Yves Deville

Design, implementation, and evaluation of the constraint language cc (FD)

This paper describes the design, implementation, and applications of the constraint logic language cc(FD). cc(FD) is a declarative nondeterministic constraint logic language over finite domains based on the cc framework [33], an extension of the Constraint Logic Programming (CLP) scheme [21]. Its constraint solver includes (nonlinear) arithmetic constraints over natural numbers which are approximated using domain and interval consistency. The main novelty of cc (FD) is the inclusion of a number of general-purpose combinators, in particular cardinality, constructive disjunction, and blocking implication, in conjunction with new constraint operations such as constraint entailment and generalization. These combinators significantly improve the operational expressiveness, extensibility, and flexibility of CLP languages and allow issues such as the definition of nonprimitive constraints and disjunctions to be tackled at the language level. The implementation of cc (FD) (about 40,000 lines of C) includes a WAM-based engine [44], optimal are-consistency algorithms based on AC-5 [40], and incremental implementation of the combinators. Results on numerous problems, including scheduling, resource allocation, sequencing, packing, and hamiltonian paths are reported and indicate that cc(FD) comes close to procedural languages on a number of combinatorial problems. In addition, a small cc(FD) program was able to find the optimal solution and prove optimality to a famous 10/10 disjunctive scheduling problem [29], which was left open for more than 20 years and finally solved in 1986

CP(Graph): introducing a graph computation domain in constraint programming

In an increasing number of domains such as bioinformatics, combinatorial graph problems arise. We propose a novel way to solve these problems, mainly those that can be translated to constrained subgraph finding. Our approach extends constraint programming by introducing CP(Graph), a new computation domain focused on graphs including a new type of variable: graph domain variables as well as constraints over these variables and their propagators. These constraints are subdivided into kernel constraints and additional constraints formulated as networks of kernel constraints. For some of these constraints a dedicated global constraint and its associated propagator are sketched. CP(Graph) is integrated with finite domain and finite sets computation domains, allowing the combining of constraints of these domains with graph constraints. A prototype of CP(Graph) built over finite domains and finite sets in Oz is presented. And we show that a problem of biochemical network analysis can be very simply described and solved within CP(Graph).

NeAT: a toolbox for the analysis of biological networks, clusters, classes and pathways

The network analysis tools (NeAT) (http://rsat.ulb.ac.be/neat/) provide a user-friendly web access to a collection of modular tools for the analysis of networks (graphs) and clusters (e.g. microarray clusters, functional classes, etc.). A first set of tools supports basic operations on graphs (comparison between two graphs, neighborhood of a set of input nodes, path finding and graph randomization). Another set of programs makes the connection between networks and clusters (graph-based clustering, cliques discovery and mapping of clusters onto a network). The toolbox also includes programs for detecting significant intersections between clusters/classes (e.g. clusters of co-expression versus functional classes of genes). NeAT are designed to cope with large datasets and provide a flexible toolbox for analyzing biological networks stored in various databases (protein interactions, regulation and metabolism) or obtained from high-throughput experiments (two-hybrid, mass-spectrometry and microarrays). The web interface interconnects the programs in predefined analysis flows, enabling to address a series of questions about networks of interest. Each tool can also be used separately by entering custom data for a specific analysis. NeAT can also be used as web services (SOAP/WSDL interface), in order to design programmatic workflows and integrate them with other available resources.

The aMAZE LightBench: a web interface to a relational database of cellular processes

The aMAZE LightBench (http://www.amaze.ulb. ac.be/) is a web interface to the aMAZE relational database, which contains information on gene expression, catalysed chemical reactions, regulatory interactions, protein assembly, as well as metabolic and signal transduction pathways. It allows the user to browse the information in an intuitive way, which also reflects the underlying data model. Moreover links are provided to literature references, and whenever appropriate, to external databases.

Logic Program Synthesis

This paper presents an overview and a survey of logic program synthesis. Logic program synthesis is interpreted here in a broad way; it is concerned with the following question: given a specification, how do we get a logic program satisfying the specification? Logic programming provides a uniquely nice and uniform framework for program synthesis since the specification, the synthesis process, and the resulting program can all be expressed in logic. Three main approaches to logic program synthesis by formal methods are described: constructive synthesis, deductive synthesis, and inductive synthesis. Related issues such as correctness and verification, as well as synthesis by informal methods, are briefly presented. Our presentation is made coherent by employing a unified framework of terminology and notation, and by using the same running example for all the approaches covered. This paper thus intends to provide an assessment of existing work and a framework for future research in logic program synthesis.

