Data mining the yeast genome in a lazy functional language

Clare, A. and King R.D. (2003) Data mining the yeast genome in a lazy functional language. In Practical Aspects of Declarative Languages (PADL'03) (won Best/Most Practical Paper award).

Un formalisme pour la traçabilité des transformations

Dans le développement logiciel en industrie, les documents de spécification jouent un rôle important pour la communication entre les analystes et les développeurs. Cependant, avec le temps, les changements de personel et les échéances toujours plus courtes, ces documents sont souvent obsolètes ou incohérents avec l'état effectif du système, i.e., son code source. Pourtant, il est nécessaire que les composants du système logiciel soient conservés à jour et cohérents avec leurs documents de spécifications pour faciliter leur développement et maintenance et, ainsi, pour en réduire les coûts. Maintenir la cohérence entre spécification et code source nécessite de pouvoir représenter les changements sur les uns et les autres et de pouvoir appliquer ces changements de manière cohérente et automatique. Nous proposons une solution permettant de décrire une représentation d'un logiciel ainsi qu'un formalisme mathématique permettant de décrire et de manipuler l'évolution des composants de ces représentations. Le formalisme est basé sur les triplets de Hoare pour représenter les transformations et sur la théorie des groupes et des homomorphismes de groupes pour manipuler ces transformations et permettrent leur application sur les différentes représentations du système. Nous illustrons notre formalisme sur deux représentations d'un système logiciel : PADL, une représentation architecturale de haut niveau (semblable à UML), et JCT, un arbre de syntaxe abstrait basé sur Java. Nous définissons également des transformations représentant l'évolution de ces représentations et la transposition permettant de reporter les transformations d'une représentation sur l'autre. Enfin, nous avons développé et décrivons brièvement une implémentation de notre illustration, un plugiciel pour l'IDE Eclipse détectant les transformations effectuées sur le code par les développeurs et un générateur de code pour l'intégration de nouvelles représentations dans l'implémentation.

Modélisation et implémentation des patrons de conception

Mémoire numérisé par la Division de la gestion de documents et des archives de l'Université de Montréal

Mucociliary clearance and its relation with the level of physical activity in daily life in healthy smokers and nonsmokers

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Obesity and Physical Activity in the Daily Life of Patients with COPD

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Transporte mucociliar e atividade física na vida diária de fumantes saudáveis

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Physical Activity In Daily Life In Brazilian COPD Patients During and After Exacerbation

Background: Although hospitalization is recognized as an important cause of reduction in physical activity in daily life (PADL) in COPD, there is only one study evaluating this effect, and it was performed in European COPD patients who have a lower PADL than that of South American COPD patients. Objectives: To investigate the effect of hospitalization due to acute exacerbation of PADL in Brazilian COPD patients and to evaluate the factors that determines the physical activity levels during hospitalization and after discharge. Methods: PADL was quantified using a 3-axis accelerometer on the 3rd day of hospitalization and 1 month after discharge in Brazilian COPD patients who were hospitalized due to disease exacerbation. Six-minute walking distance (6MWD), lower limb strength and pulmonary function were also evaluated. Results: A total of 20 patients completed the study. During hospitalization, patients spent most of the time (87%) lying down or sitting; however, 1 month after they were walking >40 min/day. In addition, patients with prior hospitalization had a lower level of physical activity compared to those without a previous history of hospitalization. The time spent walking during hospitalization was significantly explained by the quadriceps strength (r(2) = 0.29; p < 0.05), while 1 month after, the time spent walking was only significantly explained by the 6MWD (r(2) = 0.51; p = 0.02). Conclusions: Brazilian COPD patients are inactive during hospitalization but become active 1 month after discharge. Previously hospitalized are more inactive both during and after exacerbation. The quadriceps strength and 6MWD explain the physical activity levels during hospitalization and at home, respectively.

Profiling for run-time checking of computational properties and performance debugging in logic programs

Although several profiling techniques for identifying performance bottlenecks in logic programs have been developed, they are generally not automatic and in most cases they do not provide enough information for identifying the root causes of such bottlenecks. This complicates using their results for guiding performance improvement. We present a profiling method and tool that provides such explanations. Our profiler associates cost centers to certain program elements and can measure different types of resource-related properties that affect performance, preserving the precedence of cost centers in the cali graph. It includes an automatic method for detecting procedures that are performance bottlenecks. The profiling tool has been integrated in a previously developed run-time checking framework to allow verification of certain properties when they cannot be verified statically. The approach allows checking global computational properties which require complex instrumentation tracking information about previous execution states, such as, e.g., that the execution time accumulated by a given procedure is not greater than a given bound. We have built a prototype implementation, integrated it in the Ciao/CiaoPP system and successfully applied it to performance improvement, automatic optimization (e.g., resource-aware specialization of programs), run-time checking, and debugging of global computational properties (e.g., resource usage) in Prolog programs.

