crf2.java

这是一个matlab的java实现。里面有许多内容。请大家慢慢捉摸。

		// terms of "weights", not "costs".
		
		public Matrix getParameters (Matrix m)
		{
			assert (m instanceof DenseVector && ((Vector)m).singleSize() == numParameters);
			DenseVector parameters = (DenseVector)m;
			int pi = 0;
			for (int i = 0; i < numStates(); i++) {
				State s = (State) getState (i);
				parameters.setValue (pi++, -s.initialCost);
				parameters.setValue (pi++, -s.finalCost);
			}
			for (int i = 0; i < weights.length; i++) {
				parameters.setValue (pi++, defaultWeights[i]);
				int nl = weights[i].numLocations();
				for (int j = 0; j < nl; j++)
					parameters.setValue (pi++, weights[i].valueAtLocation(j));
			}
			return parameters;
		}

		public void setParameters (Matrix m) {
			assert (m instanceof DenseVector && ((DenseVector)m).singleSize() == numParameters);
			cachedCostStale = cachedGradientStale = true;
			DenseVector parameters = (DenseVector)m;
			int pi = 0;
			for (int i = 0; i < numStates(); i++) {
				State s = (State) getState (i);
				s.initialCost = -parameters.value (pi++);
				s.finalCost = -parameters.value (pi++);
			}
			for (int i = 0; i < weights.length; i++) {
				defaultWeights[i] = parameters.value (pi++);
				int nl = weights[i].numLocations();
				for (int j = 0; j < nl; j++)
					weights[i].setValueAtLocation (j, parameters.value (pi++));
			}
		}

		public double getParameter (int[] indices) {
			assert (indices.length == 1);
			int index = indices[0];
			int numStateParms = 2 * numStates();
			if (index < numStateParms) {
				State s = (State)getState(index / 2);
				if (index % 2 == 0)
					return -s.initialCost;
				else
					return -s.finalCost;
			} else {
				index -= numStateParms;
				for (int i = 0; i < weights.length; i++) {
					if (index == 0)
						return defaultWeights[i];
					index--;
					if (index < weights[i].numLocations())
						return weights[i].valueAtLocation (index);
					else
						index -= weights[i].numLocations();
				}
				throw new IllegalArgumentException ("index too high = "+indices[0]);
			}
		}

		public void setParameter (int[] indices, double value) {
			cachedCostStale = cachedGradientStale = true;
			assert (indices.length == 1);
			int index = indices[0];
			int numStateParms = 2 * numStates();
			if (index < numStateParms) {
				State s = (State)getState(index / 2);
				if (index % 2 == 0)
					s.initialCost = -value;
				else
					s.finalCost = -value;
			} else {
				index -= numStateParms;
				for (int i = 0; i < weights.length; i++) {
					if (index == 0) {
						defaultWeights[i] = value;
						return;
					} else
						index--;
					if (index < weights[i].numLocations()) {
						weights[i].setValueAtLocation (index, value);
					} else
						index -= weights[i].numLocations();
				}
				throw new IllegalArgumentException ("index too high = "+indices[0]);
			}
		}


		// Minus log probability of the training sequence labels
		public double getCost ()
		{
			if (cachedCostStale) {
				cachedCost = 0;
				cachedGradientStale = true;
				// Instance costs must either always or never be included in
				// the total costs; we can't just sometimes skip a cost
				// because it is infinite, this throws off the total costs.
				boolean initializingInfiniteCosts = false;
				if (infiniteCosts == null) {
					infiniteCosts = new BitSet ();
					initializingInfiniteCosts = true;
				}
				// Clear the sufficient statistics that we are about to fill
				for (int i = 0; i < numStates(); i++) {
					State s = (State)getState(i);
					s.initialExpectation = 0;
					s.finalExpectation = 0;
				}
				for (int i = 0; i < weights.length; i++) {
					expectations[i].setAll (0.0);
					defaultExpectations[i] = 0.0;
				}
				// Calculate the cost of each instance, and also fill in expectations
				double unlabeledCost, labeledCost, cost;
				for (int ii = 0; ii < trainingSet.size(); ii++) {
					Instance instance = trainingSet.getInstance(ii);
					FeatureVectorSequence input = (FeatureVectorSequence) instance.getData();
					FeatureSequence output = (FeatureSequence) instance.getTarget();
					labeledCost = forwardBackward (input, output, false).getCost();
					if (Double.isInfinite (labeledCost))
						logger.warning (instance.getName().toString() + " has infinite labeled cost.\n"
														+(instance.getSource() != null ? instance.getSource() : ""));
					unlabeledCost = forwardBackward (input, true).getCost ();
					if (Double.isInfinite (unlabeledCost))
						logger.warning (instance.getName().toString() + " has infinite unlabeled cost.\n"
														+(instance.getSource() != null ? instance.getSource() : ""));
					// Here cost is -log(conditional probability correct label sequence)
					cost = labeledCost - unlabeledCost;
					logger.info("Instance "+ii+" CRF.MinimizableCRF.getCost = "+cost);
					if (Double.isInfinite(cost)) {
						logger.warning (instance.getName().toString() + " has infinite cost; skipping.");
						if (initializingInfiniteCosts)
							infiniteCosts.set (ii);
						else if (!infiniteCosts.get(ii))
							throw new IllegalStateException ("Instance i used to have non-infinite cost, "
																							 +"but now it has infinite cost.");
						continue;
					} else {
						cachedCost += cost;
					}
				}
				
