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Timestamp:
08/29/18 18:16:05 (6 years ago)
Author:
abeham
Message:

#2457:

  • Changed calculation of correlation length (using limit introduced Hordijk 1996)
  • Changed RuggednessCalculator (no more a HL item)
  • Added additional, information-analysis-based features for directed walks
  • Added generic DirectedWalk algorithm (as described in thesis)
  • Made OneSizeInstanceProvider parametrizable
  • Adapted program for analyzing problem instance reidentification
Location:
branches/2457_ExpertSystem/HeuristicLab.Analysis.FitnessLandscape/3.3/Analysis
Files:
4 edited

Legend:

Unmodified
Added
Removed

  • branches/2457_ExpertSystem/HeuristicLab.Analysis.FitnessLandscape/3.3/Analysis/InformationAnalyzer.cs

    r15279 r16096  
    2020#endregion
    2121
     22using System.Linq;
    2223using HeuristicLab.Common;
    2324using HeuristicLab.Core;
    … …  
    2728using HeuristicLab.Parameters;
    2829using HeuristicLab.Persistence.Default.CompositeSerializers.Storable;
    29 using System.Linq;
    30 using System;
    3130
    3231namespace HeuristicLab.Analysis.FitnessLandscape {
    … …  
    125124      var ic = new DoubleValue(analysis.InformationContent.FirstOrDefault());
    126125      InformationContentParameter.ActualValue = ic;
    127       AddOrUpdateResult(results, InformationContentParameter.Name, ic);
     126      results.AddOrUpdateResult(InformationContentParameter.Name, ic);
    128127      var pic = new DoubleValue(analysis.PartialInformationContent.FirstOrDefault());
    129128      PartialInformationContentParameter.ActualValue = pic;
    130       AddOrUpdateResult(results, PartialInformationContentParameter.Name, pic);
     129      results.AddOrUpdateResult(PartialInformationContentParameter.Name, pic);
    131130      var dbi = new DoubleValue(analysis.DensityBasinInformation.FirstOrDefault());
    132131      DensityBasinInformationParameter.ActualValue = dbi;
    133       AddOrUpdateResult(results, DensityBasinInformationParameter.Name, dbi);
     132      results.AddOrUpdateResult(DensityBasinInformationParameter.Name, dbi);
    134133      var @is = new DoubleValue(analysis.InformationStability);
    135134      InformationStabilityParameter.ActualValue = @is;
    136       AddOrUpdateResult(results, InformationStabilityParameter.Name, @is);
     135      results.AddOrUpdateResult(InformationStabilityParameter.Name, @is);
    137136      var regularity = new DoubleValue(1.0 * analysis.Regularity / qualities.Count);
    138137      RegularityParameter.ActualValue = regularity;
    139       AddOrUpdateResult(results, RegularityParameter.Name, regularity);
     138      results.AddOrUpdateResult(RegularityParameter.Name, regularity);
    140139      var diversity = new DoubleValue(1.0 * analysis.Diversity / qualities.Count);
    141140      DiversityParameter.ActualValue = diversity;
    142       AddOrUpdateResult(results, DiversityParameter.Name, diversity);
     141      results.AddOrUpdateResult(DiversityParameter.Name, diversity);
    143142      var totalEntropy = new DoubleValue(analysis.TotalEntropy.FirstOrDefault());
    144143      TotalEntropyParameter.ActualValue = totalEntropy;
    145       AddOrUpdateResult(results, TotalEntropyParameter.Name, totalEntropy);
     144      results.AddOrUpdateResult(TotalEntropyParameter.Name, totalEntropy);
    146145      var peakIc = new DoubleValue(analysis.PeakInformationContent.Value);
    147146      PeakInformationContentParameter.ActualValue = peakIc;
    148       AddOrUpdateResult(results, PeakInformationContentParameter.Name, peakIc);
     147      results.AddOrUpdateResult(PeakInformationContentParameter.Name, peakIc);
    149148      var peakDbi = new DoubleValue(analysis.PeakDensityBasinInformation.Value);
    150149      PeakDensityBasinInformationParameter.ActualValue = peakDbi;
    151       AddOrUpdateResult(results, PeakDensityBasinInformationParameter.Name, peakDbi);
     150      results.AddOrUpdateResult(PeakDensityBasinInformationParameter.Name, peakDbi);
    152151
    153152      var itable = GetInformationTable(analysis);
    154       AddOrUpdateResult(results, InformationAnalysisParameter.Name, itable);
     153      results.AddOrUpdateResult(InformationAnalysisParameter.Name, itable);
    155154      return base.Apply();
    156155    }
    … …  
    176175      return dt;
    177176    }
    178 
    179     private static void AddOrUpdateResult(ResultCollection results, string name, IItem item, bool clone = false) {
    180       IResult r;
    181       if (!results.TryGetValue(name, out r)) {
    182         results.Add(new Result(name, clone ? (IItem)item.Clone() : item));
    183       } else r.Value = clone ? (IItem)item.Clone() : item;
    184     }
    185177  }
    186178}

