public override IPeakScoringModel Train(IList <IList <float[]> > targets, IList <IList <float[]> > decoys, LinearModelParams initParameters,
bool includeSecondBest = false, bool preTrain = true, IProgressMonitor progressMonitor = null)
{
return(ChangeProp(ImClone(this), im =>
{
int nWeights = initParameters.Weights.Count;
var weights = new double [nWeights];
for (int i = 0; i < initParameters.Weights.Count; ++i)
{
weights[i] = double.IsNaN(initParameters.Weights[i]) ? double.NaN : DEFAULT_WEIGHTS[i];
}
var parameters = new LinearModelParams(weights);
ScoredGroupPeaksSet decoyTransitionGroups = new ScoredGroupPeaksSet(decoys);
ScoredGroupPeaksSet targetTransitionGroups = new ScoredGroupPeaksSet(targets);
targetTransitionGroups.ScorePeaks(parameters.Weights);
if (includeSecondBest)
{
ScoredGroupPeaksSet secondBestTransitionGroups;
targetTransitionGroups.SelectTargetsAndDecoys(out targetTransitionGroups, out secondBestTransitionGroups);
foreach (var secondBestGroup in secondBestTransitionGroups.ScoredGroupPeaksList)
{
decoyTransitionGroups.Add(secondBestGroup);
}
}
decoyTransitionGroups.ScorePeaks(parameters.Weights);
im.UsesDecoys = decoys.Count > 0;
im.UsesSecondBest = includeSecondBest;
im.Parameters = parameters.RescaleParameters(decoyTransitionGroups.Mean, decoyTransitionGroups.Stdev);
}));
}
public void SelectTargetsAndDecoys(out ScoredGroupPeaksSet targetScoredGroupPeaksSet, out ScoredGroupPeaksSet decoyScoredGroupPeaksSet)
{
targetScoredGroupPeaksSet = new ScoredGroupPeaksSet();
decoyScoredGroupPeaksSet = new ScoredGroupPeaksSet();
foreach (var scoredGroupPeaks in _scoredGroupPeaksList)
{
var secondHighestPeak = scoredGroupPeaks.SecondHighestPeak;
if (!secondHighestPeak.IsEmpty)
{
var decoyScoredGroupPeaks = new ScoredGroupPeaks();
decoyScoredGroupPeaks.Add(secondHighestPeak);
decoyScoredGroupPeaksSet.Add(decoyScoredGroupPeaks);
}
// Copy all other peaks to target.
var targetScoredGroupPeaks = new ScoredGroupPeaks();
foreach (var peak in scoredGroupPeaks.ScoredPeaks)
{
if (!ReferenceEquals(peak.Features, secondHighestPeak.Features))
{
targetScoredGroupPeaks.Add(peak);
}
}
targetScoredGroupPeaksSet.Add(targetScoredGroupPeaks);
}
}
public void SelectTargetsAndDecoys(out ScoredGroupPeaksSet targetScoredGroupPeaksSet, out ScoredGroupPeaksSet decoyScoredGroupPeaksSet)
{
targetScoredGroupPeaksSet = new ScoredGroupPeaksSet();
decoyScoredGroupPeaksSet = new ScoredGroupPeaksSet();
foreach (var scoredGroupPeaks in _scoredGroupPeaksList)
{
var secondHighestPeak = scoredGroupPeaks.SecondHighestPeak;
if (secondHighestPeak != null)
{
var decoyScoredGroupPeaks = new ScoredGroupPeaks();
decoyScoredGroupPeaks.Add(secondHighestPeak);
decoyScoredGroupPeaksSet.Add(decoyScoredGroupPeaks);
}
// Copy all other peaks to target.
var targetScoredGroupPeaks = new ScoredGroupPeaks();
foreach (var peak in scoredGroupPeaks.ScoredPeaks)
{
if (peak != secondHighestPeak)
{
targetScoredGroupPeaks.Add(peak);
}
}
targetScoredGroupPeaksSet.Add(targetScoredGroupPeaks);
}
}
private const int MAX_TRAINING_MEMORY = 512 * 1024 * 1024; // 512 MB
/// <summary>
/// Calculate new weight factors for one iteration of the refinement process. This is the heart
/// of the MProphet algorithm.
/// </summary>
/// <param name="iteration">Iteration number (special processing happens for iteration 0).</param>
/// <param name="targetTransitionGroups">Target transition groups.</param>
/// <param name="decoyTransitionGroups">Decoy transition groups.</param>
/// <param name="includeSecondBest">Include the second best peaks in the targets as additional decoys?</param>
/// <param name="weights">Array of weights per calculator.</param>
/// <param name="decoyMean">Output mean of decoy transition groups.</param>
/// <param name="decoyStdev">Output standard deviation of decoy transition groups.</param>
/// <param name="colinearWarning">Set to true if colinearity was detected.</param>
private void CalculateWeights(
int iteration,
ScoredGroupPeaksSet targetTransitionGroups,
ScoredGroupPeaksSet decoyTransitionGroups,
bool includeSecondBest,
double[] weights,
out double decoyMean,
out double decoyStdev,
ref bool colinearWarning)
{
if (includeSecondBest)
{
ScoredGroupPeaksSet secondBestTransitionGroups;
targetTransitionGroups.SelectTargetsAndDecoys(out targetTransitionGroups, out secondBestTransitionGroups);
foreach (var secondBestGroup in secondBestTransitionGroups.ScoredGroupPeaksList)
{
decoyTransitionGroups.Add(secondBestGroup);
}
}
// Select true target peaks using a q-value cutoff filter.
