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Merge pull request #1771 from cmu-phil/vbc-05-16-2
Introducing LocalGraphConfusion and its corresponding Precision and Recall classes
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tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/statistic/LocalGraphPrecision.java
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| @@ -0,0 +1,30 @@ | ||
| package edu.cmu.tetrad.algcomparison.statistic; | ||
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| import edu.cmu.tetrad.algcomparison.statistic.utils.LocalGraphConfusion; | ||
| import edu.cmu.tetrad.data.DataModel; | ||
| import edu.cmu.tetrad.graph.Graph; | ||
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| public class LocalGraphPrecision implements Statistic { | ||
| @Override | ||
| public String getAbbreviation() { | ||
| return "LGP"; | ||
| } | ||
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| @Override | ||
| public String getDescription() { | ||
| return "Local Graph Precision"; | ||
| } | ||
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| @Override | ||
| public double getValue(Graph trueGraph, Graph estGraph, DataModel dataModel) { | ||
| LocalGraphConfusion lgConfusion = new LocalGraphConfusion(trueGraph, estGraph); | ||
| int lgTp = lgConfusion.getTp(); | ||
| int lgFp = lgConfusion.getFp(); | ||
| return lgTp / (double) (lgTp + lgFp); | ||
| } | ||
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| @Override | ||
| public double getNormValue(double value) { | ||
| return value; | ||
| } | ||
| } |
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tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/statistic/LocalGraphRecall.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,30 @@ | ||
| package edu.cmu.tetrad.algcomparison.statistic; | ||
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| import edu.cmu.tetrad.algcomparison.statistic.utils.LocalGraphConfusion; | ||
| import edu.cmu.tetrad.data.DataModel; | ||
| import edu.cmu.tetrad.graph.Graph; | ||
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| public class LocalGraphRecall implements Statistic { | ||
| @Override | ||
| public String getAbbreviation() { | ||
| return "LGR"; | ||
| } | ||
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| @Override | ||
| public String getDescription() { | ||
| return "Local Graph Recall"; | ||
| } | ||
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| @Override | ||
| public double getValue(Graph trueGraph, Graph estGraph, DataModel dataModel) { | ||
| LocalGraphConfusion lgConfusion = new LocalGraphConfusion(trueGraph, estGraph); | ||
| int lgTp = lgConfusion.getTp(); | ||
| int lgFn = lgConfusion.getFn(); | ||
| return lgTp / (double) (lgTp + lgFn); | ||
| } | ||
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| @Override | ||
| public double getNormValue(double value) { | ||
| return value; | ||
| } | ||
| } |
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...d-lib/src/main/java/edu/cmu/tetrad/algcomparison/statistic/utils/LocalGraphConfusion.java
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| @@ -0,0 +1,224 @@ | ||
| package edu.cmu.tetrad.algcomparison.statistic.utils; | ||
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| import edu.cmu.tetrad.graph.*; | ||
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| import java.util.HashSet; | ||
| import java.util.List; | ||
| import java.util.Set; | ||
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| /** | ||
| * A confusion matrix for local graph accuracy check --i.e. TP, FP, TN, FN for counts of a combination of | ||
| * arrowhead and precision. | ||
| */ | ||
| public class LocalGraphConfusion { | ||
| /** | ||
| * The true positive count. | ||
| */ | ||
| private int tp; | ||
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| /** | ||
| * The true negative count. | ||
| */ | ||
| private int tn; | ||
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| /** | ||
