arXiv subjects

Jorma Tarhio

Publications and source records attributed to Jorma Tarhio.

2 recordsLinked to original sources

arXiv2016

Technology Beats Algorithms (in Exact String Matching)

More than 120 algorithms have been developed for exact string matching within the last 40 years. We show by experiments that the \naive{} algorithm exploiting SIMD instructions of modern CPUs (with symbols compared in a special order) is the fastest one for patterns of length up to about 50 symbols and extremely good for longer patterns and small alphabets. The algorithm compares 16 or 32 characters in parallel by applying SSE2 or AVX2 instructions, respectively. Moreover, it uses loop peeling to further speed up the searching phase. We tried several orders for comparisons of pattern symbols and the increasing order of their probabilities in the text was the best.

cs.DS↗

arXiv2014

Alternative Algorithms for Lyndon Factorization

We present two variations of Duval's algorithm for computing the Lyndon factorization of a word. The first algorithm is designed for the case of small alphabets and is able to skip a significant portion of the characters of the string, for strings containing runs of the smallest character in the alphabet. Experimental results show that it is faster than Duval's original algorithm, more than ten times in the case of long DNA strings. The second algorithm computes, given a run-length encoded string $R$ of length $ρ$, the Lyndon factorization of $R$ in $O(ρ)$ time and constant space.

cs.DS↗