Dataset associated with "Polyhedral Optimizations of RNA-RNA Interaction Computations"
Studying RNA-RNA interaction has led to major successes in the treatment of some cancers, including colon, breast and pancreatic cancer by suppressing the gene expression involved in the development of these diseases. The problem with such programs is that they are computationally and memory intensive: O(N4 ) space and O(N6 ) time complexity. Moreover, the entire application is complicated and involves many mutually recursive data variables. We address the problem of speeding up a surrogate kernel (named OSPSQ) that captures the main dependence pattern found in two widely used RNA-RNA ...
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