Fernando M. A. Silva

Mooshak: a Web-based multi-site programming contest system

This paper presents a new Web‐based system, Mooshak, to handle programming contests. The system acts as a full contest manager as well as an automatic judge for programming contests. Mooshak innovates in a number of aspects: it has a scalable architecture that can be used from small single server contests to complex multi‐site contests with simultaneous public online contests and redundancy; it has a robust data management system favoring simple procedures for storing, replicating, backing up data and failure recovery using persistent objects; it has automatic judging capabilities to assist human judges in the evaluation of programs; it has built‐in safety measures to prevent users from interfering with the normal progress of contests. Mooshak is an open system implemented on the Linux operating system using the Apache HTTP server and the Tcl scripting language.

On applying or-parallelism and tabling to logic programs

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 programs 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 Prologs evaluation strategy – SLD resolution – often limits the potential of the logic programming paradigm. The past years have therefore seen widening efforts at increasing Prologs declarativeness and expressiveness. Tabling has proved to be a viable technique to efficiently overcome SLDs 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 Yaps 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.

g-tries: an efficient data structure for discovering network motifs

In this paper we propose a novel specialized data structure that we call g-trie, designed to deal with collections of subgraphs. The main conceptual idea is akin to a prefix tree in the sense that we take advantage of common topology by constructing a multiway tree where the descendants of a node share a common substructure. We give algorithms to construct a g-trie, to list all stored subgraphs, and to find occurrences on another graph of the subgraphs stored in the g-trie. We evaluate the implementation of this structure and its associated algorithms on a set of representative benchmark biological networks in order to find network motifs. To assess the efficiency of our algorithms we compare their performance with other known network motif algorithms also implemented in the same common platform. Our results show that indeed, g-tries are a feasible, adequate and very efficient data structure for network motifs discovery, clearly outperforming previous algorithms and data structures.

YapOr: an Or-Parallel Prolog System Based on Environment Copying

YapOr is an or-parallel system that extends the Yap Prolog system to exploit implicit or-parallelism in Prolog programs. It is based on the environment copying model, as first implemented in Muse. The development of YapOr required solutions for some important issues, such as designing the data structures to support parallel processing, implementing incremental copying technique, developing a memory organization able to answer with efficiency to parallel processing and to incremental copying in particular, implementing the scheduler strategies, designing an interface between the scheduler and the engine, implementing the sharing work process, and implementing support to the cut builtin. An initial evaluation of YapOr performance showed that it achieves very good performance on a large set of benchmark programs. Indeed, YapOr compares favorably with a mature parallel Prolog system such as Muse, both in terms of base speed and in terms of speedups.

Distribution and Mobility with Lexical Scoping in Process Calculi

Abstract We propose a simple model of distribution for mobile processes, independent of the underlying calculus. Conventional processes compute within sites; inter-site computation is achieved by message sending and object migration, both obeying a lexical scope. We focus on the semantics of networks, on programming practice, and on physical realization with current technology.

On a Tabling Engine That Can Exploit Or-Parallelism

Tabling is an implementation technique that improves the declarativeness and expressiveness of Prolog by reusing solutions to goals. Quite a few interesting applications of tabling have been developed in the last few years, and several are by nature non-deterministic. This raises the question of whether parallel search techniques can be usedto improve the performance of tabledapplications.In this work we demonstrate that the mechanisms proposed to parallelize search in the context of SLD resolution naturally generalize to parallel tabledcomputations, and that resulting systems can achieve goodp erformance on multi-processors. To do so, we present the OPTYap parallel engine. In our system individual SLG engines communicate data through stack copying. Completion is detected through a novel parallel completion algorithm that builds upon the data structures proposed for or-parallelism. Scheduling is simplified by building on previous research on or-parallelism. We show initial performance results for our implementation. Our best result is for an actual application, model checking, where we obtain linear speedups.

G-Tries: a data structure for storing and finding subgraphs

The ability to find and count subgraphs of a given network is an important non trivial task with multidisciplinary applicability. Discovering network motifs or computing graphlet signatures are two examples of methodologies that at their core rely precisely on the subgraph counting problem. Here we present the g-trie, a data-structure specifically designed for discovering subgraph frequencies. We produce a tree that encapsulates the structure of the entire graph set, taking advantage of common topologies in the same way a prefix tree takes advantage of common prefixes. This avoids redundancy in the representation of the graphs, thus allowing for both memory and computation time savings. We introduce a specialized canonical labeling designed to highlight common substructures and annotate the g-trie with a set of conditional rules that break symmetries, avoiding repetitions in the computation. We introduce a novel algorithm that takes as input a set of small graphs and is able to efficiently find and count them as induced subgraphs of a larger network. We perform an extensive empirical evaluation of our algorithms, focusing on efficiency and scalability on a set of diversified complex networks. Results show that g-tries are able to clearly outperform previously existing algorithms by at least one order of magnitude.

Parallel Implementation of Decision Tree Learning Algorithms

In the fields of data mining and machine learning the amount of data available for building classifiers is growing very fast. Therefore, there is a great need for algorithms that are capable of building classifiers from very-large datasets and, simultaneously, being computationally efficient and scalable. One possible solution is to employ parallelism to reduce the amount of time spent in building classifiers from very-large datasets and keeping the classification accuracy. This work first overviews some strategies for implementing decision tree construction algorithms in parallel based on techniques such as task parallelism, data parallelism and hybrid parallelism. We then describe a new parallel implementation of the C4.5 decision tree construction algorithm. Even though the implementation of the algorithm is still in final development phase, we present some experimental results that can be used to predict the expected behavior of the algorithm.

Comparison of Co-authorship Networks across Scientific Fields Using Motifs

Comparing scientific production across different fields of knowledge is commonly controversial and subject to disagreement. Such comparisons are often based on quantitative indicators, such as papers per researcher, and data normalization is very difficult to accomplish. Different approaches can provide new insight and in this paper we focus on the comparison of different scientific fields based on their research collaboration networks. We use co-authorship networks where nodes are researchers and the edges show the existing co-authorship relations between them. Our comparison methodology is based on network motifs, which are over represented patterns, or sub graphs. We derive motif fingerprints for 22 scientific fields based on 29 different small motifs found in the corresponding co-authorship networks. These fingerprints provide a metric for assessing similarity among scientific fields, and our analysis shows that the discrimination power of the 29 motif types is not identical. We use a co-authorship dataset built from over 15,361 publications inducing a co-authorship network with over 32,842 researchers. Our results also show that we can group different fields according to their fingerprints, supporting the notion that some fields present higher similarity and can be more easily compared.

Parallel discovery of network motifs

Many natural structures can be naturally represented by complex networks. Discovering network motifs, which are overrepresented patterns of inter-connections, is a computationally hard task related to graph isomorphism. Sequential methods are hindered by an exponential execution time growth when we increase the size of motifs and networks. In this article we study the opportunities for parallelism in existing methods and propose new parallel strategies that adapt and extend one of the most efficient serial methods known from the Fanmod tool. We propose both a master-worker strategy and one with distributed control, in which we employ a randomized receiver initiated methodology capable of providing dynamic load balancing during the whole computation process. Our strategies are capable of dealing both with exact and approximate network motif discovery. We implement and apply our algorithms to a set of representative networks and examine their scalability up to 128 processing cores. We obtain almost linear speedups, showcasing the efficiency of our proposed approach and are able to reach motif sizes that were not previously achievable using conventional serial algorithms.