A Study in function optimization with the breeder genetic algorithm

Optimization is concerned with the finding of global optima (hence the name) of problems that can be cast in the form of a function of several variables and constraints thereof. Among the searching methods, {em Evolutionary Algorithms} have been shown to be adaptable and general tools that have often outperformed traditional {em ad hoc} methods. The {em Breeder Genetic Algorithm} (BGA) combines a direct representation with a nice conceptual simplicity. This work contains a general description of the algorithm and a detailed study on a collection of function optimization tasks. The results show that the BGA is a powerful and reliable searching algorithm. The main discussion concerns the choice of genetic operators and their parameters, among which the family of Extended Intermediate Recombination (EIR) is shown to stand out. In addition, a simple method to dynamically adjust the operator is outlined and found to greatly improve on the already excellent overall performance of the algorithm.Postprint (published version

Bayesian semi non-negative matrix factorisation

Non-negative Matrix Factorisation (NMF) has become a standard method for source identification when data, sources and mixing coefficients are constrained to be positive-valued. The method has recently been extended to allow for negative-valued data and sources in the form of Semi-and Convex-NMF. In this paper, we re-elaborate Semi-NMF within a full Bayesian framework. This provides solid foundations for parameter estimation and, importantly, a principled method to address the problem of choosing the most adequate number of sources to describe the observed data. The proposed Bayesian Semi-NMF is preliminarily evaluated here in a real neuro-oncology problem.Peer ReviewedPostprint (published version

Instance and feature weighted k-nearest-neighbors algorithm

We present a novel method that aims at providing a more stable selection of feature subsets when variations in the training process occur. This is accomplished by using an instance-weighting process -assigning different importances to instances as a preprocessing step to a feature weighting method that is independent of the learner, and then making good use of both sets of computed weigths in a standard Nearest-Neighbours classifier. We report extensive experimentation in well-known benchmarking datasets as well as some challenging microarray gene expression problems. Our results show increases in stability for most subset sizes and most problems, without compromising prediction accuracy.Peer ReviewedPostprint (published version

Heterogeneous Kohonen networks

A large number of practical problems involves elements that are described as a mixture of qualitative and quantitative infomation, and whose description is probably incomplete. The self-organizing map is an effective tool for visualization of high-dimensional continuous data. In this work, we extend the network and training algorithm to cope with heterogeneous information, as well as missing values. The classification performance on a collection of benchmarking data sets is compared in different configurations. Various visualization methods are suggested to aid users interpret post-training results.Peer ReviewedPostprint (author's final draft

Feature selection algorithms: a survey and experimental evaluation

In view of the substantial number of existing feature selection algorithms, the need arises to count on criteria that enables to adequately decide which algorithm to use in certain situations. This work reviews several fundamental algorithms found in the literature and assesses their performance in a controlled scenario. A scoring measure ranks the algorithms by taking into account the amount of relevance, irrelevance and redundance on sample data sets. This measure computes the degree of matching between the output given by the algorithm and the known optimal solution. Sample size effects are also studied.Postprint (published version

Linguloidean brachiopods from the Lower Ordovician (Tremadocian) of northwestern Argentina

The new obolid Torobolus subplanus gen. et sp. nov., from the lower Temadocian Devendeus Formation, the new species Libecoviella tilcarensis and Leptembolon argentinum, and Ectenoglossa sp. from upper Tremadocian beds of the Santa Rosita Formation are described and ilustrated. Libecoviella is typical of the upper Tremadocian and Floian strata of the Prague basin (Trenice and Klabava formations, respectively) and it has been reported recently from Australia. Leptembolon has been recorded in the same Bohemian formations, but together with other taxa it forms the Thysanotos-Leptembolon Association present in northern Estonia and a series of high-latitude terranes. The record of Leptembolon and Libecoviella in the high- to temperate-latitude Central Andean region attests for a peri-Gondwanan distribution of these genera. The presence of Bohemian-like obolids in northwestern Argentina suggests a migratory route linking the Central Andean basin with north Gondwana and Perunica along the clastic platforms fringing the North African and Brazilian shieldsFil: Benedetto, Juan Luis Arnaldo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Centro de Investigaciones en Ciencias de la Tierra. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Centro de Investigaciones en Ciencias de la Tierra; ArgentinaFil: Muñoz, Diego Fernando. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Centro de Investigaciones en Ciencias de la Tierra. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Centro de Investigaciones en Ciencias de la Tierra; Argentin

Exploiting the accumulated evidence for gene selection in microarray gene expression data

Machine Learning methods have of late made signicant efforts to solving multidisciplinary problems in the field of cancer classification using microarray gene expression data. Feature subset selection methods can play an important role in the modeling process, since these tasks are characterized by a large number of features and a few observations, making the modeling a non-trivial undertaking. In this particular scenario, it is extremely important to select genes by taking into account the possible interactions with other gene subsets. This paper shows that, by accumulating the evidence in favour (or against) each gene along the search process, the obtained gene subsets may constitute better solutions, either in terms of predictive accuracy or gene size, or in both. The proposed technique is extremely simple and applicable at a negligible overhead in cost.Postprint (published version

The eoorthid brachiopod Apheoorthina in the Lower Ordovician of NW Argentina and the dispersal pathways along western Gondwana

The eoorthid brachiopod Apheoorthina is reported for the first time from the Lower Ordovician of NW Argentina. It is represented by a species similar to A. ferrigena from the Tremadocian of the Prague Basin, increasing the faunal affinities between the Central Andean Basin and the South European microcontinents, in particular the Bohemian region (Perunica). Nine out of the fourteen brachiopod genera reported from the Tremadocian of the Central Andean Basin (~64 %) are shared with the Mediterranean region, four of which (~ 28 %) have been recorded in the Prague Basin, and two (Kvania and Apheoorthina) are restricted to the Central Andes and Perunica. Dispersal pathways around Gondwana are analyzed in the light of major factors affecting large-scale distribution of brachiopods (environment, larval capacity for dispersal, oceanic currents).The presence in Apheoorthina aff. ferrigena of a well-preserved larval protegulum measuring 420 μm in width and 210 μm in length strongly suggests that this species had planktotrophic larvae capable of long-distance dispersal. According to recent oceanatmosphere general circulation models for the Ordovician Period, the Central Andean margin was dominated by the cold-water Antarctica Current. Despite the complex nonzonal pattern produced by current deflections around the peri-Gondwanan microcontinents, the general westward circulation sense favoured larval dispersal from the Andean region to North Africa, Avalonia, the Armorican Terrane Assemblage, and Perunica. On the other hand, the eastwards flowing Gondwana Current connected the North Gondwana waters with the South American epicontinental seas, which could explain the reversed migration of some brachiopods.Fil: Muñoz, Diego Fernando. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Centro de Investigaciones en Ciencias de la Tierra. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Centro de Investigaciones en Ciencias de la Tierra; ArgentinaFil: Benedetto, Juan Luis Arnaldo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Centro de Investigaciones en Ciencias de la Tierra. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Centro de Investigaciones en Ciencias de la Tierra; Argentin