private NaiveBayesClassifier<L, F> trainClassifier(
int[][] data,
int[] labels,
int numFeatures,
int numClasses,
Index<L> labelIndex,
Index<F> featureIndex) {
Set<L> labelSet = Generics.newHashSet();
NBWeights nbWeights = trainWeights(data, labels, numFeatures, numClasses);
Counter<L> priors = new ClassicCounter<L>();
double[] pr = nbWeights.priors;
for (int i = 0; i < pr.length; i++) {
priors.incrementCount(labelIndex.get(i), pr[i]);
labelSet.add(labelIndex.get(i));
}
Counter<Pair<Pair<L, F>, Number>> weightsCounter =
new ClassicCounter<Pair<Pair<L, F>, Number>>();
double[][][] wts = nbWeights.weights;
for (int c = 0; c < numClasses; c++) {
L label = labelIndex.get(c);
for (int f = 0; f < numFeatures; f++) {
F feature = featureIndex.get(f);
Pair<L, F> p = new Pair<L, F>(label, feature);
for (int val = 0; val < wts[c][f].length; val++) {
Pair<Pair<L, F>, Number> key = new Pair<Pair<L, F>, Number>(p, Integer.valueOf(val));
weightsCounter.incrementCount(key, wts[c][f][val]);
}
}
}
return new NaiveBayesClassifier<L, F>(weightsCounter, priors, labelSet);
}
/**
* Returns a list of all modes in the Collection. (If the Collection has multiple items with the
* highest frequency, all of them will be returned.)
*/
public static <T> Set<T> modes(Collection<T> values) {
Counter<T> counter = new ClassicCounter<T>(values);
List<Double> sortedCounts = CollectionUtils.sorted(counter.values());
Double highestCount = sortedCounts.get(sortedCounts.size() - 1);
Counters.retainAbove(counter, highestCount);
return counter.keySet();
}
/**
* The examples are assumed to be a list of RFVDatum. The datums are assumed to contain the zeroes
* as well.
*/
@Override
@Deprecated
public NaiveBayesClassifier<L, F> trainClassifier(List<RVFDatum<L, F>> examples) {
RVFDatum<L, F> d0 = examples.get(0);
int numFeatures = d0.asFeatures().size();
int[][] data = new int[examples.size()][numFeatures];
int[] labels = new int[examples.size()];
labelIndex = new HashIndex<L>();
featureIndex = new HashIndex<F>();
for (int d = 0; d < examples.size(); d++) {
RVFDatum<L, F> datum = examples.get(d);
Counter<F> c = datum.asFeaturesCounter();
for (F feature : c.keySet()) {
if (featureIndex.add(feature)) {
int fNo = featureIndex.indexOf(feature);
int value = (int) c.getCount(feature);
data[d][fNo] = value;
}
}
labelIndex.add(datum.label());
labels[d] = labelIndex.indexOf(datum.label());
}
int numClasses = labelIndex.size();
return trainClassifier(data, labels, numFeatures, numClasses, labelIndex, featureIndex);
}
/**
* Returns a list of featured thresholded by minPrecision and sorted by their frequency of
* occurrence. precision in this case, is defined as the frequency of majority label over total
* frequency for that feature.
*
* @return list of high precision features.
*/
private List<F> getHighPrecisionFeatures(
GeneralDataset<L, F> dataset, double minPrecision, int maxNumFeatures) {
int[][] feature2label = new int[dataset.numFeatures()][dataset.numClasses()];
for (int f = 0; f < dataset.numFeatures(); f++) Arrays.fill(feature2label[f], 0);
int[][] data = dataset.data;
int[] labels = dataset.labels;
for (int d = 0; d < data.length; d++) {
int label = labels[d];
// System.out.println("datum id:"+d+" label id: "+label);
if (data[d] != null) {
// System.out.println(" number of features:"+data[d].length);
for (int n = 0; n < data[d].length; n++) {
feature2label[data[d][n]][label]++;
}
}
}
Counter<F> feature2freq = new ClassicCounter<F>();
for (int f = 0; f < dataset.numFeatures(); f++) {
int maxF = ArrayMath.max(feature2label[f]);
int total = ArrayMath.sum(feature2label[f]);
double precision = ((double) maxF) / total;
F feature = dataset.featureIndex.get(f);
if (precision >= minPrecision) {
feature2freq.incrementCount(feature, total);
}
}
if (feature2freq.size() > maxNumFeatures) {
Counters.retainTop(feature2freq, maxNumFeatures);
}
// for(F feature : feature2freq.keySet())
// System.out.println(feature+" "+feature2freq.getCount(feature));
// System.exit(0);
return Counters.toSortedList(feature2freq);
}
public static Counter<String> getWeightCounterFromArray(String[] weightNames, double[] wtsArr) {
Counter<String> wts = new ClassicCounter<String>();
for (int i = 0; i < weightNames.length; i++) {
wts.setCount(weightNames[i], wtsArr[i]);
}
return wts;
}
/**
* Add a scaled (positive) random vector to a weights vector.
