
Allende, C., Sohn, E., & Little, C. (2015). Treelink: data integration, clustering and visualization of phylogenetic trees. BMC Bioinformatics, 16, 6 pp.
Abstract: Background: Phylogenetic trees are central to a wide range of biological studies. In many of these studies, tree nodes need to be associated with a variety of attributes. For example, in studies concerned with viral relationships, tree nodes are associated with epidemiological information, such as location, age and subtype. Gene trees used in comparative genomics are usually linked with taxonomic information, such as functional annotations and events. A wide variety of tree visualization and annotation tools have been developed in the past, however none of them are intended for an integrative and comparative analysis. Results: Treelink is a platformindependent software for linking datasets and sequence files to phylogenetic trees. The application allows an automated integration of datasets to trees for operations such as classifying a tree based on a field or showing the distribution of selected data attributes in branches and leafs. Genomic and proteonomic sequences can also be linked to the tree and extracted from internal and external nodes. A novel clustering algorithm to simplify trees and display the most divergent clades was also developed, where validation can be achieved using the data integration and classification function. Integrated geographical information allows ancestral character reconstruction for phylogeographic plotting based on parsimony and likelihood algorithms. Conclusion: Our software can successfully integrate phylogenetic trees with different data sources, and perform operations to differentiate and visualize those differences within a tree. File support includes the most popular formats such as newick and csv. Exporting visualizations as images, cluster outputs and genomic sequences is supported. Treelink is available as a web and desktop application at http://www. treelinkapp. com.



Allende, H., Bravo, D., & Canessa, E. (2010). Robust design in multivariate systems using genetic algorithms. Qual. Quant., 44(2), 315–332.
Abstract: This paper presents a methodology based oil genetic algorithms, which finds feasible and reasonably adequate Solutions to problems of robust design in multivariate systems. We use a genetic algorithm to determine the appropriate control factor levels for simultaneously optimizing all of the responses of the system, considering the noise factors which affect it. The algorithm is guided by a desirability function which works with only one fitness function although the system May have many responses. We validated the methodology using data obtained from a real system and also from a process simulator, considering univariate and multivariate systems. In all cases, the methodology delivered feasible solutions, which accomplished the goals of robust design: obtain responses very close to the target values of each of them, and with minimum variability. Regarding the adjustment of the mean of each response to the target value, the algorithm performed very well. However, only in some of the multivariate cases, the algorithm was able to significantly reduce the variability of the responses.



Allende, H., Elias, C., & Torres, S. (2004). Estimation of the option prime: Microsimulation of backward stochastic differential equations. Int. Stat. Rev., 72(1), 107–121.
Abstract: A mathematical statistical model is needed to obtain an option prime and create a hedging strategy. With formulas derived from stochastic differential equations, the primes for US Dollar/Chilean Pesos currency options using a prime calculator are obtained. Furthermore, a backward simulation of the option prime trajectory is used with a numerical method created for backward stochastic differential equations. The use of statistics in finance is highly important in order to develop complex products.



Allende, H., Salas, R., & Moraga, C. (2003). A robust and effective learning algorithm for feedforward neural networks based on the influence function. Lect. Notes Comput. Sc., 2652, 28–36.
Abstract: The learning process of the Feedforward Artificial Neural Networks relies on the data, though a robustness analysis of the parameter estimates of the model must be done due to the presence of outlying observations in the data. In this paper we seek the robust properties in the parameter estimates in the sense that the influence of aberrant observations or outliers in the estimate is bounded so the neural network is able to model the bulk of data. We also seek a trade off between robustness and efficiency under a Gaussian model. An adaptive learning procedure that seeks both aspects is developed. Finally we show some simulations results applied to the RESEX time series.



AllendeCid, H., Canessa, E., Quezada, A., & Allende, H. (2011). An Improved Fuzzy RuleBased Automated Trading Agent. Stud. Inform. Control, 20(2), 135–142.
Abstract: In this paper an improved Fuzzy RuleBased Trading Agent is presented. The proposal consists in adding machinelearningbased methods to improve the overall performance of an automated agent that trades in futures markets. The modified Fuzzy RuleBased Trading Agent has to decide whether to buy or sell goods, based on the spot and futures time series, gaining a profit from the price speculation. The proposal consists first in changing the membership functions of the fuzzy inference model (Gaussian and Sigmoidal, instead of triangular and trapezoidal). Then using the NFAR (NeuroFuzzy Autoregressive) model the relevant lags of the time series are detected, and finally a fuzzy inference system (SelfOrganizing NeuroFuzzy Inference System) is implemented to aid the decision making process of the agent. Experimental results demonstrate that with the addition of these techniques, the improved agent considerably outperforms the original one.



