Change formulas for the following integral numeric characteristics:

Entropy (Amount of information / identification information). Descriptive information amount. And as a consequence Uniformity and Regularity characteristics calculation also changed. Also refactored almost all integral characteristics calculators and fixed some tests.
intervals-mining-lab · Oct 28, 2024 · ff25e2c · ff25e2c
1 parent 9d5d8f3
commit ff25e2c
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diff --git a/Libiada.Core.Tests/Core/ChainsStorage.cs b/Libiada.Core.Tests/Core/ChainsStorage.cs
@@ -25,111 +25,109 @@ public static class ChainsStorage
     /// </summary>
     public static List<Chain> Chains =>
     [
-        // B B A A C B A C C B
-        // _ _ A A _ _ A _ _ _
-        // B B _ _ _ B _ _ _ B
-        // _ _ _ _ C _ _ C C _
-        new Chain("BBAACBACCB"), // 0
-
-        // A C T T G A T A C G
-        // A _ _ _ _ A _ A _ _
-        // _ C _ _ _ _ _ _ C _
-        // _ _ T T _ _ T _ _ _
-        // _ _ _ _ G _ _ _ _ G
-        new Chain("ACTTGATACG"), // 1
-
-        // C C A C G C T T A C
-        // C C _ C _ C _ _ _ C
-        // _ _ A _ _ _ _ _ A _
-        // _ _ _ _ G _ _ _ _ _
-        // _ _ _ _ _ _ T T _ _
-        new Chain("CCACGCTTAC"), // 2
-
-        // C G
-        // C _
-        // _ G
-        new Chain("CG"), // 3
-
-        // C C C C
-        // C C C C
-        new Chain("CCCC"), // 4
-
-        // A C G T
-        // A _ _ _
-        // _ C _ _
-        // _ _ G _
-        // _ _ _ T
-        new Chain("ACGT"), // 5
-
-        // A A A A C G T
-        // A A A A _ _ _
-        // _ _ _ _ C _ _
-        // _ _ _ _ _ G _
-        // _ _ _ _ _ _ T
-        new Chain("AAAACGT"), // 6
-
-        // T A
-        // T _
-        // _ A
-        new Chain("TA"), // 7
-
-        // T T T T
-        // T T T T
-        new Chain("TTTT"), // 8
-
-        // A B C A B C A B C
-        // A _ _ A _ _ A _ _
-        // _ B _ _ B _ _ B _
-        // _ _ C _ _ C _ _ C
-        new Chain("ABCABCABC"), // 9
-
-        // C B C A B C A B C
-        // - _ _ A _ _ A _ _
-        // _ B _ _ B _ _ B _
-        // C _ C _ _ C _ _ C
-        new Chain("CBCABCABC"), // 10
-
-        // A B A A B C A B C
-        // A _ A A _ _ A _ _
-        // _ B _ _ B _ _ B _
-        // _ _ _ _ _ C _ _ C
-        new Chain("ABAABCABC"), // 11
-
-        // A B B A B C A B C
-        // A _ _ A _ _ A _ _
-        // _ B B _ B _ _ B _
-        // _ _ _ _ _ C _ _ C
-        new Chain("ABBABCABC"), // 12
-
-        // A B C A B B A B C
-        // A _ _ A _ _ A _ _
-        // _ B _ _ B B _ B _
-        // _ _ C _ _ _ _ _ C
-        new Chain("ABCABBABC"), // 13
-
-        // A B C A B C A A C
-        // A _ _ A _ _ A A _
-        // _ B _ _ B _ _ _ _
-        // _ _ C _ _ C _ _ C
-        new Chain("ABCABCAAC"), // 14
-
-        // A B C A B C A C C
-        // A _ _ A _ _ A _ _
-        // _ B _ _ B _ _ _ _
-        // _ _ C _ _ C _ C C
-        new Chain("ABCABCACC"), // 15
-
-        // A B C A B C A B B
-        // A _ _ A _ _ A _ _
-        // _ B _ _ B _ _ B B
-        // _ _ C _ _ C _ _ _
-        new Chain("ABCABCABB"), // 16
-
-        // A B C A B C A B C
-        // A _ _ A _ _ A _ _
-        // _ B _ _ B _ _ B _
-        // _ _ C _ _ C _ _ C
-        new Chain("ABCABCABC"), // 17
+        // 0 B B A A C B A C C B
+        //   _ _ A A _ _ A _ _ _
+        //   B B _ _ _ B _ _ _ B
+        //   _ _ _ _ C _ _ C C _
+        new Chain("BBAACBACCB"),
+
+        // 1 A C T T G A T A C G
+        //   A _ _ _ _ A _ A _ _
+        //   _ C _ _ _ _ _ _ C _
+        //   _ _ T T _ _ T _ _ _
+        //   _ _ _ _ G _ _ _ _ G
+        new Chain("ACTTGATACG"),
+
+        // 2 C C A C G C T T A C
+        //   C C _ C _ C _ _ _ C
+        //   _ _ A _ _ _ _ _ A _
+        //   _ _ _ _ G _ _ _ _ _
+        //   _ _ _ _ _ _ T T _ _
+        new Chain("CCACGCTTAC"),
+
+        // 3 C G
+        //   C _
+        //   _ G
+        new Chain("CG"),
+
+        // 4 C C C C
+        new Chain("CCCC"),
+
+        // 5 A C G T
+        //   A _ _ _
+        //   _ C _ _
+        //   _ _ G _
+        //   _ _ _ T
+        new Chain("ACGT"),
+
+        // 6 A A A A C G T
+        //   A A A A _ _ _
+        //   _ _ _ _ C _ _
+        //   _ _ _ _ _ G _
+        //   _ _ _ _ _ _ T
+        new Chain("AAAACGT"),
+
+        // 7 T A
+        //   T _
+        //   _ A
+        new Chain("TA"),
+
+        // 8 T T T T
+        new Chain("TTTT"),
+
+        // 9 A B C A B C A B C
+        //   A _ _ A _ _ A _ _
+        //   _ B _ _ B _ _ B _
+        //   _ _ C _ _ C _ _ C
+        new Chain("ABCABCABC"),
+
+        // 10 C B C A B C A B C
+        //    - _ _ A _ _ A _ _
+        //    _ B _ _ B _ _ B _
+        //    C _ C _ _ C _ _ C
+        new Chain("CBCABCABC"),
+
+        // 11 A B A A B C A B C
+        //    A _ A A _ _ A _ _
+        //    _ B _ _ B _ _ B _
+        //    _ _ _ _ _ C _ _ C
+        new Chain("ABAABCABC"),
+
+        // 12 A B B A B C A B C
+        //    A _ _ A _ _ A _ _
+        //    _ B B _ B _ _ B _
+        //    _ _ _ _ _ C _ _ C
+        new Chain("ABBABCABC"),
+
+        // 13 A B C A B B A B C
+        //    A _ _ A _ _ A _ _
+        //    _ B _ _ B B _ B _
+        //    _ _ C _ _ _ _ _ C
+        new Chain("ABCABBABC"),
+
+        // 14 A B C A B C A A C
+        //    A _ _ A _ _ A A _
+        //    _ B _ _ B _ _ _ _
+        //    _ _ C _ _ C _ _ C
+        new Chain("ABCABCAAC"),
+
+        // 15 A B C A B C A C C
+        //    A _ _ A _ _ A _ _
+        //    _ B _ _ B _ _ _ _
+        //    _ _ C _ _ C _ C C
+        new Chain("ABCABCACC"),
+
+        // 16 A B C A B C A B B
+        //    A _ _ A _ _ A _ _
+        //    _ B _ _ B _ _ B B
+        //    _ _ C _ _ C _ _ _
+        new Chain("ABCABCABB"),
+
+        // 17 A B C A B C A B C
+        //    A _ _ A _ _ A _ _
+        //    _ B _ _ B _ _ B _
+        //    _ _ C _ _ C _ _ C
+        new Chain("ABCABCABC"),
 
