670 lines
22 KiB
Java
670 lines
22 KiB
Java
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/*
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* Copyright (C) 2007 by
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*
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* Xuan-Hieu Phan
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* hieuxuan@ecei.tohoku.ac.jp or pxhieu@gmail.com
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* Graduate School of Information Sciences
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* Tohoku University
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*
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* Cam-Tu Nguyen
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* ncamtu@gmail.com
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* College of Technology
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* Vietnam National University, Hanoi
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*
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* JGibbsLDA is a free software; you can redistribute it and/or modify
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* it under the terms of the GNU General Public License as published
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* by the Free Software Foundation; either version 2 of the License,
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* or (at your option) any later version.
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*
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* JGibbsLDA is distributed in the hope that it will be useful, but
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* WITHOUT ANY WARRANTY; without even the implied warranty of
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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* GNU General Public License for more details.
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*
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* You should have received a copy of the GNU General Public License
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* along with JGibbsLDA; if not, write to the Free Software Foundation,
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* Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
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*/
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package jgibblda;
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import java.io.BufferedReader;
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import java.io.BufferedWriter;
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import java.io.File;
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import java.io.FileInputStream;
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import java.io.FileNotFoundException;
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import java.io.FileOutputStream;
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import java.io.IOException;
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import java.io.InputStreamReader;
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import java.io.OutputStreamWriter;
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import java.util.ArrayList;
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import java.util.Collections;
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import java.util.StringTokenizer;
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import java.util.zip.GZIPInputStream;
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import java.util.zip.GZIPOutputStream;
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import gnu.trove.list.array.TIntArrayList;
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import gnu.trove.map.hash.TIntObjectHashMap;
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public class Model {
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//---------------------------------------------------------------
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// Class Variables
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//---------------------------------------------------------------
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public static String tassignSuffix = ".tassign.gz"; // suffix for topic assignment file
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public static String thetaSuffix = ".theta.gz"; // suffix for theta (topic - document distribution) file
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public static String phiSuffix = ".phi.gz"; // suffix for phi file (topic - word distribution) file
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public static String othersSuffix = ".others.gz"; // suffix for containing other parameters
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public static String twordsSuffix = ".twords.gz"; // suffix for file containing words-per-topics
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public static String wordMapSuffix = ".wordmap.gz"; // suffix for file containing word to id map
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//---------------------------------------------------------------
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// Model Parameters and Variables
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//---------------------------------------------------------------
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public String dir = "./";
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public String dfile = "trndocs.dat";
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public boolean unlabeled = false;
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public String modelName = "model";
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public LDADataset data; // link to a dataset
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public int M = 0; // dataset size (i.e., number of docs)
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public int V = 0; // vocabulary size
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public int K = 100; // number of topics
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public double alpha; // LDA hyperparameters
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public double beta = 0.01; // LDA hyperparameters
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public int niters = 1000; // number of Gibbs sampling iteration
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public int nburnin = 500; // number of Gibbs sampling burn-in iterations
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public int samplingLag = 5;// Gibbs sampling sample lag
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public int numSamples = 1; // number of samples taken
