Learning Bayesian Networks with Bounded Tree-Width via Guided Search

Bounding the tree-width of a Bayesian network can reduce the chance of overfitting, and allows exact inference to be performed efficiently. Several existing algorithms tackle the problem of learning bounded tree-width Bayesian networks by learning from k-trees as super-structures, but they do not scale to large domains and/or large tree-width. We propose a guided search algorithm to find k-trees with maximum Informative scores, which is a measure of quality for the k-tree in yielding good Bayesian networks. The algorithm achieves close to optimal performance compared to exact solutions in small domains, and can discover better networks than existing approximate methods can in large domains. It also provides an optimal elimination order of variables that guarantees small complexity for later runs of exact inference. Comparisons with well-known approaches in terms of learning and inference accuracy illustrate its capabilities.

Lichenicidin biosynthesis and search for novel antibacterial peptides

A estirpe Bacillus licheniformis I89 possui a capacidade de produzir alguns compostos com actividade antibacteriana. No presente estudo, a separação desses compostos foi realizada através da aplicação de vários procedimentos, incluindo extracção em fase sólida e cromatografia liquida de alta pressão. Dois destes compostos bioactivos constituem o lantibiótico de classe II lichenicidina e são caracterizados pela massas molecular de 3250 Da (Bliα) e 3020 Da (Bliβ). O cluster responsável pela biossíntese da lichenicidina foi heterologamente expresso em Escherichia coli, constituindo a primeira descrição da produção de um lantibiótico totalmente in vivo num hospedeiro Gram-negativo. Este sistema foi subsequentemente explorado com o objectivo de relacionar cada proteína codificada no cluster genético da lichenicidina na produção dos péptidos Bliα e Bliβ. O desenvolvimento do sistema de trans complementação possibilitou a produção de variantes destes péptidos. A análise das massas moleculares destas variantes assim como a análise dos padrões de fragmentação obtidos por MS/MS permitiu a revisão de algumas das características estruturais previamente proposta para Bliα e Bliβ. A análise dos genes hipoteticamente envolvidos na protecção da estirpe produtora contra a acção antibiótica da lichenicidina revelou, que em E. coli, a sua ausência não resulta no aumento da susceptibilidade a este composto. Verificou-se também que a presença destes genes não é essencial para a produção de lichenicidina em E. coli. Foi também confirmado experimentalmente que a membrana externa da E. coli constitui uma barreira natural para a entrada dos péptidos na célula. De facto, uma das características intrigantes da produção de lichenicidina por uma bactéria de Gram negativo reside no mecanismo de transporte dos dois péptidos através da membrana externa. Neste estudo foi demonstrado que na ausência da proteína de membrana TolC, a massa molecular de Bliα e Bliβ não foi identificada no sobrenadante de E. coli, demonstrando assim que a sua presença no ambiente extra-celular não se devia a um processo de lise bacteriana. Foi ainda avaliada a capacidade da maquinaria biossintética da lichenicidina para produzir o lantibiótico haloduracina, através do processamento de chimeras lichenicidina-haloduracina, contudo, os resultados foram negativos. Verificou-se ainda que em determinadas condições de incubação, a diferenciação da morfologia original da estirpe B. licheniformis I89 pode ocorrer. Esta dissociação implicou a transição da colónia parental e rugosa para uma colónia de aparência mais simples e suave. Desta forma, as diferenças das duas morfologias em termos de taxa de crescimento, esporulação e actividade antibiótica foram investigadas. Considerando especificamente Bliα e Bliβ verificou-se que a abundância destes péptidos nas culturas do fenótipo fino é geralmente inferior aquela identificada nas culturas do fenótipo parental. Por último, a diversidade de elementos genéticos constituintes de péptido sintetases não ribossomais (NRPS) foi investigada em lagoas no centro de Portugal e em solos provenientes de caves do sul de Portugal, revelando a presença de potenciais novas NRPS nestes ambientes.

