'A Bayesian Optimisation Algorithm for the Nurse Scheduling Problem'

Abstract- A Bayesian optimization algorithm for the nurse scheduling problem is presented, which involves choosing a suitable scheduling rule from a set for each nurse's assignment. Unlike our previous work that used GAs to implement implicit learning, the learning in the proposed algorithm is explicit, i.e. eventually, we will be able to identify and mix building blocks directly. The Bayesian optimization algorithm is applied to implement such explicit learning by building a Bayesian network of the joint distribution of solutions. The conditional probability of each variable in the network is computed according to an initial set of promising solutions. Subsequently, each new instance for each variable is generated by using the corresponding conditional probabilities, until all variables have been generated, i.e. in our case, a new rule string has been obtained. Another set of rule strings will be generated in this way, some of which will replace previous strings based on fitness selection. If stopping conditions are not met, the conditional probabilities for all nodes in the Bayesian network are updated again using the current set of promising rule strings. Computational results from 52 real data instances demonstrate the success of this approach. It is also suggested that the learning mechanism in the proposed approach might be suitable for other scheduling problems.

Packings and coverings of the complete graph with trees

In this thesis, we define the spectrum problem for packings (coverings) of G to be the problem of finding all graphs H such that a maximum G-packing (minimum G- covering) of the complete graph with the leave (excess) graph H exists. The set of achievable leave (excess) graphs in G-packings (G-coverings) of the complete graph is called the spectrum of leave (excess) graphs for G. Then, we consider this problem for trees with up to five edges. We will prove that for any tree T with up to five edges, if the leave graph in a maximum T-packing of the complete graph Kn has i edges, then the spectrum of leave graphs for T is the set of all simple graphs with i edges. In fact, for these T and i and H any simple graph with i edges, we will construct a maximum T-packing of Kn with the leave graph H. We will also show that for any tree T with k ≤ 5 edges, if the excess graph in a minimum T-covering of the complete graph Kn has i edges, then the spectrum of excess graphs for T is the set of all simple graphs and multigraphs with i edges, except for the case that T is a 5-star, for which the graph formed by four multiple edges is not achievable when n = 12.

Bumps and rings in a two-dimensional neural field: splitting and rotational instabilities

In this paper we consider instabilities of localised solutions in planar neural field firing rate models of Wilson-Cowan or Amari type. Importantly we show that angular perturbations can destabilise spatially localised solutions. For a scalar model with Heaviside firing rate function we calculate symmetric one-bump and ring solutions explicitly and use an Evans function approach to predict the point of instability and the shapes of the dominant growing modes. Our predictions are shown to be in excellent agreement with direct numerical simulations. Moreover, beyond the instability our simulations demonstrate the emergence of multi-bump and labyrinthine patterns. With the addition of spike-frequency adaptation, numerical simulations of the resulting vector model show that it is possible for structures without rotational symmetry, and in particular multi-bumps, to undergo an instability to a rotating wave. We use a general argument, valid for smooth firing rate functions, to establish the conditions necessary to generate such a rotational instability. Numerical continuation of the rotating wave is used to quantify the emergent angular velocity as a bifurcation parameter is varied. Wave stability is found via the numerical evaluation of an associated eigenvalue problem.

A Hybrid Genetic Algorithm to Solve a Logt-Sizing and Scheduling Problem

Abstract: This paper reports a lot-sizing and scheduling problem, which minimizes inventory and backlog costs on m parallel machines with sequence-dependent set-up times over t periods. Problem solutions are represented as product subsets ordered and/or unordered for each machine m at each period t. The optimal lot sizes are determined applying a linear program. A genetic algorithm searches either over ordered or over unordered subsets (which are implicitly ordered using a fast ATSP-type heuristic) to identify an overall optimal solution. Initial computational results are presented, comparing the speed and solution quality of the ordered and unordered genetic algorithm approaches.

'A Bayesian Optimisation Algorithm for the Nurse Scheduling Problem'

Abstract- A Bayesian optimization algorithm for the nurse scheduling problem is presented, which involves choosing a suitable scheduling rule from a set for each nurse's assignment. Unlike our previous work that used GAs to implement implicit learning, the learning in the proposed algorithm is explicit, i.e. eventually, we will be able to identify and mix building blocks directly. The Bayesian optimization algorithm is applied to implement such explicit learning by building a Bayesian network of the joint distribution of solutions. The conditional probability of each variable in the network is computed according to an initial set of promising solutions. Subsequently, each new instance for each variable is generated by using the corresponding conditional probabilities, until all variables have been generated, i.e. in our case, a new rule string has been obtained. Another set of rule strings will be generated in this way, some of which will replace previous strings based on fitness selection. If stopping conditions are not met, the conditional probabilities for all nodes in the Bayesian network are updated again using the current set of promising rule strings. Computational results from 52 real data instances demonstrate the success of this approach. It is also suggested that the learning mechanism in the proposed approach might be suitable for other scheduling problems.

