Automatic Repair of Real Bugs: An Experience Report on the Defects4J Dataset

Defects4J is a large, peer-reviewed, structured dataset of real-world Java bugs. Each bug in Defects4J is provided with a test suite and at least one failing test case that triggers the bug. In this paper, we report on an experiment to explore the effectiveness of automatic repair on Defects4J. The result of our experiment shows that 47 bugs of the Defects4J dataset can be automatically repaired by state-of- the-art repair. This sets a baseline for future research on automatic repair for Java. We have manually analyzed 84 different patches to assess their real correctness. In total, 9 real Java bugs can be correctly fixed with test-suite based repair. This analysis shows that test-suite based repair suffers from under-specified bugs, for which trivial and incorrect patches still pass the test suite. With respect to practical applicability, it takes in average 14.8 minutes to find a patch. The experiment was done on a scientific grid, totaling 17.6 days of computation time. All their systems and experimental results are publicly available on Github in order to facilitate future research on automatic repair

Automatic Repair of Real Bugs in Java: A Large-Scale Experiment on the Defects4J Dataset

update for oadoi on Nov 02 2018International audienceDefects4J is a large, peer-reviewed, structured dataset of real-world Java bugs. Each bug in Defects4J comes with a test suite and at least one failing test case that triggers the bug. In this paper, we report on an experiment to explore the effectiveness of automatic test-suite based repair on Defects4J. The result of our experiment shows that the considered state-of-the-art repair methods can generate patches for 47 out of 224 bugs. However, those patches are only test-suite adequate, which means that they pass the test suite and may potentially be incorrect beyond the test-suite satisfaction correctness criterion. We have manually analyzed 84 different patches to assess their real correctness. In total, 9 real Java bugs can be correctly repaired with test-suite based repair. This analysis shows that test-suite based repair suffers from under-specified bugs, for which trivial or incorrect patches still pass the test suite. With respect to practical applicability, it takes on average 14.8 minutes to find a patch. The experiment was done on a scientific grid, totaling 17.6 days of computation time. All the repair systems and experimental results are publicly available on Github in order to facilitate future research on automatic repair

Parasite-induced suppression of aggregation under predation risk in a freshwater amphipod: sociality of infected amphipods.

7 pagesInternational audienceRecent findings suggest that grouping with conspecifics is part of the behavioural defences developed by amphipod crustaceans to face predation risk by fish. Amphipods commonly serve as intermediate hosts for trophically transmitted parasites. These parasites are known for their ability to alter intermediate host phenotype in a way that promotes predation by definitive hosts, where they reproduce. If aggregation in amphipods dilutes the risk to be preyed on by fish, then it may dilute the probability of transmission for the parasite using fish as definitive hosts. Using experimental infections, we tested whether infection with the fish acanthocephalan Pomphorhynchus laevis alters attraction to conspecifics in the amphipod intermediate host Gammarus pulex. We also measured G. pulex's activity and reaction to light to detect potential links between changes in aggregation and changes in other behaviours. The attraction to conspecifics in the presence of predator cue, a behaviour found in uninfected gammarids, was cancelled by the infection, while phototaxis was reversed and activity unchanged. We found no correlation between the three behaviours in infected amphipods, while activity and aggregation were negatively correlated in uninfected individuals after the detection of predation cue. The physiological causes and the adaptive value of aggregation suppression are discussed in the context of a multidimensional manipulation

Vers une approche « rhétorique » en TAL : application à la veille épidémiologique multilingue

National audienceUsually, Natural Language Processing (NLP) systems rely on local analysis (morphology, syntax and semantics). In this study we present how an alternative approach can be based on rhetorics. The principles presented in this study are genre-dependent rather than language-dependent. They are intended to facilitate a multilingual news analysis in order to perform an epidemic surveillance task.L'approche traditionnelle en Traitement Automatique des Langues (TAL) se base sur une batterie d'analyses très complexes (morphologique, syntaxique, sémantique...) qui ne sont pas stabilisées pour la plupart des langues. Or, contrairement à une opinion bien répandue dans le domaine du TAL, l'analyse efficace de la langue ne provient pas nécessairement d'une description exhaustive de tous les phénomènes. Au contraire, à partir de l'exemple de la veille épidémiologique sur la presse Internet nous montrons comment les principes rhétoriques propres à un genre textuel sont utiles pour l'analyse automatique de texte. En effet, certains de ces principes sont aisément transposables en langage informatique, c'est à dire aisément « traduisibles » en algorithmes. Ainsi, les règles rhétoriques et communicationnelles qui régissent le genre journalistique fournissent une grille d'analyse simple et efficace pour construire un système d'analyse automatique de la presse à visée multilingue. Lire l'article sur : https://www.researchgate.net/publication/281950859_Vers_une_approche_rhetorique_en_TAL_application_a_la_veille_epidemiologique_multilingue

Alignement endogène de documents, une approche multilingue et multi-échelle

CAEN-BU Sciences et STAPS (141182103) / SudocSudocFranceF

Automatic Repair of Real Bugs: An Experience Report on the Defects4J Dataset

Automatic software repair aims to reduce human effort for fixing bugs. Various automatic repair approaches have emerged in recent years. In this paper, we report on an experiment on automatically repairing 224 bugs of a real-world and publicly available bug dataset, Defects4J. We investigate the results of three repair methods, GenProg (repair via random search), Kali (repair via exhaustive search), and Nopol (repair via constraint based search). We conduct our investigation with five research questions: fixability, patch correctness, ill-defined bugs, performance, and fault localizability. Our implementations of GenProg, Kali, and Nopol fix together 41 out of 224 (18%) bugs with 59 different patches. This can be viewed as a baseline for future usage of Defects4J for automatic repair research. In addition, manual analysis of sampling 42 of 59 generated patches shows that only 8 patches are undoubtedly correct. This is a novel piece of evidence that there is large room for improvement in the area of test suite based repair

KKL-35 Exhibits Potent Antibiotic Activity against Legionella Species Independently of trans-Translation Inhibition

International audiencetrans-Translation is a ribosome-rescue system that is ubiquitous in bacteria. Small molecules defining a new family of oxadiazole compounds that inhibit trans-translation have been found to have broad-spectrum antibiotic activity. We sought to determine the activity of KKL-35, a potent member of the oxadiazole family, against the human pathogen Legionella pneumophila and other related species that can also cause Legionnaires' disease (LD). Consistent with the essential nature of trans-translation in L. pneumophila, KKL-35 inhibited the growth of all tested strains at submicromolar concentrations. KKL-35 was also active against other LD-causing Legionella species. KKL-35 remained equally active against L. pneumophila mutants that have evolved resistance to macrolides. KKL-35 inhibited the multiplication of L. pneumophila in human macrophages at several stages of infection. No resistant mutants could be obtained, even during extended and chronic exposure. Surprisingly, KKL-35 was not synergistic with other ribosome-targeting antibiotics and did not induce the filamentation phenotype observed in cells defective for trans-translation. Importantly, KKL-35 remained active against L. pneumophila mutants expressing an alternate ribosome-rescue system and lacking transfer-messenger RNA, the essential component of trans-translation. These results indicate that the antibiotic activity of KKL-35 is not related to the specific inhibition of trans-translation and its mode of action remains to be identified. In conclusion, KKL-35 is an effective antibacterial agent against the intracellular pathogen L. pneumophila with no detectable resistance development. However, further studies are needed to better understand its mechanism of action and to assess further the potential of oxadiazoles in treatment