*
* @param wts
* @param scale
*/
public static void randomizeWeightsInPlace(Counter<String> wts, double scale) {
for (String feature : wts.keySet()) {
double epsilon = Math.random() * scale;
double newValue = wts.getCount(feature) + epsilon;
wts.setCount(feature, newValue);
}
}
/**
* 67% of time spent in LogConditionalObjectiveFunction.rvfcalculate() 29% of time spent in
* dataset construction (11% in RVFDataset.addFeatures(), 7% rvf incrementCount(), 11% rest)
*
* <p>Single threaded, 4700 ms Multi threaded, 700 ms
*
* <p>With same data, seed 42, 245 ms With reordered accesses for cacheing, 195 ms Down to 80% of
* the time, not huge but a win nonetheless
*
* <p>with 8 cpus, a 6.7x speedup -- almost, but not quite linear, pretty good
*/
public static void benchmarkRVFLogisticRegression() {
RVFDataset<String, String> data = new RVFDataset<>();
for (int i = 0; i < 10000; i++) {
Random r = new Random(42);
Counter<String> features = new ClassicCounter<>();
boolean cl = r.nextBoolean();
for (int j = 0; j < 1000; j++) {
double value;
if (cl && i % 2 == 0) {
value = (r.nextDouble() * 2.0) - 0.6;
} else {
value = (r.nextDouble() * 2.0) - 1.4;
}
features.incrementCount("f" + j, value);
}
data.add(new RVFDatum<>(features, "target:" + cl));
}
LinearClassifierFactory<String, String> factory = new LinearClassifierFactory<>();
long msStart = System.currentTimeMillis();
factory.trainClassifier(data);
long delay = System.currentTimeMillis() - msStart;
System.out.println("Training took " + delay + " ms");
}
public Counter<K> uncompress(CompressedFeatureVector cvf) {
Counter<K> c = new ClassicCounter<>();
for (int i = 0; i < cvf.keys.size(); i++) {
c.incrementCount(inverse.get(cvf.keys.get(i)), cvf.values.get(i));
}
return c;
}
@SuppressWarnings({"unchecked"})
@Override
protected void fillFeatures(
Pair<Mention, ClusteredMention> input,
Counter<Feature> inFeatures,
Boolean output,
Counter<Feature> outFeatures) {
// --Input Features
for (Object o : ACTIVE_FEATURES) {
if (o instanceof Class) {
// (case: singleton feature)
Option<Double> count = new Option<Double>(1.0);
Feature feat = feature((Class) o, input, count);
if (count.get() > 0.0) {
inFeatures.incrementCount(feat, count.get());
}
} else if (o instanceof Pair) {
// (case: pair of features)
Pair<Class, Class> pair = (Pair<Class, Class>) o;
Option<Double> countA = new Option<Double>(1.0);
Option<Double> countB = new Option<Double>(1.0);
Feature featA = feature(pair.getFirst(), input, countA);
Feature featB = feature(pair.getSecond(), input, countB);
if (countA.get() * countB.get() > 0.0) {
inFeatures.incrementCount(
new Feature.PairFeature(featA, featB), countA.get() * countB.get());
}
}
}
// --Output Features
if (output != null) {
outFeatures.incrementCount(new Feature.CoreferentIndicator(output), 1.0);
}
}
public static <T> Counter<T> featureValueCollectionToCounter(Collection<FeatureValue<T>> c) {
Counter<T> counter = new ClassicCounter<T>();
for (FeatureValue<T> fv : c) {
counter.incrementCount(fv.name, fv.value);
}
return counter;
}
private double[] getModelProbs(Datum<L, F> datum) {
double[] condDist = new double[labeledDataset.numClasses()];
Counter<L> probCounter = classifier.probabilityOf(datum);
for (L label : probCounter.keySet()) {
int labelID = labeledDataset.labelIndex.indexOf(label);
condDist[labelID] = probCounter.getCount(label);
}
return condDist;
}
@Test
public void tokenMatch() {
String[] text = new String[] {"what", "tv", "program", "have", "hugh", "laurie", "create"};
String[] pattern = new String[] {"program", "create"};
Counter<String> match =
TokenLevelMatchFeatures.extractTokenMatchFeatures(
Arrays.asList(text), Arrays.asList(pattern), true);
assertEquals(0.5, match.getCount("prefix"), 0.00001);
