Ctakes ytex conceptgraph

ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/IntrinsicInfoContentEvaluatorImpl.java

@@ -460,8 +460,16 @@ private Set<String> getSubsumers(ConcRel concept,
 				}
 			}
 		}
-		if (calcDepth)
-			depthArray[concept.getNodeIndex()] = (short) (parentMaxDepth + 1);
+
+		// Compute the current depth of the concept node
+		if (calcDepth) {
+			// Dummy concept has no length
+			if ( concept.getConceptID().contentEquals("C0000000") ) { 
+				depthArray[concept.getNodeIndex()] = (short) (0);
+			} else {
+				depthArray[concept.getNodeIndex()] = (short) (parentMaxDepth + 1);
+			}
+		}
 		// add the concept itself to the set of subsumers
 		subsumers.add(concept.getConceptID());
 		// add this to the cache - copy the key so that this can be gc'ed as

ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/metric/IntrinsicLCHMetric.java

@@ -24,33 +24,43 @@
  * compute intrinsic LCH as in eqn 28 from
  * http://dx.doi.org/10.1016/j.jbi.2011.03.013
  * 
- * Scale to unit interval
+ * This version is NOT scaled to the unit metric
  * 
  * @author vijay
  * 
  */
 public class IntrinsicLCHMetric extends BaseSimilarityMetric {
-	double logMaxIC2 = 0d;
-
-	public IntrinsicLCHMetric(ConceptSimilarityService simSvc, Double maxIC) {
-		super(simSvc);
-		if (maxIC != null)
-			this.logMaxIC2 = Math.log(2 * maxIC.doubleValue()) + 1d;
-	}
+
+	double maxIC2 = 0d;
 
 	@Override
 	public double similarity(String concept1, String concept2,
 			Map<String, Double> conceptFilter, SimilarityInfo simInfo) {
-		double sim = 0d;
-		if (logMaxIC2 != 0d) {
+
+		if (maxIC2 != 0d) {
+
 			double ic1 = simSvc.getIC(concept1, true);
 			double ic2 = simSvc.getIC(concept2, true);
 			double lcsIC = initLcsIC(concept1, concept2, conceptFilter,
 					simInfo, true);
-			sim = 1 - (Math.log(ic1 + ic2 - 2 * (lcsIC) + 1) / logMaxIC2);
-
+
+			// Compute the Intrinsic LCH metric
+			double sim = Math.log( (ic1 + ic2 - (2d * lcsIC) + 1d) / maxIC2) * -1.0d;
+			return sim;
+
 		}
-		return sim;
+		return 0d;		
+
 	}
+
+	public IntrinsicLCHMetric(ConceptSimilarityService simSvc, Double maxIC) {
+		super(simSvc);
+		if (maxIC != null) {
+			// Compute the denominator of the Intrinsic LCH metric
+			this.maxIC2 = 2.0d * maxIC.doubleValue();
+		}
+	}
+
+
 
 }

ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/metric/JaccardMetric.java

@@ -42,7 +42,15 @@ public double similarity(String concept1, String concept2,
 			return 0d;
 		double ic1 = simSvc.getIC(concept1, true);
 		double ic2 = simSvc.getIC(concept2, true);
-		return lcsIC / (ic1 + ic2 - lcsIC);
+
+		//
+		// Test that we get a positive denominator
+		//
+		if ( ic1 + ic2 > lcsIC ) {
+			return lcsIC / (ic1 + ic2 - lcsIC);
+		} else {
+			return 0d;
+		}
 	}
 
 }

ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/metric/LCHMetric.java

@@ -20,22 +20,36 @@
 
 import java.util.Map;
 
+/**
+ * 
+ * This metric is an implementation of the semantic relatedness measure described
+ * by Leacock and Chodorow (1998).
+ * 
+ * See reference paper: https://aclanthology.org/J06-1003.pdf
+ * Page 19, Sec 2.5.3 (7)
+ * 
+ * sim(c1,c2) = -log ( len(c1,c2) / 2 * max_depth )
+ * 
+ */
 public class LCHMetric extends BaseSimilarityMetric {
 	/**
-	 * log(max depth * 2)
+	 * natural log(max depth * 2)
 	 */
-	double logdm = 0d;
+	double maxDepth = 0d;
 