Altimiras, F., UszczynskaRatajczak, B., Camara, F., Vlasova, A., Palumbo, E., Newhouse, S., et al. (2017). Brain Transcriptome Sequencing of a Natural Model of Alzheimer's Disease. Front. Aging Neurosci., 9, 8 pp.



AlvarezGerding, X., CortesBullemore, R., Medina, C., RomeroRomero, J. L., InostrozaBlancheteau, C., Aquea, F., et al. (2015). Improved Salinity Tolerance in Carrizo Citrange Rootstock through Overexpression of Glyoxalase System Genes. Biomed Res. Int., 827951, 7 pp.
Abstract: Citrus plants are widely cultivated around the world and, however, are one of the most salt stress sensitive crops. To improve salinity tolerance, transgenic Carrizo citrange rootstocks that overexpress glyoxalase I and glyoxalase II genes were obtained and their salt stress tolerance was evaluated. Molecular analysis showed high expression for both glyoxalase genes (BjGlyI and PgGlyII) in 5H03 and 5H04 lines. Under control conditions, transgenic and wild type plants presented normal morphology. In salinity treatments, the transgenic plants showed less yellowing, marginal burn in lower leaves and showed less than 40% of leaf damage compared with wild type plants. The transgenic plants showed a significant increase in the dry weight of shoot but there are no differences in the root and complete plant dry weight. In addition, a higher accumulation of chlorine is observed in the roots in transgenic line 5H03 but in shoot it was lower. Also, the wild type plant accumulated around 20% more chlorine in the shoot compared to roots. These results suggest that heterologous expression of glyoxalase system genes could enhance salt stress tolerance in Carrizo citrange rootstock and could be a good biotechnological approach to improve the abiotic stress tolerance in woody plant species.



AlvarezMiranda, E., & Pereira, J. (2017). Designing and constructing networks under uncertainty in the construction stage: Definition and exact algorithmic approach. Comput. Oper. Res., 81, 178–191.
Abstract: The present work proposes a novel Network Optimization problem whose core is to combine both network design and network construction scheduling under uncertainty into a single twostage robust optimization model. The firststage decisions correspond to those of a classical network design problem, while the secondstage decisions correspond to those of a network construction scheduling problem (NCS) under uncertainty. The resulting problem, which we will refer to as the TwoStage Robust Network Design and Construction Problem (2SRNDC), aims at providing a modeling framework in which the design decision not only depends on the design costs (e.g., distances) but also on the corresponding construction plan (e.g., time to provide service to costumers). We provide motivations, mixed integer programming formulations, and an exact algorithm for the 2SRNDC. Experimental results on a large set of instances show the effectiveness of the model in providing robust solutions, and the capability of the proposed algorithm to provide good solutions in reasonable running times. (C) 2017 Elsevier Ltd. All rights reserved.



AlvarezMiranda, E., & Pereira, J. (2019). On the complexity of assembly line balancing problems. Comput. Oper. Res., 108, 182–186.
Abstract: Assembly line balancing is a family of combinatorial optimization problems that has been widely studied in the literature due to its simplicity and industrial applicability. Most line balancing problems are NPhard as they subsume the bin packing problem as a special case. Nevertheless, it is common in the line balancing literature to cite [A. Gutjahr and G. Nemhauser, An algorithm for the line balancing problem, Management Science 11 (1964) 308315] in order to assess the computational complexity of the problem. Such an assessment is not correct since the work of Gutjahr and Nemhauser predates the concept of NPhardness. This work points at over 50 publications since 1995 with the aforesaid error. (C) 2019 Elsevier Ltd. All rights reserved.



Anabalon, A. (2012). Exact black holes and universality in the backreaction of nonlinear sigma models with a potential in (A)dS(4). J. High Energy Phys., (6), 18 pp.
Abstract: The aim of this paper is to construct accelerated, stationary and axisymmetric exact solutions of the Einstein theory with self interacting scalar fields in (A)dS4. To warm up, the backreaction of the (non)minimally coupled scalar field is solved, the scalar field equations are integrated and all the potentials compatible with the metric ansatz and Einstein gravity are found. With these results at hand the nonlinear sigma model is tackled. The scalar field Lagrangian is generic; neither the coupling to the curvature, neither the metric in the scalar manifold nor the potential, are fixed ab initio. The unique assumption in the analysis is the metric ansatz: it has the form of the most general Petrov type D vacuum solution of general relativity; it is a a cohomogeneity two Weyl rescaling of the Carter metric and therefore it has the typical PlebanskiDemianski form with two arbitrary functions of one variable and one arbitrary function of two variables. It is shown, by an straightforward manipulation of the field equations, that the metric is completely integrable without necessity of specifiying anything in the scalar Lagrangian. This results is that the backreaction of the scalar fields, within this class of metrics, is universal. The metric functions generically show an explicit dependence on a dynamical exponent that allows to smoothly connect this new family of solutions with the actual PlebanskiDemianski spacetime. The remaining field equations imply that the scalar fields follow geodesics in the scalar manifold with an affine parameter given by a nonlinear function of the spacetime coordinates and define the onshell form of the potential plus a functional equation that it has to satisfy. To further find the exact form of the potential the simplest case associated to a flat scalar manifold is taken. The most general potential compatible with the Einstein theory and the metric ansatz is constructed in this case and it is shown that it has less symmetry than the maximal compact subgroup of the coset construction. Finally, the most general family of (A) dS4 static hairy black holes is explicitly constructed and its properties are outlined.