var qValueCutoff = (iteration == 0 ? 0.15 : 0.02);
var truePeaks = targetTransitionGroups.SelectTruePeaks(qValueCutoff, Lambda, decoyTransitionGroups);
var decoyPeaks = decoyTransitionGroups.SelectMaxPeaks();
// Omit first feature during first iteration, since it is used as the initial score value.
weights[0] = (iteration == 0) ? double.NaN : 0;
var featureCount = weights.Count(w => !double.IsNaN(w));
// Copy target and decoy peaks to training data array.
int totalTrainingPeaks = truePeaks.Count + decoyTransitionGroups.Count;
// Calculate the maximum number of training peaks (8 bytes per score - double, featurCount + 1 scores per peak)
int maxTrainingPeaks = MAX_TRAINING_MEMORY / 8 / (featureCount + 1);
var trainData = new double[Math.Min(totalTrainingPeaks, maxTrainingPeaks), featureCount + 1];
if (totalTrainingPeaks < maxTrainingPeaks)
{
for (int i = 0; i < truePeaks.Count; i++)
{
CopyToTrainData(truePeaks[i].Features, trainData, weights, i, 1);
}
for (int i = 0; i < decoyPeaks.Count; i++)
{
CopyToTrainData(decoyPeaks[i].Features, trainData, weights, i + truePeaks.Count, 0);
}
}
else
{
double proportionTrue = truePeaks.Count * 1.0 / totalTrainingPeaks;
int truePeakCount = (int)Math.Round(maxTrainingPeaks * proportionTrue);
int i = 0;
foreach (var peak in truePeaks.RandomOrder())
{
if (i < truePeakCount)
{
CopyToTrainData(peak.Features, trainData, weights, i, 1);
}
else
{
break;
}
i++;
}
int decoyPeakCount = maxTrainingPeaks - truePeakCount;
i = 0;
foreach (var peak in decoyPeaks.RandomOrder())
{
if (i < decoyPeakCount)
{
CopyToTrainData(peak.Features, trainData, weights, i + truePeakCount, 0);
}
else
{
break;
}
i++;
}
}
// Use Linear Discriminant Analysis to find weights that separate true and decoy peak scores.
int info;
double[] weightsFromLda;
alglib.fisherlda(
trainData,
trainData.GetLength(0),
trainData.GetLength(1) - 1,
2,
out info,
out weightsFromLda);
// Check for colinearity.
if (info == 2)
{
colinearWarning = true;
}
// Unpack weights array.
for (int i = 0, j = 0; i < weights.Length; i++)
{
if (!double.IsNaN(weights[i]))
{
weights[i] = weightsFromLda[j++];
}
}
// Recalculate all peak scores.
targetTransitionGroups.ScorePeaks(weights);
decoyTransitionGroups.ScorePeaks(weights);
// If the mean target score is less than the mean decoy score, then the
// weights came out negative, and all the weights and scores must be negated to
// restore the proper ordering.
if (targetTransitionGroups.Mean < decoyTransitionGroups.Mean)
{
for (int i = 0; i < weights.Length; i++)
{
weights[i] *= -1;
}
targetTransitionGroups.ScorePeaks(weights);
decoyTransitionGroups.ScorePeaks(weights);
}
decoyMean = decoyTransitionGroups.Mean;
decoyStdev = decoyTransitionGroups.Stdev;
}
private const int MAX_TRAINING_MEMORY = 512 * 1024 * 1024; // 512 MB
/// <summary>
/// Calculate new weight factors for one iteration of the refinement process. This is the heart
/// of the MProphet algorithm.
/// </summary>
/// <param name="documentPath">The path to the current document for writing score distributions</param>
/// <param name="targetTransitionGroups">Target transition groups.</param>
/// <param name="decoyTransitionGroups">Decoy transition groups.</param>
/// <param name="includeSecondBest">Include the second best peaks in the targets as additional decoys?</param>
/// <param name="nonParametricPValues">Non-parametric p values used in selecting true peaks if true</param>
/// <param name="qValueCutoff">The q value cut-off for true peaks in the training</param>
/// <param name="weights">Array of weights per calculator.</param>
/// <param name="decoyMean">Output mean of decoy transition groups.</param>
/// <param name="decoyStdev">Output standard deviation of decoy transition groups.</param>
/// <param name="colinearWarning">Set to true if colinearity was detected.</param>
private int CalculateWeights(string documentPath,
ScoredGroupPeaksSet targetTransitionGroups,
ScoredGroupPeaksSet decoyTransitionGroups,
bool includeSecondBest,
bool nonParametricPValues,
double qValueCutoff,
double[] weights,
out double decoyMean,
out double decoyStdev,
ref bool colinearWarning)
{
if (includeSecondBest)
{
ScoredGroupPeaksSet secondBestTransitionGroups;
targetTransitionGroups.SelectTargetsAndDecoys(out targetTransitionGroups, out secondBestTransitionGroups);
foreach (var secondBestGroup in secondBestTransitionGroups.ScoredGroupPeaksList)
{
decoyTransitionGroups.Add(secondBestGroup);
}
}
// Select true target peaks using a q-value cutoff filter.
