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Tree Automata for Code Selection
, 1994
"... We deal with the generation of code selectors in compiler backends. The fundamental concepts are systematically derived from the theory of regular tree grammars and finite tree automata. We use this general approach to construct algorithms that generalize and improve existing methods. 1 Introduction ..."
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Cited by 28 (0 self)
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We deal with the generation of code selectors in compiler backends. The fundamental concepts are systematically derived from the theory of regular tree grammars and finite tree automata. We use this general approach to construct algorithms that generalize and improve existing methods. 1 Introduction A code generator for a compiler is applied to an intermediate representation (IR) of the input program that has been computed during preceding phases of compilation. This intermediate representation can be viewed as code for an abstract machine. The task of code generation is to translate this code into an efficient sequence of instructions for a concrete machine. Besides register allocation and instruction scheduling (for processors with pipelined architectures), code selection, i.e., the selection of instructions, is one subtask of code generation. It is especially important for CISC (Complex I nstruction Set Computer) architectures where there are usually many possibilities to generat...
Explaining and Controlling Ambiguity in Dynamic Programming
, 2000
"... . Ambiguity in dynamic programming arises from two independent sources, the nonuniqueness of optimal solutions and the particular recursion scheme by which the search space is evaluated. Ambiguity, unless explicitly considered, leads to unnecessarily complicated, inflexible, and sometimes even ..."
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Cited by 25 (10 self)
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. Ambiguity in dynamic programming arises from two independent sources, the nonuniqueness of optimal solutions and the particular recursion scheme by which the search space is evaluated. Ambiguity, unless explicitly considered, leads to unnecessarily complicated, inflexible, and sometimes even incorrect dynamic programming algorithms. Building upon the recently developed algebraic approach to dynamic programming, we formalize the notions of ambiguity and canonicity. We argue that the use of canonical yield grammars leads to transparent and versatile dynamic programming algorithms. They provide a master copy of recurrences, that can solve all DP problems in a welldefined domain. We demonstrate the advantages of such a systematic approach using problems from the areas of RNA folding and pairwise sequence comparison. 1 Motivation and Overview 1.1 Ambiguity Issues in Dynamic Programming Dynamic Programming (DP) solves combinatorial optimization problems. It is a classical p...
A Systematic Approach to Dynamic Programming in Bioinformatics
, 1999
"... Motivation: Dynamic programming is probably the most popular programming method in bioinformatics. Sequence comparison, gene recognition, RNA structure prediction and hundreds of other problems are solved by ever new variants of dynamic programming. Currently, the development of a successful dynamic ..."
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Cited by 25 (9 self)
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Motivation: Dynamic programming is probably the most popular programming method in bioinformatics. Sequence comparison, gene recognition, RNA structure prediction and hundreds of other problems are solved by ever new variants of dynamic programming. Currently, the development of a successful dynamic programming algorithm is a matter of experience, talent, and luck. The typical matrix recurrence relations that make up a dynamic programming algorithm are intricate to construct, and difficult to implement reliably. No general problem independent guidance is available. Results: This article introduces a systematic method for constructing dynamic programming solutions to problems in biosequence analysis. By a conceptual splitting of the algorithm into a recognition and an evaluation phase, algorithm development is simplified considerably, and correct recurrences can be derived systematically. Without additional effort, the method produces an early, executable prototype expressed in a funct...
Code generation based on formal BURS theory and heuristic search
 Acta Informatica
, 1997
"... BURS theory provides a powerful mechanism to efficiently generate pattern matches in a given expression tree. BURS, which stands for bottomup rewrite system, is based on term rewrite systems, to which costs are added. We formalise the
underlying theory, and derive an algorithm that computes all pat ..."
