The past few years have seen a surge of interest in the field of probabilistic logic learning and statistical relational learning. In this endeavor, many probabilistic logics have been developed. ProbLog is a recent probabilistic extension of Prolog motivated by the mining of large biological networks. In ProbLog, facts can be labeled with probabilities. These facts are treated as mutually independent random variables that indicate whether these facts belong to a randomly sampled program. Different kinds of queries can be posed to ProbLog programs. We introduce algorithms that allow the efficient execution of these queries, discuss their implementation on top of the YAP-Prolog system, and evaluate their performance in the context of large networks of biological entities.

We analyzed the current status (as of the end of August 2008) of human mitochondrial genomes deposited in GenBank, amounting to 5140 complete or coding-region sequences, in order to present an overall picture of the diversity present in the mitochondrial DNA of the global human population. To perform this task, we developed mtDNA-GeneSyn, a computer tool that identifies and exhaustedly classifies the diversity present in large genetic data sets. The diversity observed in the 5140 human mitochondrial genomes was compared with all possible transitions and transversions from the standard human mitochondrial reference genome. This comparison showed that tRNA and rRNA secondary structures have a large effect in limiting the diversity of the human mitochondrial sequences, whereas for the protein-coding genes there is a bias toward less variation at the second codon positions. The analysis of the observed amino acid variations showed a tolerance of variations that convert between the amino acids V, I, A, M, and T. This defines a group of amino acids with similar chemical properties that can interconvert by a single transition.

Yet Another Prolog (YAP) is a Prolog system originally developed in the mid-eighties and that has been under almost constant development since then. This paper presents the general structure and design of the YAP system, focusing on three important contributions to the Logic Programming community. First, it describes the main techniques used in YAP to achieve an efficient Prolog engine. Second, most Logic Programming systems have a rather limited indexing algorithm. YAP contributes to this area by providing a dynamic indexing mechanism, or just-in-time indexer. Third, a important contribution of the YAP system has been the integration of both or-parallelism and tabling in a single Logic Programming system.

Abstract. The past few years have seen a surge of interest in the field of probabilistic logic learning or statistical relational learning. In this endeavor, many probabilistic logics have been developed. ProbLog is a recent probabilistic extension of Prolog motivated by the mining of large biological networks. In ProbLog, facts can be labeled with mutually independent probabilities that they belong to a randomly sampled program. Different kinds of queries can be posed to ProbLog programs. We introduce algorithms that allow the efficient execution of these queries, discuss their implementation on top of the YAP-Prolog system, and evaluate their performance in the context of large networks of biological entities.

Logic Programming languages, such as Prolog, provide a high-level, declarative approach to programming. Logic Programming offers great potential for implicit parallelism, thus allowing parallel systems to often reduce a program's execution time without programmer intervention. We believe that for complex applications that take several hours, if not days, to return an answer, even limited speedups from parallel execution can directly translate to very significant productivity gains.It has been argued that Prolog's evaluation strategy -SLD resolution -often limits the potential of the logic programming paradigm. The past years have therefore seen widening efforts at increasing Prolog's declarativeness and expressiveness. Tabling has proved to be a viable technique to efficiently overcome SLD's susceptibility to infinite loops and redundant subcomputations.Our research demonstrates that implicit or-parallelism is a natural fit for logic programs with tabling. To substantiate this belief, we have designed and implemented an or-parallel tabling engine -OPTYap -and we used a shared-memory parallel machine to evaluate its performance. To the best of our knowledge, OPTYap is the first implementation of a parallel tabling engine for logic programming systems. OPTYap builds on Yap's efficient sequential Prolog engine. Its execution model is based on the SLG-WAM for tabling, and on the environment copying for or-parallelism.Preliminary results indicate that the mechanisms proposed to parallelize search in the context of SLD resolution can indeed be effectively and naturally generalized to parallelize tabled computations, and that the resulting systems can achieve good performance on shared-memory parallel machines. More importantly, it emphasizes our belief that through applying or-parallelism and tabling to logic programs the range of applications for Logic Programming can be increased.

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Multi-threading is currently supported by several well-known Prolog systems providing a highly portable solution for applications that can benefit from concurrency. When multi-threading is combined with tabling, we can exploit the power of higher procedural control and declarative semantics. However, despite the availability of both threads and tabling in some Prolog systems, the implementation of these two features implies complex ties to each other and to the underlying engine. Until now, XSB was the only Prolog system combining multi-threading with tabling. In XSB, tables may be either private or shared between threads. While thread-private tables are easier to implement, shared tables have all the associated issues of locking, synchronization and potential deadlocks. In this paper, we propose an alternative view to XSB's approach. In our proposal, each thread views its tables as private but, at the engine level, we use a common table space where tables are shared among all threads. We present three designs for our common table space approach: No-Sharing (NS) (similar to XSB's private tables), Subgoal-Sharing (SS) and Full-Sharing (FS). The primary goal of this work was to reduce the memory usage for the table space but, our experimental results, using the YapTab tabling system with a local evaluation strategy, show that we can also achieve significant reductions on running time.

Abstract. Tabled evaluation has been proved an effective method to improve several aspects of goal-oriented query evaluation, including termination and complexity. Several "native" implementations of tabled evaluation have been developed which offer good performance, but many of them require significant changes to the underlying Prolog implementation, including the compiler and the abstract machine. Approaches based on program transformation, which tend to minimize changes to both the Prolog compiler and the abstract machine, have also been proposed, but they often result in lower efficiency. We explore some techniques aimed at combining the best of these worlds, i.e., developing an extensible implementation which requires minimal modifications to the compiler and the abstract machine, and with reasonably good performance. Our preliminary experiments indicate promising results.