Peter J. Stuckey

MUSTANG: A multiple structural alignment algorithm

Multiple structural alignment is a fundamental problem in structural genomics. In this article, we define a reliable and robust algorithm, MUSTANG (MUltiple STructural AligNment AlGorithm), for the alignment of multiple protein structures. Given a set of protein structures, the program constructs a multiple alignment using the spatial information of the Cα atoms in the set. Broadly based on the progressive pairwise heuristic, this algorithm gains accuracy through novel and effective refinement phases. MUSTANG reports the multiple sequence alignment and the corresponding superposition of structures. Alignments generated by MUSTANG are compared with several handcurated alignments in the literature as well as with the benchmark alignments of 1033 alignment families from the HOMSTRAD database. The performance of MUSTANG was compared with DALI at a pairwise level, and with other multiple structural alignment tools such as POSA, CE‐MC, MALECON, and MultiProt. MUSTANG performs comparably to popular pairwise and multiple structural alignment tools for closely related proteins, and performs more reliably than other multiple structural alignment methods on hard data sets containing distantly related proteins or proteins that show conformational changes. Proteins 2006.

MiniZinc: towards a standard CP modelling language

There is no standard modelling language for constraint programming (CP) problems. Most solvers have their own modelling language. This makes it difficult for modellers to experiment with different solvers for a problem. In this paper we present MiniZinc, a simple but expressive CP modelling language which is suitable for modelling problems for a range of solvers and provides a reasonable compromise between many design possibilities. Equally importantly, we also propose a low-level solver-input language called FlatZinc, and a straightforward translation from MiniZinc to FlatZinc that preserves all solver-supported global constraints. This lets a solver writer support MiniZinc with a minimum of effort-- they only need to provide a simple FlatZinc front-end to their solver, and then combine it with an existing MiniZinc-to-FlatZinc translator. Such a front-end may then serve as a stepping stone towards a full MiniZinc implementation that is more tailored to the particular solver. A standard language for modelling CP problems will encourage experimentation with and comparisons between different solvers. Although MiniZinc is not perfect--no standard modelling language will be--we believe its simplicity, expressiveness, and ease of implementation make it a practical choice for a standard language.

Computational Logic — CL 2000

Syntax for Variable Binders: An Overview . . . . . . . . . . . . . . . . . . . . 239 Dale Miller Goal-Directed Proof Search in Multiple-Conclusioned Intuitionistic Logic . . 254 James Harland, Tatjana Lutovac, and Michael Winikoff Efficient EM Learning with Tabulation for Parameterized Logic Programs . 269 Yoshitaka Kameya and Taisuke Sato Model Generation Theorem Proving with Finite Interval Constraints . . . . . 285 Reiner Hähnle, Ryuzo Hasegawa, and Yasuyuki Shirai Combining Mobile Processes and Declarative Programming . . . . . . . . . . . . . 300 Rachid Echahed and Wendelin Serwe

A Hybrid Algorithm for the Examination Timetabling Problem

Examination timetabling is a well-studied combinatorial optimization problem. We present a new hybrid algorithm for examination timetabling, consisting of three phases: a constraint programming phase to develop an initial solution, a simulated annealing phase to improve the quality of solution, and a hill climbing phase for further improvement. The examination timetabling problem at the University of Melbourne is introduced, and the hybrid method is proved to be superior to the current method employed by the University. Finally, the hybrid method is compared to established methods on the publicly available data sets, and found to perform well in comparison.

The semantics of constraint logic programs

Abstract The Constraint Logic Programming (CLP) Scheme was introduced by Jaffar and Lassez. The scheme gave a formal framework, based on constraints, for the basic operational, logical and algebraic semantics of an extended class of logic programs. This paper presents for the first time the semantic foundations of CLP in a self-contained and complete package. The main contributions are threefold. First, we extend the original conference paper by presenting definitions and basic semantic constructs from first principles, giving new and complete proofs for the main lemmas. Importantly, we clarify which theorems depend on conditions such as solution compactness, satisfaction completeness and independence of constraints. Second, we generalize the original results to allow for incompleteness of the constraint solver. This is important since almost all CLP systems use an incomplete solver. Third, we give conditions on the (possibly incomplete) solver which ensure that the operational semantics is confluent, that is, has independence of literal scheduling.