Anabalon, A., & Astefanesei, D. (2013). On attractor mechanism of AdS(4) black holes. Phys. Lett. B, 727(45), 568–572.
Abstract: We construct a general family of exact nonextremal 4dimensional black holes in AdS gravity with U(1) gauge fields nonminimally coupled to a dilaton and a nontrivial dilaton potential. These black holes can have spherical, toroidal, and hyperbolic horizon topologies. We use the entropy function formalism to obtain the near horizon data in the extremal limit. Due to the nontrivial selfinteraction of the scalar field, the zero temperature black holes can have a finite horizon area even if only the electric field is turned on. (C) 2013 Elsevier B.V. All rights reserved.



Anabalon, A., & Astefanesei, D. (2014). Black holes in omegadeformed gauged N=8 supergravity. Phys. Lett. B, 732, 137–141.
Abstract: Motivated by the recently found 4dimensional omegadeformed gauged supergravity, we investigate the black hole solutions within the single scalar field consistent truncations of this theory. We construct black hole solutions that have spherical, toroidal, and hyperbolic horizon topologies. The scalar field is regular everywhere outside the curvature singularity and the stressenergy tensor satisfies the null energy condition. When the parameter CO does not vanish, there is a degeneracy in the spectrum of black hole solutions for boundary conditions that preserve the asymptotic Antide Sitter symmetries. These boundary conditions correspond to multitrace deformations in the dual field theory. (C) 2014 The Authors. Published by Elsevier B.V.



Anabalon, A., & Batista, C. (2016). A class of integrable metrics. Phys. Rev. D, 93(6), 13 pp.
Abstract: In four dimensions, the most general metric admitting two commuting Killing vectors and a ranktwo Killing tensor can be parametrized by ten arbitrary functions of a single variable. We show that picking a special vierbein, reducing the system to eight functions, implies the existence of two geodesic and sharefree, null congruences, generated by two principal null directions of the Weyl tensor. Thus, if the spacetime is an Einstein manifold, the GoldbergSachs theorem implies it is Petrov type D, and by explicit construction, is in the Carter class. Hence, our analysis provides a straightforward connection between the most general integrable structure and the Carter family of spacetimes.



Anabalon, A., & Cisterna, A. (2012). Asymptotically (anti) de Sitter black holes and wormholes with a selfinteracting scalar field in four dimensions. Phys. Rev. D, 85(8), 6 pp.
Abstract: The aim of this paper is to report on the existence of a wide variety of exact solutions, ranging from black holes to wormholes, when a conformally coupled scalar field with a selfinteracting potential containing a linear, a cubic and a quartic self interaction is taken as a source of the energymomentum tensor, in the Einstein theory with a cosmological constant. Among all the solutions there are two particularly interesting. On the one hand, the spherically symmetric black holes when the cosmological constant is positive; they are shown to be everywhere regular, namely, there is no singularity neither inside nor outside the event horizon. On the other hand, there are spherically symmetric and topological wormholes that connect two asymptotically (anti) de Sitter regions with a different value for the cosmological constant. The regular black holes and the wormholes are supported by everywhere regular scalar field configurations.



Anabalon, A., & Deruelle, N. (2013). Mechanical stability of asymptotically flat black holes with minimally coupled scalar hair. Phys. Rev. D, 88(6), 9 pp.
Abstract: We show that the asymptotically flat hairy black holes, solutions of the Einstein field equations minimally coupled to a scalar field, previously discovered by one of us, present mode instability against linear radial perturbations. It is also shown that the number of unstable modes is finite and their frequencies can be made arbitrarily small.



