An extensible benchmark and tooling for comparing reverse engineering approaches

Various tools exist to reverse engineer software source code and generate design information, such as UML projections. Each has specific strengths and weaknesses, however no standardised benchmark exists that can be used to evaluate and compare their performance and effectiveness in a systematic manner. To facilitate such comparison in this paper we introduce the Reverse Engineering to Design Benchmark (RED-BM), which consists of a comprehensive set of Java-based targets for reverse engineering and a formal set of performance measures with which tools and approaches can be analysed and ranked. When used to evaluate 12 industry standard tools performance figures range from 8.82\% to 100\% demonstrating the ability of the benchmark to differentiate between tools. To aid the comparison, analysis and further use of reverse engineering XMI output we have developed a parser which can interpret the XMI output format of the most commonly used reverse engineering applications, and is used in a number of tools

Using a new high-throughput video-tracking platform to assess behavioural changes in Daphnia magna exposed to neuro-active drugs

© 2019. ElsevierOne of the major challenges that faces today regulatory risk assessment is to speed up the way of assessing threshold sublethal detrimental effects of existing and new chemical products. Recently advances in imaging allows to monitor in real time the behaviour of individuals under a given stress. Light is a common stress for many different organisms. Fish larvae and many invertebrate species respond to light altering their behaviour. The water flea Daphnia magna as many other zooplanktonic species has a marked diel vertical phototactic swimming behaviour against light due to fish predation. The aim of this study was to develop a high throughput image analysis to study changes in the vertical swimming behaviour to light of D. magna first reproductive adult females exposed to 0.1 and 1 µg/L of four psychiatric drugs: diazepam, fluoxetine, propranolol and carbamazepine during their entire life. Experiments were conducted using a new custom designed vertical oriented four 50 mL chamber device controlled by the Noldus software (Netherlands). Changes in speed, preferred area (bottom vs upper areas) and animal aggregation were analysed using groups of animals under consecutive periods of dark and apical light stimulus of different intensities. Obtained results indicated that light intensity increased the speed but low light intensities allowed to better discriminate individual responses to the studied drugs. The four tested drugs decreased the response of exposed organisms to light: individuals move less, were closer to the bottom and at low light intensities were closer each other. At high light intensities, however, exposed individuals were less aggregated. Propranolol, carbamazepine and fluoxetine were the compounds effecting most the behaviour. Our results indicated that psychiatric drugs at environmental relevant concentrations alter the vertical phototactic behaviour of D. magna individuals and that it is possible to develop appropriate high-throughput image analysis devices to measure those responses.Peer ReviewedPostprint (author's final draft

Clone Detection in Matlab Stateflow Models

Matlab Simulink is one of the leading tools for model based software development in the automotive industry. One extension to Simulink is Stateflow, which allows the user to embed Statecharts as components in a Simulink Model. These state machines contain nested states, an action language that describes events, guards, conditions and actions and complex transitions. As Stateflow has become increasingly important in Simulink models for the automotive sector, we extend previous work on clone detection of Simulink models to Stateflow components

Asymmetric Actor Critic for Image-Based Robot Learning

Deep reinforcement learning (RL) has proven a powerful technique in many sequential decision making domains. However, Robotics poses many challenges for RL, most notably training on a physical system can be expensive and dangerous, which has sparked significant interest in learning control policies using a physics simulator. While several recent works have shown promising results in transferring policies trained in simulation to the real world, they often do not fully utilize the advantage of working with a simulator. In this work, we exploit the full state observability in the simulator to train better policies which take as input only partial observations (RGBD images). We do this by employing an actor-critic training algorithm in which the critic is trained on full states while the actor (or policy) gets rendered images as input. We show experimentally on a range of simulated tasks that using these asymmetric inputs significantly improves performance. Finally, we combine this method with domain randomization and show real robot experiments for several tasks like picking, pushing, and moving a block. We achieve this simulation to real world transfer without training on any real world data.Comment: Videos of experiments can be found at http://www.goo.gl/b57WT

Group emotion modelling and the use of middleware for virtual crowds in video-games

In this paper we discuss the use of crowd simulation in video-games to augment their realism. Using previous works on emotion modelling and virtual crowds we define a game world in an urban context. To achieve that, we explore a biologically inspired human emotion model, investigate the formation of groups in crowds, and examine the use of physics middleware for crowds. Furthermore, we assess the realism and computational performance of the proposed approach. Our system runs at interactive frame-rate and can generate large crowds which demonstrate complex behaviour

