Lenient (overlap) evaluation for Mallet

LenientMultiSegmentationEvaluator.java

package cc.mallet.fst;

import java.text.DecimalFormat;
import java.util.LinkedList;
import java.util.List;

import cc.mallet.types.FeatureVector;
import cc.mallet.types.Instance;
import cc.mallet.types.InstanceList;
import cc.mallet.types.Sequence;

//import org.javatuples.Pair;

/**
 * Lenient (overlap) evaluation. Only works when evaluating one instancelist<br>
 * Usage:
 * 
 * <pre>
 * CRFTrainerByThreadedLabelLikelihood trainer = new CRFTrainerByThreadedLabelLikelihood(
 *         crf, 4);
 * String[] tags = new String[] { &quot;I&quot; }; // *I*nside, *O*utside
 * String[] continueTags = tags; // same
 * trainer.train(trainingSet);
 * 
 * MultiSegmentationEvaluator evalOrig = new MultiSegmentationEvaluator(
 *         new InstanceList[] { testingSet },//
 *         new String[] { &quot;thetest&quot; }, tags, continueTags);
 * evalOrig.evaluate(trainer); // eval at end of training
 * 
 * MyLenientMultiSegmentationEvaluator evalLenient = new MyLenientMultiSegmentationEvaluator(
 *         new InstanceList[] { testingSet },//
 *         new String[] { &quot;thelenienttest&quot; }, tags, continueTags, true);
 * evalLenient.evaluate(trainer);
 * 
 * System.out.println(&quot;Strict eval:&quot; + eval + &quot;, lenient eval:&quot; + evalLenient);
 * </pre>
 * 
 * @see MultiSegmentationEvaluator
 * @author [email protected]
 */
public class LenientMultiSegmentationEvaluator extends
        MultiSegmentationEvaluator {

    private boolean printMissclassified;

    /**
     * @param printMissclassified
     *            whether to output a detailed report of TP, FT and the sentence
     *            to sys.out
     */
    public LenientMultiSegmentationEvaluator(InstanceList[] instanceLists,
            String[] instanceListDescriptions, Object[] segmentStartTags,
            Object[] segmentContinueTags, boolean printMissclassified) {
        super(instanceLists, instanceListDescriptions, segmentStartTags,
                segmentContinueTags);
        this.printMissclassified = printMissclassified;
    }

    protected static final DecimalFormat f = new DecimalFormat("0.####");

    protected double precision, recall, f1;

    public double getPrecision() {
        return precision;
    }

    public double getRecall() {
        return recall;
    }

    public double getF1() {
        return f1;
    }

    public String getReport() {
        return "precision=" + f.format(precision) + " recall="
                + f.format(recall) + " f1=" + f.format(f1);
    }

    @Override
    public String toString() {
        return getReport();
    }

    @SuppressWarnings("rawtypes")
    public void evaluateInstanceList(TransducerTrainer tt, InstanceList data,
            String description) {
        Transducer model = tt.getTransducer();

        int trueCnt = 0;// int predCnt = 0;
        int tp = 0;
        int fp = 0;

        for (int i = 0; i < data.size(); i++) {
            Instance instance = data.get(i);
            Sequence input = (Sequence) instance.getData();

            Sequence trueOutput = (Sequence) instance.getTarget();
            Sequence predOutput = model.transduce(input);
            if ((input.size() != trueOutput.size()) || //
                    (predOutput.size() != trueOutput.size())) {
                throw new RuntimeException("inputs do not match");
            }

            List<Pair<Integer, Integer>> trueAnnots = new LinkedList<Pair<Integer, Integer>>(), predAnnots = new LinkedList<Pair<Integer, Integer>>();
            // -1 for non-start, otherwise start index
            int lastTrue = -1, lastPred = -1;

            StringBuilder sentencePrint = new StringBuilder();
            for (int j = 0; j < trueOutput.size(); j++) {

                // 1. Find out if this j is a I (in true and pred)
                boolean isTrue = false, isPred = false;
                // Count true segment starts
                for (int n = 0; n < segmentStartTags.length; n++) {
                    if (segmentStartTags[n].equals(trueOutput.get(j))) {
                        isTrue = true;
                        break;
                    }
                }
                // Count predicted segment starts
                for (int n = 0; n < segmentStartTags.length; n++) {
                    if (segmentStartTags[n].equals(predOutput.get(j))) {
                        isPred = true;
                    }
                }
                // Count true segment continue
                for (int n = 0; n < segmentContinueTags.length; n++) {
                    if (segmentContinueTags[n].equals(trueOutput.get(j))) {
                        isTrue = true;
                        break;
                    }
                }
                // Count predicted segment continue
                for (int n = 0; n < segmentContinueTags.length; n++) {
                    if (segmentContinueTags[n].equals(predOutput.get(j))) {
                        isPred = true;
                    }
                }

