auto-optimize speeds up genomics tool fimo ~20x with bit-identical results
jmschreiber91 · x · 2026-10-11
jmschrei's auto-optimize loop struck again, this time on the motif scanning tool fimo: per-motif lookup tables over precomputed sequence codes enable early-abandon tests that skip any window provably below threshold, plus rebuilt DataFrame and p-value stages.
Benchmark time dropped from 1.483s to 0.0727s (20x), with every hit and p-value bitwise identical and scores within 3.6e-15. The optimization is merged into memesuite-lite main.
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