U-curve: A branch-and-bound optimization algorithm for U-shaped cost functions on Boolean lattices applied to the feature selection problem

This paper presents the formulation of a combinatorial optimization problem with the following characteristics: (i) the search space is the power set of a finite set structured as a Boolean lattice; (ii) the cost function forms a U-shaped curve when applied to any lattice chain. This formulation applies for feature selection in the context of pattern recognition. The known approaches for this problem are branch-and-bound algorithms and heuristics that explore partially the search space. Branch-and-bound algorithms are equivalent to the full search, while heuristics are not. This paper presents a branch-and-bound algorithm that differs from the others known by exploring the lattice structure and the U-shaped chain curves of the search space. The main contribution of this paper is the architecture of this algorithm that is based on the representation and exploration of the search space by new lattice properties proven here. Several experiments, with well known public data, indicate the superiority of the proposed method to the sequential floating forward selection (SFFS), which is a popular heuristic that gives good results in very short computational time. In all experiments, the proposed method got better or equal results in similar or even smaller computational time. (C) 2009 Elsevier Ltd. All rights reserved.

A multi-GPU algorithm for large-scale neuronal networks

Large-scale simulations of parts of the brain using detailed neuronal models to improve our understanding of brain functions are becoming a reality with the usage of supercomputers and large clusters. However, the high acquisition and maintenance cost of these computers, including the physical space, air conditioning, and electrical power, limits the number of simulations of this kind that scientists can perform. Modern commodity graphical cards, based on the CUDA platform, contain graphical processing units (GPUs) composed of hundreds of processors that can simultaneously execute thousands of threads and thus constitute a low-cost solution for many high-performance computing applications. In this work, we present a CUDA algorithm that enables the execution, on multiple GPUs, of simulations of large-scale networks composed of biologically realistic Hodgkin-Huxley neurons. The algorithm represents each neuron as a CUDA thread, which solves the set of coupled differential equations that model each neuron. Communication among neurons located in different GPUs is coordinated by the CPU. We obtained speedups of 40 for the simulation of 200k neurons that received random external input and speedups of 9 for a network with 200k neurons and 20M neuronal connections, in a single computer with two graphic boards with two GPUs each, when compared with a modern quad-core CPU. Copyright (C) 2010 John Wiley & Sons, Ltd.

An algorithm for automatic checking of exercises in a dynamic geometry system: iGeom

One of the key issues in e-learning environments is the possibility of creating and evaluating exercises. However, the lack of tools supporting the authoring and automatic checking of exercises for specifics topics (e.g., geometry) drastically reduces advantages in the use of e-learning environments on a larger scale, as usually happens in Brazil. This paper describes an algorithm, and a tool based on it, designed for the authoring and automatic checking of geometry exercises. The algorithm dynamically compares the distances between the geometric objects of the student`s solution and the template`s solution, provided by the author of the exercise. Each solution is a geometric construction which is considered a function receiving geometric objects (input) and returning other geometric objects (output). Thus, for a given problem, if we know one function (construction) that solves the problem, we can compare it to any other function to check whether they are equivalent or not. Two functions are equivalent if, and only if, they have the same output when the same input is applied. If the student`s solution is equivalent to the template`s solution, then we consider the student`s solution as a correct solution. Our software utility provides both authoring and checking tools to work directly on the Internet, together with learning management systems. These tools are implemented using the dynamic geometry software, iGeom, which has been used in a geometry course since 2004 and has a successful track record in the classroom. Empowered with these new features, iGeom simplifies teachers` tasks, solves non-trivial problems in student solutions and helps to increase student motivation by providing feedback in real time. (c) 2008 Elsevier Ltd. All rights reserved.