                // 2. Do we start a new /already are in a BR (in true and pred)?
                // start new True?
                String prefix = " "; // for debug
                if (lastTrue == -1 && isTrue == true) {
                    prefix += "<G";
                    lastTrue = j; // just register for later

                } else if (lastTrue != -1 && isTrue == false) {
                    trueAnnots.add(new Pair<Integer, Integer>(lastTrue, j));
                    lastTrue = -1;
                    prefix += "G>";
                }
                // else do nothing (either it continues out or continues in)

                // start new Pred?
                if (lastPred == -1 && isPred == true) {
                    prefix += "<S";
                    lastPred = j; // just register for later

                } else if (lastPred != -1 && isPred == false) {
                    predAnnots.add(new Pair<Integer, Integer>(lastPred, j));
                    lastPred = -1;
                    prefix += "S>";
                }
                // else do nothing (either it continues out or continues in

                sentencePrint.append(prefix + getText(input, j));
            }
            if (printMissclassified)
                System.out.println(sentencePrint);

            // 3. Count tp, fp; add to total counts
            int _truePositives = 0;
            for (Pair<Integer, Integer> expected : trueAnnots) {
                boolean _localFN = true;
                for (Pair<Integer, Integer> actual : predAnnots) {
                    if (overlap(expected, actual)) {
                        _truePositives++;
                        _localFN = false;
                        break;// external_loop;
                    }
                }
                if (_localFN && printMissclassified) {// false negative
                    System.out.println("FN: " + getText(input, expected));
                }
            }
            int _falsePositives = 0;
            for (Pair<Integer, Integer> actual : predAnnots) {
                boolean _localTP = false;
                for (Pair<Integer, Integer> expected : trueAnnots) {
                    if (overlap(expected, actual)) {
                        _localTP = true;
                        break;// external_loop;
                    }
                }
                if (!_localTP) {
                    _falsePositives++;
                    if (printMissclassified)
                        System.out.println("FP: " + getText(input, actual));
                }
            }

            tp += _truePositives;
            fp += _falsePositives;
            trueCnt += trueAnnots.size();
            // predCnt += predAnnots.size();
        }

        precision = (tp + 0d) / (tp + fp + 0d);
        recall = (tp + 0d) / (trueCnt + 0d);
        f1 = 2 * precision * recall / (precision + recall);
    }

    private String getText(@SuppressWarnings("rawtypes") Sequence input,
            Pair<Integer, Integer> annot) {
        StringBuilder sb = new StringBuilder();
        for (int i = annot.getKey(); i < annot.getValue(); i++) {
            sb.append(getText(input, i) + " ");
        }
        return sb.toString();
    }

    // /** Here we do a lenient comparison */
    // // TODO add more comparisons, see TestEvaluator
    // protected boolean areTheSameLenient(Pair<Integer, Integer> expected,
    // Pair<Integer, Integer> actual) {
    // if (expected.getKey() < actual.getValue()
    // && expected.getValue() > actual.getKey()) {
    // return true;
    // }
    // return false;
    //
    // }

    /** Here we do a lenient comparison */
    protected boolean overlap(Pair<Integer, Integer> expected,
            Pair<Integer, Integer> actual) {
        // // a1 then a2
        // if (a2.getBegin() - a1.getEnd() > 0)
        // return Position.before;
        //
        // // a2 then a1
        // if (a1.getBegin() - a2.getEnd() > 0)
        // return Position.after;
        //
        // // overlap
        // return Position.overlap;
        //

        if (expected.getKey() < actual.getValue()
                && actual.getKey() < expected.getValue()) {
            return true;
        }
        return false;

    }

    // /** Here we do a EXACT comparison */
    // protected boolean areTheSame(Pair<Integer, Integer> expected,
    // Pair<Integer, Integer> actual) {
    // if (expected.getKey() == actual.getKey()
    // && expected.getValue() == actual.getValue()) {
    // return true;
    // }
    // return false;
    // }

    protected static String getText(
            @SuppressWarnings("rawtypes") Sequence input, int j) {
        FeatureVector fv = (FeatureVector) input.get(j);
        for (int idx : fv.getIndices()) {

            Object ooo = fv.getAlphabet().lookupObject(idx);
            if (ooo.toString().startsWith("text=")
                    && !ooo.toString().matches("^.+?\\/[-\\+]\\d$")) {
                return ooo.toString().substring(5);
            }
        }
        return "";
    }
}