  • branches/2457_ExpertSystem/HeuristicLab.Analysis.FitnessLandscape/3.3/Analysis/RuggednessAnalyzer.cs

    r13583 r16096  
    2020#endregion
    2121
     22using System.Linq;
    2223using HeuristicLab.Common;
    2324using HeuristicLab.Core;
    … …  
    2728using HeuristicLab.Parameters;
    2829using HeuristicLab.Persistence.Default.CompositeSerializers.Storable;
    29 using System.Linq;
    3030
    3131namespace HeuristicLab.Analysis.FitnessLandscape {
    32   [Item("Ruggedness Analyzer", "Analyzes autocorrelation for one mutation step and correlation length.")]
     32  [Item("Ruggedness Analyzer", "Analyzes autocorrelation for one mutation step and correlation length. Correlation length is calculated according to the statistical correlation length defined by Hordijk, W., 1996. A measure of landscapes. Evolutionary computation, 4(4), pp.335-360.")]
    3333  [StorableClass]
    3434  public class RuggednessAnalyzer : SingleSuccessorOperator, IQualityTrailAnalyzer {
    … …  
    5050      get { return (LookupParameter<IntValue>)Parameters["CorrelationLength"]; }
    5151    }
     52    public ValueLookupParameter<DoubleValue> LimitParameter {
     53      get { return (ValueLookupParameter<DoubleValue>)Parameters["Limit"]; }
     54    }
    5255    #endregion
    5356
    … …  
    6063      Parameters.Add(new LookupParameter<DoubleValue>("AutoCorrelation1", "Autocorrelation for one mutation step."));
    6164      Parameters.Add(new LookupParameter<IntValue>("CorrelationLength", "The correlation length."));
     65      Parameters.Add(new ValueLookupParameter<DoubleValue>("Limit", "The limit for the statistical correlation length, if left empty 2 / sqrt(n), where n = length of walk will be used, as defined by Hordijk 1996."));
    6266    }
    6367
    … …  
    7074      if (qualityTrail == null || qualityTrail.Rows.Count <= 0) return base.Apply();
    7175      var results = ResultsParameter.ActualValue;
     76      var limit = LimitParameter.ActualValue?.Value;
    7277      double[] autocorrelationValues;
    73       var correlationLength = RuggednessCalculator.CalculateCorrelationLength(qualityTrail.Rows.First().Values.ToArray(), out autocorrelationValues);
     78      var correlationLength = RuggednessCalculator.CalculateCorrelationLength(qualityTrail.Rows.First().Values.ToArray(), out autocorrelationValues, limit);
    7479      var cl = new IntValue(correlationLength);
    7580      CorrelationLengthParameter.ActualValue = cl;
    76       AddOrUpdateResult(results, CorrelationLengthParameter.Name, cl);
     81      results.AddOrUpdateResult(CorrelationLengthParameter.Name, cl);
    7782      var ac1 = new DoubleValue(autocorrelationValues.Length > 1 ? autocorrelationValues[1] : 0.0);
    7883      AutoCorrelation1Parameter.ActualValue = ac1;
    79       AddOrUpdateResult(results, AutoCorrelation1Parameter.Name, ac1);
     84      results.AddOrUpdateResult(AutoCorrelation1Parameter.Name, ac1);
    8085      return base.Apply();
    81     }
    82 
    83     private static void AddOrUpdateResult(ResultCollection results, string name, IItem item, bool clone = false) {
    84       IResult r;
    85       if (!results.TryGetValue(name, out r)) {
    86         results.Add(new Result(name, clone ? (IItem)item.Clone() : item));
    87       } else r.Value = clone ? (IItem)item.Clone() : item;
    8886    }
    8987  }