In search of reliable centimeter-level indoor positioning: a smartphone-based approach

This thesis describes the design and implementation of a reliable centimeter-level indoor positioning system fully compatible with a conventional smartphone. The proposed system takes advantage of the smartphone audio I/O and processing capabilities to perform acoustic ranging in the audio band using non-invasive audio signals and it has been developed having in mind applications that require high accuracy, such as augmented reality, virtual reality, gaming and audio guides. The system works in a distributed operation mode, i.e. each smartphone is able to obtain its own position using only acoustic signals. To support the positioning system, a Wireless Sensor Network (WSN) of synchronized acoustic beacons is used. To keep the infrastructure in sync we have developed an Automatic Time Synchronization and Syntonization (ATSS) protocol with a standard deviation of the sync offset error below 1.25 μs. Using an improved Time Difference of Arrival (TDoA) estimation approach (which takes advantage of the beacon signals’ periodicity) and by performing Non-Line-of-Sight (NLoS) mitigation, we were able to obtain very stable and accurate position estimates with an absolute mean error of less than 10 cm in 95% of the cases and a mean standard deviation of 2.2 cm for a position refresh period of 350 ms.

The effect of redundancy and neutrality in genetic search

An experimental study aimed at assessing the influence of redundancy and neutrality on the performance of an (1+1)-ES evolution strategy modeled using Markov chains and applied to NK fitness landscapes is presented. For the study, two families of redundant binary representations, one non-neutral family which is based on linear transformations and that allows the phenotypic neighborhoods to be designed in a simple and effective way, and the neutral family based on the mathematical formulation of error control codes are used. The results indicate whether redundancy or neutrality affects more strongly the behavior of the algorithm used.

Optimised search heuristics: combining metaheuristics and exact methods to solve scheduling problems

Tese dout., Matemática, Investigação Operacional, Universidade do Algarve, 2009

Information search in web archives

Tese de doutoramento, Informática (Engenharia Informática), Universidade de Lisboa, Faculdade de Ciências, 2014

Local strategic partnerships in England: the continuing search for collaborative advantage, leadership and strategy in urban governance

Local Strategic Partnerships are being established in England to provide an inclusive, collaborative and strategic focus to regeneration strategies at the local level. They are also required to rationalise the proliferation of local and micro-partnerships set up by a succession of funding initiatives over the last 25 years. This article explores their remit, resources and membership and discusses how this initiative relates to theoretical work on urban governance, community engagement and leadership. It concludes by debating whether urban policy in England is now entering a new and more advanced phase based on inter-organisational networks with a strategic purpose. But questions remain about whether the institutional capacity is sufficient to deliver strong local leadership, accountability and community engagement.

Natural deduction system in paraconsistent setting: proof search for PCont

This paper continues a systematic approach to build natural deduction calculi and corresponding proof procedures for non-classical logics. Our attention is now paid to the framework of paraconsistent logics. These logics are used, in particular, for reasoning about systems where paradoxes do not lead to the `deductive explosion', i.e., where formulae of the type `A follows from false', for any A, are not valid. We formulate the natural deduction system for the logic PCont, explain its main concepts, define a proof searching technique and illustrate it by examples. The presentation is accompanied by demonstrating the correctness of these developments.

Specifying and analysing networks of processes in CSPt (or in search of associativity)

In proposing theories of how we should design and specify networks of processes it is necessary to show that the semantics of any language we use to write down the intended behaviours of a system has several qualities. First in that the meaning of what is written on the page reflects the intention of the designer; second that there are no unexpected behaviours that might arise in a specified system that are hidden from the unsuspecting specifier; and third that the intention for the design of the behaviour of a network of processes can be communicated clearly and intuitively to others. In order to achieve this we have developed a variant of CSP, called CSPt, designed to solve the problems of termination of parallel processes present in the original formulation of CSP. In CSPt we introduced three parallel operators, each with a different kind of termination semantics, which we call synchronous, asynchronous and race. These operators provide specifiers with an expressive and flexible tool kit to define the intended behaviour of a system in such a way that unexpected or unwanted behaviours are guaranteed not to take place. In this paper we extend out analysis of CSPt and introduce the notion of an alphabet diagram that illustrates the different categories of events that can arise in the parallel composition of processes. These alphabet diagrams are then used to analyse networks of three processes in parallel with the aim of identifying sufficient constraints to ensure associativity of their parallel composition. Having achieved this we then proceed to prove associativity laws for the three parallel operators of CSPt. Next, we illustrate how to design and construct a network of three processes that satisfy the associativity law, using the associativity theorem and alphabet diagrams. Finally, we outline how this could be achieved for more general networks of processes.