Ligand-induced monoubiquitination of BIK1 regulates plant immunity

The detection of microorganism-associated ligands by plant cells activates a signalling cascade in which the kinase BIK1 is monoubiquinated, released from the FLS2-BAK1 complex, and internalized by endocytosis. Recognition of microbe-associated molecular patterns (MAMPs) by pattern recognition receptors (PRRs) triggers the first line of inducible defence against invading pathogens(1-3). Receptor-like cytoplasmic kinases (RLCKs) are convergent regulators that associate with multiple PRRs in plants(4). The mechanisms that underlie the activation of RLCKs are unclear. Here we show that when MAMPs are detected, the RLCK BOTRYTIS-INDUCED KINASE 1 (BIK1) is monoubiquitinated following phosphorylation, then released from the flagellin receptor FLAGELLIN SENSING 2 (FLS2)-BRASSINOSTEROID INSENSITIVE 1-ASSOCIATED KINASE 1 (BAK1) complex, and internalized dynamically into endocytic compartments. The Arabidopsis E3 ubiquitin ligases RING-H2 FINGER A3A (RHA3A) and RHA3B mediate the monoubiquitination of BIK1, which is essential for the subsequent release of BIK1 from the FLS2-BAK1 complex and activation of immune signalling. Ligand-induced monoubiquitination and endosomal puncta of BIK1 exhibit spatial and temporal dynamics that are distinct from those of the PRR FLS2. Our study reveals the intertwined regulation of PRR-RLCK complex activation by protein phosphorylation and ubiquitination, and shows that ligand-induced monoubiquitination contributes to the release of BIK1 family RLCKs from the PRR complex and activation of PRR signalling

Induced chromosome deletions cause hypersociability and other features of Williams-Beuren syndrome in mice

The neurodevelopmental disorder Williams-Beuren syndrome is caused by spontaneous similar to 1.5 Mb deletions comprising 25 genes on human chromosome 7q11.23. To functionally dissect the deletion and identify dosage-sensitive genes, we created two half-deletions of the conserved syntenic region on mouse chromosome 5G2. Proximal deletion (PD) mice lack Gtf2i to Limk1, distal deletion (DD) mice lack Limk1 to Fkbp6, and the double heterozygotes (D/P) model the complete human deletion. Gene transcript levels in brain are generally consistent with gene dosage. Increased sociability and acoustic startle response are associated with PD, and cognitive defects with DD. Both PD and D/P males are growth-retarded, while skulls are shortened and brains are smaller in DD and D/P. Lateral ventricle (LV) volumes are reduced, and neuronal cell density in the somatosensory cortex is increased, in PD and D/P. Motor skills are most impaired in D/P. Together, these partial deletion mice replicate crucial aspects of the human disorder and serve to identify genes and gene networks contributing to the neural substrates of complex behaviours and behavioural disorders

Event-B in the Institutional Framework: Defining a Semantics, Modularisation Constructs and Interoperability for a Specification Language

Event-B is an industrial-strength specification language for verifying the properties of a given system’s specification. It is supported by its Eclipse-based IDE, Rodin, and uses the process of refinement to model systems at different levels of abstraction. Although a mature formalism, Event-B has a number of limitations. In this thesis, we demonstrate that Event-B lacks formally defined modularisation constructs. Additionally, interoperability between Event-B and other formalisms has been achieved in an ad hoc manner. Moreover, although a formal language, Event-B does not have a formal semantics. We address each of these limitations in this thesis using the theory of institutions. The theory of institutions provides a category-theoretic way of representing a formalism. Formalisms that have been represented as institutions gain access to an array of generic specification-building operators that can be used to modularise specifications in a formalismindependent manner. In the theory of institutions, there are constructs (known as institution (co)morphisms) that provide us with the facility to create interoperability between formalisms in a mathematically sound way. The main contribution of this thesis is the definition of an institution for Event-B, EVT, which allows us to address its identified limitations. To this end, we formally define a translational semantics from Event- B to EVT. We show how specification-building operators can provide a unified set of modularisation constructs for Event-B. In fact, the institutional framework that we have incorporated Event-B into is more accommodating to modularisation than the current state-of-the-art for Rodin. Furthermore, we present institution morphisms that facilitate interoperability between the respective institutions for Event-B and UML. This approach is more generic than the current approach to interoperability for Event-B and in fact, allows access to any formalism or logic that has already been defined as an institution. Finally, by defining EVT, we have outlined the steps required in order to include similar formalisms into the institutional framework. Hence, this thesis acts as a template for defining an institution for a specification language