From Boolean Equalities to Constraints

Although functional as well as logic languages use equality to discriminate between logically different cases, the operational meaning of equality is different in such languages. Functional languages reduce equational expressions to their Boolean values, True or False, logic languages use unification to check the validity only and fail otherwise. Consequently, the language Curry, which amalgamates functional and logic programming features, offers two kinds of equational expressions so that the programmer has to distinguish between these uses. We show that this distinction can be avoided by providing an analysis and transformation method that automatically selects the appropriate operation. Without this distinction in source programs, the language design can be simplified and the execution of programs can be optimized. As a consequence, we show that one kind of equational expressions is sufficient and unification is nothing else than an optimization of Boolean equality

PhyloPattern: regular expressions to identify complex patterns in phylogenetic trees

<p>Abstract</p> <p>Background</p> <p>To effectively apply evolutionary concepts in genome-scale studies, large numbers of phylogenetic trees have to be automatically analysed, at a level approaching human expertise. Complex architectures must be recognized within the trees, so that associated information can be extracted.</p> <p>Results</p> <p>Here, we present a new software library, PhyloPattern, for automating tree manipulations and analysis. PhyloPattern includes three main modules, which address essential tasks in high-throughput phylogenetic tree analysis: node annotation, pattern matching, and tree comparison. PhyloPattern thus allows the programmer to focus on: i) the use of predefined or user defined annotation functions to perform immediate or deferred evaluation of node properties, ii) the search for user-defined patterns in large phylogenetic trees, iii) the pairwise comparison of trees by dynamically generating patterns from one tree and applying them to the other.</p> <p>Conclusion</p> <p>PhyloPattern greatly simplifies and accelerates the work of the computer scientist in the evolutionary biology field. The library has been used to automatically identify phylogenetic evidence for domain shuffling or gene loss events in the evolutionary histories of protein sequences. However any workflow that relies on phylogenetic tree analysis, could be automated with PhyloPattern.</p

Compiling a Functional Logic Language: The Fair Scheme

Abstract. We present a compilation scheme for a functional logic programming language. The input program to our compiler is a constructor-based graph rewrit-ing system in a non-confluent, but well-behaved class. This input is an interme-diate representation of a functional logic program in a language such as Curry or T OY. The output program from our compiler consists of three procedures that make recursive calls and execute both rewrite and pull-tab steps. This output is an intermediate representation that is easy to encode in any number of programming languages. Our design evolves the Basic Scheme of Antoy and Peters by removing the “left bias ” that prevents obtaining results of some computations—a behavior related to the order of evaluation, which is counter to declarative programming. The benefits of this evolution are not only the strong completeness of computa-tions, but also the provability of non-trivial properties of these computations. We rigorously describe the compiler design and prove some of its properties. To state and prove these properties, we introduce novel definitions of “need ” and “fail-ure. ” For non-confluent constructor-based rewriting systems these concepts are more appropriate than the classic definition of need of Huet and Levy