public static void main(String[] args) {
    try {
      String corpusFile = args[0];
      String goldSet = args[1];
      File outputDir = new File(args[2]);

      SystemConfig systemConfig = DriverUtils.configure(args);
      systemConfig.setAnnotationSetName(Constants.GS_NP, goldSet);

      Trainer trainer = new Trainer(systemConfig);
      FeatureGenerator featureGenerator = new FeatureGenerator(systemConfig);

      // get corpus
      Corpus c = DriverUtils.loadFiles(corpusFile);

      Preprocessor preprocessor = new Preprocessor(systemConfig);
      preprocessor.preprocess(c, false);

      // generate features
      String featureSetName = featureGenerator.generateFeatures(c, true);

      // train classifier
      Classifier classifier = trainer.runLearner(c, outputDir, featureSetName);
      System.out.println("classifier trained: " + classifier.getName());

    } catch (IOException e) {
      e.printStackTrace();
    } catch (ConfigurationException e) {
      e.printStackTrace();
    }
  }
Esempio n. 2
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  static boolean computeLogMi(
      FeatureGenerator featureGen,
      double lambda[],
      DoubleMatrix2D Mi_YY,
      DoubleMatrix1D Ri_Y,
      boolean takeExp,
      boolean reuseM,
      boolean initMDone) {

    if (reuseM && initMDone) {
      Mi_YY = null;
    } else initMDone = false;
    if (Mi_YY != null) Mi_YY.assign(0);
    Ri_Y.assign(0);
    while (featureGen.hasNext()) {
      Feature feature = featureGen.next();
      int f = feature.index();
      int yp = feature.y();
      int yprev = feature.yprev();
      float val = feature.value();
      //	    System.out.println(feature.toString());

      if (yprev < 0) {
        // this is a single state feature.
        double oldVal = Ri_Y.getQuick(yp);
        Ri_Y.setQuick(yp, oldVal + lambda[f] * val);
      } else if (Mi_YY != null) {
        Mi_YY.setQuick(yprev, yp, Mi_YY.getQuick(yprev, yp) + lambda[f] * val);
        initMDone = true;
      }
    }
    if (takeExp) {
      for (int r = Ri_Y.size() - 1; r >= 0; r--) {
        Ri_Y.setQuick(r, expE(Ri_Y.getQuick(r)));
        if (Mi_YY != null)
          for (int c = Mi_YY.columns() - 1; c >= 0; c--) {
            Mi_YY.setQuick(r, c, expE(Mi_YY.getQuick(r, c)));
          }
      }
    }
    return initMDone;
  }
Esempio n. 3
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 static boolean computeLogMi(
     FeatureGenerator featureGen,
     double lambda[],
     DataSequence dataSeq,
     int i,
     DoubleMatrix2D Mi_YY,
     DoubleMatrix1D Ri_Y,
     boolean takeExp,
     boolean reuseM,
     boolean initMDone) {
   featureGen.startScanFeaturesAt(dataSeq, i);
   return computeLogMi(featureGen, lambda, Mi_YY, Ri_Y, takeExp, reuseM, initMDone);
 }
Esempio n. 4
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  protected void init(CRF model, DataIter data, double[] l) {
    edgeGen = model.edgeGen;
    lambda = l;
    numY = model.numY;
    diter = data;
    featureGenerator = model.featureGenerator;
    numF = featureGenerator.numFeatures();

    gradLogli = new double[numF];
    diag = new double[numF]; // needed by the optimizer
    ExpF = new double[lambda.length];
    initMatrices();
    reuseM = params.reuseM;
    if (params.miscOptions.getProperty("cache", "false").equals("true")) {
      featureGenCache = new FeatureGenCache(featureGenerator);
      featureGenerator = featureGenCache;
    } else featureGenCache = null;
  }
Esempio n. 5
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  public void compute() {

    alpha_Y.assign(1);
    initMDone = false;
    boolean doScaling = params.doScaling;

    if ((beta_Y == null) || (beta_Y.length < dataSeq.length())) {
      beta_Y = new DenseDoubleMatrix1D[2 * dataSeq.length()];
      for (int i = 0; i < beta_Y.length; i++) beta_Y[i] = new DenseDoubleMatrix1D(numY);

