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Merge pull request #186 from cicirello/fix-tau-related
Fixed efficiency issues in Kendall tau distance and related distances
2 parents 1b5f56d + d400dd0 commit 1cf37aa

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‎CHANGELOG.md‎

Lines changed: 10 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -4,7 +4,7 @@ All notable changes to this project will be documented in this file.
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The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
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and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
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7-
## [Unreleased] - 2022-02-15
7+
## [Unreleased] - 2022-02-17
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### Added
1010

@@ -21,6 +21,15 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
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### Other
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24+
## [3.1.1] - 2022-02-17
25+
26+
### Fixed
27+
* Fixed inefficient memory usage in KendallTauDistance (issue #183)
28+
* Fixed inefficient memory usage in KendallTauSequenceDistance (issue #184)
29+
* Fixed inefficient memory usage in WeightedKendallTauDistance (issue #185)
30+
* Fixed inefficiency in WeightedKendallTauDistance related to redundant computation (issue #182)
31+
32+
2433
## [3.1.0] - 2022-02-15
2534

2635
### Added

‎src/main/java/org/cicirello/permutations/distance/KendallTauDistance.java‎

Lines changed: 16 additions & 10 deletions
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,6 @@
11
/*
2-
* Copyright 2014, 2015, 2017-2022 Vincent A. Cicirello, <https://www.cicirello.org/>.
2+
* JavaPermutationTools: A Java library for computation on permutations and sequences.
3+
* Copyright (C) 2014, 2015, 2017-2022 Vincent A. Cicirello, <https://www.cicirello.org/>.
34
*
45
* This file is part of JavaPermutationTools (https://jpt.cicirello.org/).
56
*
@@ -74,7 +75,7 @@ public int distance(Permutation p1, Permutation p2) {
7475
for (int i = 0; i < arrayP2.length; i++) {
7576
arrayP2[i] = invP1[p2.get(i)];
7677
}
77-
return countInversions(arrayP2);
78+
return countInversions(arrayP2, 0, arrayP2.length-1);
7879
}
7980

8081
@Override
@@ -83,15 +84,21 @@ public int max(int length) {
8384
return (length*(length - 1))>>1;
8485
}
8586

86-
private int countInversions(int[] array) {
87-
if (array.length <= 1) return 0;
88-
int m = array.length >> 1;
89-
int[] left = Arrays.copyOfRange(array, 0, m);
90-
int[] right = Arrays.copyOfRange(array, m, array.length);
91-
int count = countInversions(left) + countInversions(right);
87+
private int countInversions(int[] array, int first, int last) {
88+
if (last <= first) {
89+
return 0;
90+
}
91+
int m = (first + last) >> 1;
92+
return countInversions(array, first, m) + countInversions(array, m+1, last) + merge(array, first, m+1, last+1);
93+
}
94+
95+
private int merge(int[] array, int first, int midPlus, int lastPlus) {
96+
int[] left = Arrays.copyOfRange(array, first, midPlus);
97+
int[] right = Arrays.copyOfRange(array, midPlus, lastPlus);
9298
int i = 0;
9399
int j = 0;
94-
int k = 0;
100+
int k = first;
101+
int count = 0;
95102
while (i < left.length && j < right.length) {
96103
if (left[i] < right[j]) {
97104
array[k] = left[i];
@@ -117,5 +124,4 @@ private int countInversions(int[] array) {
117124
}
118125
return count;
119126
}
120-
121127
}

‎src/main/java/org/cicirello/permutations/distance/WeightedKendallTauDistance.java‎

Lines changed: 19 additions & 12 deletions
Original file line numberDiff line numberDiff line change
@@ -100,7 +100,7 @@ public double distancef(Permutation p1, Permutation p2) {
100100
w[arrayP2[i]] = weights[p2.get(i)];
101101
}
102102

103-
return countWeightedInversions(arrayP2, w);
103+
return countWeightedInversions(arrayP2, w, 0, arrayP2.length-1);
104104
}
105105

106106
/**
@@ -115,26 +115,33 @@ public double maxf(int length) {
115115
return maxDistance;
116116
}
117117