         // 18 _ _ _ _ _ _ _ _ _ _
         new Chain(
@@ -189,7 +187,12 @@ public static class ChainsStorage
         // 29 _ _ _ _ _ C _ _ _ _
         new Chain(
             [0, 0, 0, 0, 0, 1, 0, 0, 0, 0],
-            [NullValue.Instance(), Elements["C"]])
+            [NullValue.Instance(), Elements["C"]]),
+
+        // 30 A B A A B
+        //    A _ A A _
+        //    _ B _ _ B
+        new Chain("ABAAB")
 
     ];
 

diff --git a/...a.Core.Tests/Core/Characteristics/Calculators/CongenericCalculators/ElementsCountTests.cs b/...a.Core.Tests/Core/Characteristics/Calculators/CongenericCalculators/ElementsCountTests.cs
@@ -19,13 +19,13 @@ public class ElementsCountTests : CongenericCalculatorsTests<ElementsCount>
     /// The value.
     /// </param>
     [TestCase(0, 3)]
-    [TestCase(1, 3)]
-    [TestCase(2, 3)]
-    [TestCase(3, 3)]
+    [TestCase(1, 4)]
+    [TestCase(2, 1)]
+    [TestCase(3, 1)]
     [TestCase(4, 3)]
-    [TestCase(5, 3)]
+    [TestCase(5, 5)]
     public void CongenericCalculationTest(int index, double value)
     {
-        CongenericChainCharacteristicTest(0, Link.NotApplied, value);
+        CongenericChainCharacteristicTest(index, Link.NotApplied, value);
     }
 }
diff --git a/...ada.Core.Tests/Core/Characteristics/Calculators/FullCalculators/AverageRemotenessTests.cs b/...ada.Core.Tests/Core/Characteristics/Calculators/FullCalculators/AverageRemotenessTests.cs
@@ -26,6 +26,7 @@ public class AverageRemotenessTests : FullCalculatorsTests<AverageRemoteness>
     [TestCase(0, Link.End, 1.017)]
     [TestCase(0, Link.Both, 1.0828)]
     [TestCase(0, Link.Cycle, 1.234)]
+    [TestCase(30, Link.Start, 0.7169925)]
     public void ChainCalculationTest(int index, Link link, double value)
     {
         ChainCharacteristicTest(index, link, value);