Combining static analysis and profiling for estimating execution times

Effective static analyses have been proposed which infer bounds on the number of resolutions. These have the advantage of being independent from the platform on which the programs are executed and have been shown to be useful in a number of applications, such as granularity control in parallel execution. On the other hand, in distributed computation scenarios where platforms with different capabilities come into play, it is necessary to express costs in metrics that include the characteristics of the platform. In particular, it is specially interesting to be able to infer upper and lower bounds on actual execution times. With this objective in mind, we propose an approach which combines compile-time analysis for cost bounds with a one-time profiling of a given platform in order to determine the valúes of certain parameters for that platform. These parameters calibrate a cost model which, from then on, is able to compute statically time bound functions for procedures and to predict with a significant degree of accuracy the execution times of such procedures in that concrete platform. The approach has been implemented and integrated in the CiaoPP system.

Efficient top-down set-sharing analysis using cliques

Abstract. We study the problem of efficient, scalable set-sharing analysis of logic programs. We use the idea of representing sharing information as a pair of abstract substitutions, one of which is a worst-case sharing representation called a clique set, which was previously proposed for the case of inferring pair-sharing. We use the clique-set representation for (1) inferring actual set-sharing information, and (2) analysis within a top-down framework. In particular, we define the new abstract functions required by standard top-down analyses, both for sharing alone and also for the case of including freeness in addition to sharing. We use cliques both as an alternative representation and as widening, defining several widening operators. Our experimental evaluation supports the conclusión that, for inferring set-sharing, as it was the case for inferring pair-sharing, precisión losses are limited, while useful efficieney gains are obtained. We also derive useful conclusions regarding the interactions between thresholds, precisión, efficieney and cost of widening. At the limit, the clique-set representation allowed analyzing some programs that exceeded memory capacity using classical sharing representations.

Improving the compilation of prolog to C using moded types and determinism information

We describe the current status of and provide performance results for a prototype compiler of Prolog to C, ciaocc. ciaocc is novel in that it is designed to accept different kinds of high-level information, typically obtained via an automatic analysis of the initial Prolog program and expressed in a standardized language of assertions. This information is used to optimize the resulting C code, which is then processed by an off-the-shelf C compiler. The basic translation process essentially mimics the unfolding of a bytecode emulator with respect to the particular bytecode corresponding to the Prolog program. This is facilitated by a flexible design of the instructions and their lower-level components. This approach allows reusing a sizable amount of the machinery of the bytecode emulator: predicates already written in C, data definitions, memory management routines and áreas, etc., as well as mixing emulated bytecode with native code in a relatively straightforward way. We report on the performance of programs compiled by the current versión of the system, both with and without analysis information.

A generic persistence model for CLP systems (and two useful implementations)

This paper describes a model of persistence in (C)LP languages and two different and practically very useful ways to implement this model in current systems. The fundamental idea is that persistence is a characteristic of certain dynamic predicates (Le., those which encapsulate state). The main effect of declaring a predicate persistent is that the dynamic changes made to such predicates persist from one execution to the next one. After proposing a syntax for declaring persistent predicates, a simple, file-based implementation of the concept is presented and some examples shown. An additional implementation is presented which stores persistent predicates in an external datábase. The abstraction of the concept of persistence from its implementation allows developing applications which can store their persistent predicates alternatively in files or databases with only a few simple changes to a declaration stating the location and modality used for persistent storage. The paper presents the model, the implementation approach in both the cases of using files and relational databases, a number of optimizations of the process (using information obtained from static global analysis and goal clustering), and performance results from an implementation of these ideas.

A generic persistence model for CLP systems

This paper describes a model of persistence in (C)LP languages and two different and practically very useful ways to implement this model in current systems. The fundamental idea is that persistence is a characteristic of certain dynamic predicates (i.e., those which encapsulate state). The main effect of declaring a predicate persistent is that the dynamic changes made to such predicates persist from one execution to the next one. After proposing a syntax for declaring persistent predicates, a simple, file-based implementation of the concept is presented and some examples shown. An additional implementation is presented which stores persistent predicates in an external database. The abstraction of the concept of persistence from its implementation allows developing applications which can store their persistent predicates alternatively in files or databases with only a few simple changes to a declaration stating the location and modality used for persistent storage. The paper presents the model, the implementation approach in both the cases of using files and relational databases, a number of optimizations of the process (using information obtained from static global analysis and goal clustering), and performance results from an implementation of these ideas.

Supporting pruning in tabled LP

This paper analyzes issues which appear when supporting pruning operators in tabled LP. A version of the once/1 control predicate tailored for tabled predicates is presented, and an implementation analyzed and evaluated. Using once/1 with answer-on-demand strategies makes it possible to avoid computing unneeded solutions for problems which can benefit from tabled LP but in which only a single solution is needed, such as model checking and planning. The proposed version of once/1 is also directly applicable to the efficient implementation of other optimizations, such as early completion, cut-fail loops (to, e.g., prune at the top level), if-then-else, and constraint-based branch-and-bound optimization. Although once/1 still presents open issues such as dependencies of tabled solutions on program history, our experimental evaluation confirms that it provides an arbitrarily large efficiency improvement in several application areas.