Wyniki wyszukiwania - BazTech

1

New models and algorithms for RNA pseudoknot order assignment

Zok Tomasz, Badura Jan, Swat Sylwester, Figurski Kacper, Popenda Mariusz, Antczak Maciej

International Journal of Applied Mathematics and Computer Science

|

2020

|

Vol. 30, no. 2

315--324

EN

The pseudoknot is a specific motif of the RNA structure that highly influences the overall shape and stability of a molecule. It occurs when nucleotides of two disjoint single-stranded fragments of the same chain, separated by a helical fragment, interact with each other and form base pairs. Pseudoknots are characterized by great topological diversity, and their systematic description is still a challenge. In our previous work, we have introduced the pseudoknot order: a new coefficient representing the topological complexity of the pseudoknotted RNA structure. It is defined as the minimum number of base pair set decompositions, aimed to obtain the unknotted RNA structure. We have suggested how it can be useful in the interpretation and understanding of a hierarchy of RNA folding. However, it is not trivial to unambiguously identify pseudoknots and determine their orders in an RNA structure. Therefore, since the introduction of this coefficient, we have worked on the method to reliably assign pseudoknot orders in correspondence to the mechanisms that control the biological process leading to their formation in the molecule. Here, we introduce a novel graph coloring-based model for the problem of pseudoknot order assignment. We show a specialized heuristic operating on the proposed model and an alternative integer programming algorithm. The performance of both approaches is compared with that of state-of-the-art algorithms which so far have been most efficient in solving the problem in question. We summarize the results of computational experiments that evaluate our new methods in terms of classification quality on a representative data set originating from the non-redundant RNA 3D structure repository.

2

Modele i metody kolorowania grafów. Część II

Kubale M.

Przegląd Elektrotechniczny

|

2012

|

R. 88, nr 11a

51-55

PL

Niniejszy artykuł jest drugą częścią 2-odcinkowego cyklu przeglądowego na temat modeli i metod kolorowania grafów. Przedstawiono w nim najważniejsze, z punktu widzenia zastosowań, modele kolorowania grafów. W szczególności pokazano różne kryteria i ograniczenia modyfikujące kolorowanie klasyczne. Ponieważ kolorowanie we wszystkich tych odmianach i wariantach jest NP-trudne, podano oszacowania na liczbę chromatyczną (indeks chromatyczny) oraz podano potencjalne zastosowania rozważanych modeli w problemach naukowo-technicznych.

EN

This is the second of a couple of review papers on models and methods of graph coloring. We present herein the main models of graph coloring from a practical point of view. In particular, we show various criteria and modifications of classical coloring model. Since graph coloring is NP-hard in various modifications and variants, we give simple bounds on the chromatic number (chromatic index) as well as we give potential applications of the chromatic methods in science and technology.

3

Modele i metody kolorowania grafów. Część I

Kubale M.

Przegląd Elektrotechniczny

|

2010

|

R. 86, nr 9

115-117

PL

Niniejszy artykuł jest pierwszą częścią 2-odcinkowego cyklu przeglądowego na temat modeli i metod kolorowania grafów. Przedstawiono w nim najważniejsze, z punktu widzenia zastosowań, modele kolorowania grafów. W szczególności pokazano: (1) co można kolorować w grafie (np. wierzchołki, krawędzie, końcówki, ściany, jednocześnie wierzchołki i krawędzie) oraz (2) jak można kolorować (np. dzielenie kolorów, zawijanie kolorów). Ponieważ kolorowanie we wszystkich tych odmianach i wariantach jest NP-trudne, podajemy oszacowania na liczbę chromatyczną (indeks chromatyczny) oraz podajemy potencjalne zastosowania rozważanych modeli w problemach naukowo-technicznych.

EN

This is the first of a couple of review papers on models and methods of graph coloring. We present herein the main models of graph coloring from a practical point of view. In particular, we show: (1) what elements of a graph can be colored (e.g. vertices, edges, faces, incidences) and (2) how these elements can be colored (e.g. fractional coloring, circular coloring). Since graph coloring is NP-hard in various modifications and variants, we give simple bounds on the chromatic number (chromatic index) as well as we give potential applications of the chromatic methods in science and technology.

4

Parallel tabu search for graph coloring problem

Dąbrowski J., Kubale M.

Prace Naukowe Politechniki Warszawskiej. Elektronika

|

2006

|

z. 156

87-95

EN

Tabu search is a simple, yet powerful meta-heuristic based on local search that has been often used to solve combinatorial optimization problems like the graph coloring problem. This paper presents current taxonomy of parallel tabu search algorithms and compares three parallelization techniques applied to Tabucol, a sequential TS algorithm for graph coloring. The experirnental results are based on graphs available from the DIMACS benchmark suite.