clusters[CurrentMinimumDistance.Item2]);
AlphaJ = calculateMeanAlpha(clusters[CurrentMinimumDistance.Item2], clusters[CurrentMinimumDistance.Item1]);
Beta = 0;
Gamma = 0;
break;
case HACDistanceStyle.SLink:
AlphaI = 0.5;
AlphaJ = 0.5;
Beta = 0;
Gamma = -0.5;
break;
case HACDistanceStyle.Ward:
//has to be implemented inside matrix update loop
//as requires values for cluster k
break;
}
//handle cluster merging in list
InterimClusterList[CurrentMinimumDistance.Item1].Merge(InterimClusterList[CurrentMinimumDistance.Item2]);
InterimClusterList.RemoveAt(CurrentMinimumDistance.Item2);
updateClusterIndexes(InterimClusterList);
//handles removal of subsumed cluster's distances from distance matrix
if (CurrentMinimumDistance.Item1 < CurrentMinimumDistance.Item2)
{
Winner = CurrentMinimumDistance.Item1;
}
else
{
//if the item 1 value is further down the distances matrix than the row/column to be removed
Winner = CurrentMinimumDistance.Item1 - 1;
}
InterimMatrix = (DenseMatrix)InterimMatrix.RemoveColumn(CurrentMinimumDistance.Item2).RemoveRow(CurrentMinimumDistance.Item2);
Parallel.For(0, InterimMatrix.RowCount, i =>
{
//recalculate distances from new cluster to all other clusters
if (style == HACDistanceStyle.Ward)
{
AlphaI = calculateWardAlpha(clusters[CurrentMinimumDistance.Item1], clusters[CurrentMinimumDistance.Item2], clusters[i]);
AlphaJ = calculateWardAlpha(clusters[CurrentMinimumDistance.Item2], clusters[CurrentMinimumDistance.Item1], clusters[i]);
Beta = calculateWardBeta(clusters[CurrentMinimumDistance.Item1], clusters[CurrentMinimumDistance.Item2], clusters[i]);
Gamma = 0;
}
double DistanceIJ = nextDistance;
double DistanceIK = currentDistanceMatrix[CurrentMinimumDistance.Item1, i];
double DistanceJK = currentDistanceMatrix[CurrentMinimumDistance.Item2, i];
InterimMatrix[Winner, i] = runLanceWilliamsEquation(DistanceIK, DistanceJK, DistanceIJ, AlphaI, AlphaJ, Beta, Gamma);
InterimMatrix[i, Winner] = InterimMatrix[Winner, i];
InterimMatrix[Winner, Winner] = artificialMax;
});
lastDistance = nextDistance;
nextDistance = InterimMatrix.Values.Min();
if (!stopped)
{
currentDistanceMatrix = (DenseMatrix)InterimMatrix.Clone();
double XValue = InterimClusterList[Winner].XValue;
Tuple <string, string, double, double> ThisDendroEntry = new Tuple <string, string, double, double>(clusters[CurrentMinimumDistance.Item1].ClusterID, clusters[CurrentMinimumDistance.Item2].ClusterID, lastDistance, XValue);
dendrogram.Add(ThisDendroEntry);
clusters = InterimClusterList;
iterator++;
stopped = StoppingConditionMet();
}
else
{
Parallel.ForEach(clusters, Clust => {
Clust.SetCentroidAsMean();
});
stopped = true;
}
}
else
{
stopped = true;
}
}
else
{
Parallel.ForEach(clusters, Clust => {
Clust.SetCentroidAsMean();
});
}
}