Introducing Sapling: Accelerating Suffix Array Queries with Learned Data Models with @melanie_kirsche and http://arundas.org . https://www.biorxiv.org/content/10.1101/2020.01.29.925768v1 …pic.twitter.com/SyeHlwHIvV
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We were deeply inspired by The Case for Learned Index Structures by @tim_kraska et al (plus conversations with @JeffDean last year): https://arxiv.org/abs/1712.01208 . I see huge potential for these ideas in the future
It is a classic CS space-time tradeoff, and with a tiny amount of space overhead (0.1%) we can double the performance over @TheGeneMyers' optimal suffix array search algorithm. If we allow for more space can push it even faster.pic.twitter.com/TOYEFxuh5T
What is kmer value in these graphs?
This was with 21-mers but is robust except if you use very short kmers. The function also becomes more complicated if you really skew the GC content but you have to go beyond anything that exists in naturepic.twitter.com/JkYT6RD6BK
this is brilliant
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