FlashSimilarity for faster flash entropy, cosine, modified cosine computation #827
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Add flash modcos
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julianpollmann
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Oct 6, 2025
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New fast similarity score computation inspired by the Flash Entropy from Li and Fiehn (2023).
This is based on first creating a m/z index (
_LibraryIndex) that contains ALL fragments of the dataset ordered by m/z. This allows much faster computation than, for instance,CosineGreedyorModifiedCosine.In the current implementation it is possible to chose differnt score types:
score_typecan bespectral entropyorcosinematching_modecan befragment,neutral_lossorhybrid(hybrid being a combination of both fragments and neutral losses)The computation of modified cosine scores is then a combination of
cosinewithhybridmatching mode.I quickly compared
CosineGreedywithFlashSimilarity(cosine mode) and blink (see #829 ). This shows that FlashSimilarity is not scaling as well as Blink for the presented task (all-vs-all comparisons), but is MUCH faster than CosineGreedy, by about 100x. In addition, and unlike Blink, FlashSimilarity is no approximation but computes the exact same scores as CosineGreedy.FlashSimlaritynow also allows to compute the modified cosine scores (exact same as with currentModifiedCosine) about 100x faster.