      scale = new double[2 * dataSeq.length()];
      scale[dataSeq.length() - 1] = (doScaling) ? numY : 1;
      beta_Y[dataSeq.length() - 1].assign(1.0 / scale[dataSeq.length() - 1]);
    }
    beta.add(beta_Y[dataSeq.length() - 1]);
    // System.out.println("Beta "+beta_Y[3].toString());
    for (int i = dataSeq.length() - 1; i > 0; i--) {
      if (params.debugLvl > 2) {
        Util.printDbg("Features fired");
        // featureGenerator.startScanFeaturesAt(dataSeq, i);
        // while (featureGenerator.hasNext()) {
        // Feature feature = featureGenerator.next();
        // Util.printDbg(feature.toString());
        // }
      }

      // compute the Mi matrix
      // System.out.println("MI previous" +Mi_YY.toString());
      initMDone =
          Trainer.computeLogMi(
              featureGenerator, lambda, dataSeq, i, Mi_YY, Ri_Y, true, reuseM, initMDone);
      // System.out.println("MI "+Mi_YY.toString());
      tmp_Y.assign(beta_Y[i]);
      tmp_Y.assign(Ri_Y, multFunc);
      RobustMath.Mult(Mi_YY, tmp_Y, beta_Y[i - 1], 1, 0, false, edgeGen);

      // need to scale the beta-s to avoid overflow
      scale[i - 1] = doScaling ? beta_Y[i - 1].zSum() : 1;
      if ((scale[i - 1] < 1) && (scale[i - 1] > -1)) scale[i - 1] = 1;
      constMultiplier.multiplicator = 1.0 / scale[i - 1];
      beta_Y[i - 1].assign(constMultiplier);
      // System.out.println("Beta "+beta_Y[i - 1].toString() + " ");
      beta.add(beta_Y[i - 1]);
    }

    double thisSeqLogli = 0;
    System.out.println("\n");
    // Mi_YY.assign(0);
    alpha_temp = new DenseDoubleMatrix1D[2 * dataSeq.length()];
    for (int i = 0; i < dataSeq.length(); i++) alpha_temp[i] = new DenseDoubleMatrix1D(numY);

    for (int i = 0; i < dataSeq.length(); i++) {
      // compute the Mi matrix
      //
      initMDone =
          Trainer.computeLogMi(
              featureGenerator, lambda, dataSeq, i, Mi_YY, Ri_Y, true, reuseM, initMDone);
      // System.out.println("MI: " + Mi_YY.toString());
      // find features that fire at this position..
      featureGenerator.startScanFeaturesAt(dataSeq, i);

      if (i > 0) {
        tmp_Y.assign(alpha_Y);
        RobustMath.Mult(Mi_YY, tmp_Y, newAlpha_Y, 1, 0, true, edgeGen);
        // Mi_YY.zMult(tmp_Y, newAlpha_Y,1,0,true);
        newAlpha_Y.assign(Ri_Y, multFunc);
      } else {
        newAlpha_Y.assign(Ri_Y);
      }
      while (featureGenerator.hasNext()) {
        Feature feature = featureGenerator.next();
        int f = feature.index();

        int yp = feature.y();
        int yprev = feature.yprev();
        float val = feature.value();
        if ((dataSeq.y(i) == yp)
            && (((i - 1 >= 0) && (yprev == dataSeq.y(i - 1))) || (yprev < 0))) {

          thisSeqLogli += val * lambda[f];
        }
      }

      alpha_Y.assign(newAlpha_Y);
      // now scale the alpha-s to avoid overflow problems.
      constMultiplier.multiplicator = 1.0 / scale[i];
      alpha_Y.assign(constMultiplier);
      alpha_temp[i].assign(newAlpha_Y);
      alpha_temp[i].assign(constMultiplier);
      // System.out.println("ALpha "+alpha_Y.toString());
      alpha.add(alpha_temp[i]);
      if (params.debugLvl > 2) {
        System.out.println("Alpha-i " + alpha_Y.toString());
        System.out.println("Ri " + Ri_Y.toString());
        System.out.println("Mi " + Mi_YY.toString());
        System.out.println("Beta-i " + beta_Y[i].toString());
      }
    }

