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3 Annals of Computer Science and Information Systems

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Efficient Computation of RNA Partition Functions Using McCaskill’s Algorithm

Zhao Chunchun, Sahni Sartaj

Annals of Computer Science and Information Systems

2020

Vol. 21

449--452

We develop efficient single- and multi-core algorithms to compute partition functions for RNA sequences. Our algorithms, which are based on McCaskill's algorithm, are benchmarked against state-of-the-art fast algorithms obtained using the parallelizing source-to-source compilers PLUTO and TRACO. On our Intel I9 computational platform, our best single core algorithm takes up to 81.2% less time than the single core algorithm resulting from PLUTO, which is faster than that obtained from TRACO. Our best multi-core algorithm takes up to 84.7% less time than the multi-core algorithm obtained using TRACO when run with 20 threads (our I9 has 10 cores and supports hyperthreading); the TRACO multi-core algorithm is faster than the PLUTO one.

Parallel cache-efficient code for computing the McCaskill partition functions

Palkowski Marek, Bielecki Wlodzimierz

Annals of Computer Science and Information Systems

2019

Vol. 18

207--210

We present parallel tiled optimized McCaskill's partition functions computation code. That CPU and memory intensive dynamic programming task is within computational biology. To optimize code, we use the authorial source-to-source TRACO compiler and compare obtained code performance with that generated with the state-of-the-art PluTo compiler based on the affine transformations framework (ATF). For the considered task, PluTo is able to generate only serial highly cache efficient code without any parallelism. A TRACO tiling and parallelizing strategy uses the transitive closure of a dependence graph to avoid affine function calculation. First, for each loop nest statement, rectangular tiles are formed. Then those tiles are corrected to be valid under lexicographical order if necessary. A correction is carried out by means of applying transitive closure. The validity of tiles guarantees that the inter-tile dependence graph is acyclic. So, a valid schedule for target tiles can be derived and applied to generate parallel tiled code. For this purpose, the ISL scheduler is used. An experimental study carried out on a multi-core computer demonstrates considerable speed-up of generated code for the larger number of threads. Generated parallel tiled code overcomes that generated with the PluTo compiler.

Development of a flexible Mizar tokenizer and parser for information retrieval system

Nakasho Kazuhisa

Annals of Computer Science and Information Systems

2019

Vol. 18

77--80

In this paper, we explain the development of a new Mizar tokenizer and parser program as a component of a search system that works on the Mizar Mathematical Library. The existing Mizar tokenizer and parser can handle only an article as a whole written in the Mizar language, however, the newly developed program can deal with a snippet of a Mizar article. In particular, since it is possible to handle a snippet of an article without specifying a vocabulary section of an environment part, it is expected that user input efforts will be greatly reduced.