An all-substrings common subsequence algorithm

Given two strings A and B of lengths n(a) and n(b), n(a) <= n(b), respectively, the all-substrings longest common subsequence (ALCS) problem obtains, for every substring B` of B, the length of the longest string that is a subsequence of both A and B. The ALCS problem has many applications, such as finding approximate tandem repeats in strings, solving the circular alignment of two strings and finding the alignment of one string with several others that have a common substring. We present an algorithm to prepare the basic data structure for ALCS queries that takes O(n(a)n(b)) time and O(n(a) + n(b)) space. After this preparation, it is possible to build that allows any LCS length to be retrieved in constant time. Some trade-offs between the space required and a matrix of size O(n(b)(2)) the querying time are discussed. To our knowledge, this is the first algorithm in the literature for the ALCS problem. (C) 2007 Elsevier B.V. All rights reserved.

A semi-Markov multistate model for estimation of the mean quality-adjusted survival for non-progressive processes

We discuss the estimation of the expected value of the quality-adjusted survival, based on multistate models. We generalize an earlier work, considering the sojourn times in health states are not identically distributed, for a given vector of covariates. Approaches based on semiparametric and parametric (exponential and Weibull distributions) methodologies are considered. A simulation study is conducted to evaluate the performance of the proposed estimator and the jackknife resampling method is used to estimate the variance of such estimator. An application to a real data set is also included.

Efficient solutions to robust, semi-implicit discretizations of the immersed boundary method

The immersed boundary method is a versatile tool for the investigation of flow-structure interaction. In a large number of applications, the immersed boundaries or structures are very stiff and strong tangential forces on these interfaces induce a well-known, severe time-step restriction for explicit discretizations. This excessive stability constraint can be removed with fully implicit or suitable semi-implicit schemes but at a seemingly prohibitive computational cost. While economical alternatives have been proposed recently for some special cases, there is a practical need for a computationally efficient approach that can be applied more broadly. In this context, we revisit a robust semi-implicit discretization introduced by Peskin in the late 1970s which has received renewed attention recently. This discretization, in which the spreading and interpolation operators are lagged. leads to a linear system of equations for the inter-face configuration at the future time, when the interfacial force is linear. However, this linear system is large and dense and thus it is challenging to streamline its solution. Moreover, while the same linear system or one of similar structure could potentially be used in Newton-type iterations, nonlinear and highly stiff immersed structures pose additional challenges to iterative methods. In this work, we address these problems and propose cost-effective computational strategies for solving Peskin`s lagged-operators type of discretization. We do this by first constructing a sufficiently accurate approximation to the system`s matrix and we obtain a rigorous estimate for this approximation. This matrix is expeditiously computed by using a combination of pre-calculated values and interpolation. The availability of a matrix allows for more efficient matrix-vector products and facilitates the design of effective iterative schemes. We propose efficient iterative approaches to deal with both linear and nonlinear interfacial forces and simple or complex immersed structures with tethered or untethered points. One of these iterative approaches employs a splitting in which we first solve a linear problem for the interfacial force and then we use a nonlinear iteration to find the interface configuration corresponding to this force. We demonstrate that the proposed approach is several orders of magnitude more efficient than the standard explicit method. In addition to considering the standard elliptical drop test case, we show both the robustness and efficacy of the proposed methodology with a 2D model of a heart valve. (C) 2009 Elsevier Inc. All rights reserved.

NEW CHARACTERIZATIONS OF COMPLETE SPACELIKE SUBMANIFOLDS IN SEMI-RIEMANNIAN SPACE FORMS

In this paper we study n-dimensional complete spacelike submanifolds with constant normalized scalar curvature immersed in semi-Riemannian space forms. By extending Cheng-Yau`s technique to these ambients, we obtain results to such submanifolds satisfying certain conditions on both the squared norm of the second fundamental form and the mean curvature. We also characterize compact non-negatively curved submanifolds in De Sitter space of index p.

Spectral flow and iteration of closed semi-Riemannian geodesics

We introduce the notion of spectral flow along a periodic semi-Riemannian geodesic, as a suitable substitute of the Morse index in the Riemannian case. We study the growth of the spectral flow along a closed geodesic under iteration, determining its asymptotic behavior.