118-
private double countWeightedInversions(int[] array, double[] w) {
119-
if (array.length <= 1) return 0;
120-
int m = array.length >> 1;
121-
int[] left = Arrays.copyOfRange(array, 0, m);
122-
int[] right = Arrays.copyOfRange(array, m, array.length);
123-
double weightedCount = countWeightedInversions(left, w) + countWeightedInversions(right, w);
118+
private double countWeightedInversions(int[] array, double[] w, int first, int last) {
119+
if (last <= first) {
120+
return 0;
121+
}
122+
int m = (first + last) >> 1;
123+
return countWeightedInversions(array, w, first, m) + countWeightedInversions(array, w, m+1, last) + merge(array, w, first, m+1, last+1);
124+
}
125+
126+
private double merge(int[] array, double[] w, int first, int midPlus, int lastPlus) {
127+
int[] left = Arrays.copyOfRange(array, first, midPlus);
128+
int[] right = Arrays.copyOfRange(array, midPlus, lastPlus);
124129
int i = 0;
125130
int j = 0;
126-
int k = 0;
131+
int k = first;
132+
double weightedCount = 0;
133+
double leftWeights = 0;
134+
for (int x = 0; x < left.length; x++) {
135+
leftWeights += w[left[x]];
136+
}
127137
while (i < left.length && j < right.length) {
128138
if (left[i] < right[j]) {
139+
leftWeights -= w[left[i]];
129140
array[k] = left[i];
130141
i++;
131142
k++;
132143
} else {
133144
// inversions
134-
double leftWeights = 0;
135-
for (int x = i; x < left.length; x++) {
136-
leftWeights += w[left[x]];
137-
}
138145
weightedCount += w[right[j]] * leftWeights;
139146
array[k] = right[j];
140147
j++;

‎src/main/java/org/cicirello/sequences/distance/KendallTauSequenceDistance.java‎

Lines changed: 27 additions & 20 deletions
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,6 @@
11
/*
2-
* Copyright 2018-2021 Vincent A. Cicirello, <https://www.cicirello.org/>.
2+
* JavaPermutationTools: A Java library for computation on permutations and sequences.
3+
* Copyright (C) 2018-2021 Vincent A. Cicirello, <https://www.cicirello.org/>.
34
*
45
* This file is part of JavaPermutationTools (https://jpt.cicirello.org/).
56
*
@@ -76,7 +77,6 @@
7677
* Industrial Networks and Intelligent Systems, 7(23), Article e1, April 2020.</p>
7778
*
7879
* @author <a href=https://www.cicirello.org/ target=_top>Vincent A. Cicirello</a>, <a href=https://www.cicirello.org/ target=_top>https://www.cicirello.org/</a>
79-
* @version 5.13.2021
8080
*/
8181
public final class KendallTauSequenceDistance implements SequenceDistanceMeasurer {
8282

@@ -128,7 +128,7 @@ public int distance(int[] s1, int[] s2) {
128128
int numLabels = USE_HASHMAP ? relabelElementsWithHash(s1,s2,relabeling) : relabelElements(s1,s2,relabeling);
129129
Bucket[][] buckets = bucketSortElements(relabeling, numLabels);
130130
int[] mapping = mapElements(buckets, relabeling.length);
131-
return countInversions(mapping);
131+
return countInversions(mapping, 0, mapping.length-1);
132132
}
133133

134134
/**
@@ -144,7 +144,7 @@ public int distance(long[] s1, long[] s2) {
144144
int numLabels = USE_HASHMAP ? relabelElementsWithHash(s1,s2,relabeling) : relabelElements(s1,s2,relabeling);
145145
Bucket[][] buckets = bucketSortElements(relabeling, numLabels);
146146
int[] mapping = mapElements(buckets, relabeling.length);
147-
return countInversions(mapping);
147+
return countInversions(mapping, 0, mapping.length-1);
148148
}
149149

150150
/**
@@ -160,7 +160,7 @@ public int distance(short[] s1, short[] s2) {
160160
int numLabels = USE_HASHMAP ? relabelElementsWithHash(s1,s2,relabeling) : relabelElements(s1,s2,relabeling);
161161
Bucket[][] buckets = bucketSortElements(relabeling, numLabels);
162162
int[] mapping = mapElements(buckets, relabeling.length);
163-
return countInversions(mapping);
163+
return countInversions(mapping, 0, mapping.length-1);
164164
}
165165

166166
/**
@@ -176,7 +176,7 @@ public int distance(byte[] s1, byte[] s2) {
176176
int numLabels = USE_HASHMAP ? relabelElementsWithHash(s1,s2,relabeling) : relabelElements(s1,s2,relabeling);
177177
Bucket[][] buckets = bucketSortElements(relabeling, numLabels);
178178
int[] mapping = mapElements(buckets, relabeling.length);
179-
return countInversions(mapping);
179+
return countInversions(mapping, 0, mapping.length-1);
180180
}
181181

