CLP-based protein fragment assembly

The paper investigates a novel approach, based on Constraint Logic Programming (CLP), to predict the 3D conformation of a protein via fragments assembly. The fragments are extracted by a preprocessor-also developed for this work- from a database of known protein structures that clusters and classifies the fragments according to similarity and frequency. The problem of assembling fragments into a complete conformation is mapped to a constraint solving problem and solved using CLP. The constraint-based model uses a medium discretization degree Ca-side chain centroid protein model that offers efficiency and a good approximation for space filling. The approach adapts existing energy models to the protein representation used and applies a large neighboring search strategy. The results shows the feasibility and efficiency of the method. The declarative nature of the solution allows to include future extensions, e.g., different size fragments for better accuracy.Comment: special issue dedicated to ICLP 201

An abstract machine for restricted and-parallel execution of logic programs

Although the sequential execution speed of logic programs has been greatly improved by the concepts introduced in the Warren Abstract Machine (WAM), parallel execution represents the only way to increase this speed beyond the natural limits of sequential systems. However, most proposed parallel logic programming execution models lack the performance optimizations and storage efficiency of sequential systems. This paper presents a parallel abstract machine which is an extension of the WAM and is thus capable of supporting ANDParallelism without giving up the optimizations present in sequential implementations. A suitable instruction set, which can be used as a target by a variety of logic programming languages, is also included. Special instructions are provided to support a generalized version of "Restricted AND-Parallelism" (RAP), a technique which reduces the overhead traditionally associated with the run-time management of variable binding conflicts to a series of simple run-time checks, which select one out of a series of compiled execution graphs

Offline Specialisation in Prolog Using a Hand-Written Compiler Generator

The so called "cogen approach" to program specialisation, writing a compiler generator instead of a specialiser, has been used with considerable success in partial evaluation of both functional and imperative languages. This paper demonstrates that the "cogen" approach is also applicable to the specialisation of logic programs (called partial deduction when applied to pure logic programs) and leads to effective specialisers. Moreover, using good binding-time annotations, the speed-ups of the specialised programs are comparable to the speed-ups obtained with online specialisers. The paper first develops a generic approach to offline partial deduction and then a specific offline partial deduction method, leading to the offline system LIX for pure logic programs. While this is a usable specialiser by itself, its specialisation strategy is used to develop the "cogen" system LOGEN. Given a program, a specification of what inputs will be static, and an annotation specifying which calls should be unfolded, LOGEN generates a specialised specialiser for the program at hand. Running this specialiser with particular values for the static inputs results in the specialised program. While this requires two steps instead of one, the efficiency of the specialisation process is improved in situations where the same program is specialised multiple times. The paper also presents and evaluates an automatic binding-time analysis that is able to derive the annotations. While the derived annotations are still suboptimal compared to hand-crafted ones, they enable non-expert users to use the LOGEN system in a fully automated way Finally, LOGEN is extended so as to directly support a large part of Prolog's declarative and non-declarative features and so as to be able to perform so called mixline specialisations. In mixline specialisation some unfolding decisions depend on the outcome of tests performed at specialisation time instead of being hardwired into the specialiser