cdec cleanup, remove bayesian stuff, parsing stuff

1 files changed, 0 insertions, 257 deletions

diff --git a/gi/posterior-regularisation/prjava/src/phrase/Trainer.java b/gi/posterior-regularisation/prjava/src/phrase/Trainer.java
deleted file mode 100644
index 6f302b20..00000000
--- a/gi/posterior-regularisation/prjava/src/phrase/Trainer.java
+++ /dev/null
@@ -1,257 +0,0 @@
-package phrase;
-
-import io.FileUtil;
-import joptsimple.OptionParser;
-import joptsimple.OptionSet;
-import java.io.File;
-import java.io.IOException;
-import java.io.PrintStream;
-import java.util.List;
-import java.util.Random;
-import java.util.concurrent.ExecutorService;
-import java.util.concurrent.Executors;
-
-import phrase.Corpus.Edge;
-
-import arr.F;
-
-public class Trainer 
-{
-	public static void main(String[] args) 
-	{
-        OptionParser parser = new OptionParser();
-        parser.accepts("help");
-        parser.accepts("in").withRequiredArg().ofType(File.class);
-        parser.accepts("in1").withRequiredArg().ofType(File.class);
-        parser.accepts("test").withRequiredArg().ofType(File.class);
-        parser.accepts("out").withRequiredArg().ofType(File.class);
-        parser.accepts("start").withRequiredArg().ofType(File.class);
-        parser.accepts("parameters").withRequiredArg().ofType(File.class);
-        parser.accepts("topics").withRequiredArg().ofType(Integer.class).defaultsTo(5);
-        parser.accepts("iterations").withRequiredArg().ofType(Integer.class).defaultsTo(10);
-        parser.accepts("threads").withRequiredArg().ofType(Integer.class).defaultsTo(0);
-        parser.accepts("scale-phrase").withRequiredArg().ofType(Double.class).defaultsTo(0.0);
-        parser.accepts("scale-context").withRequiredArg().ofType(Double.class).defaultsTo(0.0);
-        parser.accepts("seed").withRequiredArg().ofType(Long.class).defaultsTo(0l);
-        parser.accepts("convergence-threshold").withRequiredArg().ofType(Double.class).defaultsTo(1e-6);
-        parser.accepts("variational-bayes");
-        parser.accepts("alpha-emit").withRequiredArg().ofType(Double.class).defaultsTo(0.1);
-        parser.accepts("alpha-pi").withRequiredArg().ofType(Double.class).defaultsTo(0.0001);
-        parser.accepts("agree-direction");
-        parser.accepts("agree-language");
-        parser.accepts("no-parameter-cache");
-        parser.accepts("skip-large-phrases").withRequiredArg().ofType(Integer.class).defaultsTo(5);
-        OptionSet options = parser.parse(args);
-
-        if (options.has("help") || !options.has("in"))
-        {
-        	try {
-				parser.printHelpOn(System.err);
-			} catch (IOException e) {
-				System.err.println("This should never happen.");
-				e.printStackTrace();
-			}
-        	System.exit(1);     
-        }
-		
-		int tags = (Integer) options.valueOf("topics");
-		int iterations = (Integer) options.valueOf("iterations");
-		double scale_phrase = (Double) options.valueOf("scale-phrase");
-		double scale_context = (Double) options.valueOf("scale-context");
-		int threads = (Integer) options.valueOf("threads");
-		double threshold = (Double) options.valueOf("convergence-threshold");
-		boolean vb = options.has("variational-bayes");
-		double alphaEmit = (vb) ? (Double) options.valueOf("alpha-emit") : 0;
-		double alphaPi = (vb) ? (Double) options.valueOf("alpha-pi") : 0;
-		int skip = (Integer) options.valueOf("skip-large-phrases");
-		
-		if (options.has("seed"))
-			F.rng = new Random((Long) options.valueOf("seed"));
-		
-		ExecutorService threadPool = null;
-		if (threads > 0)
-			threadPool = Executors.newFixedThreadPool(threads);			
-		
-		if (tags <= 1 || scale_phrase < 0 || scale_context < 0 || threshold < 0)
-		{
-			System.err.println("Invalid arguments. Try again!");
-			System.exit(1);
-		}
-		
-		Corpus corpus = null;
-		File infile = (File) options.valueOf("in");
-		Corpus corpus1 = null;
-		File infile1 = (File) options.valueOf("in1");
-		try {
-			System.out.println("Reading concordance from " + infile);
-			corpus = Corpus.readFromFile(FileUtil.reader(infile));
-			corpus.printStats(System.out);
-			if(options.has("in1")){
-				corpus1 = Corpus.readFromFile(FileUtil.reader(infile1));
-				corpus1.printStats(System.out);
-			}
-		} catch (IOException e) {
-			System.err.println("Failed to open input file: " + infile);
-			e.printStackTrace();
-			System.exit(1);
-		}
-				
-		if (!(options.has("agree-direction")||options.has("agree-language")))