| * The false positive count. | ||
| */ | ||
| private int fp; | ||
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| /** | ||
| * The false positive count. | ||
| */ | ||
| private int fn; | ||
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| /** | ||
| * Constructs a new LocalGraphConfusion object from the given graphs. | ||
| * @param trueGraph The true graph | ||
| * | ||
| * @param estGraph The estimated graph | ||
| */ | ||
| public LocalGraphConfusion(Graph trueGraph, Graph estGraph) { | ||
| this.tp = 0; | ||
| this.tn = 0; | ||
| this.fp = 0; | ||
| this.fn = 0; | ||
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| // STEP0: Create lookups for both true graph and estimated graph. | ||
| // trueGraphLookup is the same structure as trueGraph's structure but node objects replaced by estimated graph nodes. | ||
| Graph trueGraphLookup = GraphUtils.replaceNodes(trueGraph, estGraph.getNodes()); | ||
| // estGraphLookup is the same structure as estGraph's structure but node objects replaced by true graph nodes. | ||
| Graph estGraphLookup = GraphUtils.replaceNodes(estGraph, trueGraph.getNodes()); | ||
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| // STEP1: Check for Adjacency. | ||
| /** | ||
| * True | ||
| * Y N | ||
| * --------------------- | ||
| * Y | TP FP | ||
| * Est | -------------------- | ||
| * N | FN TN | ||
| * ----------------------- | ||
| */ | ||
| // STEP 1.1: Create allUnoriented base on trueGraphLookup and estimatedGraph | ||
| Set<Edge> allUnoriented = new HashSet<>(); | ||
| for (Edge edge: trueGraphLookup.getEdges()) { | ||
| allUnoriented.add(Edges.undirectedEdge(edge.getNode1(), edge.getNode2())); | ||
| } | ||
| for (Edge edge: estGraph.getEdges()) { | ||
| allUnoriented.add(Edges.undirectedEdge(edge.getNode1(), edge.getNode2())); | ||
| } | ||
| // STEP 1.2: Iterate through allUnoriented to record confusion metrix | ||
| for (Edge u: allUnoriented) { | ||
| Node node1 = u.getNode1(); | ||
| Node node2 = u.getNode2(); | ||
| if (estGraph.isAdjacentTo(node1, node2)) { // Est: Y | ||
| if (trueGraphLookup.isAdjacentTo(node1, node2)) { // True: Y | ||
| this.tp++; | ||
| } else { // True: N | ||
| this.fp++; | ||
| } | ||
| } else { // Est: N | ||
| if (trueGraphLookup.isAdjacentTo(node1, node2)) { // True: Y | ||
| this.fn++; | ||
| } else { // True: N | ||
| this.tn++; | ||
| } | ||
| } | ||
| } | ||
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| // STEP2: Check for Orientation(i.e. Arrowhead), so we need to check both endpoints of an edge. | ||
| /** | ||
| * True | ||
| * -> <- ...(None) | ||
| * --------------------------- | ||
| * -> | TP FP,FN / (Do not repeat count, as we checked for it in Adj step) | ||
| * Est | -------------------------- | ||
| * <- | FP, FN TP / | ||
| * | -------------------------- | ||
| * -- | FN FN / | ||
| * | -------------------------- | ||
| * ...| / / / | ||
| * ----------------------------- | ||
| * | ||
| */ | ||
| // STEP2.1: Check through the true graph | ||
| for (Edge tle: trueGraphLookup.getEdges()) { | ||
| // STEP2.1.1: Get corresponding endpoint in Est graph lookup | ||
| List<Edge> estGraphLookupEdges = estGraphLookup.getEdges(tle.getNode1(), tle.getNode2()); | ||
| Edge ele; // estimated lookup graph edge | ||
| if (estGraphLookupEdges.size() == 1) { | ||
| ele = estGraphLookupEdges.iterator().next(); | ||
| } else { | ||
| ele = estGraphLookup.getDirectedEdge(tle.getNode1(), tle.getNode2()); | ||
| } | ||
| Endpoint ep1Est = null; | ||
| Endpoint ep2Est = null; | ||
| if (ele != null) { | ||
| ep1Est = ele.getProximalEndpoint(tle.getNode1()); | ||
| ep2Est = ele.getProximalEndpoint(tle.getNode2()); | ||
| } | ||
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| // STEP2.1.2: Get corresponding endpoint in true graph lookup | ||
| List<Edge> trueGraphLookupEdges = trueGraphLookup.getEdges(tle.getNode1(), tle.getNode1()); | ||
| Edge tle2; | ||
| if (trueGraphLookupEdges.size() == 1) { | ||