				// Incorporate prior on parameters
				if (usingHyperbolicPrior) {
					// Hyperbolic prior
					for (int i = 0; i < numStates(); i++) {
						State s = (State) getState (i);
						if (!Double.isInfinite(s.initialCost))
							cachedCost += (hyperbolicPriorSlope / hyperbolicPriorSharpness
														 * Math.log (Maths.cosh (hyperbolicPriorSharpness * -s.initialCost)));
						if (!Double.isInfinite(s.finalCost))
							cachedCost += (hyperbolicPriorSlope / hyperbolicPriorSharpness
														 * Math.log (Maths.cosh (hyperbolicPriorSharpness * -s.finalCost)));
					}
					for (int i = 0; i < weights.length; i++) {
						cachedCost += (hyperbolicPriorSlope / hyperbolicPriorSharpness
													 * Math.log (Maths.cosh (hyperbolicPriorSharpness * defaultWeights[i])));
						for (int j = 0; j < weights[i].numLocations(); j++) {
							double w = weights[i].valueAtLocation(j);
							if (!Double.isInfinite(w))
								cachedCost += (hyperbolicPriorSlope / hyperbolicPriorSharpness
															 * Math.log (Maths.cosh (hyperbolicPriorSharpness * w)));
						}
					}
				} else {
					// Gaussian prior
					double priorDenom = 2 * gaussianPriorVariance;
					for (int i = 0; i < numStates(); i++) {
						State s = (State) getState (i);
						if (!Double.isInfinite(s.initialCost))
							cachedCost += s.initialCost * s.initialCost / priorDenom;
						if (!Double.isInfinite(s.finalCost))
							cachedCost += s.finalCost * s.finalCost / priorDenom;
					}
					for (int i = 0; i < weights.length; i++) {
						if (!Double.isInfinite(defaultWeights[i]))
							cachedCost += defaultWeights[i] * defaultWeights[i] / priorDenom;
						for (int j = 0; j < weights[i].numLocations(); j++) {
							double w = weights[i].valueAtLocation (j);
							if (!Double.isInfinite(w))
								cachedCost += w * w / priorDenom;
						}
					}
				}
				cachedCostStale = false;
				logger.info ("getCost() (-loglikelihood) = "+cachedCost);
				logger.fine ("getCost() (-loglikelihood) = "+cachedCost);
				//crf.print();
			}
			return cachedCost;
		}

		private boolean checkForNaN ()
		{
			for (int i = 0; i < weights.length; i++) {
				assert (!weights[i].isNaN());
				assert (constraints == null || !constraints[i].isNaN());
				assert (expectations == null || !expectations[i].isNaN());
				assert (!Double.isNaN(defaultExpectations[i]));
				assert (!Double.isNaN(defaultConstraints[i]));
			}
			for (int i = 0; i < numStates(); i++) {
				State s = (State) getState (i);
				assert (!Double.isNaN (s.initialExpectation));
				assert (!Double.isNaN (s.initialConstraint));
				assert (!Double.isNaN (s.initialCost));
				assert (!Double.isNaN (s.finalExpectation));
				assert (!Double.isNaN (s.finalConstraint));
				assert (!Double.isNaN (s.finalCost));
			}
			return true;
		}
	
