Performance optimization of tree edit distance #102
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…flow operation can be simplified when comparing binary trees
…g time of the dense tree comparison example * The time measurement does not seem to work inside the actual test (the test produces out of memory error)
… of using stream API * Profiling showed that this would speed up tree edit distance computation by ~20%
* Using these methods in ZhangUnorderedTreeEditDistance allows to speed up distance computation by 20 to 40% depending on test case
* Performance improve: ~20-60%
…idimap objects in ZhangUnorderedTreeEditDistance
…y time, when needed from the graph
The idea is that the Zhang algorithm makes a copy of the input trees as "CachedTree". The CachedTree allows to store tree cost, forest cost, attribute, index etc. which makes the algorithm faster.
stefanhahmann
changed the title
Instead, introduce a new class Node that can be implemented by CachedTree This allows that TreeUtils.getAllAttributes() can be reused in the constructor for ZhangUnorderedTreeEditDistance
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Resolves #59
This PR adds mainly 4 optimizations:
In total, this PR gains a speed up of up to ~90%
As Benchmark mainly this demo has been used:
mastodon-deep-lineage/src/test/java/org/mastodon/mamut/treesimilarity/ZhangUnorderedTreeEditDistanceTest.java
Line 313 in be8120c
or this mastodon file
flatSim2_be_2aba_1bab.zip
with these settings