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public int liter = 0; // the iteration at which the model was saved
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public int twords = 20; // print out top words per each topic
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// Estimated/Inferenced parameters
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public double[][] theta = null; // theta: document - topic distributions, size M x K
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public double[][] phi = null; // phi: topic-word distributions, size K x V
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// Temp variables while sampling
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public TIntArrayList[] z = null; // topic assignments for words, size M x doc.size()
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protected int[][] nw = null; // nw[i][j]: number of instances of word/term i assigned to topic j, size V x K
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protected int[][] nd = null; // nd[i][j]: number of words in document i assigned to topic j, size M x K
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protected int[] nwsum = null; // nwsum[j]: total number of words assigned to topic j, size K
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protected int[] ndsum = null; // ndsum[i]: total number of words in document i, size M
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protected ArrayList<TIntObjectHashMap<int[]>> nw_inf = null; // nw[m][i][j]: number of instances of word/term i assigned to topic j in doc m, size M x V x K
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protected int[][] nwsum_inf = null; // nwsum[m][j]: total number of words assigned to topic j in doc m, size M x K
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// temp variables for sampling
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protected double[] p = null;
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//---------------------------------------------------------------
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// Constructors
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//---------------------------------------------------------------
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public Model(LDACmdOption option) throws FileNotFoundException, IOException
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{
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this(option, null);
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}
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public Model(LDACmdOption option, Model trnModel) throws FileNotFoundException, IOException
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{
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modelName = option.modelName;
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K = option.K;
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alpha = option.alpha;
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if (alpha < 0.0)
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alpha = 50.0 / K;
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if (option.beta >= 0)
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beta = option.beta;
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niters = option.niters;
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nburnin = option.nburnin;
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samplingLag = option.samplingLag;
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dir = option.dir;
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if (dir.endsWith(File.separator))
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dir = dir.substring(0, dir.length() - 1);
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dfile = option.dfile;
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unlabeled = option.unlabeled;
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twords = option.twords;
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// initialize dataset
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data = new LDADataset();
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// process trnModel (if given)
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if (trnModel != null) {
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data.setDictionary(trnModel.data.localDict);
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K = trnModel.K;
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// use hyperparameters from model (if not overridden in options)
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if (option.alpha < 0.0)
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alpha = trnModel.alpha;
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if (option.beta < 0.0)
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beta = trnModel.beta;
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}
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// read in data
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data.readDataSet(dir + File.separator + dfile, unlabeled);
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}
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//---------------------------------------------------------------
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// Init Methods
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//---------------------------------------------------------------
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/**
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* Init parameters for estimation or inference
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*/
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public boolean init(boolean random)
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{
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if (random) {
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M = data.M;
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V = data.V;
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z = new TIntArrayList[M];
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} else {
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if (!loadModel()) {
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System.out.println("Fail to load word-topic assignment file of the model!");
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return false;
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}
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// debug output
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System.out.println("Model loaded:");
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System.out.println("\talpha:" + alpha);