		public Matrix getCostGradient (Matrix m)
		{
			// Gradient is -(constraint - expectation - parameters/gaussianPriorVariance)
			// == (expectation + parameters/gaussianPriorVariance - constraint)
			// This might be opposite from what you are used to seeing, this
			// is because this is the gradient of the "cost" and the
			// gradient should point "up-hill", which is actually away from
			// the direction we want to parameters to go.
			if (cachedGradientStale) {
				if (cachedCostStale)
					// This will fill in the this.expectation
					getCost ();
				assert (checkForNaN());
				Vector g = (Vector) m;
				int gi = 0;
				for (int i = 0; i < numStates(); i++) {
					State s = (State) getState (i);
					cachedGradient.setValue (gi++, (Double.isInfinite(s.initialCost)
																					? 0.0
																					: (s.initialExpectation
																						 + (usingHyperbolicPrior
																								? (hyperbolicPriorSlope
																									 * Maths.tanh (-s.initialCost)
																									 * hyperbolicPriorSharpness)
																								: ((-s.initialCost) / gaussianPriorVariance))
																						 - s.initialConstraint)));
					cachedGradient.setValue (gi++, (Double.isInfinite (s.finalCost)
																					? 0.0
																					: s.finalExpectation
																					+ (usingHyperbolicPrior
																						 ? (hyperbolicPriorSlope
																								* Maths.tanh (-s.finalCost)
																								* hyperbolicPriorSharpness)
																						 : ((-s.finalCost) / gaussianPriorVariance))
																					- s.finalConstraint));
				}
				if (usingHyperbolicPrior) {
					// Hyperbolic prior
					for (int i = 0; i < weights.length; i++) {
						cachedGradient.setValue (gi++, (Double.isInfinite (defaultWeights[i])
																							? 0.0
																							: (defaultExpectations[i]
																								 + (hyperbolicPriorSlope
																										* Maths.tanh (defaultWeights[i])
																										* hyperbolicPriorSharpness)
																								 - defaultConstraints[i])));
						if (printGradient)
							System.out.println ("CRF gradient["+crf.getWeightsName(i)+"][<DEFAULT_FEATURE>]="+cachedGradient.value(gi-1));
						for (int j = 0; j < weights[i].numLocations(); j++) {
							cachedGradient.setValue (gi++, (Double.isInfinite (weights[i].valueAtLocation(j))
																							? 0.0
																							: (expectations[i].valueAtLocation(j)
																								 + (hyperbolicPriorSlope
																										* Maths.tanh (weights[i].valueAtLocation(j))
																										* hyperbolicPriorSharpness)
																								 - constraints[i].valueAtLocation(j))));
							if (printGradient)
								System.out.println ("CRF gradient["+crf.getWeightsName(i)+"]["+inputAlphabet.lookupObject(j)+"]="+cachedGradient.value(gi-1));								
						}
					}
				} else {
					// Gaussian prior
					for (int i = 0; i < weights.length; i++) {
						cachedGradient.setValue (gi++, (Double.isInfinite (defaultWeights[i])
																							? 0.0
																							: (defaultExpectations[i]
																								 + defaultWeights[i] / gaussianPriorVariance
																								 - defaultConstraints[i])));
						if (printGradient)
							System.out.println ("CRF gradient["+crf.getWeightsName(i)+"][<DEFAULT_FEATURE>]="+cachedGradient.value(gi-1));
						for (int j = 0; j < weights[i].numLocations(); j++) {
							cachedGradient.setValue (gi++, (Double.isInfinite (weights[i].valueAtLocation(j))
																							? 0.0
																							: (expectations[i].valueAtLocation(j)
																								 + weights[i].valueAtLocation(j) / gaussianPriorVariance
																								 - constraints[i].valueAtLocation(j))));
							if (printGradient)
								System.out.println ("CRF gradient["+crf.getWeightsName(i)+"]["+inputAlphabet.lookupObject(j)+"]="+cachedGradient.value(gi-1));
						}
					}
				}
				// xxx Show the feature with maximum gradient
				cachedGradientStale = false;
				assert (!cachedGradient.isNaN());
			}
			m.set (cachedGradient);
			printGradient = false;
			return m;
		}

		//Serialization of MinimizableCRF
		
		private static final long serialVersionUID = 1;
		private static final int CURRENT_SERIAL_VERSION = 0;
	
		private void writeObject (ObjectOutputStream out) throws IOException {
			out.writeInt (CURRENT_SERIAL_VERSION);
			out.writeObject(trainingSet);
			out.writeDouble(cachedCost);
			out.writeObject(cachedGradient);
			out.writeObject(infiniteCosts);
			out.writeInt(numParameters);
			out.writeObject(crf);
		}
		
		private void readObject (ObjectInputStream in) throws IOException, ClassNotFoundException {
			int version = in.readInt ();
			trainingSet = (InstanceList) in.readObject();
			cachedCost = in.readDouble();
			cachedGradient = (DenseVector) in.readObject();
			infiniteCosts = (BitSet) in.readObject();
			numParameters = in.readInt();
			crf = (CRF2)in.readObject();
		}

	}



	public class State extends Transducer.State implements Serializable
	{
		// Parameters indexed by destination state, feature index