var truePeaks = targetTransitionGroups.SelectTruePeaks(decoyTransitionGroups, qValueCutoff, Lambda, nonParametricPValues);
var decoyPeaks = decoyTransitionGroups.SelectMaxPeaks();
WriteDistributionInfo(documentPath, targetTransitionGroups, decoyTransitionGroups); // Only if asked to do so in command-line arguments
// Better to let a really poor model through for the user to see than to give an error message here
if (((double)truePeaks.Count) * 10 * 1000 < decoyPeaks.Count) // Targets must be at least 0.01% of decoys (still rejects zero)
{
throw new InvalidDataException(string.Format(Resources.MProphetPeakScoringModel_CalculateWeights_Insufficient_target_peaks___0__with__1__decoys__detected_at__2___FDR_to_continue_training_, truePeaks.Count, decoyPeaks.Count, qValueCutoff * 100));
}
if (((double)decoyPeaks.Count) * 1000 < truePeaks.Count) // Decoys must be at least 0.1% of targets
{
throw new InvalidDataException(string.Format(Resources.MProphetPeakScoringModel_CalculateWeights_Insufficient_decoy_peaks___0__with__1__targets__to_continue_training_, decoyPeaks.Count, truePeaks.Count));
}
var featureCount = weights.Count(w => !double.IsNaN(w));
// Copy target and decoy peaks to training data array.
int totalTrainingPeaks = truePeaks.Count + decoyTransitionGroups.Count;
// Calculate the maximum number of training peaks (8 bytes per score - double, featurCount + 1 scores per peak)
int maxTrainingPeaks = MAX_TRAINING_MEMORY / 8 / (featureCount + 1);
var trainData = new double[Math.Min(totalTrainingPeaks, maxTrainingPeaks), featureCount + 1];
if (totalTrainingPeaks < maxTrainingPeaks)
{
for (int i = 0; i < truePeaks.Count; i++)
{
CopyToTrainData(truePeaks[i].Features, trainData, weights, i, 1);
}
for (int i = 0; i < decoyPeaks.Count; i++)
{
CopyToTrainData(decoyPeaks[i].Features, trainData, weights, i + truePeaks.Count, 0);
}
}
else
{
double proportionTrue = truePeaks.Count * 1.0 / totalTrainingPeaks;
int truePeakCount = (int)Math.Round(maxTrainingPeaks * proportionTrue);
int i = 0;
foreach (var peak in truePeaks.RandomOrder(ArrayUtil.RANDOM_SEED))
{
if (i < truePeakCount)
{
CopyToTrainData(peak.Features, trainData, weights, i, 1);
}
else
{
break;
}
i++;
}
int decoyPeakCount = maxTrainingPeaks - truePeakCount;
i = 0;
foreach (var peak in decoyPeaks.RandomOrder(ArrayUtil.RANDOM_SEED))
{
if (i < decoyPeakCount)
{
CopyToTrainData(peak.Features, trainData, weights, i + truePeakCount, 0);
}
else
{
break;
}
i++;
}
}
// Use Linear Discriminant Analysis to find weights that separate true and decoy peak scores.
int info;
double[] weightsFromLda;
alglib.fisherlda(
trainData,
trainData.GetLength(0),
trainData.GetLength(1) - 1,
2,
out info,
out weightsFromLda);
// Check for colinearity.
if (info == 2)
{
colinearWarning = true;
}
// Unpack weights array.
for (int i = 0, j = 0; i < weights.Length; i++)
{
if (!double.IsNaN(weights[i]))
{
weights[i] = weightsFromLda[j++];
}
}
// Recalculate all peak scores.
targetTransitionGroups.ScorePeaks(weights);
decoyTransitionGroups.ScorePeaks(weights);
// If the mean target score is less than the mean decoy score, then the
// weights came out negative, and all the weights and scores must be negated to
// restore the proper ordering.
if (targetTransitionGroups.Mean < decoyTransitionGroups.Mean)
{
for (int i = 0; i < weights.Length; i++)
{
weights[i] *= -1;
}
targetTransitionGroups.ScorePeaks(weights);
decoyTransitionGroups.ScorePeaks(weights);
}
decoyMean = decoyTransitionGroups.Mean;
decoyStdev = decoyTransitionGroups.Stdev;
return(truePeaks.Count);
}