Problem-Based SRS: método para especificação de requisitos de software baseado em problemas

Requirements specification has long been recognized as critical activity in software development processes because of its impact on project risks when poorly performed. A large amount of studies addresses theoretical aspects, propositions of techniques, and recommended practices for Requirements Engineering (RE). To be successful, RE have to ensure that the specified requirements are complete and correct what means that all intents of the stakeholders in a given business context are covered by the requirements and that no unnecessary requirement was introduced. However, the accurate capture the business intents of the stakeholders remains a challenge and it is a major factor of software project failures. This master’s dissertation presents a novel method referred to as “Problem-Based SRS” aiming at improving the quality of the Software Requirements Specification (SRS) in the sense that the stated requirements provide suitable answers to real customer ́s businesses issues. In this approach, the knowledge about the software requirements is constructed from the knowledge about the customer ́s problems. Problem-Based SRS consists in an organization of activities and outcome objects through a process that contains five main steps. It aims at supporting the software requirements engineering team to systematically analyze the business context and specify the software requirements, taking also into account a first glance and vision of the software. The quality aspects of the specifications are evaluated using traceability techniques and axiomatic design principles. The cases studies conducted and presented in this document point out that the proposed method can contribute significantly to improve the software requirements specification.

Optimization of the Ion Source-Mass Spectrometry Parameters in Non-Steroidal Anti-Inflammatory and Analgesic Pharmaceuticals Analysis by a Design of Experiments Approach

The flow rates of drying and nebulizing gas, heat block and desolvation line temperatures and interface voltage are potential electrospray ionization parameters as they may enhance sensitivity of the mass spectrometer. The conditions that give higher sensitivity of 13 pharmaceuticals were explored. First, Plackett-Burman design was implemented to screen significant factors, and it was concluded that interface voltage and nebulizing gas flow were the only factors that influence the intensity signal for all pharmaceuticals. This fractionated factorial design was projected to set a full 2(2) factorial design with center points. The lack-of-fit test proved to be significant. Then, a central composite face-centered design was conducted. Finally, a stepwise multiple linear regression and subsequently an optimization problem solving were carried out. Two main drug clusters were found concerning the signal intensities of all runs of the augmented factorial design. p-Aminophenol, salicylic acid, and nimesulide constitute one cluster as a result of showing much higher sensitivity than the remaining drugs. The other cluster is more homogeneous with some sub-clusters comprising one pharmaceutical and its respective metabolite. It was observed that instrumental signal increased when both significant factors increased with maximum signal occurring when both codified factors are set at level +1. It was also found that, for most of the pharmaceuticals, interface voltage influences the intensity of the instrument more than the nebulizing gas flowrate. The only exceptions refer to nimesulide where the relative importance of the factors is reversed and still salicylic acid where both factors equally influence the instrumental signal. Graphical Abstract ᅟ.

Comparison of five popular normalization methods using a spike-in proteomics data set

Mass spectrometry (MS)-based proteomics has seen significant technical advances during the past two decades and mass spectrometry has become a central tool in many biosciences. Despite the popularity of MS-based methods, the handling of the systematic non-biological variation in the data remains a common problem. This biasing variation can result from several sources ranging from sample handling to differences caused by the instrumentation. Normalization is the procedure which aims to account for this biasing variation and make samples comparable. Many normalization methods commonly used in proteomics have been adapted from the DNA-microarray world. Studies comparing normalization methods with proteomics data sets using some variability measures exist. However, a more thorough comparison looking at the quantitative and qualitative differences of the performance of the different normalization methods and at their ability in preserving the true differential expression signal of proteins, is lacking. In this thesis, several popular and widely used normalization methods (the Linear regression normalization, Local regression normalization, Variance stabilizing normalization, Quantile-normalization, Median central tendency normalization and also variants of some of the forementioned methods), representing different strategies in normalization are being compared and evaluated with a benchmark spike-in proteomics data set. The normalization methods are evaluated in several ways. The performance of the normalization methods is evaluated qualitatively and quantitatively on a global scale and in pairwise comparisons of sample groups. In addition, it is investigated, whether performing the normalization globally on the whole data or pairwise for the comparison pairs examined, affects the performance of the normalization method in normalizing the data and preserving the true differential expression signal. In this thesis, both major and minor differences in the performance of the different normalization methods were found. Also, the way in which the normalization was performed (global normalization of the whole data or pairwise normalization of the comparison pair) affected the performance of some of the methods in pairwise comparisons. Differences among variants of the same methods were also observed.