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Cited by 17 (2 self)
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BURS theory provides a powerful mechanism to efficiently generate pattern matches in a given expression tree. BURS, which stands for bottomup rewrite system, is based on term rewrite systems, to which costs are added. We formalise the
underlying theory, and derive an algorithm that computes all pattern matches. This algorithm terminates if the term rewrite system is finite. We couple this algorithm with
the wellknown search algorithm A* that carries out pattern selection. The search algorithm is directed by a cost heuristic that estimates the minimum cost of code that
has yet to be generated. The advantage of using a search algorithm is that we need to compute only those costs that may be part of an optimal rewrite sequence (and not the costs of all possible rewrite sequences as in dynamic programming). A system that implements the algorithms presented in this work has been built.
Global Code Selection for Directed Acyclic Graphs
, 1994
"... . We describe a novel technique for code selection based on dataflow graphs, which arise naturally in the domain of digital signal processing. Code selection is the optimized mapping of abstract operations to partial machine instructions. The presented method performs an important task within t ..."
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Cited by 11 (2 self)
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. We describe a novel technique for code selection based on dataflow graphs, which arise naturally in the domain of digital signal processing. Code selection is the optimized mapping of abstract operations to partial machine instructions. The presented method performs an important task within the retargetable microcode generator CBC, which was designed to cope with the requirements arising in the context of custom digital signal processor (DSP) programming. The algorithm exploits a graph representation in which controlflow is modeled by scopes. 1 Introduction In the domain of mediumthroughput digital signal processing, microprogrammable processor cores are frequently chosen for system realization. By adding dedicated hardware (accelerator paths), these cores are tailored to the needs of new applications. Optimized processor modules can be reused, which is a major benefit compared to highlevel synthesis [28] where a completely new design is developed for each application. ...
A declarative approach to the development of dynamic programming algorithms, applied to RNA folding
, 1998
"... A new approach to the systematic development of dynamic programming algorithms is presented and applied to RNA folding. Analyses of the potential foldings of an RNA molecule have mainly been restricted to energy minimization over all feasible secondary structures. In order to develop more specific a ..."
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Cited by 6 (5 self)
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A new approach to the systematic development of dynamic programming algorithms is presented and applied to RNA folding. Analyses of the potential foldings of an RNA molecule have mainly been restricted to energy minimization over all feasible secondary structures. In order to develop more specific analyses, we split up the traditional dynamic programming approach into a structure recognition and an evaluation phase. Regular tree grammars are used to describe the recognized class of structures. This allows to analyse for presence (or even absence) of very specific structures in the folding space of an RNA molecule. An EBNFlike notation for tree grammars is developed. It turns into a recognizer by interpreting the EBNFoperators as parser combinators; the polynomial efficiency of dynamic programming is regained by the introduction of tabulating yield parsers. folding space evaluator, described in terms of higherorder functions.
Matching and Significance Evaluation of Combined SequenceStructure Motifs in RNA
 Z. PHYS. CHEM
, 2001
"... The discipline of Algebraic Dynamic Programming is a powerful method to design and implement versatile pattern matching algorithms on sequences; here we consider mixed sequence and secondary structure motifs in RNA. A recurring challenge when designing new pattern matchers is to provide a statis ..."
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Cited by 3 (0 self)
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The discipline of Algebraic Dynamic Programming is a powerful method to design and implement versatile pattern matching algorithms on sequences; here we consider mixed sequence and secondary structure motifs in RNA. A recurring challenge when designing new pattern matchers is to provide a statistical analysis of pattern significance. We demonstrate
Code Generation = A* + BURS
 Compiler Construction
, 1996
"... A system called BURS that is based on term rewrite systems and a search algorithm A* are combined to produce a code generator that generates optimal code. The theory underlying BURS is redeveloped, formalised and explained in this work. The search algorithm uses a cost heuristic that is derived fro ..."
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Cited by 1 (1 self)
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A system called BURS that is based on term rewrite systems and a search algorithm A* are combined to produce a code generator that generates optimal code. The theory underlying BURS is redeveloped, formalised and explained in this work. The search algorithm uses a cost heuristic that is derived from the term rewrite system to direct the search. The advantage of using a search algorithm is that we need to compute only those costs that may be part of an optimal rewrite sequence.