Constraint satisfaction over connected row-convex constraints

This paper studies constraint satisfaction over connected row-convex (CRC) constraints. It shows that CRC constraints are closed under composition, intersection, and transposition, the basic operations of path-consistency algorithms. This establishes that path consistency over CRC constraints produces a minimal and decomposable network and is thus a polynomial-time decision procedure for CRC networks. This paper also presents a new path-consistency algorithm for CRC constraints running in time O(n(3)d(2)) and space O(n(2)d), where n is the number of variables and d is the size of the largest domain, improving the traditional time and space complexity by orders of magnitude. The paper also shows how to construct CRC constraints by conjunction and disjunction of a set of basic CRC constraints, highlighting how CRC constraints generalize monotone constraints and presenting interesting subclasses of CRC constraints. Experimental results show that the algorithm behaves well in practice

A distributed arc-consistency algorithm

Consistency techniques are an efficient way of tackling constraint satisfaction problems (CSP). In particular, various are-consistency algorithms have been designed such as the rime optimal AC-4 sequential algorithm of Mohr and Henderson (1986). In this paper, we present a new distributed are-consistency algorithm, called DisAC-4. DisAC-4 is based on AC-4, and is a coarse-grained parallel algorithm designed for distributed memory computers using message passing communication. Termination and correctness of the algorithm are proven. Theoretical complexities and experimental results are given. Both show linear speedup with respect to the number of processors. The strong point of DisAC-4 is its suitability to be implemented on very common hardware infrastructures like networks of workstations and/or PCs as well as on intensive computing parallel mainframes

Solving subgraph isomorphism problems with constraint programming

The subgraph isomorphism problem consists in deciding if there exists a copy of a pattern graph in a target graph. We introduce in this paper a global constraint and an associated filtering algorithm to solve this problem within the context of constraint programming. The main idea of the filtering algorithm is to label every node with respect to its relationships with other nodes of the graph, and to define a partial order on these labels in order to express compatibility of labels for subgraph isomorphism. This partial order over labels is used to filter domains. Labelings can also be strengthened by adding information from the labels of neighbors. Such a strengthening can be applied iteratively until a fixpoint is reached. Practical experiments illustrate that our new filtering approach is more effective on difficult instances of scale free graphs than state-of-the-art algorithms and other constraint programming approaches.

Synthesis of Programs in Computational Logic

Since the early days of programming and automated reasoning, researchers have developed methods for systematically constructing programs from their specifications. Especially the last decade has seen a flurry of activities including the advent of specialized conferences, such as LOPSTR, covering the synthesis of programs in computational logic. In this paper we analyze and compare three state-of-the-art methods for synthesizing recursive programs in computational logic. The three approaches are constructive/deductive synthesis, schema-guided synthesis, and inductive synthesis. Our comparison is carried out in a systematic way where, for each approach, we describe the key ideas and synthesize a common running example. In doing so, we explore the synergies between the approaches, which we believe are necessary in order to achieve progress over the next decade in this field.

Design, Implementation, and Evaluation of the Constraint Language cc(FD)

This paper describes the design, implementation, and applications of the constraint logic language cc(FD). cc(FD) is a declarative nondeterministic constraint logic language over finite domains based on the cc framework, an extension of the CLP scheme. Its constraint solver includes (nonlinear) arithmetic constraints over natural numbers which are approximated using domain and interval consistency. The main novelty of cc(FD) is the inclusion of a number of general-purpose combinators, in particular cardinality, constructive disjunction, and blocking implication, in conjunction with new constraint operations such as constraint entailment and generalization. These combinators significantly improve the operational expressiveness, extensibility, and flexibility of CLP languages and allow issues such as the definition of non-primitive constraints and disjunctions to be tackled at the language level. The implementation of cc(FD) (about 40,000 lines of C) includes a WAM-based engine, optimal arc-consistency algorithms based on AC-5, and incremental implementation of the combinators. Results on numerous problems, including scheduling, resource allocation, sequencing, packing, and hamiltonian paths are reported, and indicate that cc(FD) comes close to procedural languages on a number of combinatorial problems. In addition, a small cc(FD) program was able to find the optimal solution and prove optimality to a famous 10/10 disjunctive scheduling problem, which was left open for more than 20 years and finally solved in 1988.