public virtual void TestGetSummaryForInstance(GraphicalModel[] dataset, ConcatVector weights)
{
LogLikelihoodDifferentiableFunction fn = new LogLikelihoodDifferentiableFunction();
foreach (GraphicalModel model in dataset)
{
double goldLogLikelihood = LogLikelihood(model, (ConcatVector)weights);
ConcatVector goldGradient = DefinitionOfDerivative(model, (ConcatVector)weights);
ConcatVector gradient = new ConcatVector(0);
double logLikelihood = fn.GetSummaryForInstance(model, (ConcatVector)weights, gradient);
NUnit.Framework.Assert.AreEqual(logLikelihood, Math.Max(1.0e-3, goldLogLikelihood * 1.0e-2), goldLogLikelihood);
// Our check for gradient similarity involves distance between endpoints of vectors, instead of elementwise
// similarity, b/c it can be controlled as a percentage
ConcatVector difference = goldGradient.DeepClone();
difference.AddVectorInPlace(gradient, -1);
double distance = Math.Sqrt(difference.DotProduct(difference));
// The tolerance here is pretty large, since the gold gradient is computed approximately
// 5% still tells us whether everything is working or not though
if (distance > 5.0e-2)
{
System.Console.Error.WriteLine("Definitional and calculated gradient differ!");
System.Console.Error.WriteLine("Definition approx: " + goldGradient);
System.Console.Error.WriteLine("Calculated: " + gradient);
}
NUnit.Framework.Assert.AreEqual(distance, 5.0e-2, 0.0);
}
}
/*
* @Theory
* public void testOptimizeLogLikelihoodWithConstraints(AbstractBatchOptimizer optimizer,
* @ForAll(sampleSize = 5) @From(LogLikelihoodFunctionTest.GraphicalModelDatasetGenerator.class) GraphicalModel[] dataset,
* @ForAll(sampleSize = 2) @From(LogLikelihoodFunctionTest.WeightsGenerator.class) ConcatVector initialWeights,
* @ForAll(sampleSize = 2) @InRange(minDouble = 0.0, maxDouble = 5.0) double l2regularization) throws Exception {
* Random r = new Random(42);
*
* int constraintComponent = r.nextInt(initialWeights.getNumberOfComponents());
* double constraintValue = r.nextDouble();
*
* if (r.nextBoolean()) {
* optimizer.addSparseConstraint(constraintComponent, 0, constraintValue);
* } else {
* optimizer.addDenseConstraint(constraintComponent, new double[]{constraintValue});
* }
*
* // Put in some constraints
*
* AbstractDifferentiableFunction<GraphicalModel> ll = new LogLikelihoodDifferentiableFunction();
* ConcatVector finalWeights = optimizer.optimize(dataset, ll, initialWeights, l2regularization, 1.0e-9, false);
* System.err.println("Finished optimizing");
*
* assertEquals(constraintValue, finalWeights.getValueAt(constraintComponent, 0), 1.0e-9);
*
* double logLikelihood = getValueSum(dataset, finalWeights, ll, l2regularization);
*
* // Check in a whole bunch of random directions really nearby that there is no nearby point with a higher log
* // likelihood
* for (int i = 0; i < 1000; i++) {
* int size = finalWeights.getNumberOfComponents();
* ConcatVector randomDirection = new ConcatVector(size);
* for (int j = 0; j < size; j++) {
* if (j == constraintComponent) continue;
* double[] dense = new double[finalWeights.isComponentSparse(j) ? finalWeights.getSparseIndex(j) + 1 : finalWeights.getDenseComponent(j).length];
* for (int k = 0; k < dense.length; k++) {
* dense[k] = (r.nextDouble() - 0.5) * 1.0e-3;
* }
* randomDirection.setDenseComponent(j, dense);
* }
*
* ConcatVector randomPerturbation = finalWeights.deepClone();
* randomPerturbation.addVectorInPlace(randomDirection, 1.0);
*
* double randomPerturbedLogLikelihood = getValueSum(dataset, randomPerturbation, ll, l2regularization);
*
* // Check that we're within a very small margin of error (around 3 decimal places) of the randomly
* // discovered value
*
* if (logLikelihood < randomPerturbedLogLikelihood - (1.0e-3 * Math.max(1.0, Math.abs(logLikelihood)))) {
* System.err.println("Thought optimal point was: " + logLikelihood);
* System.err.println("Discovered better point: " + randomPerturbedLogLikelihood);
* }
*
* assertTrue(logLikelihood >= randomPerturbedLogLikelihood - (1.0e-3 * Math.max(1.0, Math.abs(logLikelihood))));
* }
* }
*/
private double GetValueSum <T>(T[] dataset, ConcatVector weights, AbstractDifferentiableFunction <T> fn, double l2regularization)
{
double value = 0.0;
foreach (T t in dataset)
{
value += fn.GetSummaryForInstance(t, weights, new ConcatVector(0));
}
return((value / dataset.Length) - (weights.DotProduct(weights) * l2regularization));
}
public virtual void Run()
{
// Multithreading stuff
int numThreads = Math.Max(1, Runtime.GetRuntime().AvailableProcessors());
IList <T>[] queues = (IList <T>[])(new IList[numThreads]);
Random r = new Random();
// Allocate work to make estimated cost of work per thread as even as possible
if (this.useThreads)
{
for (int i = 0; i < numThreads; i++)
