MPI parallel programming of mixed integer optimization problems using CPLEX with COIN-OR

The aim of this technical report is to present some detailed explanations in order to help to understand and use the Message Passing Interface (MPI) parallel programming for solving several mixed integer optimization problems. We have developed a C++ experimental code that uses the IBM ILOG CPLEX optimizer within the COmputational INfrastructure for Operations Research (COIN-OR) and MPI parallel computing for solving the optimization models under UNIX-like systems. The computational experience illustrates how can we solve 44 optimization problems which are asymmetric with respect to the number of integer and continuous variables and the number of constraints. We also report a comparative with the speedup and efficiency of several strategies implemented for some available number of threads.

A Passage to India: from novel to film. Some problems of "translation"

Eguíluz, Federico; Merino, Raquel; Olsen, Vickie; Pajares, Eterio; Santamaría, José Miguel (eds.)

Factors associated with chronic pain in patients with bipolar depression: a cross-sectional study

Background: While pain is frequently associated with unipolar depression, few studies have investigated the link between pain and bipolar depression. In the present study we estimated the prevalence and characteristics of pain among patients with bipolar depression treated by psychiatrists in their regular clinical practice. The study was designed to identify factors associated with the manifestation of pain in these patients.- Methods:Patients diagnosed with bipolar disorder (n=121) were selected to participate in a cross-sectional study in which DSM-IV-TR criteria were employed to identify depressive episodes. The patients were asked to describe any pain experienced during the study, and in the 6 weeks beforehand, by means of a Visual Analogical Scale (VAS).- Results: Over half of the bipolar depressed patients (51.2%, 95% CI: 41.9%–60.6%), and 2/3 of the female experienced concomitant pain. The pain was of moderate to severe intensity and prolonged duration, and it occurred at multiple sites, significantly limiting the patient’s everyday activities. The most important factors associated with the presence of pain were older age, sleep disorders and delayed diagnosis of bipolar disorder.- Conclusions: Chronic pain is common in bipolar depressed patients, and it is related to sleep disorders and delayed diagnosis of their disorder. More attention should be paid to study the presence of pain in bipolar depressed patients, in order to achieve more accurate diagnoses and to provide better treatment options.

Role of G protein coupled inwardly rectifier K+ channels (GIRK) on the neurobiology depression

353 págs.

Adaptive Scalable SVD Unit for Fast Processing of Large LSE Problems

Singular Value Decomposition (SVD) is a key linear algebraic operation in many scientific and engineering applications. In particular, many computational intelligence systems rely on machine learning methods involving high dimensionality datasets that have to be fast processed for real-time adaptability. In this paper we describe a practical FPGA (Field Programmable Gate Array) implementation of a SVD processor for accelerating the solution of large LSE problems. The design approach has been comprehensive, from the algorithmic refinement to the numerical analysis to the customization for an efficient hardware realization. The processing scheme rests on an adaptive vector rotation evaluator for error regularization that enhances convergence speed with no penalty on the solution accuracy. The proposed architecture, which follows a data transfer scheme, is scalable and based on the interconnection of simple rotations units, which allows for a trade-off between occupied area and processing acceleration in the final implementation. This permits the SVD processor to be implemented both on low-cost and highend FPGAs, according to the final application requirements.

Problems when generating virtual models representing real objects: Hondarribia walls

[EN] This paper is based in the following project:

A common axiom for classical division rules for claims problems

In this paper we introduce a new axiom, denoted claims separability, that is satisfied by several classical division rules defined for claims problems. We characterize axiomatically the entire family of division rules that satisfy this new axiom. In addition, employing claims separability, we characterize the minimal overlap rule, given by O'Neill (1982), Piniles rule and the rules in the TAL-family, introduced by Moreno-Ternero and Villar (2006), which includes the uniform gains rule, the uniform losses rule and the Talmud rule.

miRNA polymorphisms are associated with risk of developing chronic lymphocytic leukemia

Chronic Lymphocytic Leukemia (CLL) is the most frequent leukemia of adults in Western countries and shows a ~8.5-fold increased relative risk in first-degree relatives. Up to date several studies have identified low-penetrance susceptibility alleles in CLL. Nevertheless, these studies scarcely study regions that do not encode proteins such as microRNAs (miRNAs). Abnormalities in miRNAs, as altered expression patterns and mutations, have been described in CLL, suggesting their implication in the development of the disease. Polymorphisms in these miRNAs may deregulate miRNAs expression levels and affect to the miRNA function. However, despite accumulating evidence that inherited genetic variation in miRNA genes can contribute to the predisposition for CLL, the role of these in the risk of CLL has not been extensively studied. Therefore, the aim of this study was to find new genetic markers of risk to CLL. To that end, we made a systematic search for SNPs in miRNAs and miRNAs deregulated in CLL and genotyped 213 polymorphisms in 401 samples of Spanish individuals. The literature search resulted in more than 100 miRNAs deregulated in CLL and 43 polymorphisms studied in the disease. Out of 213 genotyped SNPs, 13 showed to be significantly associated with CLL risk. rs2682818 in pre-mature miR618 was the most significant result, with 0.49 fold decreased risk to CLL. Interestingly, a previous study associated this SNP with an increased risk of developing follicular lymphoma. Secondly, rs10173558 SNP in mir- 1302-4 showed the highest risk association, with a 5.24 fold increased risk, but there were no previous works studying it. Finally, rs61992671 in miR412, previously associated with CLL risk, showed also association in our sample. In conclusion, we find 13 alleles which could contribute to the risk of CLL. However, new large-scale studies including functional analyses will be needed to validate our findings.

