Improving the structure MCMC sampler for Bayesian networks by introducing a new edge reversal move

Applications of Bayesian networks in systems biology are computationally demanding due to the large number of model parameters. Conventional MCMC schemes based on proposal moves in structure space tend to be too slow in mixing and convergence, and have recently been superseded by proposal moves in the space of node orders. A disadvantage of the latter approach is the intrinsic inability to specify the prior probability on network structures explicitly. The relative paucity of different experimental conditions in contemporary systems biology implies a strong influence of the prior probability on the posterior probability and, hence, the outcome of inference. Consequently, the paradigm of performing MCMC proposal moves in order rather than structure space is not entirely satisfactory. In the present article, we propose a new and more extensive edge reversal move in the original structure space, and we show that this significantly improves the convergence of the classical structure MCMC scheme.     

Artificial institutions: a model of institutional reality for open multiagent systems

Software agents’ ability to interact within different open systems, designed by different groups, presupposes an agreement on an unambiguous definition of a set of concepts, used to describe the context of the interaction and the communication language the agents can use. Agents’ interactions ought to allow for reliable expectations on the possible evolution of the system; however, in open systems interacting agents may not conform to predefined specifications. A possible solution is to define interaction environments including a normative component, with suitable rules to regulate the behaviour of agents. To tackle this problem we propose an application-independent metamodel of artificial institutions that can be used to define open multiagent systems. In our view an artificial institution is made up by an ontology that models the social context of the interaction, a set of authorizations to act on the institutional context, a set of linguistic conventions for the performance of institutional actions and a system of norms that are necessary to constrain the agents’ actions.     

Measuring the structural similarity among XML documents and DTDs

Measuring the structural similarity between an XML document and a DTD has many relevant applications that range from document classification and approximate structural queries on XML documents to selective dissemination of XML documents and document protection. The problem is harder than measuring structural similarity among documents, because a DTD can be considered as a generator of documents. Thus, the problem is to evaluate the similarity between a document and a set of documents. An effective structural similarity measure should face different requirements that range from considering the presence and absence of required elements, as well as the structure and level of the missing and extra elements to vocabulary discrepancies due to the use of synonymous or syntactically similar tags. In the paper, starting from these requirements, we provide a definition of the measure and present an algorithm for matching a document against a DTD to obtain their structural similarity. Finally, experimental results to assess the effectiveness of the approach are presented.     

High power GaN‐HEMT SPDT switches for microwave applications

In this article, the design, fabrication, and on‐wafer test of X‐Band and 2–18 GHz wideband high‐power SPDT MMIC switches in AlGaN/GaN technology are presented. The switches have demonstrated state‐of‐the‐art performance and RF fabrication yield better than 65%. Linear and power measurements for different control voltages have been reported and an explanation of the dependence of the power performances on the control voltage is given. In particular, the X‐band switch exhibits a 0.4 dB compression level at 10 GHz when driven by a 38 dBm input signal. The wideband switch shows a compression level of 1 dB at an input drive higher than 38 dBm across the entire bandwidth. © 2009 Wiley Periodicals, Inc. Int J RF and Microwave CAE, 2009.     

Molecular modeling of tricyclic compounds with anilino substituents and their intercalation complexes with DNA sequences

Although 9-anilinoacridines are among the best studied antitumoral intercalators, there are few studies about the effect of isosteric substitution of a benzene moiety for a heterocycle ring in the acridine framework. According to these studies, this approach may lead to effective cytotoxic agents, but good cytotoxic activity depends on structural requirements in the aniline ring which differ from those in 9-anilinoacridines. The present paper deals with molecular modeling studies of some 9-anilino substituted tricyclic compounds and their intercalation complexes (in various DNA sequences) resulting from docking the compounds into various DNA sequences. As expected, the isosteric substitution in 9-anilinoacridines influences the LUMO energy values and orbital distribution, the dipole moment, electrostatic charges and the conformation of the anilino ring. Other important differences are observed during the docking studies, for example, changes in the spatial arrangement of the tricyclic nucleus and the anilino ring at the intercalation site. Semiempirical calculations of the intercalation complexes show that the isosteric replacement of a benzene ring in the acridine nucleus affects not only DNA affinity but also base pair selectivity. These findings explain, at least partially, the different structural requirements observed in several 9-anilino substituted tricyclic compounds for cytotoxic activity. Thus, the data presented here may guide the rational design of new agents with different DNA binding properties and/or a cytotoxic profile by isosteric substitution of known intercalators.     

