Package edu.pitt.dbmi.algo.resampling

Class GeneralResamplingTest

java.lang.Object
edu.pitt.dbmi.algo.resampling.GeneralResamplingTest
public class GeneralResamplingTest extends Object
Created by mahdi on 1/16/17.

Updated: Chirayu Kong Wongchokprasitti, PhD on 9/13/2018

  • Constructor Details

    • GeneralResamplingTest

      public GeneralResamplingTest(DataSet data, Algorithm algorithm, int numberResampling, double percentResamplingSize, boolean resamplingWithReplacement, int edgeEnsemble, boolean addOriginalDataset)
      Constructor.
      Parameters:
      data - the data set.
      algorithm - the algorithm.
      numberResampling - the number of resampling.
      percentResamplingSize - the percent resampling size.
      resamplingWithReplacement - whether resampling with replacement.
      edgeEnsemble - the edge ensemble.
      addOriginalDataset - whether to add the original dataset.

    • GeneralResamplingTest

      public GeneralResamplingTest(List<DataSet> dataSets, MultiDataSetAlgorithm multiDataSetAlgorithm, int numberResampling, double percentResamplingSize, boolean resamplingWithReplacement, int edgeEnsemble, boolean addOriginalDataset)
      Constructor.
      Parameters:
      dataSets - the data sets.
      multiDataSetAlgorithm - the multi data set algorithm.
      numberResampling - the number of resampling.
      percentResamplingSize - the percent resampling size.
      resamplingWithReplacement - whether resampling with replacement.
      edgeEnsemble - the edge ensemble.
      addOriginalDataset - whether to add the original dataset.

  • Method Details

    • getAdjConfusionMatrix

      public static int[][] getAdjConfusionMatrix(Graph truth, Graph estimate)
      Constructor.
      Parameters:
      truth - the true graph.
      estimate - the estimated graph.

    • getEdgeTypeConfusionMatrix

      public static int[][] getEdgeTypeConfusionMatrix(Graph truth, Graph estimate)
      Constructor.
      Parameters:
      truth - the true graph.
      estimate - the estimated graph.

    • setVerbose

      public void setVerbose(boolean verbose)
      Sets whether verbose output should be produced.
      Parameters:
      verbose - whether verbose output should be produced.

    • getOut

      public PrintStream getOut()
      Returns:
      the output stream that output (except for log output) should be sent to.

    • setOut

      public void setOut(PrintStream out)
      Sets the output stream that output (except for log output) should be sent to. By default System.out.
      Parameters:
      out - the output stream that output (except for log output) should be sent to.

    • setParameters

      public void setParameters(Parameters parameters)
      Sets the parameters.
      Parameters:
      parameters - the parameters.

    • setKnowledge

      public void setKnowledge(Knowledge knowledge)
      Sets the background knowledge.
      Parameters:
      knowledge - the knowledge object, specifying forbidden and required edges.

    • setExternalGraph

      public void setExternalGraph(Graph externalGraph)
      Sets the initial graph.

    • search

      public Graph search()
      Runs the resampling test.
      Returns:
      the graph.

    • setScoreWrapper

      public void setScoreWrapper(ScoreWrapper scoreWrapper)
      Sets the score wrapper.
      Parameters:
      scoreWrapper - the score wrapper.

    • setIndTestWrapper

      public void setIndTestWrapper(IndependenceWrapper independenceWrapper)
      Sets the independence wrapper.
      Parameters:
      independenceWrapper - the independence wrapper.

    • getGraphs

      public List<Graph> getGraphs()
      Returns the individual bootstrap result graphs.
      Returns:
      A list of these Graphs.