Abstract
A consequence of ILP systems being implemented in Prolog or using Prolog libraries is that, usually, these systems use a Prolog internal database to store and manipulate data. However, in real-world problems, the original data is rarely in Prolog format. In fact, the data is often kept in Relational Database Management Systems (RDBMS) and then converted to a format acceptable by the ILP system. Therefore, a more interesting approach is to link the ILP system to the RDBMS and manipulate the data without converting it. This scheme has the advantage of being more scalable since the whole data does not need to be loaded into memory by the ILP system. In this paper we study several approaches of coupling ILP systems with RDBMS systems and evaluate their impact on performance. We propose to use a Deductive Database (DDB) system to transparently translate the hypotheses to relational algebra expressions. The empirical evaluation performed shows that the execution time of ILP algorithms can be effectively reduced using a DDB and that the size of the problems can be increased due to a non-memory storage of the data.

Abstract
We describe the MyYapDB, a deductive database system coupling the Yap Prolog compiler and the MySQL DBMS. We use our OPTYap extension of the Yap compiler, which is the first available system that can exploit parallelism from tabled logic programs. We describe the major features of the system, give a simplified description of the implementation and present a performance comparison of using static facts or accessing the facts as MySQL tuples for a simple example.

Abstract
An interesting feature of current Prolog systems is the ability to define external Prolog predicates that can be written in other languages. However, an important drawback of these interfaces is the fact that they lack some important features necessary to improve both the efficiency and the transparent integration of the Prolog system and the external predicates. Such an example is the cut operation. This operation is used quite often in Prolog programs, both for efficiency and semantic preservation. However, its use after a call to an externally defined predicate can have undesired effects. For example, if we have a pending connection to another application, or if we have memory blocks allocated by an external predicate, when a cut operation occurs, we may not be able to perform generic destruct actions, such as closing the pending connection or freeing the unnecessary memory. In this work, we propose an extension of the interface architecture that allows to associate generic user-defined functions with external predicates, in such a way that the Prolog engine transparently executes them when a cut operation occurs. We describe the implementation details of our proposal in the context of the Yap Prolog system.

Abstract
One of the main advantages of Logic Programming (LP) is that it provides an excellent framework for the parallel execution of programs. In this work we investigate novel techniques to efficiently exploit parallelism from real-world applications in low cost multi-core architectures. To achieve these goals, we revive and redesign the YapOr system to exploit or-parallelism based on a multi-threaded implementation. Our new approach takes full advantage of the state-of-the-art fast and optimized YAP Prolog engine and shares the underlying execution environment, scheduler and most of the data structures used to support YapOr's model. Initial experiments with our new approach consistently achieve almost linear speedups for most of the applications, proving itself as a good alternative for exploiting implicit parallelism in the currently available low cost multi-core architectures.

Abstract
Despite the availability of both multithreading and tabling in some Prolog systems, the implementation of these two features, such that they work together, implies complex ties to one another and to the underlying engine. In recent work, we have proposed an approach to combine multithreading with tabling, implemented on top of the Yap Prolog system, whose primary goal was to reduce memory usage for the table space. Regarding the execution times, we observed some problems related to Yap's memory allocator, which is based on the operating system's default memory allocator, when running programs that allocate a higher number of data structures in the table space. In this paper, we propose a more efficient and scalable memory allocator for multithreaded tabled evaluation of logic programs. Our goal is to minimize the performance degradation that the system suffers when it is exposed to simultaneous memory requests made by multiple threads. For that, we propose a memory allocator based on local and global pages, to split memory among specific data structures and different threads, together with a strategy where data structures of the same type are pre-allocated within a page. Experimental results show that our new memory allocator can effectively reduce the execution time and scale better, when increasing the number of threads, than the original allocator.

Abstract
The analysis of considerable numbers of DNA sequences is largely dependent on the development of simple software tools for automatically process the genetic data deposited on public databases. However, there are some difficulties in the automation process due to diverse synonyms being used as qualifiers for genes and some inconsistencies in gene locations between related Primate species, this fact happening even in the carefully curated database RefSeq. Here, we present mtDNA GeneEXtractor, a Windows based computer tool developed for the extraction of information for particular gene/regions from mammal mitochondrial DNA sequences deposited under GenBank format. The tool was quite efficient in retrieving organized information for comparative mtDNA gene/region diversity analyses when tested for the evaluation of transition/transversion ratios in humans and between Primates. Taking phylogenetic information into account to avoid redundancy due to ancestry-sharing, the transition/transversion ratios in the 13 protein-coding genes had a mean value of 12.46 for Primates (from 6.46 in ND2 to 17.04 in COX1) and higher (34.74) but more heterogeneous (ranging from 17.30 in ND5 to 74.39 in ND4) in a worldwide human database. The similar patterns of transition/transversion ratios in all positions and in only four fold degenerate positions show no evidence for selection in the 13 mtDNA protein-coding genes.