Fluid Ontologies in the Search for MH370

This paper gives an account of the disappearance of Malaysian Airways Flight MH370 into the southern Indian Ocean in March 2014 and analyses the rare glimpses into remote ocean space this incident opened up. It follows the tenuous clues as to where the aeroplane might have come to rest after it disappeared from radar screens – seven satellite pings, hundreds of pieces of floating debris and six underwater sonic recordings – as ways of entering into and thinking about ocean space. The paper pays attention to and analyses this space on three registers – first, as a fluid, more-than-human materiality with particular properties and agencies; second, as a synthetic situation, a composite of informational bits and pieces scopically articulated and augmented; and third, as geopolitics, delineated by the protocols of international search and rescue. On all three registers – as matter, as data and as law – the ocean is shown to be ontologically fluid, a world defined by movement, flow and flux, posing intractable difficulties for human interactions with it.

Ant colony search algorithm for the optimal power flow problem

To maintain a power system within operation limits, a level ahead planning it is necessary to apply competitive techniques to solve the optimal power flow (OPF). OPF is a non-linear and a large combinatorial problem. The Ant Colony Search (ACS) optimization algorithm is inspired by the organized natural movement of real ants and has been successfully applied to different large combinatorial optimization problems. This paper presents an implementation of Ant Colony optimization to solve the OPF in an economic dispatch context. The proposed methodology has been developed to be used for maintenance and repairing planning with 48 to 24 hours antecipation. The main advantage of this method is its low execution time that allows the use of OPF when a large set of scenarios has to be analyzed. The paper includes a case study using the IEEE 30 bus network. The results are compared with other well-known methodologies presented in the literature.

Voices in search of a reader: the polyphonic writing of António Lobo Antunes

This paper aims at analysing the writing of the Portuguese author António Lobo Antunes, considered one of the major writers in European Literature with 26 books published, by focusing on the strategies deployed in his texts of creating micro-narratives within the main frame, and conveying the elements of individual and collective memory, past and present, the self and the others, using various voices and silences. Lobo Antunes incorporates in his writing his background as a psychiatrist at a Mental Hospital in Lisbon, until 1985 (when he decided to commit exclusively to writing), his experience as a doctor in the Portuguese Colonial War battlefield, but also the daily routines of the pre and post 25th of April 1974 (Portuguese Revolution) with subtle and ironic details of the life of the middle and upper class of Lisbon‘s society: from the traumas of the war to the simple story of the janitor, or the couple who struggles to keep their marriage functional, everything serves as material to develop and interweave a complex plot, that a lot of readers find too enwrapped and difficult to follow through. Some excerpts taken from his first three novels and books of Chronicles and his later novel – Ontem não te Vi em Babilónia (2006) – will be put forward to exemplify the complexity of the writing and the main difficulties of the reader, lost in a multitude of narrators‘ voices. Recently, Lobo Antunes has commented on his work stating: What I write can be read in the darkness. This paper aims at throwing some light by unfolding some of the strategies employed to defy new borders in the process of reading.

Economic, environmental and mixed objective functions in non-linear process optimization using simulated annealing and tabu search

Screening of topologies developed by hierarchical heuristic procedures can be carried out by comparing their optimal performance. In this work we will be exploiting mono-objective process optimization using two algorithms, simulated annealing and tabu search, and four different objective functions: two of the net present value type, one of them including environmental costs and two of the global potential impact type. The hydrodealkylation of toluene to produce benzene was used as case study, considering five topologies with different complexities mainly obtained by including or not liquid recycling and heat integration. The performance of the algorithms together with the objective functions was observed, analyzed and discussed from various perspectives: average deviation of results for each algorithm, capacity for producing high purity product, screening of topologies, objective functions robustness in screening of topologies, trade-offs between economic and environmental type objective functions and variability of optimum solutions.