Crossing textual and visual content in different application scenarios

This paper deals with multimedia information access. We propose two new approaches for hybrid text-image information processing that can be straightforwardly generalized to the more general multimodal scenario. Both approaches fall in the trans-media pseudo-relevance feedback category. Our first method proposes using a mixture model of the aggregate components, considering them as a single relevance concept. In our second approach, we define trans-media similarities as an aggregation of monomodal similarities between the elements of the aggregate and the new multimodal object. We also introduce the monomodal similarity measures for text and images that serve as basic components for both proposed trans-media similarities. We show how one can frame a large variety of problem in order to address them with the proposed techniques: image annotation or captioning, text illustration and multimedia retrieval and clustering. Finally, we present how these methods can be integrated in two applications: a travel blog assistant system and a tool for browsing the Wikipedia taking into account the multimedia nature of its content.

Efficient application identification and the temporal and spatial stability of classification schema

Motivated by the importance of accurate identification for a range of applications, this paper compares and contrasts the effective and efficient classification of network-based applications using behavioral observations of network-traffic and those using deep-packet inspection.Importantly, throughout our work we are able to make comparison with data possessing an accurate, independently determined ground-truth that describes the actual applications causing the network-traffic observed.In a unique study in both the spatial-domain: comparing across different network-locations and in the temporal-domain: comparing across a number of years of data, we illustrate the decay in classification accuracy across a range of application–classification mechanisms. Further, we document the accuracy of spatial classification without training data possessing spatial diversity.Finally, we illustrate the classification of UDP traffic. We use the same classification approach for both stateful flows (TCP) and stateless flows based upon UDP. Importantly, we demonstrate high levels of accuracy: greater than 92% for the worst circumstance regardless of the application.     

Landscape-aware location-privacy protection in location-based services

Mobile network providers have developed a variety of location-based services (LBSs), such as friend-finder, point of interest services, emergency rescue and many other safety and security services. The protection of location-privacy has consequently become a key aspect to the success of LBSs, since users consider their own physical location and movements highly privacy-sensitive, and demand for solutions able to protect such an information in a variety of environments. The idea behind location-privacy protection is that the individual should be able to set the level at which the location information is released to avoid undesired exploitation by a potential attacker: one of the approaches to this problem is given by the application of spatial obfuscation techniques, actuated by a trusted agent, and consisting in artificial perturbations of the location information collected by sensing technologies, before its disclosure to third parties. In many situations, however, landscape/map information can help a third party to perform Bayesian inference over spatially obfuscated data and to refine the user’s location estimate up to a violation of the original user’s location-privacy requirements. The goal of this paper is to provide a map-dependent obfuscation procedure that enables the release of the maximum possible user’s location information, that does not lead to a violation of the original user’s location-privacy requirements, even when refined through map-based inference.     

Product features and task effects on experienced richness, control and engagement in voicemail browsing

A recent focus is on creating engaging user experiences with digital products and services such as voicemail. This study aims to design towards increased levels of engagement in voicemail browsing by using the ‘Richness, Control and Engagement’ (RC & E) framework. This framework explains the levels of engagement in terms of the levels of richness and control that are shaped by the features of a product and the user’s expertise. A product was developed that utilized gestures and sound to access digital voicemail contents. An experiment was conducted in which 28 participants interacted with the product while varying (1) the number of features of the user interface, (2) the amount of voicemail content and (3) the type of task. Results showed that the levels of engagement could be predicted according to the levels of richness and control experienced when a task-term was added to the framework. Implications of the refined RC & E framework for interaction design practice are discussed.