    Zx = alpha_Y.zSum();
    System.out.println("Zx: " + Zx);
  } /* end of computeBeta */
Esempio n. 6
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  protected double computeFunctionGradientLL(double lambda[], double grad[]) {
    double logli = 0;
    try {
      for (int f = 0; f < lambda.length; f++) {
        grad[f] = -1 * lambda[f] * params.invSigmaSquare;
        logli -= ((lambda[f] * lambda[f]) * params.invSigmaSquare) / 2;
      }
      diter.startScan();
      if (featureGenCache != null) featureGenCache.startDataScan();
      for (int numRecord = 0; diter.hasNext(); numRecord++) {
        DataSequence dataSeq = (DataSequence) diter.next();
        if (featureGenCache != null) featureGenCache.nextDataIndex();
        if (params.debugLvl > 1) {
          Util.printDbg("Read next seq: " + numRecord + " logli " + logli);
        }
        alpha_Y.assign(0);
        for (int f = 0; f < lambda.length; f++) ExpF[f] = RobustMath.LOG0;

        if ((beta_Y == null) || (beta_Y.length < dataSeq.length())) {
          beta_Y = new DenseDoubleMatrix1D[2 * dataSeq.length()];
          for (int i = 0; i < beta_Y.length; i++) beta_Y[i] = new DenseDoubleMatrix1D(numY);
        }
        // compute beta values in a backward scan.
        // also scale beta-values to 1 to avoid numerical problems.
        beta_Y[dataSeq.length() - 1].assign(0);
        for (int i = dataSeq.length() - 1; i > 0; i--) {
          if (params.debugLvl > 2) {
            /*  Util.printDbg("Features fired");
            featureGenerator.startScanFeaturesAt(dataSeq, i);
            while (featureGenerator.hasNext()) {
            Feature feature = featureGenerator.next();
            Util.printDbg(feature.toString());
            }
            */
          }

          // compute the Mi matrix
          initMDone =
              computeLogMi(
                  featureGenerator, lambda, dataSeq, i, Mi_YY, Ri_Y, false, reuseM, initMDone);
          tmp_Y.assign(beta_Y[i]);
          tmp_Y.assign(Ri_Y, sumFunc);
          RobustMath.logMult(Mi_YY, tmp_Y, beta_Y[i - 1], 1, 0, false, edgeGen);
        }

        double thisSeqLogli = 0;
        for (int i = 0; i < dataSeq.length(); i++) {
          // compute the Mi matrix
          initMDone =
              computeLogMi(
                  featureGenerator, lambda, dataSeq, i, Mi_YY, Ri_Y, false, reuseM, initMDone);
          // find features that fire at this position..
          featureGenerator.startScanFeaturesAt(dataSeq, i);

          if (i > 0) {
            tmp_Y.assign(alpha_Y);
            RobustMath.logMult(Mi_YY, tmp_Y, newAlpha_Y, 1, 0, true, edgeGen);
            newAlpha_Y.assign(Ri_Y, sumFunc);
          } else {
            newAlpha_Y.assign(Ri_Y);
          }

          while (featureGenerator.hasNext()) {
            Feature feature = featureGenerator.next();
            int f = feature.index();

            int yp = feature.y();
            int yprev = feature.yprev();
            float val = feature.value();

            if ((dataSeq.y(i) == yp)
                && (((i - 1 >= 0) && (yprev == dataSeq.y(i - 1))) || (yprev < 0))) {
              grad[f] += val;
              thisSeqLogli += val * lambda[f];
              if (params.debugLvl > 2) {
                System.out.println("Feature fired " + f + " " + feature);
              }
            }

            if (yprev < 0) {
              ExpF[f] =
                  RobustMath.logSumExp(
                      ExpF[f], newAlpha_Y.get(yp) + RobustMath.log(val) + beta_Y[i].get(yp));
            } else {
              ExpF[f] =
                  RobustMath.logSumExp(
                      ExpF[f],
                      alpha_Y.get(yprev)
                          + Ri_Y.get(yp)
                          + Mi_YY.get(yprev, yp)
                          + RobustMath.log(val)
                          + beta_Y[i].get(yp));
            }
          }
          alpha_Y.assign(newAlpha_Y);