On the semi-Riemannian bumpy metric theorem

We prove the semi-Riemannian bumpy metric theorem using equivariant variational genericity. The theorem states that, on a given compact manifold M, the set of semi-Riemannian metrics that admit only nondegenerate closed geodesics is generic relatively to the C(k)-topology, k=2, ..., infinity, in the set of metrics of a given index on M. A higher-order genericity Riemannian result of Klingenberg and Takens is extended to semi-Riemannian geometry.

Maslov index in semi-Riemannian submersions

We study focal points and Maslov index of a horizontal geodesic gamma : I -> M in the total space of a semi-Riemannian submersion pi : M -> B by determining an explicit relation with the corresponding objects along the projected geodesic pi omicron gamma : I -> B in the base space. We use this result to calculate the focal Maslov index of a (spacelike) geodesic in a stationary spacetime which is orthogonal to a timelike Killing vector field.

Associated Family of G-Structure Preserving Minimal Immersions in Semi-Riemannian Manifolds

We prove the existence of an associated family of G-structure preserving minimal immersions into semi-Riemannian manifolds endowed with a compatible infinitesimally homogeneous G-structure. We will study in more details minimal embeddings into product of space forms.

COMPARISON RESULTS FOR CONJUGATE AND FOCAL POINTS IN SEMI-RIEMANNIAN GEOMETRY VIA MASLOV INDEX

We prove an estimate on the difference of Maslov indices relative to the choice of two distinct reference Lagrangians of a continuous path in the Lagrangian Grassmannian of a symplectic space. We discuss some applications to the study of conjugate and focal points along a geodesic in a semi-Riemannian manifold.

Thermal analysis and compatibility studies of prednicarbate with excipients used in semi solid pharmaceutical form

Differential Scanning Calorimetry (DSC), thermogravimetry/derivative thermogravimetry (TG/DTG) and infrared spectroscopy (IR) techniques were used to investigate the compatibility between prednicarbate and several excipients commonly used in semi solid pharmaceutical form. The thermoanalytical studies of 1:1 (m/m) drug/excipient physical mixtures showed that the beginning of the first thermal decomposition stage of the prednicarbate (T (onset) value) was decreased in the presence of stearyl alcohol and glyceryl stearate compared to the drug alone. For the binary mixture of drug/sodium pirrolidone carboxilate the first thermal decomposition stage was not changed, however the DTG peak temperature (T (peak DTG)) decreased. The comparison of the IR spectra of the drug, the physical mixtures and of the thermally treated samples confirmed the thermal decomposition of prednicarbate. By the comparison of the thermal profiles of 1:1 prednicarbate:excipients mixtures (methylparaben, propylparaben, carbomer 940, acrylate crosspolymer, lactic acid, light liquid paraffin, isopropyl palmitate, myristyl lactate and cetyl alcohol) no interaction was observed.

Pharmacogenetics of Warfarin: Development of a Dosing Algorithm for Brazilian Patients

A dosing algorithm including genetic (VKORC1 and CYP2C9 genotypes) and nongenetic factors (age, weight, therapeutic indication, and cotreatment with amiodarone or simvastatin) explained 51% of the variance in stable weekly warfarin doses in 390 patients attending an anticoagulant clinic in a Brazilian public hospital. The VKORC1 3673G>A genotype was the most important predictor of warfarin dose, with a partial R(2) value of 23.9%. Replacing the VKORC1 3673G>A genotype with VKORC1 diplotype did not increase the algorithm`s predictive power. We suggest that three other single-nucleotide polymorphisms (SNPs) (5808T>G, 6853G>C, and 9041G>A) that are in strong linkage disequilibrium (LD) with 3673G>A would be equally good predictors of the warfarin dose requirement. The algorithm`s predictive power was similar across the self-identified ""race/color"" subsets. ""Race/color"" was not associated with stable warfarin dose in the multiple regression model, although the required warfarin dose was significantly lower (P = 0.006) in white (29 +/- 13 mg/week, n = 196) than in black patients (35 +/- 15 mg/week, n = 76).