コード例 #1
0
ファイル: Sparsifier.java プロジェクト: mmathioudakis/spine
  public static ICModel runSparsifier(
      SocialNetwork socNet,
      ObservationsReader observations,
      ICModel originalModel,
      int sparseSize,
      Sparsifier sparse,
      int numOfChunks,
      boolean reportPartial) {
    LOGGER.info(
        "Arcs: total in social network="
            + socNet.getArcs().size()
            + ", with non-zero probability="
            + originalModel.getProbs().cardinality()
            + ", target k="
            + sparseSize);

    LOGGER.info("Begin creating sparsified model");
    ICModel sparseModel = sparse.sparsify(sparseSize, numOfChunks, observations, reportPartial);
    LOGGER.info("Done creating sparsified model");

    LOGGER.info("Begin measuring the resulting sparsified model");

    // Report change in log likelihood
    double sparsifiedLogL =
        sparseModel.getLogLikelihoodIgnoringParentInformation(sparse.getAuxiliary());
    LOGGER.info("SPARSIFIED log likelihood (ignoring parent information)=" + sparsifiedLogL);
    double originalLogL =
        originalModel.getLogLikelihoodIgnoringParentInformation(sparse.getAuxiliary());
    LOGGER.info("ORIGINAL log likelihood (ignoring parent information)=" + originalLogL);

    LOGGER.info("End measuring the resulting sparsified model");
    return sparseModel;
  }
コード例 #2
0
ファイル: Sparsifier.java プロジェクト: mmathioudakis/spine
  public static void main(String[] args) throws Exception {

    final SimpleJSAP jsap =
        new SimpleJSAP(
            Sparsifier.class.getName(),
            "Estimates and sparsifies a propagation model from a set of observations.",
            new Parameter[] {
              new FlaggedOption(
                  "social-network",
                  JSAP.STRING_PARSER,
                  JSAP.NO_DEFAULT,
                  JSAP.REQUIRED,
                  's',
                  "social-network",
                  "The file containing the social network graph"),
              new FlaggedOption(
                  "probabilities",
                  JSAP.STRING_PARSER,
                  JSAP.NO_DEFAULT,
                  JSAP.REQUIRED,
                  'p',
                  "probabilities",
                  "The file containing the propagation probabilities"),
              new FlaggedOption(
                  "candidate-selection-policy",
                  JSAP.STRING_PARSER,
                  CandidateSelectionPolicy.DEFAULT_CANDIDATE_SELECTION_POLICY
                      .getClass()
                      .getSimpleName(),
                  JSAP.REQUIRED,
                  'c',
                  "candidate-selection-policy",
                  "The name of the candidate selection policy"),
              new FlaggedOption(
                  "auxiliary-basename",
                  JSAP.STRING_PARSER,
                  JSAP.NO_DEFAULT,
                  JSAP.NOT_REQUIRED,
                  JSAP.NO_SHORTFLAG,
                  "auxiliary-basename",
                  "The base name for reading a pre-computed auxiliary structure"),
              new FlaggedOption(
                  "input",
                  JSAP.STRING_PARSER,
                  JSAP.NO_DEFAULT,
                  JSAP.REQUIRED,
                  'i',
                  "input",
                  "The file containing the observations"),
              new FlaggedOption(
                  "sparsifier",
                  JSAP.STRING_PARSER,
                  DEFAULT_SPARSIFIER.getSimpleName(),
                  JSAP.NOT_REQUIRED,
                  'f',
                  "sparsifier",
                  "The sparsifier to run, from this list: "
                      + StringUtils.join(Reflection.subClasses(Sparsifier.class), ',')),
              new FlaggedOption(
                  "sparse-model-size",
                  JSAP.INTEGER_PARSER,
                  JSAP.NO_DEFAULT,
                  JSAP.NOT_REQUIRED,
                  'k',
                  "sparse-model-size",
                  "The size of the sparse model"),
              new FlaggedOption(
                  "number-of-chunks",
                  JSAP.INTEGER_PARSER,
                  JSAP.NO_DEFAULT,
                  JSAP.NOT_REQUIRED,
                  'r',
                  "number-of-chunks",
                  "The number of chunks to be sparsified in parralel"),
              new FlaggedOption(
                  "output",
                  JSAP.STRING_PARSER,
                  JSAP.NO_DEFAULT,
                  JSAP.NOT_REQUIRED,
                  'o',
                  "output",
                  "File to dump sparsified model to"),
              new FlaggedOption(
                  "measures-file",
                  JSAP.STRING_PARSER,
                  JSAP.NO_DEFAULT,
                  JSAP.NOT_REQUIRED,
                  'z',
                  "measures-file",
                  "Save measures of partial models to file"),
              new FlaggedOption(
                  "debug-file",
                  JSAP.STRING_PARSER,
                  JSAP.NO_DEFAULT,
                  JSAP.NOT_REQUIRED,
                  'd',
                  "debug-file",
                  "Save debug information to file"),
              new Switch(
                  "with-fraction",
                  'n',
                  "with-fraction",
                  "Disable the computation of the 'fraction of covered propagations'."),
              new Switch(
                  "incremental-likelihood",
                  JSAP.NO_SHORTFLAG,
                  "incremental-likelihood",
                  "Performs incremental computation of likelihood, for sparsifications methods that support this option (faster, experimental)."),
            });

    final JSAPResult jsapResult = jsap.parse(args);
    if (jsap.messagePrinted()) {
      return;
    }

