An improved Four-Russians method and sparsified Four-Russians algorithm for RNA folding
نویسندگان
چکیده
منابع مشابه
Time and Space Efficient Algorithms for RNA Folding with the Four-Russians Technique
In this paper, we develop new algorithms for the basic RNA folding problem. Given an RNA sequence that contains n nucleotides, the goal of the problem is to compute a pseudoknot-free secondary structure that maximizes the number of base pairs in the sequence. We show that there exists a dynamic programming algorithm that can solve the problem in time O( n 3 log2 n ) while using only O( n 2 log2...
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Solving a dense linear system of boolean equations is the final step of several cryptanalytic attacks. Examples include stream cipher cryptanalysis via XL and related algorithms, integer factorization, and attacks on the HFE public-key cryptosystem. While both Gaussian Elimination and Strassen’s Algorithm have been proposed as methods, this paper specifies an algorithm that is much faster than ...
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Bayesian computations with Hidden Markov Models (HMMs) are often avoided in practice. Instead, due to reduced running time, point estimates – maximum likelihood (ML) or maximum a posterior (MAP) – are obtained and observation sequences are segmented based on the Viterbi path, even though the lack of accuracy and dependency on starting points of the local optimization are well known. We propose ...
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We present a method of computing with matrices over very small finite fields of size larger than 2. Specifically, we show how the Method of Four Russians can be efficiently adapted to these larger fields, and introduce a row-wise matrix compression scheme that both reduces memory requirements and allows one to vectorize element operations. We also present timings which confirm the efficiency of...
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We present a new combinatorial algorithm for Boolean matrix multiplication that runs in O(n(log log n)/ log n) time. This improves the previous combinatorial algorithm by Bansal and Williams [FOCS’09] that runs in O(n(log log n)/ log n) time. Whereas Bansal and Williams’ algorithm uses regularity lemmas for graphs, the new algorithm is simple and uses entirely elementary techniques: table looku...
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ژورنال
عنوان ژورنال: Algorithms for Molecular Biology
سال: 2016
ISSN: 1748-7188
DOI: 10.1186/s13015-016-0081-9