Titre :

Modeling Dynamic Programming Problems over Sequences and Trees with Inverse Coupled Rewrite Systems

Auteur(s) :

Giegerich, Robert [Auteur]
Universität Bielefeld = Bielefeld University
Touzet, Helene [Auteur]
Bioinformatics and Sequence Analysis [BONSAI]
Laboratoire d'Informatique Fondamentale de Lille [LIFL]

Titre de la revue :

Algorithms

Pagination :

62 - 144

Éditeur :

MDPI

Date de publication :

2014

ISSN :

1999-4893

Discipline(s) HAL :

Informatique [cs]/Bio-informatique [q-bio.QM]
Informatique [cs]/Algorithme et structure de données [cs.DS]

Résumé en anglais : [en]

Dynamic programming is a classical algorithmic paradigm, which often allows the evaluation of a search space of exponential size in polynomial time. Recursive problem decomposition, tabulation of intermediate results for ...
Lire la suite >Dynamic programming is a classical algorithmic paradigm, which often allows the evaluation of a search space of exponential size in polynomial time. Recursive problem decomposition, tabulation of intermediate results for re-use, and Bellman's Principle of Optimality are its well-understood ingredients. However, algorithms often lack abstraction and are difficult to implement, tedious to debug, and delicate to modify. The present article proposes a generic framework for specifying dynamic programming problems. This framework can handle all kinds of sequential inputs, as well as tree-structured data. Biosequence analysis, document processing, molecular structure analysis, comparison of objects assembled in a hierarchic fashion, and generally, all domains come under consideration where strings and ordered, rooted trees serve as natural data representations. The new approach introduces inverse coupled rewrite systems. They describe the solutions of combinatorial optimization problems as the inverse image of a term rewrite relation that reduces problem solutions to problem inputs. This specification leads to concise yet translucent specifications of dynamic programming algorithms. Their actual implementation may be challenging, but eventually, as we hope, it can be produced automatically. The present article demonstrates the scope of this new approach by describing a diverse set of dynamic programming problems which arise in the domain of computational biology, with examples in biosequence and molecular structure analysis.Lire moins >

Langue :

Anglais

Comité de lecture :

Oui

Audience :

Internationale

Vulgarisation :

Non

Collections :

• Centre de Recherche en Informatique, Signal et Automatique de Lille (CRIStAL) - UMR 9189

Source :

Harvested from HAL