private void CrossEntropy2(ref StateDependentGammaInfo gammaInfo, double tempRareEvent)
{
IBoolean tempRareEventExpression = new EqualTo(_reExpression, new ConstantValue(tempRareEvent));
var startPC = Enumerable.Repeat(1.0, _reactions.NumReactions).ToArray();
var endPC = new double[_reactions.NumReactions];
var rateUpdateMethod = new ReactionRatesUpdateMethod(_reactions.UpdateRatesIteration2);
for (int i = 0; i < _crossEntropyRuns; i++)
{
StartRealization();
var n = new List <int[]>();
var lambda = new List <double[]>();
double weight = 1.0;
for (int j = 0; j < _reactions.NumReactions; j++)
{
n.Add(new int[(gammaInfo.IntermediatePropensityCutoff[j]).Length + 1]);
lambda.Add(new double[(gammaInfo.IntermediatePropensityCutoff[j]).Length + 1]);
}
while (CurrentTime < duration)
{
if (tempRareEventExpression.Value)
{
gammaInfo.UpdateGamma(weight, n, lambda);
break;
}
GenericStepOnce(ref weight, gammaInfo, ref startPC, ref endPC, ref n, ref lambda, rateUpdateMethod, ref _binIndex, null);
}
}
gammaInfo.SetIntermediateGamma();
}
protected virtual void GenericStepOnce(ref double weight, StateDependentGammaInfo tempGammaInfo, ref double[] startPC, ref double[] endPC, ref List <int[]> tempN, ref List <double[]> tempLambda, ReactionRatesUpdateMethod reactionRateUpdateMethod, ref int[] indexArray, BinEdgesUpdateMethod binEdgesUpdateMethod)
{
double b0 = reactionRateUpdateMethod(tempGammaInfo.IntermediateGamma, tempGammaInfo.IntermediatePropensityCutoff, tempGammaInfo.PreviousIntermediatePropensityCutoff, ref _gammaIndex, ref _binIndex);
double a0 = _reactions.CurrentRates.Sum();
if (b0 > 0.0)
{
double r = rng.GenerateUniformOO();
double tau = Math.Log(1.0 / r) / b0;
CurrentTime += tau;
if (CurrentTime < duration)
{
int mu = SelectAndFireReaction(b0);
AccumulateBiasingParameters(ref tempN, ref tempLambda, tau, mu, indexArray);
binEdgesUpdateMethod?.Invoke(ref startPC, ref endPC, a0, mu);
weight *= Math.Exp((b0 - a0) * tau) / tempGammaInfo.IntermediateGamma[mu][_gammaIndex[mu]];
}
}
else
{
CurrentTime = duration;
}
}
private void UpdateBiasingParameters(StateDependentGammaInfo gammaInfo, double intermediateRareEvent)
{
_biasingParameters.RareEvent.Thresholds.Add(intermediateRareEvent);
for (int i = 0; i < _reactions.Reactions.Count; i++)
{
var tempRareEventInfo = new BiasingParameters.RareEventInfo {
BinCount = gammaInfo.IntermediateGamma[i].Count()
};
gammaInfo.IntermediateGamma[i].CopyTo(tempRareEventInfo.Gammas, 0);
gammaInfo.IntermediatePropensityCutoff[i].CopyTo(tempRareEventInfo.Thresholds, 0);
UpdateReactionInfo(tempRareEventInfo, i);
}
}
private void RunCrossEntropy()
{
int iter = 1;
var gammaInfo = new StateDependentGammaInfo(_reactions.NumReactions, _gammaSize, _binCountThreshold);
double intermediateRareEvent = _rareEventType == 1 ? 0 : _reExpression.Value;
while (Math.Abs(intermediateRareEvent - _rareEventValue) > double.Epsilon && iter < 15)
{
Console.WriteLine("\nCross Entropy iteration " + iter + ":");
var startPC = Enumerable.Repeat(1.0, _reactions.NumReactions).ToArray();
var endPC = new double[_reactions.NumReactions];
bool rareEventFlag = false;
gammaInfo.UpdateStructure();