On the optimal usage of labelled examples in semi-supervised multi-class classification problems

In recent years, the performance of semi-supervised learning has been theoretically investigated. However, most of this theoretical development has focussed on binary classification problems. In this paper, we take it a step further by extending the work of Castelli and Cover [1] [2] to the multi-class paradigm. Particularly, we consider the key problem in semi-supervised learning of classifying an unseen instance x into one of K different classes, using a training dataset sampled from a mixture density distribution and composed of l labelled records and u unlabelled examples. Even under the assumption of identifiability of the mixture and having infinite unlabelled examples, labelled records are needed to determine the K decision regions. Therefore, in this paper, we first investigate the minimum number of labelled examples needed to accomplish that task. Then, we propose an optimal multi-class learning algorithm which is a generalisation of the optimal procedure proposed in the literature for binary problems. Finally, we make use of this generalisation to study the probability of error when the binary class constraint is relaxed.

A potential approach to claims problems

Hart and Mas Colell (1989) introduce the potential function for cooperative TU games. In this paper, we extend this approach to claims problems, also known as bankruptcy or rationing problems. We show that for appropriate subproblems, the random arrival rule, the rules in the TAL-family (which include the uniform gains rule, the uniform losses rule and the Talmud rule), the minimal overlap rule, and the proportional rule admit a potential. We also study the balanced contributions property for these rules. By means of a potential, we introduce a generalization of the random arrival rule and mixtures of the minimal overlap rule and the uniform losses rule.

Instances of combinatorial optimization problems: complexity and generation

138 p.

Helmholtz Fermi surface harmonics: an efficient approach for treating anisotropic problems involving Fermi surface integrals

We present a new efficient numerical approach for representing anisotropic physical quantities and/or matrix elements defined on the Fermi surface (FS) of metallic materials. The method introduces a set of numerically calculated generalized orthonormal functions which are the solutions of the Helmholtz equation defined on the FS. Noteworthy, many properties of our proposed basis set are also shared by the FS harmonics introduced by Philip B Allen (1976 Phys. Rev. B 13 1416), proposed to be constructed as polynomials of the cartesian components of the electronic velocity. The main motivation of both approaches is identical, to handle anisotropic problems efficiently. However, in our approach the basis set is defined as the eigenfunctions of a differential operator and several desirable properties are introduced by construction. The method is demonstrated to be very robust in handling problems with any crystal structure or topology of the FS, and the periodicity of the reciprocal space is treated as a boundary condition for our Helmholtz equation. We illustrate the method by analysing the free-electron-like lithium (Li), sodium (Na), copper (Cu), lead (Pb), tungsten (W) and magnesium diboride (MgB2)

Evaluación de la posible capacidad genotóxica de fármacos antihipertensivos: losartán e irbesartán

[es] La hipertensión arterial (AHT), estado patológico definido como la elevación persistente de la presión arterial, es considerada uno de los principales problemas de salud pública. El tratamiento de la patología se realiza preferentemente con fármacos antihipertensivos. Los pacientes se encuentran sometidos a una exposición larga e ininterrumpida a estos fármacos. Los fármacos antihipertensivos se clasifican en función del mecanismo de acción por el que logran su efecto. Una de las clases son los antagonistas de los receptores de angiotensina II (ARB). Los ARB son la última clase terapéutica incluida en la terapia antihipertensiva. En este Trabajo Fin de Grado, se ha evaluado la posible capacidad genotóxica in vitro, de dos tipos de fármacos ARB (losartán e irbesartán) mediante el empleo de uno de los métodos citogenéticos más utilizados, el ensayo de micronúcleos (MN). El índice de división nuclear (NDI) fue usado también como medida de genotoxicidad. El análisis se ha realizado en linfocitos de sangre periférica (PBL) de 10 individuos control mediante dos tipos de cultivo uno sin fármaco y otro añadiendo los fármacos a los cultivos en una concentración igual a la que se encuentra en el plasma de pacientes. Los resultados muestran un aumento estadísticamente significativo de la frecuencia de células binucleadas con micronúcleos (BNMN) pero no se observan diferencias estadísticamente significativas en el índice de división nuclear. Estos resultados sugieren un posible efecto genotóxico de los fármacos pero sería necesario llevar a cabo estudios en una población más amplia e in vivo con los mismos fármacos para confirmarlo.

Genetic Variants in MiRNA Processing Genes and Pre-MiRNAs Are Associated with the Risk of Chronic Lymphocytic Leukemia

Genome wide association studies (GWAS) have identified several low-penetrance susceptibility alleles in chronic lymphocytic leukemia (CLL). Nevertheless, these studies scarcely study regions that are implicated in non-coding molecules such as microRNAs (miRNAs). Abnormalities in miRNAs, as altered expression patterns and mutations, have been described in CLL, suggesting their implication in the development of the disease. Genetic variations in miRNAs can affect levels of miRNA expression if present in pre-miRNAs and in miRNA biogenesis genes or alter miRNA function if present in both target mRNA and miRNA sequences. Therefore, the present study aimed to evaluate whether polymorphisms in pre-miRNAs, and/or miRNA processing genes contribute to predisposition for CLL. A total of 91 SNPs in 107 CLL patients and 350 cancer-free controls were successfully analyzed using TaqMan Open Array technology. We found nine statistically significant associations with CLL risk after FDR correction, seven in miRNA processing genes (rs3805500 and rs6877842 in DROSHA, rs1057035 in DICER1, rs17676986 in SND1, rs9611280 in TNRC6B, rs784567 in TRBP and rs11866002 in CNOT1) and two in pre-miRNAs (rs11614913 in miR196a2 and rs2114358 in miR1206). These findings suggest that polymorphisms in genes involved in miRNAs biogenesis pathway as well as in pre-miRNAs contribute to the risk of CLL. Large-scale studies are needed to validate the current findings.