Automatic design of decision-tree induction algorithms tailored to flexible-receptor docking data

Background: This paper addresses the prediction of the free energy of binding of a drug candidate with enzyme InhA associated with Mycobacterium tuberculosis. This problem is found within rational drug design, where interactions between drug candidates and target proteins are verified through molecular docking simulations. In this application, it is important not only to correctly predict the free energy of binding, but also to provide a comprehensible model that could be validated by a domain specialist. Decision-tree induction algorithms have been successfully used in drug-design related applications, specially considering that decision trees are simple to understand, interpret, and validate. There are several decision-tree induction algorithms available for general-use, but each one has a bias that makes it more suitable for a particular data distribution. In this article, we propose and investigate the automatic design of decision-tree induction algorithms tailored to particular drug-enzyme binding data sets. We investigate the performance of our new method for evaluating binding conformations of different drug candidates to InhA, and we analyze our findings with respect to decision tree accuracy, comprehensibility, and biological relevance. Results: The empirical analysis indicates that our method is capable of automatically generating decision-tree induction algorithms that significantly outperform the traditional C4.5 algorithm with respect to both accuracy and comprehensibility. In addition, we provide the biological interpretation of the rules generated by our approach, reinforcing the importance of comprehensible predictive models in this particular bioinformatics application. Conclusions: We conclude that automatically designing a decision-tree algorithm tailored to molecular docking data is a promising alternative for the prediction of the free energy from the binding of a drug candidate with a flexible-receptor.

Cash balance management: A comparison between genetic algorithms and particle swarm optimization

This work aimed to apply genetic algorithms (GA) and particle swarm optimization (PSO) in cash balance management using Miller-Orr model, which consists in a stochastic model that does not define a single ideal point for cash balance, but an oscillation range between a lower bound, an ideal balance and an upper bound. Thus, this paper proposes the application of GA and PSO to minimize the Total Cost of cash maintenance, obtaining the parameter of the lower bound of the Miller-Orr model, using for this the assumptions presented in literature. Computational experiments were applied in the development and validation of the models. The results indicated that both the GA and PSO are applicable in determining the cash level from the lower limit, with best results of PSO model, which had not yet been applied in this type of problem.

A multi-objective adaptive immune algorithm for multi-application NoC mapping

Current SoC design trends are characterized by the integration of larger amount of IPs targeting a wide range of application fields. Such multi-application systems are constrained by a set of requirements. In such scenario network-on-chips (NoC) are becoming more important as the on-chip communication structure. Designing an optimal NoC for satisfying the requirements of each individual application requires the specification of a large set of configuration parameters leading to a wide solution space. It has been shown that IP mapping is one of the most critical parameters in NoC design, strongly influencing the SoC performance. IP mapping has been solved for single application systems using single and multi-objective optimization algorithms. In this paper we propose the use of a multi-objective adaptive immune algorithm (M(2)AIA), an evolutionary approach to solve the multi-application NoC mapping problem. Latency and power consumption were adopted as the target multi-objective functions. To compare the efficiency of our approach, our results are compared with those of the genetic and branch and bound multi-objective mapping algorithms. We tested 11 well-known benchmarks, including random and real applications, and combines up to 8 applications at the same SoC. The experimental results showed that the M(2)AIA decreases in average the power consumption and the latency 27.3 and 42.1 % compared to the branch and bound approach and 29.3 and 36.1 % over the genetic approach.

On the impact of disproportional samples in credit scoring models: An application to a Brazilian bank data

Statistical methods have been widely employed to assess the capabilities of credit scoring classification models in order to reduce the risk of wrong decisions when granting credit facilities to clients. The predictive quality of a classification model can be evaluated based on measures such as sensitivity, specificity, predictive values, accuracy, correlation coefficients and information theoretical measures, such as relative entropy and mutual information. In this paper we analyze the performance of a naive logistic regression model (Hosmer & Lemeshow, 1989) and a logistic regression with state-dependent sample selection model (Cramer, 2004) applied to simulated data. Also, as a case study, the methodology is illustrated on a data set extracted from a Brazilian bank portfolio. Our simulation results so far revealed that there is no statistically significant difference in terms of predictive capacity between the naive logistic regression models and the logistic regression with state-dependent sample selection models. However, there is strong difference between the distributions of the estimated default probabilities from these two statistical modeling techniques, with the naive logistic regression models always underestimating such probabilities, particularly in the presence of balanced samples. (C) 2012 Elsevier Ltd. All rights reserved.

A contribution for developing more efficient dynamic modelling algorithms of parallel robots

Parallel kinematic structures are considered very adequate architectures for positioning and orienti ng the tools of robotic mechanisms. However, developing dynamic models for this kind of systems is sometimes a difficult task. In fact, the direct application of traditional methods of robotics, for modelling and analysing such systems, usually does not lead to efficient and systematic algorithms. This work addre sses this issue: to present a modular approach to generate the dynamic model and through some convenient modifications, how we can make these methods more applicable to parallel structures as well. Kane’s formulati on to obtain the dynamic equations is shown to be one of the easiest ways to deal with redundant coordinates and kinematic constraints, so that a suitable c hoice of a set of coordinates allows the remaining of the modelling procedure to be computer aided. The advantages of this approach are discussed in the modelling of a 3-dof parallel asymmetric mechanisms.

New Improved Version of J 1 ...J 4 Interferometry Method and its Application to Nanometric Vibration Measurements

Piezoelectric ceramics, such as PZT, can generate subnanometric displacements, bu t in order to generate multi- micrometric displacements, they should be either driven by high electric voltages (hundreds of volts ), or operate at a mechanical resonant frequency (in narrow band), or have large dimensions (tens of centimeters). A piezoelectric flextensional actuator (PFA) is a device with small dimensions that can be driven by reduced voltages and can operate in the nano- and micro scales. Interferometric techniques are very adequate for the characterization of these devices, because there is no mechanical contact in the measurement process, and it has high sensitivity, bandwidth and dynamic range. A low cost open-loop homodyne Michelson interferometer is utilized in this work to experimentally detect the nanovi brations of PFAs, based on the spectral analysis of the interfero metric signal. By employing the well known J 1 ...J 4 phase demodulation method, a new and improved version is proposed, which presents the following characteristics: is direct, self-consistent, is immune to fading, and does not present phase ambiguity problems. The proposed method has resolution that is similar to the modified J 1 ...J 4 method (0.18 rad); however, differently from the former, its dynamic range is 20% larger, does not demand Bessel functions algebraic sign correction algorithms and there are no singularities when the static phase shift between the interferometer arms is equal to an integer multiple of  /2 rad. Electronic noise and random phase drifts due to ambient perturbations are taken into account in the analysis of the method. The PFA nanopositioner characterization was based on the analysis of linearity betw een the applied voltage and the resulting displacement, on the displacement frequency response and determination of main resonance frequencies.