assertEquals(0.5, match.getCount("suffix"), 0.00001);
}
private Counter<String> uniformRandom() {
Counter<String> uniformRandom =
new ClassicCounter<>(MapFactory.<String, MutableDouble>linkedHashMapFactory());
for (Map<SentenceKey, EnsembleStatistics> impl : this.impl) {
for (Map.Entry<SentenceKey, EnsembleStatistics> entry : impl.entrySet()) {
uniformRandom.setCount(entry.getKey().sentenceHash, 1.0);
}
}
return uniformRandom;
}
public static List<String> generateDict(List<String> str, int cutOff) {
Counter<String> freq = new IntCounter<>();
for (String aStr : str) freq.incrementCount(aStr);
List<String> keys = Counters.toSortedList(freq, false);
List<String> dict = new ArrayList<>();
for (String word : keys) {
if (freq.getCount(word) >= cutOff) dict.add(word);
}
return dict;
}
private Counter<String> highKLFromMean() {
// Get confidences
Counter<String> kl =
new ClassicCounter<>(MapFactory.<String, MutableDouble>linkedHashMapFactory());
for (Map<SentenceKey, EnsembleStatistics> impl : this.impl) {
for (Map.Entry<SentenceKey, EnsembleStatistics> entry : impl.entrySet()) {
kl.setCount(entry.getKey().sentenceHash, entry.getValue().averageKLFromMean());
}
}
return kl;
}
public void addCrossNumericProximity(Counter<String> features, final NumericMentionExpression e) {
List<NumericTuple> args = e.expression.arguments();
if (args.size() > 1) {
double multiplier = args.get(0).val / args.get(1).val;
features.incrementCount("abs-numeric-distance-12", Math.abs(Math.log(multiplier)));
}
if (args.size() > 2) {
double multiplier13 = args.get(0).val / args.get(2).val;
double multiplier23 = args.get(1).val / args.get(2).val;
features.incrementCount("abs-numeric-distance-13", Math.abs(Math.log(multiplier13)));
features.incrementCount("abs-numeric-distance-23", Math.abs(Math.log(multiplier23)));
}
}
/**
* TODO(gabor) JavaDoc
*
* @param tokens
* @param span
* @return
*/
public static String guessNER(List<CoreLabel> tokens, Span span) {
Counter<String> nerGuesses = new ClassicCounter<>();
for (int i : span) {
nerGuesses.incrementCount(tokens.get(i).ner());
}
nerGuesses.remove("O");
nerGuesses.remove(null);
if (nerGuesses.size() > 0 && Counters.max(nerGuesses) >= span.size() / 2) {
return Counters.argmax(nerGuesses);
} else {
return "O";
}
}
@Override
public Counter<L> scoresOf(Datum<L, F> example) {
Counter<L> scores = new ClassicCounter<>();
for (L label : labelIndex) {
Map<L, String> posLabelMap = new ArrayMap<>();
posLabelMap.put(label, POS_LABEL);
Datum<String, F> binDatum = GeneralDataset.mapDatum(example, posLabelMap, NEG_LABEL);
Classifier<String, F> binaryClassifier = getBinaryClassifier(label);
Counter<String> binScores = binaryClassifier.scoresOf(binDatum);
double score = binScores.getCount(POS_LABEL);
scores.setCount(label, score);
}
return scores;
}
private Counter<String> lowAverageConfidence() {
// Get confidences
Counter<String> lowConfidence =
new ClassicCounter<>(MapFactory.<String, MutableDouble>linkedHashMapFactory());
for (Map<SentenceKey, EnsembleStatistics> impl : this.impl) {
for (Map.Entry<SentenceKey, EnsembleStatistics> entry : impl.entrySet()) {
SentenceStatistics average = entry.getValue().mean();
for (double confidence : average.confidence) {
lowConfidence.setCount(entry.getKey().sentenceHash, 1 - confidence);
}
}
}
return lowConfidence;
}
public Object formResult() {
Set brs = new HashSet();
Set urs = new HashSet();
// scan each rule / history pair
int ruleCount = 0;
for (Iterator pairI = rulePairs.keySet().iterator(); pairI.hasNext(); ) {
if (ruleCount % 100 == 0) {
System.err.println("Rules multiplied: " + ruleCount);
}
ruleCount++;
Pair rulePair = (Pair) pairI.next();
Rule baseRule = (Rule) rulePair.first;