          if (params.debugLvl > 2) {
            System.out.println("Alpha-i " + alpha_Y.toString());
            System.out.println("Ri " + Ri_Y.toString());
            System.out.println("Mi " + Mi_YY.toString());
            System.out.println("Beta-i " + beta_Y[i].toString());
          }
        }
        double lZx = RobustMath.logSumExp(alpha_Y);
        thisSeqLogli -= lZx;
        logli += thisSeqLogli;
        // update grad.
        for (int f = 0; f < grad.length; f++) {
          grad[f] -= RobustMath.exp(ExpF[f] - lZx);
        }
        if (params.debugLvl > 1) {
          System.out.println(
              "Sequence "
                  + thisSeqLogli
                  + " logli "
                  + logli
                  + " log(Zx) "
                  + lZx
                  + " Zx "
                  + Math.exp(lZx));
        }
      }
      if (params.debugLvl > 2) {
        for (int f = 0; f < lambda.length; f++) System.out.print(lambda[f] + " ");
        System.out.println(" :x");
        for (int f = 0; f < lambda.length; f++) System.out.print(grad[f] + " ");
        System.out.println(" :g");
      }

      if (params.debugLvl > 0)
        Util.printDbg(
            "Iteration "
                + icall
                + " log-likelihood "
                + logli
                + " norm(grad logli) "
                + norm(grad)
                + " norm(x) "
                + norm(lambda));

    } catch (Exception e) {
      System.out.println("Alpha-i " + alpha_Y.toString());
      System.out.println("Ri " + Ri_Y.toString());
      System.out.println("Mi " + Mi_YY.toString());

      e.printStackTrace();
      System.exit(0);
    }
    return logli;
  }
Esempio n. 7
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  protected double computeFunctionGradient(double lambda[], double grad[]) {
    initMDone = false;

    if (params.trainerType.equals("ll")) return computeFunctionGradientLL(lambda, grad);
    double logli = 0;
    try {
      for (int f = 0; f < lambda.length; f++) {
        grad[f] = -1 * lambda[f] * params.invSigmaSquare;
        logli -= ((lambda[f] * lambda[f]) * params.invSigmaSquare) / 2;
      }
      boolean doScaling = params.doScaling;

      diter.startScan();
      if (featureGenCache != null) featureGenCache.startDataScan();
      int numRecord = 0;
      for (numRecord = 0; diter.hasNext(); numRecord++) {
        DataSequence dataSeq = (DataSequence) diter.next();
        if (featureGenCache != null) featureGenCache.nextDataIndex();
        if (params.debugLvl > 1) {
          Util.printDbg("Read next seq: " + numRecord + " logli " + logli);
        }
        alpha_Y.assign(1);
        for (int f = 0; f < lambda.length; f++) ExpF[f] = 0;

        if ((beta_Y == null) || (beta_Y.length < dataSeq.length())) {
          beta_Y = new DenseDoubleMatrix1D[2 * dataSeq.length()];
          for (int i = 0; i < beta_Y.length; i++) beta_Y[i] = new DenseDoubleMatrix1D(numY);

          scale = new double[2 * dataSeq.length()];
        }
        // compute beta values in a backward scan.
        // also scale beta-values to 1 to avoid numerical problems.
        scale[dataSeq.length() - 1] = (doScaling) ? numY : 1;
        beta_Y[dataSeq.length() - 1].assign(1.0 / scale[dataSeq.length() - 1]);
        for (int i = dataSeq.length() - 1; i > 0; i--) {
          if (params.debugLvl > 2) {
            Util.printDbg("Features fired");
            // featureGenerator.startScanFeaturesAt(dataSeq, i);
            // while (featureGenerator.hasNext()) {
            // Feature feature = featureGenerator.next();
            // Util.printDbg(feature.toString());
            // }
          }

          // compute the Mi matrix
          initMDone =
              computeLogMi(
                  featureGenerator, lambda, dataSeq, i, Mi_YY, Ri_Y, true, reuseM, initMDone);
          tmp_Y.assign(beta_Y[i]);
          tmp_Y.assign(Ri_Y, multFunc);
          RobustMath.Mult(Mi_YY, tmp_Y, beta_Y[i - 1], 1, 0, false, edgeGen);
          //		Mi_YY.zMult(tmp_Y, beta_Y[i-1]);