    // Load social network and input
    String snFilename = jsapResult.getString("social-network");
    SocialNetwork socNet = new SocialNetwork(Utilities.getIterator(snFilename));
    String obsFilename = jsapResult.getString("input");
    ObservationsReader observations = new ObservationsReader(obsFilename);

    // Load original model
    ICModel originalModel =
        new ICModel(socNet, Utilities.getIterator(jsapResult.getString("probabilities")));

    // Load candidate selection policy
    String selectionPolicyName = jsapResult.getString("candidate-selection-policy");
    Class<?> selectionPolicyClass =
        Class.forName(
            CandidateSelectionPolicy.class.getPackage().getName() + "." + selectionPolicyName);
    CandidateSelectionPolicy candidateSelectionPolicy =
        (CandidateSelectionPolicy)
            selectionPolicyClass.getConstructor(new Class[] {}).newInstance(new Object[] {});

    // Create sparsifier
    String sparsifierName = jsapResult.getString("sparsifier");
    Class<?> sparsifierClass =
        Class.forName(Sparsifier.class.getPackage().getName() + "." + sparsifierName);
    Sparsifier sparsifier =
        (Sparsifier)
            sparsifierClass
                .getConstructor(new Class[] {originalModel.getClass()})
                .newInstance(new Object[] {originalModel});
    LOGGER.info("Created a " + sparsifier.getClass().getSimpleName());

    // Set sparsifier options
    if (!jsapResult.getBoolean("with-fraction")) {
      sparsifier.disableComputationOfPartialFractionOfPropagations();
      LOGGER.info("Disabled the computation of fraction of propagations");
    }
    if (jsapResult.getBoolean("incremental-likelihood")) {
      if (sparsifier instanceof GreedySparsifier) {
        ((GreedySparsifier) sparsifier).setIncrementalLikelihoodComputation();
        LOGGER.info("Enabled incremental computation of likelihood (faster, experimental)");
      } else {
        LOGGER.warn(
            "This type of sparsifier does not accept the --incrementa-likelihood switch, ignoring");
      }
    }

    if (jsapResult.userSpecified("auxiliary-basename")) {
      // Use existing auxiliary file
      String auxiliaryBasename = jsapResult.getString("auxiliary-basename");
      ICEstimateAuxiliary auxiliary = new ICEstimateAuxiliary(socNet, observations, null);
      LOGGER.info("Loading pre-computed auxiliary variables");
      auxiliary.read(auxiliaryBasename);
      sparsifier.useAuxiliary(auxiliary);
      if (auxiliary
          .getCandidateSelectionPolicy()
          .toSpec()
          .equals(candidateSelectionPolicy.toSpec())) {
        LOGGER.info(
            "Candidate selection policy: " + auxiliary.getCandidateSelectionPolicy().toSpec());
      } else {
        throw new IllegalArgumentException(
            "The candidate selection policies do not match: auxiliary has '"
                + auxiliary.getCandidateSelectionPolicy().toSpec()
                + "', sparsifier has '"
                + candidateSelectionPolicy.toSpec()
                + "'");
      }
    } else {
      // Compute auxiliary variables
      LOGGER.info("Computing auxiliary variables");
      sparsifier.computeAuxiliary(observations, candidateSelectionPolicy);
    }

    int maxSparseSize;
    if (jsapResult.userSpecified("sparse-model-size")) {
      maxSparseSize = jsapResult.getInt("sparse-model-size");
    } else {
      maxSparseSize = originalModel.getProbs().cardinality();
      LOGGER.info(
          "Setting target number of arcs to number of arcs with non-zero probability in the original model");
    }

    // Open debug file
    if (jsapResult.userSpecified("debug-file")) {
      String debugFilename = jsapResult.getString("debug-file");
      LOGGER.info("Will write debug output to " + debugFilename);
      sparsifier.openDebugFile(debugFilename);
    }

    int numOfChunks = 1;
    if (jsapResult.userSpecified("number-of-chunks")) {
      numOfChunks = jsapResult.getInt("number-of-chunks");
    }

    ICModel sparseModel =
        runSparsifier(
            socNet, observations, originalModel, maxSparseSize, sparsifier, numOfChunks, true);

    // Write partial results to file if necessary
    if (jsapResult.userSpecified("measures-file")) {
      for (Measure m : sparsifier.partialResults.keySet()) {
        String logFilename = jsapResult.getString("measures-file");
        switch (m) {
          case LOG_L:
            logFilename = logFilename + ".logL";
            break;
          case FRACTION_OF_PROPAGATIONS:
            logFilename = logFilename + ".frac";
            break;
          default:
            break;
        }
        PrintWriter report =
            new PrintWriter(new BufferedWriter(new FileWriter(new File(logFilename))));
        LOGGER.info("Writing partial " + m.toString() + " results to " + logFilename);
        report.println("#k\t" + m.toString());
        int[] ks = sparsifier.partialResults.get(m).keySet().toArray(new int[] {});
        Arrays.sort(ks);
        for (int k : ks) {
          report.println(k + "\t" + sparsifier.partialResults.get(m).get(k));
        }
        report.close();
      }
    }

    // Dump probabilities
    if (jsapResult.userSpecified("output")) {
      String probsFilename = jsapResult.getString("output");
      PrintWriter pw = Utilities.getPW(probsFilename);
      LOGGER.info("Dumping probabilities to " + probsFilename);
      sparseModel.dumpProbabilities(pw);
      pw.close();
    }

    sparsifier.closeDebugFile();
  }