diff --git a/...ore.Tests/Core/Characteristics/Calculators/FullCalculators/DescriptiveInformationTests.cs b/...ore.Tests/Core/Characteristics/Calculators/FullCalculators/DescriptiveInformationTests.cs
@@ -21,11 +21,12 @@ public class DescriptiveInformationTests : FullCalculatorsTests<DescriptiveInfor
     /// <param name="value">
     /// The value.
     /// </param>
-    [TestCase(0, Link.None, 2.8845)]
-    [TestCase(0, Link.Start, 2.9917)]
-    [TestCase(0, Link.End, 2.9473)]
-    [TestCase(0, Link.Both, 2.9865)]
+    [TestCase(0, Link.None, 2.37956557896877)]
+    [TestCase(0, Link.Start, 2.58645791024)]
+    [TestCase(0, Link.End, 2.383831871)]
+    [TestCase(0, Link.Both, 2.52382717296366)]
     [TestCase(0, Link.Cycle, 2.971)]
+    [TestCase(30, Link.Start, 1.71450693)]
     public void ChainCalculationTest(int index, Link link, double value)
     {
         ChainCharacteristicTest(index, link, value);

diff --git a/Libiada.Core.Tests/Core/Characteristics/Calculators/FullCalculators/GeometricMeanTests.cs b/Libiada.Core.Tests/Core/Characteristics/Calculators/FullCalculators/GeometricMeanTests.cs
@@ -26,9 +26,10 @@ public class GeometricMeanTests : FullCalculatorsTests<GeometricMean>
     [TestCase(0, Link.End, 2.0237)]
     [TestCase(0, Link.Both, 2.1182)]
     [TestCase(0, Link.Cycle, 2.3522)]
+    [TestCase(30, Link.Start, 1.6437518295)]
     public void CalculationTest(int index, Link link, double value)
     {
-        ChainCharacteristicTest(0, link, value);
+        ChainCharacteristicTest(index, link, value);
     }
 
     /// <summary>

diff --git a/....Tests/Core/Characteristics/Calculators/FullCalculators/IdentificationInformationTests.cs b/....Tests/Core/Characteristics/Calculators/FullCalculators/IdentificationInformationTests.cs
@@ -21,11 +21,12 @@ public class IdentificationInformationTests : FullCalculatorsTests<Identificatio
     /// <param name="value">
     /// The value.
     /// </param>
-    [TestCase(0, Link.None, 1.5283)]
-    [TestCase(0, Link.Start, 1.581)]
-    [TestCase(0, Link.End, 1.5594)]
-    [TestCase(0, Link.Both, 1.5785)]
+    [TestCase(0, Link.None, 1.25069821459)]
+    [TestCase(0, Link.Start, 1.3709777)]
+    [TestCase(0, Link.End, 1.2532824857)]
+    [TestCase(0, Link.Both, 1.335618955)]
     [TestCase(0, Link.Cycle, 1.571)]
+    [TestCase(30, Link.Start, 0.77779373752225)]
     public void ChainCalculationTest(int index, Link link, double value)
     {
         ChainCharacteristicTest(index, link, value);

diff --git a/Libiada.Core.Tests/Core/Characteristics/Calculators/FullCalculators/PeriodicityTests.cs b/Libiada.Core.Tests/Core/Characteristics/Calculators/FullCalculators/PeriodicityTests.cs
@@ -43,9 +43,9 @@ public void ChainCalculationTest(int index, Link link, double value)
     /// <param name="value">
     /// The value.
     /// </param>
-    [TestCase(3, Link.None, 0)]
-    [TestCase(5, Link.None, 0)]
-    [TestCase(7, Link.None, 0)]
+    [TestCase(3, Link.None, 1)]
+    [TestCase(5, Link.None, 1)]
+    [TestCase(7, Link.None, 1)]
     public void NoIntervalsTest(int index, Link link, double value)
     {
         ChainCharacteristicTest(index, link, value);