Propagation via lazy clause generation

Finite domain propagation solvers effectively represent the possible values of variables by a set of choices which can be naturally modelled as Boolean variables. In this paper we describe how to mimic a finite domain propagation engine, by mapping propagators into clauses in a SAT solver. This immediately results in strong nogoods for finite domain propagation. But a naive static translation is impractical except in limited cases. We show how to convert propagators to lazy clause generators for a SAT solver. The resulting system introduces flexibility in modelling since variables are modelled dually in the propagation engine and the SAT solver, and we explore various approaches to the dual modelling. We show that the resulting system solves many finite domain problems significantly faster than other techniques.

The Cassowary linear arithmetic constraint solving algorithm

Linear equality and inequality constraints arise naturally in specifying many aspects of user interfaces, such as requiring that one window be to the left of another, requiring that a pane occupy the leftmost third of a window, or preferring that an object be contained within a rectangle if possible. Previous constraint solvers designed for user interface applications cannot handle simultaneous linear equations and inequalities efficiently. This is a major limitation, as such systems of constraints arise often in natural declarative specifications. We describe Cassowary---an incremental algorithm based on the dual simplex method, which can solve such systems of constraints efficiently. We have implemented the algorithm as part of a constraint-solving toolkit. We discuss the implementation of the toolkit, its application programming interface, and its performance.

Discovery of minimal unsatisfiable subsets of constraints using hitting set dualization

An unsatisfiable set of constraints is minimal if all its (strict) subsets are satisfiable. The task of type error diagnosis requires finding all minimal unsatisfiable subsets of a given set of constraints (representing an error), in order to generate the best explanation of the error. Similarly circuit error diagnosis requires finding all minimal unsatisfiable subsets in order to make minimal diagnoses. In this paper we present a new approach for efficiently determining all minimal unsatisfiable sets for any kind of constraints. Our approach makes use of the duality that exists between minimal unsatisfiable constraint sets and maximal satisfiable constraint sets. We show how to incrementally compute both these sets, using the fact that the complements of the maximal satisfiable constraint sets are the hitting sets of the minimal unsatisfiable constraint sets. We experimentally compare our technique to the best known method on a number of large type problems and show that considerable improvements in running time are obtained.

The Refined Operational Semantics of Constraint Handling Rules

Constraint Handling Rules (CHRs) are a high-level rule-based programming language commonly used to write constraint solvers. The theoretical operational semantics for CHRs is highly non-deterministic and relies on writing confluent programs to have a meaningful behaviour. Implementations of CHRs use an operational semantics which is considerably finer than the theoretical operational semantics, but is still non-deterministic (from the user’s perspective). This paper formally defines this refined operational semantics and proves it implements the theoretical operational semantics. It also shows how to create a (partial) confluence checker capable of detecting programs which are confluent under this semantics, but not under the theoretical operational semantics. This supports the use of new idioms in CHR programs.

The Design of the Zinc Modelling Language

Zinc is a new modelling language developed as part of the G12 project. It has four important characteristics. First, Zinc allows specification of models using a natural mathematical-like notation. To do so it supports overloaded functions and predicates and automatic coercion and provides arithmetic, finite domain and set constraints. Second, while Zinc is a relatively simple and small language, it can be readily extended to different application areas by means of powerful language constructs such as user-defined predicates and functions and constrained types. Third, Zinc provides sophisticated type and instantiation checking which allows early detection of errors in models. Finally, perhaps the main novelty in Zinc is that it is designed to support a modelling methodology in which the same conceptual model can be automatically mapped into different design models, thus allowing modellers to easily “plug and play” with different solving techniques and so choose the most appropriate for that problem. We describe in detail the various language features of Zinc and the many trade-offs we faced in its design.