Examples with ParsedFile edu.cmu.ml.proppr.util.ParsedFile used on opensource projects

Example 1 with ParsedFile

use of edu.cmu.ml.proppr.util.ParsedFile in project ProPPR by TeamCohen.

the class Diagnostic method main.

public static void main(String[] args) {
    StatusLogger status = new StatusLogger();
    try {
        int inputFiles = Configuration.USE_TRAIN;
        int outputFiles = 0;
        int constants = Configuration.USE_THREADS | Configuration.USE_THROTTLE;
        int modules = Configuration.USE_SRW;
        ModuleConfiguration c = new ModuleConfiguration(args, inputFiles, outputFiles, constants, modules);
        log.info(c.toString());
        String groundedFile = c.queryFile.getPath();
        log.info("Parsing " + groundedFile + "...");
        long start = System.currentTimeMillis();
        final ArrayLearningGraphBuilder b = new ArrayLearningGraphBuilder();
        final SRW srw = c.srw;
        final ParamVector<String, ?> params = srw.setupParams(new SimpleParamVector<String>(new ConcurrentHashMap<String, Double>(16, (float) 0.75, 24)));
        srw.setEpoch(1);
        srw.clearLoss();
        srw.fixedWeightRules().addExact("id(restart)");
        srw.fixedWeightRules().addExact("id(trueLoop)");
        srw.fixedWeightRules().addExact("id(trueLoopRestart)");
        /* DiagSrwES: */
        ArrayList<Future<PosNegRWExample>> parsed = new ArrayList<Future<PosNegRWExample>>();
        final ExecutorService trainerPool = Executors.newFixedThreadPool(c.nthreads > 1 ? c.nthreads / 2 : 1);
        final ExecutorService parserPool = Executors.newFixedThreadPool(c.nthreads > 1 ? c.nthreads / 2 : 1);
        int i = 1;
        for (String s : new ParsedFile(groundedFile)) {
            final int id = i++;
            final String in = s;
            parsed.add(parserPool.submit(new Callable<PosNegRWExample>() {

                @Override
                public PosNegRWExample call() throws Exception {
                    try {
                        //log.debug("Job start "+id);
                        //PosNegRWExample ret = parser.parse(in, b.copy());
                        log.debug("Parsing start " + id);
                        PosNegRWExample ret = new RWExampleParser().parse(in, b.copy(), srw);
                        log.debug("Parsing done " + id);
                        //log.debug("Job done "+id);
                        return ret;
                    } catch (IllegalArgumentException e) {
                        System.err.println("Problem with #" + id);
                        e.printStackTrace();
                    }
                    return null;
                }
            }));
        }
        parserPool.shutdown();
        i = 1;
        for (Future<PosNegRWExample> future : parsed) {
            final int id = i++;
            final Future<PosNegRWExample> in = future;
            trainerPool.submit(new Runnable() {