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System.out.println("\tbeta:" + beta);
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System.out.println("\tK:" + K);
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System.out.println("\tM:" + M);
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System.out.println("\tV:" + V);
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}
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p = new double[K];
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initSS();
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for (int m = 0; m < data.M; m++){
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if (random) {
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z[m] = new TIntArrayList();
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}
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// initilize for z
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int N = data.docs.get(m).length;
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for (int n = 0; n < N; n++){
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int w = data.docs.get(m).words[n];
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int topic;
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// random init a topic or load existing topic from z[m]
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if (random) {
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topic = (int)Math.floor(Math.random() * K);
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z[m].add(topic);
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} else {
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topic = z[m].get(n);
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}
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nw[w][topic]++; // number of instances of word assigned to topic j
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nd[m][topic]++; // number of words in document i assigned to topic j
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nwsum[topic]++; // total number of words assigned to topic j
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}
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ndsum[m] = N; // total number of words in document i
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}
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theta = new double[M][K];
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phi = new double[K][V];
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return true;
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}
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public boolean initInf()
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{
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nw_inf = new ArrayList<TIntObjectHashMap<int[]>>();
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nwsum_inf = new int[M][K];
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for (int m = 0; m < M; m++) {
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for (int k = 0; k < K; k++) {
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nwsum_inf[m][k] = 0;
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}
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}
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for (int m = 0; m < data.M; m++){
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nw_inf.add(m, new TIntObjectHashMap<int[]>());
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// initilize for z
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int N = data.docs.get(m).length;
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for (int n = 0; n < N; n++){
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int w = data.docs.get(m).words[n];
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int topic = z[m].get(n);
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if (!nw_inf.get(m).containsKey(w)) {
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int[] nw_inf_m_w = new int[K];
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for (int k = 0; k < K; k++) {
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nw_inf_m_w[k] = 0;
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}
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nw_inf.get(m).put(w, nw_inf_m_w);
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}
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nw_inf.get(m).get(w)[topic]++; // number of instances of word assigned to topic j in doc m
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//nw_inf[m][w][topic]++; // number of instances of word assigned to topic j in doc m
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nwsum_inf[m][topic]++; // total number of words assigned to topic j in doc m
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}
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}
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return true;
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}
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/**
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* Init sufficient stats
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*/
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protected void initSS()
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{
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nw = new int[V][K];
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for (int w = 0; w < V; w++){
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for (int k = 0; k < K; k++){
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nw[w][k] = 0;
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}
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}
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nd = new int[M][K];
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for (int m = 0; m < M; m++){
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for (int k = 0; k < K; k++){
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nd[m][k] = 0;
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}
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}
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nwsum = new int[K];
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for (int k = 0; k < K; k++){
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nwsum[k] = 0;
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}
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ndsum = new int[M];
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for (int m = 0; m < M; m++){
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ndsum[m] = 0;
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}
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}
