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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Numerical examination of ultrametricity in Nussinov-model RNA energy minima shows wide variation across 18 RNAs and strong sensitivity to nucleotide sequence permutation.
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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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Ultrametricity of Energy Minimum Configurations of RNA Secondary Structures in the Nussinov Model
Numerical examination of ultrametricity in Nussinov-model RNA energy minima shows wide variation across 18 RNAs and strong sensitivity to nucleotide sequence permutation.