Rodrigo Machado

Running AgentSpeak(L) Agents on SIM_AGENT

This paper presents what is, to the best of our knowledge, the very first successful attempt at running AgentSpeak(L) programs. AgentSpeak(L) is a programming language for BDI agents, created by Rao, with which he pointed for the first time towards bridging the gap between BDI logics and implemented BDI systems. Moreover, it has quite an elegant and neat notation for a BDI programming language, which could establish a turning point in the practice of implementing cognitive multi-agent systems, should it be turned into a working interpreter or compiler. Precisely because such (implemented) interpreter or compiler was unavailable, AgentSpeak(L)has been neglected, as have other agent-oriented programming languages with a strong theoretical support, by multi-agent system practitioners. This paper shows a way of turning AgentSpeak(L)agents into running programs within Slomans SIM_AGENT toolkit. We have called this prototype interpreter SIM_Speak, and we have tested it with a multi-agent traffic simulation. We also discuss the limitations and possible extensions to SIM_Speak.

Rule-based transformation of graph rewriting rules

Higher-order functions - the ones which manipulate other functions - have a fundamental role in Computer Science, specially in areas such as functional programming and theory of computation. Graph transformation - the rule-based modification of graphs - is also an important approach used in many contexts, as for instance, the definition of syntax and semantics of visual languages and the modelling and analysis of concurrent and non-deterministic systems. Although the algebraic double-pushout (DPO) approach to graph transformation has a vast theory, it does not present a notion of higher-order transformation, i.e., transformation of graph rewriting rules themselves. Higher-order would be required, for instance, to ease the modelling of dynamic systems through graph transformation systems, and to describe model transformations that modify graph rewriting rules. The main contribution of this work is a notion of double-pushout transformation for graph rewriting rules, where the result of the rewriting is a valid graph rule. We use DPO diagrams in the category of graph spans to describe rule transformations, and negative application conditions (NACs) in the second-order rules to enforce preservation of the rule structure. We define a model named second-order graph grammars, capable of first- and second-order derivations. Finally, we discuss alternative ways of defining second-order transformations.

Towards Test Coverage Criteria for Visual Contracts

When testing component-based or service-oriented applications we cannot always rely on coverage criteria based on source code. Instead, we have to express our requirements for testing at the interface level. Specifying interfaces by graph transformation rules, so-called visual contracts, we define model-based coverage criteria exploiting the well-known relations of causal dependency and conflict on transformation rules. To this end we establish an observational semantics for graph transformation systems with rule signatures formalising a notion of test execution, and define dependency graphs to provide a structure on which coverage can be analysed.

Stranding Events of Kogia Whales along the Brazilian Coast

The genus Kogia, which comprises only two extant species, Kogia sima and Kogia breviceps, represents one of the least known groups of cetaceans in the global ocean. In some coastal regions, however, stranding events of these species have been relatively common over the last decades. Stranding provides the opportunity to investigate the biology of these cetaceans and to explore the epidemiological aspects associated with the mortality of the organisms found on the beach. A number of disturbances (including pelagic fisheries, chemical pollution, boat strikes, and noise pollution) have been confirmed to pose a particular threat to the Kogia species. However, no study has yet investigated potential relationships between environmental conditions and stranding events. Here we analyse how a collection of environmental, physical, and biological variables, such as wind, sea surface temperature (SST), water depth, and chlorophyll-a, correlate to Kogia stranding events along the Brazilian coast. The results of our statistical analyses suggest that K. sima is more likely found in warm tropical waters, which provide an explanation for the high frequency of stranding in northeastern Brazilian coast. In contrast, K. breviceps appears to have a preference for temperate and productive waters. Wind speed results to be also an important factor for predicting Kogia strandings in Brazilian coast. Additionally, literature information in combination with our own data and analyses of stomach contents confirms that oceanic cephalopods constitute the primary nutritional source of both Kogia species. By using the available information as a qualitative proxy for habitat preference and feeding ecology, our study provides a novel and comprehensive assessment of Kogia stranding data in relation to environmental conditions along the Brazilian coast.