String baseLabel = (String) ruleToLabel.get(baseRule);
List history = (List) rulePair.second;
double totalProb = 0;
for (int depth = 1; depth <= HISTORY_DEPTH() && depth <= history.size(); depth++) {
List subHistory = history.subList(0, depth);
double c_label = labelPairs.getCount(new Pair(baseLabel, subHistory));
double c_rule = rulePairs.getCount(new Pair(baseRule, subHistory));
// System.out.println("Multiplying out "+baseRule+" with history "+subHistory);
// System.out.println("Count of "+baseLabel+" with "+subHistory+" is "+c_label);
// System.out.println("Count of "+baseRule+" with "+subHistory+" is "+c_rule );
double prob = (1.0 / HISTORY_DEPTH()) * (c_rule) / (c_label);
totalProb += prob;
for (int childDepth = 0; childDepth <= Math.min(HISTORY_DEPTH() - 1, depth); childDepth++) {
Rule rule = specifyRule(baseRule, subHistory, childDepth);
rule.score = (float) Math.log(totalProb);
// System.out.println("Created "+rule+" with score "+rule.score);
if (rule instanceof UnaryRule) {
urs.add(rule);
} else {
brs.add(rule);
}
}
}
}
System.out.println("Total states: " + stateNumberer.total());
BinaryGrammar bg = new BinaryGrammar(stateNumberer.total());
UnaryGrammar ug = new UnaryGrammar(stateNumberer.total());
for (Iterator brI = brs.iterator(); brI.hasNext(); ) {
BinaryRule br = (BinaryRule) brI.next();
bg.addRule(br);
}
for (Iterator urI = urs.iterator(); urI.hasNext(); ) {
UnaryRule ur = (UnaryRule) urI.next();
ug.addRule(ur);
}
return new Pair(ug, bg);
}
protected void tallyInternalNode(Tree lt, List parents) {
// form base rule
String label = lt.label().value();
Rule baseR = ltToRule(lt);
ruleToLabel.put(baseR, label);
// act on each history depth
for (int depth = 0, maxDepth = Math.min(HISTORY_DEPTH(), parents.size());
depth <= maxDepth;
depth++) {
List history = new ArrayList(parents.subList(0, depth));
// tally each history level / rewrite pair
rulePairs.incrementCount(new Pair(baseR, history), 1);
labelPairs.incrementCount(new Pair(label, history), 1);
}
}
protected void semanticCrossFeatures(
Counter<String> features, String prefix, Sentence str1, Sentence str2) {
double[] vec1 = embeddings.get(str1);
double[] vec2 = embeddings.get(str2);
for (int i = 0; i < vec1.length; i++)
features.incrementCount(prefix + "wv-" + i, vec1[i] - vec2[i]);
}
protected void semanticCrossFeatures(
Counter<String> features, String prefix, NumericMention mention, Sentence str2) {
double[] vec1 = embeddings.get(mention.sentence.get(), mention.token_begin, mention.token_end);
double[] vec2 = embeddings.get(str2);
for (int i = 0; i < vec1.length; i++)
features.incrementCount(prefix + "wv-" + i, vec1[i] - vec2[i]);
}
public static Set<String> featureWhiteList(FlatNBestList nbest, int minSegmentCount) {
List<List<ScoredFeaturizedTranslation<IString, String>>> nbestlists = nbest.nbestLists();
Counter<String> featureSegmentCounts = new ClassicCounter<String>();
for (List<ScoredFeaturizedTranslation<IString, String>> nbestlist : nbestlists) {
Set<String> segmentFeatureSet = new HashSet<String>();
for (ScoredFeaturizedTranslation<IString, String> trans : nbestlist) {
for (FeatureValue<String> feature : trans.features) {
segmentFeatureSet.add(feature.name);
}
}
for (String featureName : segmentFeatureSet) {
featureSegmentCounts.incrementCount(featureName);
}
}
return Counters.keysAbove(featureSegmentCounts, minSegmentCount - 1);
}
public void addCrossArgumentSemanticSimilarity(
Counter<String> features, final NumericMentionExpression e) {
List<NumericTuple> args = e.expression.arguments();
double sim = 0.;
double minSim = 0.;
double maxSim = 0.;
if (args.size() > 1) {
sim =
semanticSimilarityVW(features, "12-", args.get(0).subjSentence, args.get(1).subjSentence);
