Automated network resilience optimization using computational intelligence methods

This paper presents an automated optimization framework able to provide network administrators with resilient routing configurations for link-state protocols, such as OSPF or IS-IS. In order to deal with the formulated NP-hard optimization problems, the devised framework is underpinned by the use of computational in- telligence optimization engines, such as Multi-objective Evolutionary Algorithms (MOEAs). With the objective of demonstrating the framework capabilities, two il- lustrative Traffic Engineering methods are described, allowing to attain routing con- figurations robust to changes in the traffic demands and maintaining the network stable even in the presence of link failure events. The presented illustrative results clearly corroborate the usefulness of the proposed automated framework along with the devised optimization methods.

Using relational algebra on the specification of real world ETL processes

Modeling Extract-Transform-Load (ETL) processes of a Data Warehousing System has always been a challenge. The heterogeneity of the sources, the quality of the data obtained and the conciliation process are some of the issues that must be addressed in the design phase of this critical component. Commercial ETL tools often provide proprietary diagrammatic components and modeling languages that are not standard, thus not providing the ideal separation between a modeling platform and an execution platform. This separation in conjunction with the use of standard notations and languages is critical in a system that tends to evolve through time and which cannot be undermined by a normally expensive tool that becomes an unsatisfactory component. In this paper we demonstrate the application of Relational Algebra as a modeling language of an ETL system as an effort to standardize operations and provide a basis for uncommon ETL execution platforms.

Implementation of integral viscoelastic constitutive models in OpenFOAM® computational library

This work reports the implementation and verification of a new so lver in OpenFOAM® open source computational library, able to cope with integral viscoelastic models based on the integral upper-convected Maxwell model. The code is verified through the comparison of its predictions with analytical solutions and numerical results obtained with the differential upper-convected Maxwell model

A relational algebra approach to ETL modeling

The MAP-i Doctoral Programme in Informatics, of the Universities of Minho, Aveiro and Porto

Development of computational tools for the integrated analysis of DNA microarray data with applications in cancer research

The MAP-i Doctoral Program of the Universities of Minho, Aveiro and Porto

Da modelação matemática à simulação computacional: a experimentação matemática no ensino

Tese de Doutoramento em Ciências (área de especialização em Matemática).

Da modelação matemática à simulação computacional: a experimentação matemática no ensino

Tese de Doutoramento em Ciências (área de especialização em Matemática).

Recurrence relations for Clifford algebra-valued orthogonal polynomials

The theory of orthogonal polynomials of one real or complex variable is well established as well as its generalization for the multidimensional case. Hypercomplex function theory (or Clifford analysis) provides an alternative approach to deal with higher dimensions. In this context, we study systems of orthogonal polynomials of a hypercomplex variable with values in a Clifford algebra and prove some of their properties.

A bio-inspired computational model for motion detection

Tese de Doutoramento (Programa Doutoral em Engenharia Biomédica)

Algorithms and computational tools for metabolic flux analysis

PhD thesis in Biomedical Engineering

A linear algebra approach to OLAP

Inspired by the relational algebra of data processing, this paper addresses the foundations of data analytical processing from a linear algebra perspective. The paper investigates, in particular, how aggregation operations such as cross tabulations and data cubes essential to quantitative analysis of data can be expressed solely in terms of matrix multiplication, transposition and the Khatri–Rao variant of the Kronecker product. The approach offers a basis for deriving an algebraic theory of data consolidation, handling the quantitative as well as qualitative sides of data science in a natural, elegant and typed way. It also shows potential for parallel analytical processing, as the parallelization theory of such matrix operations is well acknowledged.

Development of computational and experimental methods for biomass composition and evaluation of its impact in genome-scale models prediction

The use of genome-scale metabolic models has been rapidly increasing in fields such as metabolic engineering. An important part of a metabolic model is the biomass equation since this reaction will ultimately determine the predictive capacity of the model in terms of essentiality and flux distributions. Thus, in order to obtain a reliable metabolic model the biomass precursors and their coefficients must be as precise as possible. Ideally, determination of the biomass composition would be performed experimentally, but when no experimental data are available this is established by approximation to closely related organisms. Computational methods however, can extract some information from the genome such as amino acid and nucleotide compositions. The main objectives of this study were to compare the biomass composition of several organisms and to evaluate how biomass precursor coefficients affected the predictability of several genome-scale metabolic models by comparing predictions with experimental data in literature. For that, the biomass macromolecular composition was experimentally determined and the amino acid composition was both experimentally and computationally estimated for several organisms. Sensitivity analysis studies were also performed with the Escherichia coli iAF1260 metabolic model concerning specific growth rates and flux distributions. The results obtained suggest that the macromolecular composition is conserved among related organisms. Contrasting, experimental data for amino acid composition seem to have no similarities for related organisms. It was also observed that the impact of macromolecular composition on specific growth rates and flux distributions is larger than the impact of amino acid composition, even when data from closely related organisms are used.

Automated network resilience optimization using computational intelligence methods

This paper presents an automated optimization framework able to provide network administrators with resilient routing configurations for link-state protocols, such as OSPF or IS-IS. In order to deal with the formulated NP-hard optimization problems, the devised framework is underpinned by the use of computational intelligence optimization engines, such as Multi-objective Evolutionary Algorithms (MOEAs). With the objective of demonstrating the framework capabilities, two illustrative Traffic Engineering methods are described, allowing to attain routing configurations robust to changes in the traffic demands and maintaining the network stable even in the presence of link failure events. The presented illustrative results clearly corroborate the usefulness of the proposed automated framework along with the devised optimization methods.

New integrative computational approaches unveil the Saccharomyces cerevisiae pheno-metabolomic fermentative profile and allow strain selection for winemaking

During must fermentation by Saccharomyces cerevisiae strains thousands of volatile aroma compounds are formed. The objective of the present work was to adapt computational approaches to analyze pheno-metabolomic diversity of a S. cerevisiae strain collection with different origins. Phenotypic and genetic characterization together with individual must fermentations were performed, and metabolites relevant to aromatic profiles were determined. Experimental results were projected onto a common coordinates system, revealing 17 statistical-relevant multi-dimensional modules, combining sets of most-correlated features of noteworthy biological importance. The present method allowed, as a breakthrough, to combine genetic, phenotypic and metabolomic data, which has not been possible so far due to difficulties in comparing different types of data. Therefore, the proposed computational approach revealed as successful to shed light into the holistic characterization of S. cerevisiae pheno-metabolome in must fermentative conditions. This will allow the identification of combined relevant features with application in selection of good winemaking strains.