 	@Override
 	public double similarity(String concept1, String concept2,
 			Map<String, Double> conceptFilter, SimilarityInfo simInfo) {
-		if (logdm != 0d) {
+		if (maxDepth != 0d) {
 			initLCSes(concept1, concept2, simInfo);
 			if (simInfo.getLcsDist() > 0) {
-				// double lch = logdm - Math.log((double) simInfo.getLcsDist());
-				// // scale to depth
-				// return lch / logdm;
-				return 1 - (Math.log((double) simInfo.getLcsDist()) / logdm);
+
+				double length = simInfo.getLcsDist();
+
+				// Compute the length between the concepts
+				double lch = Math.log(length / (double)(2 * maxDepth)) * -1.0d;
+				return lch;
+
 			}
 		}
 		return 0d;
@@ -44,7 +58,10 @@ public double similarity(String concept1, String concept2,
 	public LCHMetric(ConceptSimilarityService simSvc, Integer maxDepth) {
 		super(simSvc);
 		if (maxDepth != null) {
-			this.logdm = Math.log(2 * maxDepth);
+			// The cTakes YTEX concept graph adds a dummy node C000000
+			// which should be reduced by 1 for computing the max depth
+			// correctly
+			this.maxDepth = maxDepth - 1;
 		}
 	}
 

ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/metric/LinMetric.java

@@ -46,30 +46,39 @@ public void setIntrinsicIC(boolean intrinsicIC) {
 	@Override
 	public double similarity(String concept1, String concept2,
 			Map<String, Double> conceptFilter, SimilarityInfo simInfo) {
-		// don't bother if the concept graph is null
+
+		// Test that there is a valid concept graph
 		if (!validCG)
 			return 0d;
-		// get lcs
-		double lcsIC = initLcsIC(concept1, concept2, conceptFilter, simInfo,
-				this.intrinsicIC);
-		if (lcsIC == 0d) {
-			return 0d;
-		}
-		// get ic of concepts
+
+		// Compute the IC values for each concept
 		double ic1 = simSvc.getIC(concept1, this.intrinsicIC);
 		double ic2 = simSvc.getIC(concept2, this.intrinsicIC);
+
+		// Get the LCS with the lowest IC score
+		double lcsIC = initLcsIC(concept1, concept2, conceptFilter, simInfo,
+				this.intrinsicIC);
+
 		// if the corpus IC is 0 and the concept is not the root, then we don't
 		// have any IC on the concept and can't measure similarity - return 0
 		if (!intrinsicIC && ic1 == 0 && !rootConcept.equals(concept1))
 			return 0d;
+
 		if (!intrinsicIC && ic2 == 0 && !rootConcept.equals(concept2))
 			return 0d;
-		double denom = ic1 + ic2;
-		if (denom == 0)
-			return 0d;
-		return 2 * lcsIC / denom;
+
+		// Compute the Lin score
+		double sim = (2d * lcsIC) / ( ic1 + ic2 );
+		return sim;	
+
 	}
 
+	/**
+	 * This constructor allows us to specify if we want the standard Lin
+	 * metric or the Intrinsic Lin by passing a boolean flag
+	 * @param simSvc
+	 * @param intrinsicIC if true, then compute the intrinsic Lin metric
+	 */
 	public LinMetric(ConceptSimilarityService simSvc, boolean intrinsicIC) {
 		super(simSvc);
 		this.intrinsicIC = intrinsicIC;

ctakes-ytex/src/main/java/org/apache/ctakes/ytex/kernel/metric/WuPalmerMetric.java

@@ -20,20 +20,43 @@
 
 import java.util.Map;
 
+/**
+ * Wu-Palmer metric matches results as found in the CPAN UMLS-Similarity::wup module
+ * 
+ * @author vijay
+ * @author painter
+ * 
+ */
 public class WuPalmerMetric extends BaseSimilarityMetric {
 	@Override
 	public double similarity(String concept1, String concept2,
 			Map<String, Double> conceptFilter, SimilarityInfo simInfo) {
 		initLCSes(concept1, concept2, simInfo);
+
 		if (simInfo.getLcses().size() > 0) {
 			int lcsDepth = 0;
+
+			// Test for the LCS with the greatest depth
+			// to find the lowest common synonym
 			for (String lcs : simInfo.getLcses()) {
-				int d = simSvc.getDepth(lcs);
+
+				// The depth of the LCS is off by 1
+				int d = simSvc.getDepth(lcs) + 1;
+				// Find the max depth of the LCS
 				if (d > lcsDepth)
 					lcsDepth = d;
 			}
-			double lcsDepth2 = (double) (lcsDepth * 2);
-			return lcsDepth2 / (lcsDepth2 + (double) (simInfo.getLcsDist()-1));
+
+			//
+			// Compute Wu-Palmer Similarity:
+			//
+			double lcsDist = simInfo.getLcsDist().doubleValue();
+
+            // Adjust depth by 1 due to fake root node
+			double c1Depth = simSvc.getDepth(concept1) + 1;
+			double c2Depth = simSvc.getDepth(concept2) + 1;
+			double score = ( 2.0 * (lcsDepth) / ( c1Depth + c2Depth ) );
+			return score;
 		}
 		return 0d;
 	}