Anabalon, A., & Oliva, J. (2012). Exact hairy black holes and their modification to the universal law of gravitation. Phys. Rev. D, 86(10), 5 pp.
Abstract: In this paper two things are done. First, it is pointed out the existence of exact asymptotically flat, spherically symmetric black holes when a selfinteracting, minimally coupled scalar field is the source of the Einstein equations in four dimensions. The scalar field potential is recently found to be compatible with the hairy generalization of the PlebanskiDemianski solution of general relativity. This paper describes the spherically symmetric solutions that smoothly connect the Schwarzschild black hole with its hairy counterpart. The geometry and scalar field are everywhere regular except at the usual Schwarzschildlike singularity inside the black hole. The scalar field energy momentum tensor satisfies the nullenergy condition in the static region of spacetime. The first law holds when the parameters of the scalar field potential are fixed under thermodynamical variation. Second, it is shown that an extra, dimensionless parameter, present in the hairy solution, allows to modify the gravitational field of a spherically symmetric black hole in a remarkable way. When the dimensionless parameter is increased, the scalar field generates a flat gravitational potential that, however, asymptotically matches the Schwarzschild gravitational field. Finally, it is shown that a positive cosmological constant can render the scalar field potential convex if the parameters are within a specific rank.



Anabalon, A., Astefanesei, D., & Choque, D. (2015). On the thermodynamics of hairy black holes. Phys. Lett. B, 743, 154–159.
Abstract: We investigate the thermodynamics of a general class of exact 4dimensional asymptotically Antide Sitter hairy black hole solutions and show that, for a fixed temperature, there are small and large hairy black holes similar to the SchwarzschildAdS black hole. The large black holes have positive specific heat and so they can be in equilibrium with a thermal bath of radiation at the Hawking temperature. The relevant thermodynamic quantities are computed by using the Hamiltonian formalism and counterterm method. We explicitly show that there are first order phase transitions similar to the HawkingPage phase transition. (C) 2015 The Authors. Published by Elsevier B.V.



Anabalon, A., Astefanesei, D., & Choque, D. (2016). Hairy AdS solitons. Phys. Lett. B, 762, 80–85.
Abstract: We construct exact hairy AdS soliton solutions in Einsteindilaton gravity theory. We examine their thermodynamic properties and discuss the role of these solutions for the existence of first order phase transitions for hairy black holes. The negative energy density associated to hairy AdS solitons can be interpreted as the Casimir energy that is generated in the dual filed theory when the fermions are antiperiodic on the compact coordinate. (C) 2016 Published by Elsevier B.V.



Anabalon, A., Astefanesei, D., Choque, D., & Martinez, C. (2016). Trace anomaly and counterterms in designer gravity. J. High Energy Phys., (3), 29 pp.
Abstract: We construct concrete counterterms of the BalasubramanianKraus type for Einsteinscalar theories with designer gravity boundary conditions in AdS(4), so that the total action is fi nite onshell and satisfy a well de fi ned variational principle. We focus on scalar fi elds with the conformal mass m(2) = 2l(2) and show that the holographic mass matches the Hamiltonian mass for any boundary conditions. We compute the trace anomaly of the dual fi eld theory in the generic case, as well as when there exist logarithmic branches of nonlinear origin. As expected, the anomaly vanishes for the boundary conditions that are AdS invariant. When the anomaly does not vanish, the dual stress tensor describes a thermal gas with an equation of state related to the boundary conditions of the scalar fi eld. In the case of a vanishing anomaly, we recover the dual theory of a massless thermal gas. As an application of the formalism, we consider a general family of exact hairy black hole solutions that, for some particular values of the parameters in the moduli potential, contains solutions of fourdimensional gauged N = 8 supergravity and its omegadeformation. Using the AdS/CFT duality dictionary, they correspond to triple trace deformations of the dual fi eld theory.



Anabalon, A., Astefanesei, D., & Mann, R. (2013). Exact asymptotically flat charged hairy black holes with a dilaton potential. J. High Energy Phys., (10), 22 pp.
Abstract: We find broad classes of exact 4dimensional asymptotically flat black hole solutions in EinsteinMaxwell theories with a nonminimally coupled dilaton and its nontrivial potential. We consider a few interesting limits, in particular, a regular generalization of the dilatonic ReissnerNordstrom solution and, also, smooth deformations of supersymmetric black holes. Further examples are provided for more general dilaton potentials. We discuss the thermodynamical properties and show that the first law is satisfied. In the nonextremal case the entropy depends, as expected, on the asymptotic value of the dilaton. In the extremal limit, the entropy is determined purely in terms of charges and is independent of the asymptotic value of the dilaton. The attractor mechanism can be used as a criterion for the existence of the regular solutions. Since there is a 'competition' between the effective potential and dilaton potential, we also obtain regular extremal black hole solutions with just one U(1) gauge field turned on.