                @Override
                public void run() {
                    try {
                        PosNegRWExample ex = in.get();
                        log.debug("Training start " + id);
                        srw.trainOnExample(params, ex, status);
                        log.debug("Training done " + id);
                    } catch (InterruptedException e) {
                        e.printStackTrace();
                    } catch (ExecutionException e) {
                        e.printStackTrace();
                    }
                }
            });
        }
        trainerPool.shutdown();
        try {
            parserPool.awaitTermination(7, TimeUnit.DAYS);
            trainerPool.awaitTermination(7, TimeUnit.DAYS);
        } catch (InterruptedException e) {
            log.error("Interrupted?", e);
        }
        /* /SrwES */
        /* SrwTtwop: 
			final ExecutorService parserPool = Executors.newFixedThreadPool(c.nthreads>1?c.nthreads/2:1);
			Multithreading<String,PosNegRWExample> m = new Multithreading<String,PosNegRWExample>(log);
			m.executeJob(c.nthreads/2, new ParsedFile(groundedFile), 
					new Transformer<String,PosNegRWExample>() {
						@Override
						public Callable<PosNegRWExample> transformer(final String in, final int id) {
							return new Callable<PosNegRWExample>() {
								@Override
								public PosNegRWExample call() throws Exception {
									try {
									//log.debug("Job start "+id);
									//PosNegRWExample ret = parser.parse(in, b.copy());
									log.debug("Parsing start "+id);
									PosNegRWExample ret = new GroundedExampleParser().parse(in, b.copy());
									log.debug("Parsing done "+id);
									//log.debug("Job done "+id);
									return ret;
									} catch (IllegalArgumentException e) {
										System.err.println("Problem with #"+id);
										e.printStackTrace();
									}
									return null;
								}};
						}}, new Cleanup<PosNegRWExample>() {
							@Override
							public Runnable cleanup(final Future<PosNegRWExample> in, final int id) {
								return new Runnable(){
									@Override
									public void run() {
										try {
											final PosNegRWExample ex = in.get();
											log.debug("Cleanup start "+id);
											trainerPool.submit(new Runnable() {
													@Override
													public void run(){
														log.debug("Training start "+id);
														srw.trainOnExample(params,ex);
														log.debug("Training done "+id);
													}
												});
										} catch (InterruptedException e) {
										    e.printStackTrace(); 
										} catch (ExecutionException e) {
										    e.printStackTrace();
										}
										log.debug("Cleanup done "+id);
									}};
							}}, c.throttle);
			trainerPool.shutdown();
			try {
				trainerPool.awaitTermination(7, TimeUnit.DAYS);
			} catch (InterruptedException e) {
				log.error("Interrupted?",e);
			}

			 /SrwTtwop */
        /* all diag tasks except SrwO: 
			Multithreading<String,PosNegRWExample> m = new Multithreading<String,PosNegRWExample>(log);
			m.executeJob(c.nthreads, new ParsedFile(groundedFile), 
					new Transformer<String,PosNegRWExample>() {
						@Override
						public Callable<PosNegRWExample> transformer(final String in, final int id) {
							return new Callable<PosNegRWExample>() {
								@Override
								public PosNegRWExample call() throws Exception {
									try {
									//log.debug("Job start "+id);
									//PosNegRWExample ret = parser.parse(in, b.copy());
									log.debug("Parsing start "+id);
									PosNegRWExample ret = new GroundedExampleParser().parse(in, b.copy());
									log.debug("Parsing done "+id);
									log.debug("Training start "+id);
									srw.trainOnExample(params,ret);
									log.debug("Training done "+id);
									//log.debug("Job done "+id);
									return ret;
									} catch (IllegalArgumentException e) {
										System.err.println("Problem with #"+id);
										e.printStackTrace();
									}
									return null;
								}};
						}}, new Cleanup<PosNegRWExample>() {
							@Override
							public Runnable cleanup(final Future<PosNegRWExample> in, final int id) {
								return new Runnable(){
									//ArrayList<PosNegRWExample> done = new ArrayList<PosNegRWExample>();
									@Override
									public void run() {
										try {
											//done.add(in.get());
											in.get();
										} catch (InterruptedException e) {
										    e.printStackTrace(); 
										} catch (ExecutionException e) {
										    e.printStackTrace();
										}
										log.debug("Cleanup start "+id);
										log.debug("Cleanup done "+id);
									}};
							}}, c.throttle);
			*/
        /* SrwO:
			   Multithreading<PosNegRWExample,Integer> m = new Multithreading<PosNegRWExample,Integer>(log);
			m.executeJob(c.nthreads, new PosNegRWExampleStreamer(new ParsedFile(groundedFile),new ArrayLearningGraphBuilder()), 
						 new Transformer<PosNegRWExample,Integer>() {
						@Override
						public Callable<Integer> transformer(final PosNegRWExample in, final int id) {
							return new Callable<Integer>() {
								@Override
								public Integer call() throws Exception {
									try {
									//log.debug("Job start "+id);
									//PosNegRWExample ret = parser.parse(in, b.copy());
									log.debug("Training start "+id);
									srw.trainOnExample(params,in);
									log.debug("Training done "+id);
									//log.debug("Job done "+id);
									} catch (IllegalArgumentException e) {
										System.err.println("Problem with #"+id);
										e.printStackTrace();
									}
									return in.length();
								}};
						}}, new Cleanup<Integer>() {
							@Override
							public Runnable cleanup(final Future<Integer> in, final int id) {
								return new Runnable(){
									//ArrayList<PosNegRWExample> done = new ArrayList<PosNegRWExample>();
									@Override
									public void run() {
										try {
											//done.add(in.get());
											in.get();
										} catch (InterruptedException e) {
										    e.printStackTrace(); 
										} catch (ExecutionException e) {
										    e.printStackTrace();
										}
										log.debug("Cleanup start "+id);
										log.debug("Cleanup done "+id);
									}};
							}}, c.throttle);
			*/
        srw.cleanupParams(params, params);
        log.info("Finished diagnostic in " + (System.currentTimeMillis() - start) + " ms");
    } catch (Throwable t) {
        t.printStackTrace();
        System.exit(-1);
    }
}