  • branches/2457_ExpertSystem/HeuristicLab.Analysis.FitnessLandscape/3.3/Analysis/RuggednessCalculator.cs

    r13583 r16096  
    2020#endregion
    2121
    22 using HeuristicLab.Common;
    23 using HeuristicLab.Core;
    24 using HeuristicLab.Data;
    25 using HeuristicLab.Operators;
    26 using HeuristicLab.Parameters;
    27 using HeuristicLab.Persistence.Default.CompositeSerializers.Storable;
    2822using System;
    2923using System.Collections.Generic;
    30 using System.Linq;
    3124
    3225namespace HeuristicLab.Analysis.FitnessLandscape {
    33   [Item("Ruggedness Calculator", "Calculates ruggedness descriptors froma given quality trail.")]
    34   [StorableClass]
    35   public class RuggednessCalculator : SingleSuccessorOperator {
    36 
    37     #region Parameters
    38     public LookupParameter<DataTable> QualityTrailParameter {
    39       get { return (LookupParameter<DataTable>)Parameters["QualityTrail"]; }
    40     }
    41     public LookupParameter<IntValue> CorrelationLengthParameter {
    42       get { return (LookupParameter<IntValue>)Parameters["CorrelationLength"]; }
    43     }
    44     public LookupParameter<DoubleArray> AutoCorrelationParameter {
    45       get { return (LookupParameter<DoubleArray>)Parameters["AutoCorrelation"]; }
    46     }
    47     #endregion
    48 
    49     #region Constructors & Cloning
    50     [StorableConstructor]
    51     protected RuggednessCalculator(bool deserializing) : base(deserializing) { }
    52     protected RuggednessCalculator(RuggednessCalculator original, Cloner cloner) : base(original, cloner) { }
    53     public RuggednessCalculator() {
    54       Parameters.Add(new LookupParameter<DataTable>("QualityTrail", "Historical values of walk qualities"));
    55       Parameters.Add(new LookupParameter<IntValue>("CorrelationLength", "Average maximum distances between correlated quality values."));
    56       Parameters.Add(new LookupParameter<DoubleArray>("AutoCorrelation", "AutoCorrelation"));
    57     }
    58     public override IDeepCloneable Clone(Cloner cloner) {
    59       return new RuggednessCalculator(this, cloner);
    60     }
    61     #endregion
    62 
    63     public override IOperation Apply() {
    64       double[] qualities = QualityTrailParameter.ActualValue.Rows.First().Values.ToArray();
    65       double[] autocorrelation;
    66       CorrelationLengthParameter.ActualValue = new IntValue(CalculateCorrelationLength(qualities, out autocorrelation));
    67       AutoCorrelationParameter.ActualValue = new DoubleArray(autocorrelation);
    68       return base.Apply();
    69     }
    70 
    71     public static int CalculateCorrelationLength(double[] qualities, out double[] acf) {
     26  public static class RuggednessCalculator {
     27    /// <summary>
     28    /// Calculates statistical correlation length as defined by Hordijk, W., 1996. A measure of landscapes. Evolutionary computation, 4(4), pp.335-360.
     29    /// </summary>
     30    /// <param name="qualities">The quality trail observed.</param>
     31    /// <param name="acf">The autocorrelation values for each step s, including 0 => acf[0] = 1.</param>
     32    /// <param name="limit">The statistical limit, correlation length will be the last step before acf falls within this limit. If omitted it is calculated as 2 / sqrt(qualities.Length).</param>
     33    /// <returns>The statistical correlation length</returns>
     34    public static int CalculateCorrelationLength(double[] qualities, out double[] acf, double? limit = null) {
     35      if (!limit.HasValue) limit = 2.0 / Math.Sqrt(qualities.Length);
    7236      double[] correlations = new double[qualities.Length];
    7337      alglib.corr.corrr1dcircular(qualities, qualities.Length, qualities, qualities.Length, ref correlations);
    … …  
    8650          value = 1;
    8751        autocorrelation.Add(value);
    88         if (value < 0 && correlationLength < 0) correlationLength = counter;
     52        if (Math.Abs(value) < limit && correlationLength < 0) correlationLength = counter;
    8953      }
    9054      acf = autocorrelation.ToArray();
    9155      return correlationLength - 1;
    9256    }
    93 
    94     public static bool AnyGreaterOne(double[] values) {
    95       return values.Any(d => d > 1);
    96     }
    9757  }
    9858}