maxSim = Math.max(maxSim, sim);
minSim = Math.min(minSim, sim);
}
if (args.size() > 2) {
sim =
semanticSimilarityVW(features, "13-", args.get(0).subjSentence, args.get(2).subjSentence);
maxSim = Math.max(maxSim, sim);
minSim = Math.min(minSim, sim);
sim =
semanticSimilarityVW(features, "23-", args.get(1).subjSentence, args.get(2).subjSentence);
maxSim = Math.max(maxSim, sim);
minSim = Math.min(minSim, sim);
}
features.incrementCount("max-cross-semantic-similarity", maxSim);
features.incrementCount("min-cross-semantic-similarity", minSim);
}
public static double[] getWeightArrayFromCounter(String[] weightNames, Counter<String> wts) {
double[] wtsArr = new double[weightNames.length];
for (int i = 0; i < wtsArr.length; i++) {
wtsArr[i] = wts.getCount(weightNames[i]);
}
return wtsArr;
}
public static double scoreTranslation(
Counter<String> wts, ScoredFeaturizedTranslation<IString, String> trans) {
double s = 0;
for (FeatureValue<String> fv : trans.features) {
s += fv.value * wts.getCount(fv.name);
}
return s;
}
/**
* This should be called after the classifier has been trained and parseAndTrain has been called
* to accumulate test set
*
* <p>This will return precision,recall and F1 measure
*/
public void runTestSet(List<List<CoreLabel>> testSet) {
Counter<String> tp = new DefaultCounter<>();
Counter<String> fp = new DefaultCounter<>();
Counter<String> fn = new DefaultCounter<>();
Counter<String> actual = new DefaultCounter<>();
for (List<CoreLabel> labels : testSet) {
List<CoreLabel> unannotatedLabels = new ArrayList<>();
// create a new label without answer annotation
for (CoreLabel label : labels) {
CoreLabel newLabel = new CoreLabel();
newLabel.set(annotationForWord, label.get(annotationForWord));
newLabel.set(PartOfSpeechAnnotation.class, label.get(PartOfSpeechAnnotation.class));
unannotatedLabels.add(newLabel);
}
List<CoreLabel> annotatedLabels = this.classifier.classify(unannotatedLabels);
int ind = 0;
for (CoreLabel expectedLabel : labels) {
CoreLabel annotatedLabel = annotatedLabels.get(ind);
String answer = annotatedLabel.get(AnswerAnnotation.class);
String expectedAnswer = expectedLabel.get(AnswerAnnotation.class);
actual.incrementCount(expectedAnswer);
// match only non background symbols
if (!SeqClassifierFlags.DEFAULT_BACKGROUND_SYMBOL.equals(expectedAnswer)
&& expectedAnswer.equals(answer)) {
// true positives
tp.incrementCount(answer);
System.out.println("True Positive:" + annotatedLabel);
} else if (!SeqClassifierFlags.DEFAULT_BACKGROUND_SYMBOL.equals(answer)) {
// false positives
fp.incrementCount(answer);
System.out.println("False Positive:" + annotatedLabel);
} else if (!SeqClassifierFlags.DEFAULT_BACKGROUND_SYMBOL.equals(expectedAnswer)) {
// false negatives
fn.incrementCount(expectedAnswer);
System.out.println("False Negative:" + expectedLabel);
} // else true negatives
ind++;
}
}
actual.remove(SeqClassifierFlags.DEFAULT_BACKGROUND_SYMBOL);
}
@Override
public boolean isSimpleSplit(Counter<String> feats) {
for (String key : feats.keySet()) {
if (key.startsWith("simple&")) {
return true;
}
}
return false;
}
@Deprecated
protected void semanticSimilarity(
Counter<String> features, String prefix, Sentence str1, Sentence str2) {
Counter<String> v1 =
new ClassicCounter<>(
str1.lemmas().stream().map(String::toLowerCase).collect(Collectors.toList()));
Counter<String> v2 = new ClassicCounter<>(str2.lemmas());
// Remove any stopwords.
for (String word : stopwords) {
v1.remove(word);
v2.remove(word);
}
// take inner product.
double sim =
Counters.dotProduct(v1, v2) / (Counters.saferL2Norm(v1) * Counters.saferL2Norm(v2));
features.incrementCount(
prefix + "semantic-similarity", 2 * sim - 1); // to make it between 0 and 1.
}
