FILTR compiles bioinformatics DP recurrences with separable scheduling and pruning directives into C++ code achieving 0.95x–30x speedup over hand-optimized libraries.
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Walenz, Konstantin Berlin, Jason R
2 Pith papers cite this work, alongside 8,171 external citations. Polarity classification is still indexing.
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The anti-lexicographic SUS-anchor achieves sampling densities less than 1% above the lower bound for alphabet size 4 and k=1, substantially outperforming bidirectional anchors.
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Compiling Bioinformatics Recurrences
FILTR compiles bioinformatics DP recurrences with separable scheduling and pruning directives into C++ code achieving 0.95x–30x speedup over hand-optimized libraries.
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The anti-lexicographic SUS-anchor: a near-optimal k=1 sampling scheme
The anti-lexicographic SUS-anchor achieves sampling densities less than 1% above the lower bound for alphabet size 4 and k=1, substantially outperforming bidirectional anchors.