private void updateSourceAndDestinationVectors(int featureID, FunctionManager srcFuncManager,
			FunctionManager destFuncManager, TaskMonitor monitor) {

		/*
		 * At this point the vectors in the sourceMap and the destinationMap contain log weights for
		 * the probability that ACCEPTED MATCHED features appear in any one function in the system.
		 * Each map has the key:value pair = refFunction:featureVector.
		 * In order to account unmatched/unaccepted matches that appear in the key set that
		 * consists of possibly correlated functions, we can consider the cost of a reference
		 * switching and the cost of a reference being dropped or picked up between versions.
		 *
		 * Theoretically this should be dependent on the probability of the referenced element
		 * occurring, but for the moment we'll consider the model for a generalized switch and
		 * drop/pickup.
		 */
		monitor.setMessage("Adding unmatched references to feature vectors.");

		double pSwitch = 0.5;
		double uniqueWeight = Math.sqrt(-Math.log(pSwitch)); //arbitrary weight used to provide negative correlation

		for (Address addr : srcVectorsByAddress.keySet()) {

			int totalRefs = countFunctionRefs(sourceProgram, addr);
			LSHCosineVectorAccum srcVector = srcVectorsByAddress.get(addr);
			int numEntries = srcVector.numEntries();
			for (int i = 0; i < (totalRefs - numEntries); i++) {
				srcVector.addHash(featureID, uniqueWeight);
				++featureID;
			}
		}

		for (Address addr : destVectorsByAddress.keySet()) {

			int totalRefs = countFunctionRefs(destinationProgram, addr);
			LSHCosineVectorAccum dstVector = destVectorsByAddress.get(addr);
			int numEntries = dstVector.numEntries();
			for (int i = 0; i < (totalRefs - numEntries); i++) {
				dstVector.addHash(featureID, uniqueWeight);
				++featureID;
			}
		}
	}
Compute raw percentages for the sources and destination counts as ratios
(total references to the match):(total number of references of the correct type)
Ghidra/Features/VersionTracking/src/main/java/ghidra/feature/vt/api/correlator/program/VTAbstractReferenceProgramCorrelator.java