On the Essence of Parallel Independence for the Double-Pushout and Sesqui-Pushout Approaches

Parallel independence between transformation steps is a basic notion in the algebraic approaches to graph transformation, which is at the core of some static analysis techniques like Critical Pair Analysis. We propose a new categorical condition of parallel independence and show its equivalence with two other conditions proposed in the literature, for both left-linear and non-left-linear rules. Next we present some preliminary experimental results aimed at comparing the three conditions with respect to computational efficiency. To this aim, we implemented the three conditions, for left-linear rules only, in the Verigraph system, and used them to check parallel independence of pairs of overlapping redexes generated from some sample graph transformation systems over categories of typed graphs.

The Verigraph System for Graph Transformation

Graph transformation (GT) is a rule-based framework, suitable for modelling both static and dynamic aspects of complex systems in an intuitive yet formal manner. The algebraic approach to GT is based on category theory, allowing the instantiation of theoretical results to multiple graph-like structures (e.g. labelled or attributed graphs, Petri nets, even transformation rules themselves). There exists a rich theory of algebraic GT which underlies verification techniques such as static analysis. Current tools based on GT are implemented in a very concrete way, unlike the theory, making them hard to extend with novel theoretical results. Thus a new software system called Verigraph was created, with the goal of implementing the theory as closely as possible, while maintaining a reasonable execution time. In this paper we present the architecture of Verigraph, which enabled an almost direct implementation of the theory. We also provide a step-by-step guide to implementing a new graph model within the system, using second-order graph transformation as an example. Finally, we compare the performance of Verigraph and AGG.

Verigraph: A System for Specification and Analysis of Graph Grammars

Graph grammars are models that allow for a visual representation of both static and dynamic aspects of a system. There are several tools that allow the edition, simulation and analysis of graph grammars, each of them focusing on one kind of analysis technique or graph model. In this paper we present a new tool for simulation and analysis of graph grammars, called Verigraph, built with the following design principles: an implementation as direct as possible of formal concepts (to ease correctness arguments), a generic implementation of core algorithms (to allow its application for several graph models), and a reasonable running time. In this paper we present architectural aspects of Verigraph, together with a comparison with other similar tools in terms of available features.

Modeling and Reasoning over Distributed Systems using Aspect-Oriented Graph Grammars

Aspect-orientation is a relatively new paradigm that intro duces abstractions to modularize the implementation of system-wide policies. It is based on a composition operation, called aspect weaving, that implicitly modifies a base system by performing related changes within the system modules. Aspect-oriented graph grammars (AOGG) extend the classic graph grammar formalism by defining aspects as sets of rule-based modifications over a base graph grammar. Despite the advantages of aspect-oriented concepts regarding modularity, the implicit nature of the aspect weaving operation may also introduce issues when reasoning about the system behavior. Since in AOGGs aspect weaving is characterized by means of rule-based rewriting, we can overcome these problems by using known analysis techniques from the graph transformation literature to study aspect composition. In this paper, we present a case study of a distributed client-s erver system with global policies, modeled as an aspect-oriented graph grammar, and discuss how to use the AGG tool to identify potential conflicts in aspect weaving.

Inositol 1, 4, 5-trisphosphate-dependent nuclear calcium signals regulate angiogenesis and cell motility in triple negative breast cancer

Increases in nuclear calcium concentration generate specific biological outcomes that differ from those resulting from increased cytoplasmic calcium. Nuclear calcium effects on tumor cell proliferation are widely appreciated; nevertheless, its involvement in other steps of tumor progression is not well understood. Therefore, we evaluated whether nuclear calcium is essential in other additional stages of tumor progression, including key steps associated with the formation of the primary tumor or with the metastatic cascade. We found that nuclear calcium buffering impaired 4T1 triple negative breast cancer growth not just by decreasing tumor cell proliferation, but also by enhancing tumor necrosis. Moreover, nuclear calcium regulates tumor angiogenesis through a mechanism that involves the upregulation of the anti-angiogenic C-X-C motif chemokine 10 (CXCL10-IP10). In addition, nuclear calcium buffering regulates breast tumor cell motility, culminating in less cell invasion, likely due to enhanced vinculin expression, a focal adhesion structural protein. Together, our results show that nuclear calcium is essential for triple breast cancer angiogenesis and cell migration and can be considered as a promising strategic target for triple negative breast cancer therapy.

V: a language with extensible record accessors and a trait-based type system

This article introduces the V language, a purely functional programming language with a novel approach to records. Based on a system of type traits, V attempts to solve issues commonly found when manipulating records in purely functional programming languages.