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Changing parameters to see the impact on all the different similarity algorithms (2020.04.09)

README | Dereplication main doc | Stats: varying all parameters

General

The variable that we monitor is the median of the matchIndex of the first 200 experiments.

matchIndex is set to predictions.length if similarity is zero.

The massFilter option was not existing yet.

Parameters we test and default values

  1. Number of experiments for which matchIndex is computed: numExperiments
  2. Wether the spectra are normed in loadData or in similarity: norm
  3. What algorithm is used to compute the similarity: algorithm
  4. mergeSpan
  5. alignSpan
  6. Weight of Y values: weight

We set some default values for all these parameters, and then only vary one at a time. Here are the default values:

  1. numExperiments: 200
  2. norm: in loadData
  3. algorithm: we test all algorithms each time
  4. mergeSpan: 0.05
  5. alignSpan: 0.05
  6. weight: x^3

Results with default values

Algorithm Median
cosine 12814
czekanowski 11342
dice 9585
intersection 168
jaccard 9585
kulczynski 11342
motyka 11342

norm: in similarity (2)

Algorithm Median
cosine 12814
czekanowski 16326
dice 12964
intersection 16326
jaccard 12964
kulczynski 16326
motyka 16326

mergeSpan: 0.5 (4)

Algorithm Median
cosine 15305
czekanowski 14642
dice 14655
intersection 255
jaccard 14655
kulczynski 14642
motyka 14642

alignDelta: 0.5 (5)

Algorithm Median
cosine 36607
czekanowski 32929
dice 33408
intersection 819
jaccard 33408
kulczynski 32929
motyka 32929

mergeSpan: 0.5 and alignDelta: 0.5 (4 and 5)

Algorithm Median
cosine 15305
czekanowski 14642
dice 14655
intersection 255
jaccard 14655
kulczynski 14642
motyka 14642

weight : none (6)

Algorithm Median
cosine 15908
czekanowski 9702
dice 8086
intersection 337
jaccard 8086
kulczynski 9702
motyka 9702

weight : none, mergeSpan: 0.5 and alignDelta: 0.5 (4, 5 and 6)

(done by mistake)

Algorithm Median
cosine 32194
czekanowski 19516
dice 13614
intersection 663
jaccard 13614
kulczynski 19516
motyka 19516

More tests on the weight parameter were done in dereplicationData.md