  • branches/2457_ExpertSystem/HeuristicLab.Analysis.FitnessLandscape/3.3/Analysis/UpDownWalkAnalyzer.cs

    r13583 r16096  
    2020#endregion
    2121
     22using System.Linq;
    2223using HeuristicLab.Common;
    2324using HeuristicLab.Core;
    … …  
    2728using HeuristicLab.Parameters;
    2829using HeuristicLab.Persistence.Default.CompositeSerializers.Storable;
    29 using System.Linq;
    3030
    3131namespace HeuristicLab.Analysis.FitnessLandscape {
    … …  
    123123              var uv = new DoubleValue(topVals.Variance());
    124124              UpperVarianceParameter.ActualValue = uv;
    125               AddOrUpdateResult(results, UpperVarianceParameter.Name, uv);
     125              results.AddOrUpdateResult(UpperVarianceParameter.Name, uv);
    126126              var ul = new DoubleValue(topLengths.Average());
    127127              UpWalkLengthParameter.ActualValue = ul;
    128               AddOrUpdateResult(results, UpWalkLengthParameter.Name, ul);
     128              results.AddOrUpdateResult(UpWalkLengthParameter.Name, ul);
    129129              var ulv = new DoubleValue(topLengths.Variance());
    130130              UpWalkLenVarParameter.ActualValue = ulv;
    131               AddOrUpdateResult(results, UpWalkLenVarParameter.Name, ulv);
     131              results.AddOrUpdateResult(UpWalkLenVarParameter.Name, ulv);
    132132            }
    133133            if (bottoms.Count > 0) {
    … …  
    136136              var lv = new DoubleValue(bottomVals.Variance());
    137137              LowerVarianceParameter.ActualValue = lv;
    138               AddOrUpdateResult(results, LowerVarianceParameter.Name, lv);
     138              results.AddOrUpdateResult(LowerVarianceParameter.Name, lv);
    139139              var dl = new DoubleValue(bottomLengths.Average());
    140140              DownWalkLengthParameter.ActualValue = dl;
    141               AddOrUpdateResult(results, DownWalkLengthParameter.Name, dl);
     141              results.AddOrUpdateResult(DownWalkLengthParameter.Name, dl);
    142142              var dlv = new DoubleValue(bottomLengths.Variance());
    143143              DownWalkLenVarParameter.ActualValue = dlv;
    144               AddOrUpdateResult(results, DownWalkLenVarParameter.Name, dlv);
     144              results.AddOrUpdateResult(DownWalkLenVarParameter.Name, dlv);
    145145            }
    146146          }
    … …  
    149149      return base.Apply();
    150150    }
    151 
    152     private static void AddOrUpdateResult(ResultCollection results, string name, IItem item, bool clone = false) {
    153       IResult r;
    154       if (!results.TryGetValue(name, out r)) {
    155         results.Add(new Result(name, clone ? (IItem)item.Clone() : item));
    156       } else r.Value = clone ? (IItem)item.Clone() : item;
    157     }
    158151  }
    159152}
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