Example 2 with ParsedFile

use of edu.cmu.ml.proppr.util.ParsedFile in project ProPPR by TeamCohen.

the class GradientFinder method main.

public static void main(String[] args) {
    try {
        int inputFiles = Configuration.USE_GROUNDED | Configuration.USE_INIT_PARAMS;
        int outputFiles = Configuration.USE_GRADIENT | Configuration.USE_PARAMS;
        int modules = Configuration.USE_TRAINER | Configuration.USE_SRW | Configuration.USE_SQUASHFUNCTION;
        int constants = Configuration.USE_THREADS | Configuration.USE_EPOCHS | Configuration.USE_FORCE | Configuration.USE_FIXEDWEIGHTS;
        CustomConfiguration c = new CustomConfiguration(args, inputFiles, outputFiles, constants, modules) {

            boolean relax;

            @Override
            protected Option checkOption(Option o) {
                if (PARAMS_FILE_OPTION.equals(o.getLongOpt()) || INIT_PARAMS_FILE_OPTION.equals(o.getLongOpt()))
                    o.setRequired(false);
                return o;
            }

            @Override
            protected void addCustomOptions(Options options, int[] flags) {
                options.addOption(Option.builder().longOpt("relaxFW").desc("Relax fixedWeight rules for gradient computation (used in ProngHorn)").optionalArg(true).build());
            }

            @Override
            protected void retrieveCustomSettings(CommandLine line, int[] flags, Options options) {
                if (groundedFile == null || !groundedFile.exists())
                    usageOptions(options, flags, "Must specify grounded file using --" + Configuration.GROUNDED_FILE_OPTION);
                if (gradientFile == null)
                    usageOptions(options, flags, "Must specify gradient using --" + Configuration.GRADIENT_FILE_OPTION);
                // default to 0 epochs
                if (!options.hasOption("epochs"))
                    this.epochs = 0;
                this.relax = false;
                if (options.hasOption("relaxFW"))
                    this.relax = true;
            }