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//---------------------------------------------------------------
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// Update Methods
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//---------------------------------------------------------------
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public void updateParams()
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{
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updateTheta();
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updatePhi();
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numSamples++;
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}
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public void updateParams(Model trnModel)
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{
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updateTheta();
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updatePhi(trnModel);
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numSamples++;
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}
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public void updateTheta()
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{
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double Kalpha = K * alpha;
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for (int m = 0; m < M; m++) {
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for (int k = 0; k < K; k++) {
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if (numSamples > 1) theta[m][k] *= numSamples - 1; // convert from mean to sum
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theta[m][k] += (nd[m][k] + alpha) / (ndsum[m] + Kalpha);
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if (numSamples > 1) theta[m][k] /= numSamples; // convert from sum to mean
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}
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}
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}
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public void updatePhi()
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{
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double Vbeta = V * beta;
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for (int k = 0; k < K; k++) {
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for (int w = 0; w < V; w++) {
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if (numSamples > 1) phi[k][w] *= numSamples - 1; // convert from mean to sum
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phi[k][w] += (nw[w][k] + beta) / (nwsum[k] + Vbeta);
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if (numSamples > 1) phi[k][w] /= numSamples; // convert from sum to mean
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}
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}
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}
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// for inference
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public void updatePhi(Model trnModel)
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{
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double Vbeta = trnModel.V * beta;
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for (int k = 0; k < K; k++) {
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for (int _w = 0; _w < V; _w++) {
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if (data.lid2gid.containsKey(_w)) {
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int id = data.lid2gid.get(_w);
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if (numSamples > 1) phi[k][_w] *= numSamples - 1; // convert from mean to sum
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phi[k][_w] += (trnModel.nw[id][k] + nw[_w][k] + beta) / (trnModel.nwsum[k] + nwsum[k] + Vbeta);
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if (numSamples > 1) phi[k][_w] /= numSamples; // convert from sum to mean
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} // else ignore words that don't appear in training
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} //end foreach word
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} // end foreach topic
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}
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//---------------------------------------------------------------
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// I/O Methods
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//---------------------------------------------------------------
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/**
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* Save model
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*/
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public boolean saveModel()
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{
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return saveModel("");
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}
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public boolean saveModel(String modelPrefix)
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{
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if (!saveModelTAssign(dir + File.separator + modelPrefix + modelName + tassignSuffix)) {
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return false;
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}
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if (!saveModelOthers(dir + File.separator + modelPrefix + modelName + othersSuffix)) {
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return false;
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}
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if (!saveModelTheta(dir + File.separator + modelPrefix + modelName + thetaSuffix)) {
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return false;
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}
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//if (!saveModelPhi(dir + File.separator + modelPrefix + modelName + phiSuffix)) {
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// return false;
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//}
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if (twords > 0) {
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if (!saveModelTwords(dir + File.separator + modelPrefix + modelName + twordsSuffix)) {
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return false;
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}
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}
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if (!data.localDict.writeWordMap(dir + File.separator + modelPrefix + modelName + wordMapSuffix)) {