          // need to scale the beta-s to avoid overflow
          scale[i - 1] = doScaling ? beta_Y[i - 1].zSum() : 1;
          if ((scale[i - 1] < 1) && (scale[i - 1] > -1)) scale[i - 1] = 1;
          constMultiplier.multiplicator = 1.0 / scale[i - 1];
          beta_Y[i - 1].assign(constMultiplier);
        }

        double thisSeqLogli = 0;
        for (int i = 0; i < dataSeq.length(); i++) {
          // compute the Mi matrix
          initMDone =
              computeLogMi(
                  featureGenerator, lambda, dataSeq, i, Mi_YY, Ri_Y, true, reuseM, initMDone);
          // find features that fire at this position..
          featureGenerator.startScanFeaturesAt(dataSeq, i);

          if (i > 0) {
            tmp_Y.assign(alpha_Y);
            RobustMath.Mult(Mi_YY, tmp_Y, newAlpha_Y, 1, 0, true, edgeGen);
            //		Mi_YY.zMult(tmp_Y, newAlpha_Y,1,0,true);
            newAlpha_Y.assign(Ri_Y, multFunc);
          } else {
            newAlpha_Y.assign(Ri_Y);
          }
          while (featureGenerator.hasNext()) {
            Feature feature = featureGenerator.next();
            int f = feature.index();

            int yp = feature.y();
            int yprev = feature.yprev();
            float val = feature.value();
            if ((dataSeq.y(i) == yp)
                && (((i - 1 >= 0) && (yprev == dataSeq.y(i - 1))) || (yprev < 0))) {
              grad[f] += val;
              thisSeqLogli += val * lambda[f];
            }
            if (yprev < 0) {
              ExpF[f] += newAlpha_Y.get(yp) * val * beta_Y[i].get(yp);
            } else {
              ExpF[f] +=
                  alpha_Y.get(yprev)
                      * Ri_Y.get(yp)
                      * Mi_YY.get(yprev, yp)
                      * val
                      * beta_Y[i].get(yp);
            }
          }

          alpha_Y.assign(newAlpha_Y);
          // now scale the alpha-s to avoid overflow problems.
          constMultiplier.multiplicator = 1.0 / scale[i];
          alpha_Y.assign(constMultiplier);

          if (params.debugLvl > 2) {
            System.out.println("Alpha-i " + alpha_Y.toString());
            System.out.println("Ri " + Ri_Y.toString());
            System.out.println("Mi " + Mi_YY.toString());
            System.out.println("Beta-i " + beta_Y[i].toString());
          }
        }
        double Zx = alpha_Y.zSum();
        thisSeqLogli -= log(Zx);
        // correct for the fact that alpha-s were scaled.
        for (int i = 0; i < dataSeq.length(); i++) {
          thisSeqLogli -= log(scale[i]);
        }

        logli += thisSeqLogli;
        // update grad.
        for (int f = 0; f < grad.length; f++) grad[f] -= ExpF[f] / Zx;

        if (params.debugLvl > 1) {
          System.out.println(
              "Sequence "
                  + thisSeqLogli
                  + " logli "
                  + logli
                  + " log(Zx) "
                  + Math.log(Zx)
                  + " Zx "
                  + Zx);
        }
      }
      if (params.debugLvl > 2) {
        for (int f = 0; f < lambda.length; f++) System.out.print(lambda[f] + " ");
        System.out.println(" :x");
        for (int f = 0; f < lambda.length; f++)
          System.out.println(featureGenerator.featureName(f) + " " + grad[f] + " ");
        System.out.println(" :g");
      }

      if (params.debugLvl > 0)
        Util.printDbg(
            "Iter "
                + icall
                + " log likelihood "
                + logli
                + " norm(grad logli) "
                + norm(grad)
                + " norm(x) "
                + norm(lambda));
      if (icall == 0) {
        System.out.println("Number of training records" + numRecord);
      }
    } catch (Exception e) {
      System.out.println("Alpha-i " + alpha_Y.toString());
      System.out.println("Ri " + Ri_Y.toString());
      System.out.println("Mi " + Mi_YY.toString());

      e.printStackTrace();
      System.exit(0);
    }
    return logli;
  }