-			System.out.println("Running with " + tags + " tags " +
-					"for " + iterations + " iterations " +
-					((skip > 0) ? "skipping large phrases for first " + skip + " iterations " : "") +
-					"with scale " + scale_phrase + " phrase and " + scale_context + " context " +
-					"and " + threads + " threads");
-		else
-			System.out.println("Running agreement model with " + tags + " tags " +
-	 				"for " + iterations);
-
-	 	System.out.println();
-		
- 		PhraseCluster cluster = null;
- 		Agree2Sides agree2sides = null;
- 		Agree agree= null;
- 		VB vbModel=null;
- 		if (options.has("agree-language"))
- 			agree2sides = new Agree2Sides(tags, corpus,corpus1);
- 		else if (options.has("agree-direction"))
- 			agree = new Agree(tags, corpus);
- 		else
- 		{
- 			if (vb)	
- 			{
- 				vbModel=new VB(tags,corpus);
- 				vbModel.alpha=alphaPi;
- 				vbModel.lambda=alphaEmit;
- 	 			if (threadPool != null) vbModel.useThreadPool(threadPool);
- 			} 
- 			else 
- 			{
- 				cluster = new PhraseCluster(tags, corpus);
- 	 			if (threadPool != null) cluster.useThreadPool(threadPool);
- 				
-	 			if (options.has("no-parameter-cache")) 
-	 				cluster.cacheLambda = false;
-	 			if (options.has("start"))
-	 			{
-	 				try {
-						System.err.println("Reading starting parameters from " + options.valueOf("start"));
-						cluster.loadParameters(FileUtil.reader((File)options.valueOf("start")));
-					} catch (IOException e) {
-						System.err.println("Failed to open input file: " + options.valueOf("start"));
-						e.printStackTrace();
-					}
-	 			}
- 			}
- 		}
-				
-		double last = 0;
-		for (int i=0; i < iterations; i++)
-		{
-			double o;
-			if (agree != null)
-				o = agree.EM();
-			else if(agree2sides!=null)
-				o = agree2sides.EM();
-			else
-			{
-				if (i < skip)
-					System.out.println("Skipping phrases of length > " + (i+1));
-				
-				if (scale_phrase <= 0 && scale_context <= 0)
-				{
-					if (!vb)
-						o = cluster.EM((i < skip) ? i+1 : 0);
-					else
-						o = vbModel.EM();	
-				}
-				else
-					o = cluster.PREM(scale_phrase, scale_context, (i < skip) ? i+1 : 0);
-			}
-			
-			System.out.println("ITER: "+i+" objective: " + o);
-			
-			// sometimes takes a few iterations to break the ties
-			if (i > 5 && Math.abs((o - last) / o) < threshold)
-			{
-				last = o;
-				break;
-			}
-			last = o;
-		}
-		
-		double pl1lmax = 0, cl1lmax = 0;
-		if (cluster != null)
-		{
-			pl1lmax = cluster.phrase_l1lmax();
-			cl1lmax = cluster.context_l1lmax();
-		}
-		else if (agree != null)
-		{
-			// fairly arbitrary choice of model1 cf model2
-			pl1lmax = agree.model1.phrase_l1lmax();
-			cl1lmax = agree.model1.context_l1lmax();
-		}
-		else if (agree2sides != null)
-		{
-			// fairly arbitrary choice of model1 cf model2
-			pl1lmax = agree2sides.model1.phrase_l1lmax();
-			cl1lmax = agree2sides.model1.context_l1lmax();
-		}
-
-		System.out.println("\nFinal posterior phrase l1lmax " + pl1lmax + " context l1lmax " + cl1lmax);
-		
-		if (options.has("out"))
-		{
-			File outfile = (File) options.valueOf("out");
-			try {
-				PrintStream ps = FileUtil.printstream(outfile);
-				List<Edge> test;
-				if (!options.has("test")) // just use the training
-					test = corpus.getEdges();
-				else
-				{	// if --test supplied, load up the file
-					infile = (File) options.valueOf("test");
-					System.out.println("Reading testing concordance from " + infile);
-					test = corpus.readEdges(FileUtil.reader(infile));
-				}
-				if(vb) {
-					assert !options.has("test");
-					vbModel.displayPosterior(ps);
-				} else if (cluster != null) 
-					cluster.displayPosterior(ps, test);
-				else if (agree != null) 
-					agree.displayPosterior(ps, test);
-				else if (agree2sides != null) {
-					assert !options.has("test");
-					agree2sides.displayPosterior(ps);
-				}
-				
-				ps.close();
-			} catch (IOException e) {
-				System.err.println("Failed to open either testing file or output file");
-				e.printStackTrace();
-				System.exit(1);
-			}
-		}
-
-		if (options.has("parameters"))
-		{
-			assert !vb;
-			File outfile = (File) options.valueOf("parameters");
-			PrintStream ps;
-			try {
-				ps = FileUtil.printstream(outfile);
-				cluster.displayModelParam(ps);
-				ps.close();
-			} catch (IOException e) {
-				System.err.println("Failed to open output parameters file: " + outfile);
-				e.printStackTrace();
-				System.exit(1);
-			}
-		}
-		
-		if (cluster != null && cluster.pool != null)
-			cluster.pool.shutdown();
-	}
-}