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return false;
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}
|
||
|
|
|
||
|
|
return true;
|
||
|
|
}
|
||
|
|
|
||
|
|
/**
|
||
|
|
* Save word-topic assignments for this model
|
||
|
|
*/
|
||
|
|
public boolean saveModelTAssign(String filename) {
|
||
|
|
int i, j;
|
||
|
|
|
||
|
|
try{
|
||
|
|
BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(
|
||
|
|
new GZIPOutputStream(
|
||
|
|
new FileOutputStream(filename)), "UTF-8"));
|
||
|
|
|
||
|
|
//write docs with topic assignments for words
|
||
|
|
for (i = 0; i < data.M; i++) {
|
||
|
|
for (j = 0; j < data.docs.get(i).length; ++j) {
|
||
|
|
writer.write(data.docs.get(i).words[j] + ":" + z[i].get(j) + " ");
|
||
|
|
}
|
||
|
|
writer.write("\n");
|
||
|
|
}
|
||
|
|
|
||
|
|
writer.close();
|
||
|
|
}
|
||
|
|
catch (Exception e) {
|
||
|
|
System.out.println("Error while saving model tassign: " + e.getMessage());
|
||
|
|
e.printStackTrace();
|
||
|
|
return false;
|
||
|
|
}
|
||
|
|
return true;
|
||
|
|
}
|
||
|
|
|
||
|
|
/**
|
||
|
|
* Save theta (topic distribution) for this model
|
||
|
|
*/
|
||
|
|
public boolean saveModelTheta(String filename) {
|
||
|
|
try{
|
||
|
|
BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(
|
||
|
|
new GZIPOutputStream(
|
||
|
|
new FileOutputStream(filename)), "UTF-8"));
|
||
|
|
|
||
|
|
for (int i = 0; i < M; i++) {
|
||
|
|
for (int j = 0; j < K; j++) {
|
||
|
|
if (theta[i][j] > 0) {
|
||
|
|
writer.write(j + ":" + theta[i][j] + " ");
|
||
|
|
}
|
||
|
|
}
|
||
|
|
writer.write("\n");
|
||
|
|
}
|
||
|
|
writer.close();
|
||
|
|
}
|
||
|
|
catch (Exception e){
|
||
|
|
System.out.println("Error while saving topic distribution file for this model: " + e.getMessage());
|
||
|
|
e.printStackTrace();
|
||
|
|
return false;
|
||
|
|
}
|
||
|
|
return true;
|
||
|
|
}
|
||
|
|
|
||
|
|
/**
|
||
|
|
* Save word-topic distribution
|
||
|
|
*/
|
||
|
|
public boolean saveModelPhi(String filename)
|
||
|
|
{
|
||
|
|
try {
|
||
|
|
BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(
|
||
|
|
new GZIPOutputStream(
|
||
|
|
new FileOutputStream(filename)), "UTF-8"));
|
||
|
|
|
||
|
|
for (int i = 0; i < K; i++) {
|
||
|
|
for (int j = 0; j < V; j++) {
|
||
|
|
if (phi[i][j] > 0) {
|
||
|
|
writer.write(j + ":" + phi[i][j] + " ");
|
||
|
|
}
|
||
|
|
}
|
||
|
|
writer.write("\n");
|
||
|
|
}
|
||
|
|
writer.close();
|
||
|
|
}
|
||
|
|
catch (Exception e) {
|
||
|
|
System.out.println("Error while saving word-topic distribution:" + e.getMessage());
|
||
|
|
e.printStackTrace();
|
||
|
|
return false;
|
||
|
|
}
|
||
|
|
return true;
|
||
|
|
}
|
||
|
|
|
||
|
|
/**
|
||
|
|
* Save other information of this model
|
||
|
|
*/
|
||
|
|
public boolean saveModelOthers(String filename){
|
||
|
|
try{
|
||
|
|
BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(
|
||
|
|
new GZIPOutputStream(
|
||
|
|
new FileOutputStream(filename)), "UTF-8"));
|
||
|
|
|
||
|
|
writer.write("alpha=" + alpha + "\n");
|
||
|
|
writer.write("beta=" + beta + "\n");
|
||
|
|
writer.write("ntopics=" + K + "\n");
|
||
|
|
writer.write("ndocs=" + M + "\n");
|
||
|
|
writer.write("nwords=" + V + "\n");
|
||
|
|
writer.write("liters=" + liter + "\n");
|
||
|
|
|
||
|
|
writer.close();
|
||
|
|
}
|
||
|
|
catch(Exception e){
|
||
|
|
System.out.println("Error while saving model others:" + e.getMessage());
|
||
|
|
e.printStackTrace();
|
||
|
|
return false;
|
||
|
|
}
|
||
|
|
return true;
|
||
|
|
}
|
||
|
|
|
||
|
|
/**
|
||
|
|
* Save model the most likely words for each topic
|
||
|
|
*/
|
||
|
|
public boolean saveModelTwords(String filename){
|
||
|
|
try{
|
||
|
|
BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(
|
||
|
|
new GZIPOutputStream(
|
||
|
|
new FileOutputStream(filename)), "UTF-8"));
|
||
|
|
|
||
|
|
if (twords > V){
|
||
|
|
twords = V;
|
||
|
|
}
|
||
|
|
|
||
|
|
for (int k = 0; k < K; k++){
|
||
|
|
ArrayList<Pair> wordsProbsList = new ArrayList<Pair>();
|
||
|
|
for (int w = 0; w < V; w++){
|
||
|
|
Pair p = new Pair(w, phi[k][w], false);
|
||
|
|
|
||
|
|
wordsProbsList.add(p);
|
||
|
|
}//end foreach word
|
||
|
|
|
||
|
|
//print topic
|
||
|
|
writer.write("Topic " + k + ":\n");
|
||
|
|
Collections.sort(wordsProbsList);
|
||
|
|
|
||
|
|
for (int i = 0; i < twords; i++){
|
||
|
|
if (data.localDict.contains((Integer)wordsProbsList.get(i).first)){
|
||
|
|
String word = data.localDict.getWord((Integer)wordsProbsList.get(i).first);
|
||
|
|
|
||
|
|
writer.write("\t" + word + "\t" + wordsProbsList.get(i).second + "\n");
|
||
|
|
}
|
||
|
|
}
|
||
|
|
} //end foreach topic
|
||
|
|
|
||
|
|
writer.close();
|
||
|
|
}
|
||
|
|
catch(Exception e){
|
||
|
|
System.out.println("Error while saving model twords: " + e.getMessage());
|
||
|
|
e.printStackTrace();
|
||
|
|
return false;
|
||
|
|
}
|
||
|
|
return true;
|
||
|
|
}
|
||
|
|
|
||
|
|
/**
|
||
|
|
* Load saved model
|
||
|
|
*/
|
||
|
|
public boolean loadModel(){
|
||
|
|
if (!readOthersFile(dir + File.separator + modelName + othersSuffix))
|
||
|
|
return false;
|
||
|
|
|
||
|
|
if (!readTAssignFile(dir + File.separator + modelName + tassignSuffix))
|
||
|
|
return false;
|
||
|
|
|
||
|
|
// read dictionary
|
||
|
|
Dictionary dict = new Dictionary();
|
||
|
|
if (!dict.readWordMap(dir + File.separator + modelName + wordMapSuffix))
|
||
|
|
return false;
|
||
|
|
|
||
|
|
data.localDict = dict;
|
||
|
|
|
||
|
|
return true;
|
||
|
|
}
|
||
|
|
|
||
|
|
/**
|
||
|
|
* Load "others" file to get parameters
|
||
|
|
*/
|
||
|
|
protected boolean readOthersFile(String otherFile){
|
||
|
|
try {
|
||
|
|
BufferedReader reader = new BufferedReader(new InputStreamReader(
|
||
|
|
new GZIPInputStream(
|
||
|
|
new FileInputStream(otherFile)), "UTF-8"));
|
||
|
|
String line;
|
||
|
|
while((line = reader.readLine()) != null){
|
||
|
|
StringTokenizer tknr = new StringTokenizer(line,"= \t\r\n");
|
||
|
|
|
||
|
|
int count = tknr.countTokens();
|
||
|
|
if (count != 2)
|
||
|
|
continue;
|
||
|
|
|
||
|
|
String optstr = tknr.nextToken();
|
||
|
|
String optval = tknr.nextToken();
|
||
|
|
|
||
|
|
if (optstr.equalsIgnoreCase("alpha")){
|
||
|
|
alpha = Double.parseDouble(optval);
|
||
|
|
}
|
||
|
|
else if (optstr.equalsIgnoreCase("beta")){
|
||
|
|
beta = Double.parseDouble(optval);
|
||
|
|
}
|
||
|
|
else if (optstr.equalsIgnoreCase("ntopics")){
|
||
|
|
K = Integer.parseInt(optval);
|
||
|
|
}
|
||
|
|
else if (optstr.equalsIgnoreCase("liter")){
|
||
|
|
liter = Integer.parseInt(optval);
|
||
|
|
}
|
||
|
|
else if (optstr.equalsIgnoreCase("nwords")){
|
||
|
|
V = Integer.parseInt(optval);
|
||
|
|
}
|
||
|
|
else if (optstr.equalsIgnoreCase("ndocs")){
|
||
|
|
M = Integer.parseInt(optval);
|
||
|
|
}
|
||
|
|
else {
|
||
|
|
// any more?