Phylogenetic inference's algorithms

Phylogenetic inference consist in the search of an evolutionary tree to explain the best way possible genealogical relationships of a set of species. Phylogenetic analysis has a large number of applications in areas such as biology, ecology, paleontology, etc. There are several criterias which has been defined in order to infer phylogenies, among which are the maximum parsimony and maximum likelihood. The first one tries to find the phylogenetic tree that minimizes the number of evolutionary steps needed to describe the evolutionary history among species, while the second tries to find the tree that has the highest probability of produce the observed data according to an evolutionary model. The search of a phylogenetic tree can be formulated as a multi-objective optimization problem, which aims to find trees which satisfy simultaneously (and as much as possible) both criteria of parsimony and likelihood. Due to the fact that these criteria are different there won't be a single optimal solution (a single tree), but a set of compromise solutions. The solutions of this set are called "Pareto Optimal". To find this solutions, evolutionary algorithms are being used with success nowadays.This algorithms are a family of techniques, which aren’t exact, inspired by the process of natural selection. They usually find great quality solutions in order to resolve convoluted optimization problems. The way this algorithms works is based on the handling of a set of trial solutions (trees in the phylogeny case) using operators, some of them exchanges information between solutions, simulating DNA crossing, and others apply aleatory modifications, simulating a mutation. The result of this algorithms is an approximation to the set of the “Pareto Optimal” which can be shown in a graph with in order that the expert in the problem (the biologist when we talk about inference) can choose the solution of the commitment which produces the higher interest. In the case of optimization multi-objective applied to phylogenetic inference, there is open source software tool, called MO-Phylogenetics, which is designed for the purpose of resolving inference problems with classic evolutionary algorithms and last generation algorithms. REFERENCES [1] C.A. Coello Coello, G.B. Lamont, D.A. van Veldhuizen. Evolutionary algorithms for solving multi-objective problems. Spring. Agosto 2007 [2] C. Zambrano-Vega, A.J. Nebro, J.F Aldana-Montes. MO-Phylogenetics: a phylogenetic inference software tool with multi-objective evolutionary metaheuristics. Methods in Ecology and Evolution. En prensa. Febrero 2016.

Tabu search for the cyclic bandwidth problem

International audience

Iterated responsive threshold search for the quadratic multiple knapsack problem

International audience

Path relinking for the fixed spectrum frequency assignment problem

International audience

A Bayesian optimization algorithm for the nurse scheduling problem

A Bayesian optimization algorithm for the nurse scheduling problem is presented, which involves choosing a suitable scheduling rule from a set for each nurse’s assignment. Unlike our previous work that used GAs to implement implicit learning, the learning in the proposed algorithm is explicit, i.e. eventually, we will be able to identify and mix building blocks directly. The Bayesian optimization algorithm is applied to implement such explicit learning by building a Bayesian network of the joint distribution of solutions. The conditional probability of each variable in the network is computed according to an initial set of promising solutions. Subsequently, each new instance for each variable is generated by using the corresponding conditional probabilities, until all variables have been generated, i.e. in our case, a new rule string has been obtained. Another set of rule strings will be generated in this way, some of which will replace previous strings based on fitness selection. If stopping conditions are not met, the conditional probabilities for all nodes in the Bayesian network are updated again using the current set of promising rule strings. Computational results from 52 real data instances demonstrate the success of this approach. It is also suggested that the learning mechanism in the proposed approach might be suitable for other scheduling problems.

Bioaccumulation and effects of TBT on molluscs from southern Portugal

Tese de dout. Ciências e Tecnologias do Ambiente, Faculdade de Ciências do Mar e do Ambiente, Univ. do Algarve, 2004

Design Optimization of Nozzle Shapes for Maximum Uniformity of Exit Flow

The objective of this study is to identify the optimal designs of converging-diverging supersonic and hypersonic nozzles that perform at maximum uniformity of thermodynamic and flow-field properties with respect to their average values at the nozzle exit. Since this is a multi-objective design optimization problem, the design variables used are parameters defining the shape of the nozzle. This work presents how variation of such parameters can influence the nozzle exit flow non-uniformities. A Computational Fluid Dynamics (CFD) software package, ANSYS FLUENT, was used to simulate the compressible, viscous gas flow-field in forty nozzle shapes, including the heat transfer analysis. The results of two turbulence models, k-e and k-ω, were computed and compared. With the analysis results obtained, the Response Surface Methodology (RSM) was applied for the purpose of performing a multi-objective optimization. The optimization was performed with ModeFrontier software package using Kriging and Radial Basis Functions (RBF) response surfaces. Final Pareto optimal nozzle shapes were then analyzed with ANSYS FLUENT to confirm the accuracy of the optimization process.