Algebraic Dynamic Programming Algebraic Dynamic Programming.pdfVIP

Sequence Similarity and Dynamic Programming Robert Giegerich Lecture Notes Bioinformatics Summerschool, Bad Urach 2002 Part II Algebraic Dynamic Programming Algebraic Dynamic Programming Robert Giegerich, Carsten Meyer Faculty of Technology, Bielefeld University 33501 Bielefeld, Germany {robert,cmeyer}@techfak.uni-bielefeld.de Abstract. Dynamic programming is a classic programming technique, applicable in a wide variety of domains, like stochastic systems analy- sis, operations research, combinatorics of discrete structures, flow prob- lems, parsing with ambiguous grammars, or biosequence analysis. Yet, no methodology is available for designing such algorithms. The matrix re- currences that typically describe a dynamic programming algorithm are difficult to construct, error-prone to implement, and almost impossible to debug. This article introduces an algebraic style of dynamic programming over sequence data. We define the formal framework including a formalization of Bellman’s principle, specify an executable specification language, and show how algorithm design decisions and tuning for efficiency can be described on a convenient level of abstraction. AMAST Categories: programming methodology, specification languages, pro- gram transformation, functional programming 1 Introduction The development of successful dynamic programming recurrences is a matter of experience, talent, and luck. An anonymous re