{
queues[i] = new List <T>();
}
int[] queueEstimatedTotalCost = new int[numThreads];
foreach (T datum in this.dataset)
{
int datumEstimatedCost = this.EstimateRelativeRuntime(datum);
int minCostQueue = 0;
for (int i_1 = 0; i_1 < numThreads; i_1++)
{
if (queueEstimatedTotalCost[i_1] < queueEstimatedTotalCost[minCostQueue])
{
minCostQueue = i_1;
}
}
queueEstimatedTotalCost[minCostQueue] += datumEstimatedCost;
queues[minCostQueue].Add(datum);
}
}
while (!this.isFinished)
{
// Collect log-likelihood and derivatives
long startTime = Runtime.CurrentTimeMillis();
long threadWaiting = 0;
ConcatVector derivative = this.weights.NewEmptyClone();
double logLikelihood = 0.0;
if (this.useThreads)
{
AbstractBatchOptimizer.GradientWorker[] workers = new AbstractBatchOptimizer.GradientWorker[numThreads];
Thread[] threads = new Thread[numThreads];
for (int i = 0; i < workers.Length; i++)
{
workers[i] = new AbstractBatchOptimizer.GradientWorker(this, i, numThreads, queues[i], this.fn, this.weights);
threads[i] = new Thread(workers[i]);
workers[i].jvmThreadId = threads[i].GetId();
threads[i].Start();
}
// This is for logging
long minFinishTime = long.MaxValue;
long maxFinishTime = long.MinValue;
// This is for re-balancing
long minCPUTime = long.MaxValue;
long maxCPUTime = long.MinValue;
int slowestWorker = 0;
int fastestWorker = 0;
for (int i_1 = 0; i_1 < workers.Length; i_1++)
{
try
{
threads[i_1].Join();
}
catch (Exception e)
{
throw new RuntimeInterruptedException(e);
}
logLikelihood += workers[i_1].localLogLikelihood;
derivative.AddVectorInPlace(workers[i_1].localDerivative, 1.0);
if (workers[i_1].finishedAtTime < minFinishTime)
{
minFinishTime = workers[i_1].finishedAtTime;
}
if (workers[i_1].finishedAtTime > maxFinishTime)
{
maxFinishTime = workers[i_1].finishedAtTime;
}
if (workers[i_1].cpuTimeRequired < minCPUTime)
{
fastestWorker = i_1;
minCPUTime = workers[i_1].cpuTimeRequired;
}
if (workers[i_1].cpuTimeRequired > maxCPUTime)
{
slowestWorker = i_1;
maxCPUTime = workers[i_1].cpuTimeRequired;
}
}
threadWaiting = maxFinishTime - minFinishTime;
// Try to reallocate work dynamically to minimize waiting on subsequent rounds
// Figure out the percentage of work represented by the waiting
double waitingPercentage = (double)(maxCPUTime - minCPUTime) / (double)maxCPUTime;
int needTransferItems = (int)Math.Floor(queues[slowestWorker].Count * waitingPercentage * 0.5);
for (int i_2 = 0; i_2 < needTransferItems; i_2++)
{
int toTransfer = r.NextInt(queues[slowestWorker].Count);
T datum = queues[slowestWorker][toTransfer];
queues[slowestWorker].Remove(toTransfer);
queues[fastestWorker].Add(datum);
}
// Check for user interrupt
if (this.isFinished)
{
return;
}
}
else
{
foreach (T datum in this.dataset)
{
System.Diagnostics.Debug.Assert((datum != null));
logLikelihood += this.fn.GetSummaryForInstance(datum, this.weights, derivative);
// Check for user interrupt
if (this.isFinished)
{
return;
}
}
}
logLikelihood /= this.dataset.Length;
derivative.MapInPlace(null);
long gradientComputationTime = Runtime.CurrentTimeMillis() - startTime;
// Regularization
logLikelihood = logLikelihood - (this.l2regularization * this.weights.DotProduct(this.weights));
derivative.AddVectorInPlace(this.weights, -2 * this.l2regularization);
// Zero out the derivative on the components we're holding fixed
foreach (AbstractBatchOptimizer.Constraint constraint in this._enclosing.constraints)
{
constraint.ApplyToDerivative(derivative);
}
// If our derivative is sufficiently small, we've converged
double derivativeNorm = derivative.DotProduct(derivative);
if (derivativeNorm < this.convergenceDerivativeNorm)
{
if (!this.quiet)
{
AbstractBatchOptimizer.log.Info("Derivative norm " + derivativeNorm + " < " + this.convergenceDerivativeNorm + ": quitting");
}
break;
}
// Do the actual computation
if (!this.quiet)
{
AbstractBatchOptimizer.log.Info("[" + gradientComputationTime + " ms, threads waiting " + threadWaiting + " ms]");
}
bool converged = this._enclosing.UpdateWeights(this.weights, derivative, logLikelihood, this.optimizationState, this.quiet);
// Apply constraints to the weights vector
foreach (AbstractBatchOptimizer.Constraint constraint_1 in this._enclosing.constraints)
{
constraint_1.ApplyToWeights(this.weights);
}
if (converged)
{
break;
}
}
lock (this.naturalTerminationBarrier)
{
Sharpen.Runtime.NotifyAll(this.naturalTerminationBarrier);
}
this.isFinished = true;
}
// This sets a gold observation for a model to use as training gold data
/// <summary>
/// Gets a summary of the log-likelihood of a singe model at a point
/// <p>
/// It assumes that the models have observations for training set as metadata in
/// LogLikelihoodDifferentiableFunction.OBSERVATION_FOR_TRAINING.