diff --git a/Libiada.Core.Tests/Core/Characteristics/Calculators/FullCalculators/RegularityTests.cs b/Libiada.Core.Tests/Core/Characteristics/Calculators/FullCalculators/RegularityTests.cs
@@ -21,11 +21,12 @@ public class RegularityTests : FullCalculatorsTests<Regularity>
     /// <param name="value">
     /// The value.
     /// </param>
-    [TestCase(0, Link.None, 0.7051)]
-    [TestCase(0, Link.Start, 0.7203)]
-    [TestCase(0, Link.End, 0.6866)]
-    [TestCase(0, Link.Both, 0.70926)]
+    [TestCase(0, Link.None, 0.8547)]
+    [TestCase(0, Link.Start, 0.8332)]
+    [TestCase(0, Link.End, 0.8489)]
+    [TestCase(0, Link.Both, 0.8393)]
     [TestCase(0, Link.Cycle, 0.7917)]
+    [TestCase(30, Link.Start, 0.9587)]
     public void ChainCalculationTest(int index, Link link, double value)
     {
         ChainCharacteristicTest(index, link, value);

diff --git a/....Core.Tests/Core/Characteristics/Calculators/FullCalculators/RemotenessDispersionTests.cs b/....Core.Tests/Core/Characteristics/Calculators/FullCalculators/RemotenessDispersionTests.cs
@@ -28,7 +28,7 @@ public class RemotenessDispersionTests : FullCalculatorsTests<RemotenessDispersi
     [TestCase(0, Link.Cycle, 1.1161)]
     public void ChainCalculationTest(int index, Link link, double value)
     {
-        ChainCharacteristicTest(0, link, value);
+        ChainCharacteristicTest(index, link, value);
     }
 
     /// <summary>

diff --git a/...ts/Core/Characteristics/Calculators/FullCalculators/RemotenessKurtosisCoefficientTests.cs b/...ts/Core/Characteristics/Calculators/FullCalculators/RemotenessKurtosisCoefficientTests.cs
@@ -28,7 +28,7 @@ public class RemotenessKurtosisCoefficientTests : FullCalculatorsTests<Remotenes
     [TestCase(0, Link.Cycle, 1.337076)]
     public void ChainCalculationTest(int index, Link link, double value)
     {
-        ChainCharacteristicTest(0, link, value);
+        ChainCharacteristicTest(index, link, value);
     }
 
     /// <summary>

diff --git a/...da.Core.Tests/Core/Characteristics/Calculators/FullCalculators/RemotenessKurtosisTests.cs b/...da.Core.Tests/Core/Characteristics/Calculators/FullCalculators/RemotenessKurtosisTests.cs
@@ -28,7 +28,7 @@ public class RemotenessKurtosisTests : FullCalculatorsTests<RemotenessKurtosis>
     [TestCase(0, Link.Cycle, 1.6655934)]
     public void ChainCalculationTest(int index, Link link, double value)
     {
-        ChainCharacteristicTest(0, link, value);
+        ChainCharacteristicTest(index, link, value);
     }
 
     /// <summary>

diff --git a/...ts/Core/Characteristics/Calculators/FullCalculators/RemotenessSkewnessCoefficientTests.cs b/...ts/Core/Characteristics/Calculators/FullCalculators/RemotenessSkewnessCoefficientTests.cs
@@ -28,7 +28,7 @@ public class RemotenessSkewnessCoefficientTests : FullCalculatorsTests<Remotenes
     [TestCase(0, Link.Cycle, -0.1356234)]
     public void ChainCalculationTest(int index, Link link, double value)
     {
-        ChainCharacteristicTest(0, link, value);
+        ChainCharacteristicTest(index, link, value);
     }
 
     /// <summary>

diff --git a/...da.Core.Tests/Core/Characteristics/Calculators/FullCalculators/RemotenessSkewnessTests.cs b/...da.Core.Tests/Core/Characteristics/Calculators/FullCalculators/RemotenessSkewnessTests.cs
@@ -28,7 +28,7 @@ public class RemotenessSkewnessTests : FullCalculatorsTests<RemotenessSkewness>
     [TestCase(0, Link.Cycle, -0.1599169)]
     public void ChainCalculationTest(int index, Link link, double value)
     {
-        ChainCharacteristicTest(0, link, value);
+        ChainCharacteristicTest(index, link, value);
     }
 
     /// <summary>

diff --git a/...ests/Core/Characteristics/Calculators/FullCalculators/RemotenessStandardDeviationTests.cs b/...ests/Core/Characteristics/Calculators/FullCalculators/RemotenessStandardDeviationTests.cs
@@ -28,7 +28,7 @@ public class RemotenessStandardDeviationTests : FullCalculatorsTests<RemotenessS
     [TestCase(0, Link.Cycle, 1.0564604)]
     public void ChainCalculationTest(int index, Link link, double value)
     {
-        ChainCharacteristicTest(0, link, value);
+        ChainCharacteristicTest(index, link, value);
     }
 
     /// <summary>