rbrothers: R Package for Bayesian Multiple Change-Point Recombination Detection.

Phylogenetic recombination detection is a fundamental task in bioinformatics and evolutionary biology. Most of the computational tools developed to attack this important problem are not integrated into the growing suite of R packages for statistical analysis of molecular sequences. Here, we present an R package, rbrothers, that makes a Bayesian multiple change-point model, one of the most sophisticated model-based phylogenetic recombination tools, available to R users. Moreover, we equip the Bayesian change-point model with a set of pre- and post- processing routines that will broaden the application domain of this recombination detection framework. Specifically, we implement an algorithm that forms the set of input trees required by multiple change-point models. We also provide functionality for checking Markov chain Monte Carlo convergence and creating estimation result summaries and graphics. Using rbrothers, we perform a comparative analysis of two Salmonella enterica genes, fimA and fimH, that encode major and adhesive subunits of the type 1 fimbriae, respectively. We believe that rbrothers, available at R-Forge: http://evolmod.r-forge.r-project.org/, will allow researchers to incorporate recombination detection into phylogenetic workflows already implemented in R

Verification of interlocking systems using statistical model checking

In the railway domain, an interlocking is the system ensuring safe train traffic inside a station by controlling its active elements such as the signals or points. Modern interlockings are configured using particular data, called application data, reflecting the track layout and defining the actions that the interlocking can take. The safety of the train traffic relies thereby on application data correctness, errors inside them can cause safety issues such as derailments or collisions. Given the high level of safety required by such a system, its verification is a critical concern. In addition to the safety, an interlocking must also ensure that availability properties, stating that no train would be stopped forever in a station, are satisfied. Most of the research dealing with this verification relies on model checking. However, due to the state space explosion problem, this approach does not scale for large stations. More recently, a discrete event simulation approach limiting the verification to a set of likely scenarios, was proposed. The simulation enables the verification of larger stations, but with no proof that all the interesting scenarios are covered by the simulation. In this paper, we apply an intermediate statistical model checking approach, offering both the advantages of model checking and simulation. Even if exhaustiveness is not obtained, statistical model checking evaluates with a parametrizable confidence the reliability and the availability of the entire system.Comment: 12 pages, 3 figures, 2 table

Analysing oscillatory trends of discrete-state stochastic processes through HASL statistical model checking

The application of formal methods to the analysis of stochastic oscillators has been at the focus of several research works in recent times. In this paper we provide insights on the application of an expressive temporal logic formalism, namely the Hybrid Automata Stochastic Logic (HASL), to that issue. We show how one can take advantage of the expressive power of the HASL logic to define and assess relevant characteristics of (stochastic) oscillators

Adversarial Sample Detection for Deep Neural Network through Model Mutation Testing

Deep neural networks (DNN) have been shown to be useful in a wide range of applications. However, they are also known to be vulnerable to adversarial samples. By transforming a normal sample with some carefully crafted human imperceptible perturbations, even highly accurate DNN make wrong decisions. Multiple defense mechanisms have been proposed which aim to hinder the generation of such adversarial samples. However, a recent work show that most of them are ineffective. In this work, we propose an alternative approach to detect adversarial samples at runtime. Our main observation is that adversarial samples are much more sensitive than normal samples if we impose random mutations on the DNN. We thus first propose a measure of `sensitivity' and show empirically that normal samples and adversarial samples have distinguishable sensitivity. We then integrate statistical hypothesis testing and model mutation testing to check whether an input sample is likely to be normal or adversarial at runtime by measuring its sensitivity. We evaluated our approach on the MNIST and CIFAR10 datasets. The results show that our approach detects adversarial samples generated by state-of-the-art attacking methods efficiently and accurately.Comment: Accepted by ICSE 201