Dissection of a Bug Dataset: Anatomy of 395 Patches from Defects4J

Well-designed and publicly available datasets of bugs are an invaluable asset to advance research fields such as fault localization and program repair as they allow directly and fairly comparison between competing techniques and also the replication of experiments. These datasets need to be deeply understood by researchers: the answer for questions like "which bugs can my technique handle?" and "for which bugs is my technique effective?" depends on the comprehension of properties related to bugs and their patches. However, such properties are usually not included in the datasets, and there is still no widely adopted methodology for characterizing bugs and patches. In this work, we deeply study 395 patches of the Defects4J dataset. Quantitative properties (patch size and spreading) were automatically extracted, whereas qualitative ones (repair actions and patterns) were manually extracted using a thematic analysis-based approach. We found that 1) the median size of Defects4J patches is four lines, and almost 30% of the patches contain only addition of lines; 2) 92% of the patches change only one file, and 38% has no spreading at all; 3) the top-3 most applied repair actions are addition of method calls, conditionals, and assignments, occurring in 77% of the patches; and 4) nine repair patterns were found for 95% of the patches, where the most prevalent, appearing in 43% of the patches, is on conditional blocks. These results are useful for researchers to perform advanced analysis on their techniques' results based on Defects4J. Moreover, our set of properties can be used to characterize and compare different bug datasets.Comment: Accepted for SANER'18 (25th edition of IEEE International Conference on Software Analysis, Evolution and Reengineering), Campobasso, Ital

Phylogenetic multi-locus codon models and molecular clocks reveal the monophyly of haematophagous reduviid bugs and their evolution at the formation of South America.

We previously constructed a single molecular clock to date insect evolution that remains a cornerstone within entomological dating. The insect clock predicts that triatomine bugs, the vectors of South American trypanosomiasis, originated with the formation of South America. We addressed this hypothesis using the insectivorous reduviid bugs and their phylogenetic relationship with the haematophagous reduviid bugs, as well as their biogeographic distribution. Putative paraphyly or monophyly of Triatominae, by non-haematophagous reduviids, have both previously been hypothesized and identified. We sampled a broad range of predatory reduviids, viz. Ectrichodiinae, Emesinae, Hammacerinae, Harpactorinae, Reduviinae, Salyavatinae, Steniopodainae and Vesciinae, including both New World and Old World representatives and sequenced the nuclear 28S ribosomal gene locus and the mitochondrial loci 5' cytochrome oxidase 1 (cox1 [COI]), cox1 3', cytochrome oxidase 2 (cox2 [COII]) and cytochrome oxidase b (cob [cytb]). Robust evidence for the monophyly of Triatominae was observed in 5/5 loci using codon/nucleotide (28S) based maximum likelihood phylogenies, 3/5 loci using codon-based Bayesian phylogenies and in cox2 using amino acid Bayesian phylogenies. Several South American members of the Reduviinae, that are morphologically and phylogenetically a sister group to triatomine bugs, have a modal divergence date with the Triatominae of 109-107 million years ago (MYA). This creates a scenario where the closest (non-haematophagous) ancestor to triatomine bugs evolved immediately prior to the breakup of Gondwanaland whilst the triatomine bugs evolved 95MYA, putatively linking the origin of haematophagous behaviour to the origin of South America and in particular infers a delayed onset to the evolution of haematophagy. The placement of the enigmatic tribe Bolboderini as an ingroup to the Triatominae monophyly, confirms the 95MYA node as the most ancient in the subfamily

E-QED: Electrical Bug Localization During Post-Silicon Validation Enabled by Quick Error Detection and Formal Methods

During post-silicon validation, manufactured integrated circuits are extensively tested in actual system environments to detect design bugs. Bug localization involves identification of a bug trace (a sequence of inputs that activates and detects the bug) and a hardware design block where the bug is located. Existing bug localization practices during post-silicon validation are mostly manual and ad hoc, and, hence, extremely expensive and time consuming. This is particularly true for subtle electrical bugs caused by unexpected interactions between a design and its electrical state. We present E-QED, a new approach that automatically localizes electrical bugs during post-silicon validation. Our results on the OpenSPARC T2, an open-source 500-million-transistor multicore chip design, demonstrate the effectiveness and practicality of E-QED: starting with a failed post-silicon test, in a few hours (9 hours on average) we can automatically narrow the location of the bug to (the fan-in logic cone of) a handful of candidate flip-flops (18 flip-flops on average for a design with ~ 1 Million flip-flops) and also obtain the corresponding bug trace. The area impact of E-QED is ~2.5%. In contrast, deter-mining this same information might take weeks (or even months) of mostly manual work using traditional approaches

Self-similar disk packings as model spatial scale-free networks

The network of contacts in space-filling disk packings, such as the Apollonian packing, are examined. These networks provide an interesting example of spatial scale-free networks, where the topology reflects the broad distribution of disk areas. A wide variety of topological and spatial properties of these systems are characterized. Their potential as models for networks of connected minima on energy landscapes is discussed.Comment: 13 pages, 12 figures; some bugs fixed and further discussion of higher-dimensional packing