Edit Distance with Duplications and Contractions Revisited

Reducing the worst case running times of a family of RNA and CFG problems, using Valiant’s approach

“…The examples given here come from the fields of RNA secondary structure prediction and CFG Parsing. Recently, we have shown that this technique also applies for the Edit Distance with Duplication and Contraction problem [45], suggesting that it is possible that more problems from other domains can be similarly accelerated. While previous works describe other practical acceleration techniques for some of the mentioned problems [14,25,28,32-38], Valiant's technique, along with the Four Russians technique [28,30,31], are the only two techniques which currently allow to reduce the theoretical asymptotic worst case running times of the standard algorithms, without compromising the correctness of the computations.…”

“…While in [30] this technique was used ad hoc for accelerating RNA folding, it is possible to decouple the description of the fast matrix multiplication technique from the RNA folding algorithm, and present the algorithm of [30] in the same framework presented here. The latter special matrix multiplication variant was further accelerated in [45] to $O\left(\frac{n^3}{{qopnamelog}^{2}n}\right)$ running time, implying that RNA folding under discrete scoring schemes (e.g. [6]) can be computed in $O\left(\frac{n^3}{{qopnamelog}^{2}n}\right)$ time, instead of in $O\left(\frac{n^3{qopnamelog}^{3}qopname\; logn}{{qopnamelog}^{2}n}\right)$ time as implied by the fastest Min/Max-Plus Multiplication algorithm for general matrices [27].…”

Reducing the Worst Case Running Times of a Family of RNA and CFG Problems, Using Valiant’s Approach

“…The examples given here come from the fields of RNA secondary structure prediction and CFG Parsing. Recently, we have shown that this technique also applies for the Edit Distance with Duplication and Contraction problem [45], suggesting that it is possible that more problems from other domains can be similarly accelerated. While previous works describe other practical acceleration techniques for some of the mentioned problems [14,25,28,[32][33][34][35][36][37][38], Valiant's technique, along with the Four Russians technique [28,30,31], are the only two techniques which currently allow to reduce the theoretical asymptotic worst case running times of the standard algorithms, without compromising the correctness of the computations.…”

“…While in [30] this technique was used ad hoc for accelerating RNA folding, it is possible to decouple the description of the fast matrix multiplication technique from the RNA folding algorithm, and present the algorithm of [30] in the same framework presented here. The latter special matrix multiplication variant was further accelerated in [45] [27]. Many of the current acceleration techniques for RNA and CFG related algorithms are based on sparsification, and are applicable only to optimization problems.…”

De-Duplication Scheduling Strategy in Real-Time Data Warehouse

“…There are some researches on real-time de-duplication recently [7]. Proposed the CBLOCK which learns hash functions automatically from attribute domains and a labeled dataset consisting of duplicates; [8] proposed an objectbased de-duplication framework and an efficient object index mechanism to speed up the searching facility to identify duplicate objects; [9] proposed a buffer cache de-duplication technique for query dispatch in the field of replicated databases which has a well-known problem that different buffer caches share some identical data; [10] propose three algorithms for the problem of string edit distance with duplication and contraction operations, which improve the time complexity of previous algorithms for this problem. To our best knowledge, few works focus on the scheduling strategy of de-duplication.…”