CrossEntropy1(ref gammaInfo, ref intermediateRareEvent, ref startPC, ref endPC, ref rareEventFlag);
Console.WriteLine(" Intermediate rare event: " + intermediateRareEvent);
if (rareEventFlag)
{
Console.WriteLine("\nReached the rare event. Exiting multilevel cross entropy simulation...");
UpdateBiasingParameters(gammaInfo, intermediateRareEvent);
break;
}
gammaInfo.UpdatePropensityCutoff(startPC, endPC);
gammaInfo.UpdateStructure();
CrossEntropy2(ref gammaInfo, intermediateRareEvent);
gammaInfo.MergeBins();
UpdateBiasingParameters(gammaInfo, intermediateRareEvent);
iter++;
}
_biasingParameters.WriteParametersToJsonFile(modelInfo.Name + "_sdwSSA_CEinfo.json");
if (iter == 15)
{
throw new ApplicationException("multilevel cross entropy did not converged in 15 iterations.");
}
for (int i = 0; i < _reactions.NumReactions; i++)
{
_gamma[i] = gammaInfo.IntermediateGamma[i];
_propensityCutoff[i] = gammaInfo.IntermediatePropensityCutoff[i];
}
}
private void CrossEntropy1(ref StateDependentGammaInfo gammaInfo, ref double intermediateRareEvent, ref double[] startPC, ref double[] endPC, ref bool rareEventFlag)
{
var maxRareEventValue = new double[_crossEntropyRuns];
int counter = 0;
var rateUpdateMethod = new ReactionRatesUpdateMethod(_reactions.UpdateRatesIteration1);
var binEdgesUpdateMethod = new BinEdgesUpdateMethod(UpdateBinEdges);
for (int i = 0; i < _crossEntropyRuns; i++)
{
StartRealization();
double currentMin = _rareEventType * (_rareEventValue - _reExpression.Value);
var n = new List <int[]>();
var lambda = new List <double[]>();
double weight = 1.0;
for (int j = 0; j < _reactions.NumReactions; j++)
{
n.Add(new int[(gammaInfo.IntermediatePropensityCutoff[j]).Length + 1]);
lambda.Add(new double[(gammaInfo.IntermediatePropensityCutoff[j]).Length + 1]);
}
while (CurrentTime < duration)
{
if (_rareEventTest.Value)
{
counter++;
gammaInfo.UpdateGamma(weight, n, lambda);
break;
}
GenericStepOnce(ref weight, gammaInfo, ref startPC, ref endPC, ref n, ref lambda, rateUpdateMethod, ref _gammaIndex, binEdgesUpdateMethod);
double tempMin = _rareEventType * (_rareEventValue - _reExpression.Value);
currentMin = Math.Min(currentMin, tempMin);
}
maxRareEventValue[i] = currentMin;
}
Array.Sort(maxRareEventValue);
double ireComp = maxRareEventValue[(int)Math.Ceiling(_crossEntropyRuns * _crossEntropyThreshold)];
double pastIntermediateRareEvent = intermediateRareEvent;
intermediateRareEvent = ireComp < 0 ? _rareEventValue : _rareEventType * (_rareEventValue - ireComp);
if ((pastIntermediateRareEvent - intermediateRareEvent) * _rareEventType >= 0)
{
_crossEntropyThreshold *= 0.8;
Console.WriteLine("Cross entropy threshold changed to : " + _crossEntropyThreshold);
if (_crossEntropyThreshold * _crossEntropyRuns * 0.8 < _crossEntropyMinDataSize)
{
_crossEntropyRuns = (int)Math.Ceiling(_crossEntropyMinDataSize / _crossEntropyThreshold);
Console.WriteLine("Number of cross entropy simulations changed to : " + _crossEntropyRuns);
}
}
if (intermediateRareEvent >= _rareEventValue && counter >= (int)(_crossEntropyRuns * _crossEntropyThreshold))
{
rareEventFlag = true;
gammaInfo.SetIntermediateGamma();
}
}