/// </summary>
/// <remarks>
/// Gets a summary of the log-likelihood of a singe model at a point
/// <p>
/// It assumes that the models have observations for training set as metadata in
/// LogLikelihoodDifferentiableFunction.OBSERVATION_FOR_TRAINING. The models can also have observations fixed in
/// CliqueTree.VARIABLE_OBSERVED_VALUE, but these will be considered fixed and will not be learned against.
/// </remarks>
/// <param name="model">the model to find the log-likelihood of</param>
/// <param name="weights">the weights to use</param>
/// <returns>the gradient and value of the function at that point</returns>
public override double GetSummaryForInstance(GraphicalModel model, ConcatVector weights, ConcatVector gradient)
{
double logLikelihood = 0.0;
CliqueTree.MarginalResult result = new CliqueTree(model, weights).CalculateMarginals();
// Cache everything in preparation for multiple redundant requests for feature vectors
foreach (GraphicalModel.Factor factor in model.factors)
{
factor.featuresTable.CacheVectors();
}
// Subtract log partition function
logLikelihood -= Math.Log(result.partitionFunction);
// Quit if we have an infinite partition function
if (double.IsInfinite(logLikelihood))
{
return(0.0);
}
// Add the determined assignment by training values
foreach (GraphicalModel.Factor factor_1 in model.factors)
{
// Find the assignment, taking both fixed and training observed variables into account
int[] assignment = new int[factor_1.neigborIndices.Length];
for (int i = 0; i < assignment.Length; i++)
{
int deterministicValue = GetDeterministicAssignment(result.marginals[factor_1.neigborIndices[i]]);
if (deterministicValue != -1)
{
assignment[i] = deterministicValue;
}
else
{
int trainingObservation = System.Convert.ToInt32(model.GetVariableMetaDataByReference(factor_1.neigborIndices[i])[LogLikelihoodDifferentiableFunction.VariableTrainingValue]);
assignment[i] = trainingObservation;
}
}
ConcatVector features = factor_1.featuresTable.GetAssignmentValue(assignment).Get();
// Add the log-likelihood from this observation to the log-likelihood
logLikelihood += features.DotProduct(weights);
// Add the vector from this observation to the gradient
gradient.AddVectorInPlace(features, 1.0);
}
// Take expectations over features given marginals
// NOTE: This is extremely expensive. Not sure what to do about that
foreach (GraphicalModel.Factor factor_2 in model.factors)
{
// OPTIMIZATION:
// Rather than use the standard iterator, which creates lots of int[] arrays on the heap, which need to be GC'd,
// we use the fast version that just mutates one array. Since this is read once for us here, this is ideal.
IEnumerator <int[]> fastPassByReferenceIterator = factor_2.featuresTable.FastPassByReferenceIterator();
int[] assignment = fastPassByReferenceIterator.Current;
while (true)
{
// calculate assignment prob
double assignmentProb = result.jointMarginals[factor_2].GetAssignmentValue(assignment);
// subtract this feature set, weighted by the probability of the assignment
if (assignmentProb > 0)
{
gradient.AddVectorInPlace(factor_2.featuresTable.GetAssignmentValue(assignment).Get(), -assignmentProb);
}
// This mutates the assignment[] array, rather than creating a new one
if (fastPassByReferenceIterator.MoveNext())
{
fastPassByReferenceIterator.Current;
}
else
{
break;
}
}
}
// Uncache everything, now that the computations have completed
foreach (GraphicalModel.Factor factor_3 in model.factors)
{
factor_3.featuresTable.ReleaseCache();
}
return(logLikelihood);
}