| tle2 = trueGraphLookupEdges.iterator().next(); | ||
| } else { | ||
| tle2 = trueGraphLookup.getDirectedEdge(tle.getNode1(), tle.getNode2()); | ||
| } | ||
| Endpoint ep1True = null; | ||
| Endpoint ep2True = null; | ||
| if (tle2 != null) { | ||
| ep1True = tle2.getProximalEndpoint(tle.getNode1()); | ||
| ep2True = tle2.getProximalEndpoint(tle.getNode2()); | ||
| } | ||
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| // STEP2.1.3: Compare the endpoints | ||
| // we only care the case when the edge exist. | ||
| boolean connected = trueGraph.isAdjacentTo(tle.getNode1(), tle.getNode2()) | ||
| && estGraph.isAdjacentTo(tle.getNode1(), tle.getNode2()); | ||
| if (connected) { | ||
| if (ep1True == Endpoint.TAIL && ep2True == Endpoint.ARROW) { // True: -> | ||
| if (ep1Est == Endpoint.TAIL && ep2Est == Endpoint.ARROW) { // Est: -> | ||
| this.tp++; | ||
| } else if (ep1Est == Endpoint.ARROW && ep2Est == Endpoint.TAIL) { // Est: <- | ||
| // this.fp++; | ||
| this.fn++; | ||
| } else if (ep1Est == Endpoint.TAIL && ep2Est == Endpoint.TAIL) { // Est: -- | ||
| this.fn++; | ||
| } | ||
| } else if (ep1True == Endpoint.ARROW && ep2True == Endpoint.TAIL) { // True: <- | ||
| if (ep1Est == Endpoint.TAIL && ep2Est == Endpoint.ARROW) { // Est: -> | ||
| // this.fp++; | ||
| this.fn++; | ||
| } else if (ep1Est == Endpoint.ARROW && ep2Est == Endpoint.TAIL) { // Est: <- | ||
| this.tp++; | ||
| } else if (ep1Est == Endpoint.TAIL && ep2Est == Endpoint.TAIL) { // Est: -- | ||
| this.fn++; | ||
| } | ||
| } | ||
| } | ||
| } | ||
| // STEP2: Check through the est graph | ||
| // because est graph can have extra arrowhead that was not in true graph, which should be count as fp. | ||
| for (Edge ele: estGraphLookup.getEdges()) { | ||
| List<Edge> estGraphLookupEdges = estGraphLookup.getEdges(ele.getNode1(), ele.getNode2()); | ||
| Edge ele2; | ||
| if (estGraphLookupEdges.size() == 1) { | ||
| ele2 = estGraphLookupEdges.iterator().next(); | ||
| } else { | ||
| ele2 = estGraphLookup.getDirectedEdge(ele.getNode1(), ele.getNode2()); | ||
| } | ||
| Endpoint ep1Est = null; | ||
| Endpoint ep2Est = null; | ||
| if (ele2 != null) { | ||
| ep1Est = ele2.getProximalEndpoint(ele.getNode1()); | ||
| ep2Est = ele2.getProximalEndpoint(ele.getNode2()); | ||
| } | ||
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| List<Edge> trueGraphLookupEdges = trueGraphLookup.getEdges(ele.getNode1(), ele.getNode1()); | ||
| Edge tle; | ||
| if (trueGraphLookupEdges.size() == 1) { | ||
| tle = trueGraphLookupEdges.iterator().next(); | ||
| } else { | ||
| tle = trueGraphLookup.getDirectedEdge(ele.getNode1(), ele.getNode2()); | ||
| } | ||
| Endpoint ep1True = null; | ||
| Endpoint ep2True = null; | ||
| if (tle != null) { | ||
| ep1True = tle.getProximalEndpoint(ele.getNode1()); | ||
| ep2True = tle.getProximalEndpoint(ele.getNode2()); | ||
| } | ||
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| boolean connected = trueGraph.isAdjacentTo(ele.getNode1(), ele.getNode2()); | ||
| if (connected) { | ||
| if (ep1True == Endpoint.TAIL && ep2True == Endpoint.ARROW) { // True: -> | ||
| if (ep1Est == Endpoint.ARROW && ep2Est == Endpoint.TAIL) { // Est: <- | ||
| this.fp++; | ||
| } | ||
| // TODO VBC: Question: seems we wont encounter <-> case, is it? | ||
| } else if (ep1True == Endpoint.ARROW && ep2True == Endpoint.TAIL) { // True: <- | ||
| if (ep1Est == Endpoint.TAIL && ep2Est == Endpoint.ARROW) { // Est: -> | ||
| this.fp++; | ||
| } | ||
| } | ||
| } | ||
| } | ||
| } | ||
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| public int getTp() { | ||
| return tp; | ||
| } | ||
|
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| public int getTn() { | ||
| return tn; | ||
| } | ||
|
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| public int getFp() { | ||
| return fp; | ||
| } | ||
|
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| public int getFn() { | ||
| return fn; | ||
| } | ||
| } |
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