|
||
|
|
}
|
||
|
|
}
|
||
|
|
|
||
|
|
reader.close();
|
||
|
|
}
|
||
|
|
catch (Exception e){
|
||
|
|
System.out.println("Error while reading other file:" + e.getMessage());
|
||
|
|
e.printStackTrace();
|
||
|
|
return false;
|
||
|
|
}
|
||
|
|
return true;
|
||
|
|
}
|
||
|
|
|
||
|
|
/**
|
||
|
|
* Load word-topic assignments for this model
|
||
|
|
*/
|
||
|
|
protected boolean readTAssignFile(String tassignFile)
|
||
|
|
{
|
||
|
|
try {
|
||
|
|
int i,j;
|
||
|
|
BufferedReader reader = new BufferedReader(new InputStreamReader(
|
||
|
|
new GZIPInputStream(
|
||
|
|
new FileInputStream(tassignFile)), "UTF-8"));
|
||
|
|
|
||
|
|
String line;
|
||
|
|
z = new TIntArrayList[M];
|
||
|
|
data = new LDADataset();
|
||
|
|
data.setM(M);
|
||
|
|
data.V = V;
|
||
|
|
for (i = 0; i < M; i++){
|
||
|
|
line = reader.readLine();
|
||
|
|
StringTokenizer tknr = new StringTokenizer(line, " \t\r\n");
|
||
|
|
|
||
|
|
int length = tknr.countTokens();
|
||
|
|
|
||
|
|
TIntArrayList words = new TIntArrayList();
|
||
|
|
TIntArrayList topics = new TIntArrayList();
|
||
|
|
for (j = 0; j < length; j++){
|
||
|
|
String token = tknr.nextToken();
|
||
|
|
|
||
|
|
StringTokenizer tknr2 = new StringTokenizer(token, ":");
|
||
|
|
if (tknr2.countTokens() != 2){
|
||
|
|
System.out.println("Invalid word-topic assignment line\n");
|
||
|
|
return false;
|
||
|
|
}
|
||
|
|
|
||
|
|
words.add(Integer.parseInt(tknr2.nextToken()));
|
||
|
|
topics.add(Integer.parseInt(tknr2.nextToken()));
|
||
|
|
}//end for each topic assignment
|
||
|
|
|
||
|
|
//allocate and add new document to the corpus
|
||
|
|
Document doc = new Document(words);
|
||
|
|
data.setDoc(doc, i);
|
||
|
|
|
||
|
|
//assign values for z
|
||
|
|
z[i] = new TIntArrayList();
|
||
|
|
for (j = 0; j < topics.size(); j++){
|
||
|
|
z[i].add(topics.get(j));
|
||
|
|
}
|
||
|
|
|
||
|
|
}//end for each doc
|
||
|
|
|
||
|
|
reader.close();
|
||
|
|
}
|
||
|
|
catch (Exception e){
|
||
|
|
System.out.println("Error while loading model: " + e.getMessage());
|
||
|
|
e.printStackTrace();
|
||
|
|
return false;
|
||
|
|
}
|
||
|
|
return true;
|
||
|
|
}
|
||
|
|
}
|