            @Override
            public Object getCustomSetting(String name) {
                if ("relaxFW".equals(name))
                    return this.relax;
                return null;
            }
        };
        System.out.println(c.toString());
        ParamVector<String, ?> params = null;
        SymbolTable<String> masterFeatures = new SimpleSymbolTable<String>();
        File featureIndex = new File(c.groundedFile.getParent(), c.groundedFile.getName() + Grounder.FEATURE_INDEX_EXTENSION);
        if (featureIndex.exists()) {
            log.info("Reading feature index from " + featureIndex.getName() + "...");
            for (String line : new ParsedFile(featureIndex)) {
                masterFeatures.insert(line.trim());
            }
        }
        if (c.epochs > 0) {
            // train first
            log.info("Training for " + c.epochs + " epochs...");
            params = c.trainer.train(masterFeatures, new ParsedFile(c.groundedFile), new ArrayLearningGraphBuilder(), // create a parameter vector
            c.initParamsFile, c.epochs);
            if (c.paramsFile != null)
                ParamsFile.save(params, c.paramsFile, c);
        } else if (c.initParamsFile != null) {
            params = new SimpleParamVector<String>(Dictionary.load(new ParsedFile(c.initParamsFile)));
        } else if (c.paramsFile != null) {
            params = new SimpleParamVector<String>(Dictionary.load(new ParsedFile(c.paramsFile)));
        } else {
            params = new SimpleParamVector<String>();
        }
        // this lets prongHorn hold external features fixed for training, but still compute their gradient
        if (((Boolean) c.getCustomSetting("relaxFW"))) {
            log.info("Turning off fixedWeight rules");
            c.trainer.setFixedWeightRules(new FixedWeightRules());
        }
        ParamVector<String, ?> batchGradient = c.trainer.findGradient(masterFeatures, new ParsedFile(c.groundedFile), new ArrayLearningGraphBuilder(), params);
        ParamsFile.save(batchGradient, c.gradientFile, c);
    } catch (Throwable t) {
        t.printStackTrace();
        System.exit(-1);
    }
}

Example 3 with ParsedFile

use of edu.cmu.ml.proppr.util.ParsedFile in project ProPPR by TeamCohen.

the class Trainer method train.

public ParamVector<String, ?> train(SymbolTable<String> masterFeatures, Iterable<String> examples, LearningGraphBuilder builder, File initialParamVecFile, int numEpochs) {
    ParamVector<String, ?> initParams = null;
    if (initialParamVecFile != null) {
        log.info("loading initial params from " + initialParamVecFile);
        initParams = new SimpleParamVector<String>(Dictionary.load(new ParsedFile(initialParamVecFile), new ConcurrentHashMap<String, Double>()));
    } else {
        initParams = createParamVector();
    }
    return train(masterFeatures, examples, builder, initParams, numEpochs);
}

Example 4 with ParsedFile

use of edu.cmu.ml.proppr.util.ParsedFile in project ProPPR by TeamCohen.

the class LightweightGraphPlugin method load.

/** Return a simpleGraphComponent with all the components loaded from
        a file.  The format of the file is that each line is a tab-separated 
        triple of edgelabel, sourceNode, destNode. */
public static WamPlugin load(APROptions apr, File f, int duplicates) {
    GraphlikePlugin p = new LightweightGraphPlugin(apr, f.getName());
    ParsedFile parsed = new ParsedFile(f);
    BloomFilter<String> lines = null;
    if (duplicates > 0)
        lines = new BloomFilter<String>(1e-5, duplicates);
    boolean exceeds = false;
    for (String line : parsed) {
        String[] parts = line.split("\t");
        if (parts.length < 3)
            parsed.parseError("expected 3 tab-delimited fields; got " + parts.length);
        if (duplicates > 0) {
            if (lines.contains(line)) {
                log.warn("Skipping duplicate fact at " + f.getName() + ":" + parsed.getAbsoluteLineNumber() + ": " + line);
                continue;
            } else
                lines.add(line);
            if (!exceeds & parsed.getLineNumber() > duplicates) {
                exceeds = true;
                log.warn("Number of graph edges exceeds " + duplicates + "; duplicate detection may encounter false positives. We should add a command line option to fix this.");
            }
        }
        if (parts.length == 3) {
            p.addEdge(parts[0].trim(), parts[1].trim(), parts[2].trim());
        } else if (parts.length == 4) {
            p.addEdge(parts[0].trim(), parts[1].trim(), parts[2].trim(), Double.parseDouble(parts[3].trim()));
        }
    }
    return p;
}

Example 5 with ParsedFile

use of edu.cmu.ml.proppr.util.ParsedFile in project ProPPR by TeamCohen.

the class SparseGraphPlugin method loadArgs.

private void loadArgs(TObjectIntMap<String> args, File file) {
    log.debug("Loading args file " + file.getName() + " in String...");
    ParsedFile parsed = new ParsedFile(file);
    for (String line : parsed) args.put((line.trim()), parsed.getLineNumber());
    parsed.close();
}