public static void main (String[] args) throws IOException { if (args.length != 4) { System.err.println("Usage: MultinomialHMM [num topics] [lda state file] [lda keys file] [sequence metadata file]"); System.exit(0); } int numTopics = Integer.parseInt(args[0]); MultinomialHMM hmm = new MultinomialHMM (numTopics, args[1], 150); hmm.setGamma(1.0); hmm.setRandomSeed(1); hmm.loadAlphaFromFile(args[2]); hmm.loadSequenceIDsFromFile(args[3]); hmm.initialize(); hmm.sample(); }
sampleState (doc, random, false); out.print(stateTransitionMatrix()); out.close(); out.print(stateTopics()); out.close();
recacheStateTopicDistribution(state, allTopicsDummy); sampleState(doc, random, true);
recacheStateTopicDistribution(oldState, topicCounts); stateStateTransitions[oldState][nextState]--; if (stateStateTransitions[oldState][nextState] < 0) { System.out.println(printStateTransitions()); System.out.println(oldState + " -> " + nextState); recacheStateTopicDistribution(newState, topicCounts);
loadTopicsFromFile(topicsFilename);
sampleState (doc, random, false); out.print(stateTransitionMatrix()); out.close(); out.print(stateTopics()); out.close();
recacheStateTopicDistribution(state, allTopicsDummy); sampleState(doc, random, true);
recacheStateTopicDistribution(oldState, topicCounts); stateStateTransitions[oldState][nextState]--; if (stateStateTransitions[oldState][nextState] < 0) { System.out.println(printStateTransitions()); System.out.println(oldState + " -> " + nextState); recacheStateTopicDistribution(newState, topicCounts);
loadTopicsFromFile(topicsFilename);
public static void main (String[] args) throws IOException { if (args.length != 4) { System.err.println("Usage: MultinomialHMM [num topics] [lda state file] [lda keys file] [sequence metadata file]"); System.exit(0); } int numTopics = Integer.parseInt(args[0]); MultinomialHMM hmm = new MultinomialHMM (numTopics, args[1], 150); hmm.setGamma(1.0); hmm.setRandomSeed(1); hmm.loadAlphaFromFile(args[2]); hmm.loadSequenceIDsFromFile(args[3]); hmm.initialize(); hmm.sample(); }
sampleState (doc, random, false); out.print(stateTransitionMatrix()); out.close(); out.print(stateTopics()); out.close();
recacheStateTopicDistribution(state, allTopicsDummy); sampleState(doc, random, true);
recacheStateTopicDistribution(oldState, topicCounts); stateStateTransitions[oldState][nextState]--; if (stateStateTransitions[oldState][nextState] < 0) { System.out.println(printStateTransitions()); System.out.println(oldState + " -> " + nextState); recacheStateTopicDistribution(newState, topicCounts);
loadTopicsFromFile(topicsFilename);
public static void main (String[] args) throws IOException { if (args.length != 4) { System.err.println("Usage: MultinomialHMM [num topics] [lda state file] [lda keys file] [sequence metadata file]"); System.exit(0); } int numTopics = Integer.parseInt(args[0]); MultinomialHMM hmm = new MultinomialHMM (numTopics, args[1], 150); hmm.setGamma(1.0); hmm.setRandomSeed(1); hmm.loadAlphaFromFile(args[2]); hmm.loadSequenceIDsFromFile(args[3]); hmm.initialize(); hmm.sample(); }