182182
/**
@@ -192,7 +192,7 @@ public int distance(char[] s1, char[] s2) {
192192
int numLabels = USE_HASHMAP ? relabelElementsWithHash(s1,s2,relabeling) : relabelElements(s1,s2,relabeling);
193193
Bucket[][] buckets = bucketSortElements(relabeling, numLabels);
194194
int[] mapping = mapElements(buckets, relabeling.length);
195-
return countInversions(mapping);
195+
return countInversions(mapping, 0, mapping.length-1);
196196
}
197197

198198
/**
@@ -208,7 +208,7 @@ public int distance(String s1, String s2) {
208208
int numLabels = USE_HASHMAP ? relabelElementsWithHash(s1,s2,relabeling) : relabelElements(s1,s2,relabeling);
209209
Bucket[][] buckets = bucketSortElements(relabeling, numLabels);
210210
int[] mapping = mapElements(buckets, relabeling.length);
211-
return countInversions(mapping);
211+
return countInversions(mapping, 0, mapping.length-1);
212212
}
213213

214214
/**
@@ -224,7 +224,7 @@ public int distance(float[] s1, float[] s2) {
224224
int numLabels = USE_HASHMAP ? relabelElementsWithHash(s1,s2,relabeling) : relabelElements(s1,s2,relabeling);
225225
Bucket[][] buckets = bucketSortElements(relabeling, numLabels);
226226
int[] mapping = mapElements(buckets, relabeling.length);
227-
return countInversions(mapping);
227+
return countInversions(mapping, 0, mapping.length-1);
228228
}
229229

230230
/**
@@ -240,7 +240,7 @@ public int distance(double[] s1, double[] s2) {
240240
int numLabels = USE_HASHMAP ? relabelElementsWithHash(s1,s2,relabeling) : relabelElements(s1,s2,relabeling);
241241
Bucket[][] buckets = bucketSortElements(relabeling, numLabels);
242242
int[] mapping = mapElements(buckets, relabeling.length);
243-
return countInversions(mapping);
243+
return countInversions(mapping, 0, mapping.length-1);
244244
}
245245

246246
/**
@@ -256,7 +256,7 @@ public int distance(boolean[] s1, boolean[] s2) {
256256
int numLabels = relabelElements(s1,s2,relabeling);
257257
Bucket[][] buckets = bucketSortElements(relabeling, numLabels);
258258
int[] mapping = mapElements(buckets, relabeling.length);
259-
return countInversions(mapping);
259+
return countInversions(mapping, 0, mapping.length-1);
260260
}
261261

262262
/**
@@ -277,7 +277,7 @@ public int distance(Object[] s1, Object[] s2) {
277277

278278
Bucket[][] buckets = bucketSortElements(relabeling, numLabels);
279279
int[] mapping = mapElements(buckets, relabeling.length);
280-
return countInversions(mapping);
280+
return countInversions(mapping, 0, mapping.length-1);
281281
}
282282

283283
/**
@@ -296,7 +296,7 @@ public <T> int distance(List<T> s1, List<T> s2) {
296296

297297
Bucket[][] buckets = bucketSortElements(relabeling, numLabels);
298298
int[] mapping = mapElements(buckets, relabeling.length);
299-
return countInversions(mapping);
299+
return countInversions(mapping, 0, mapping.length-1);
300300
}
301301

302302
private int[] mapElements(Bucket[][] buckets, int seqLength) {
@@ -752,15 +752,21 @@ private int relabelElements(List<Comparable> s1, List<Comparable> s2, int[][] re
752752
}
753753

754754
// assumes all unique elements
755-
private int countInversions(int[] array) {
756-
if (array.length <= 1) return 0;
757-
int m = array.length / 2;
758-
int[] left = Arrays.copyOfRange(array, 0, m);
759-
int[] right = Arrays.copyOfRange(array, m, array.length);
760-
int count = countInversions(left) + countInversions(right);
755+
private int countInversions(int[] array, int first, int last) {
756+
if (last <= first) {
757+
return 0;
758+
}
759+
int m = (first + last) >> 1;
760+
return countInversions(array, first, m) + countInversions(array, m+1, last) + merge(array, first, m+1, last+1);
761+
}
762+
763+
private int merge(int[] array, int first, int midPlus, int lastPlus) {
764+
int[] left = Arrays.copyOfRange(array, first, midPlus);
765+
int[] right = Arrays.copyOfRange(array, midPlus, lastPlus);
761766
int i = 0;
762767
int j = 0;
763-
int k = 0;
768+
int k = first;
769+
int count = 0;
764770
while (i < left.length && j < right.length) {
765771
if (left[i] <= right[j]) {
766772
array[k] = left[i];
@@ -787,6 +793,7 @@ private int countInversions(int[] array) {
787793
return count;
788794
}
789795

796+
790797
// internal data structures below
791798

792799
private static final class Bucket {

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