arXiv subjects

L. da F. Costa

Publications and source records attributed to L. da F. Costa.

17 recordsLinked to original sources

arXiv2017

An Early Model of Transistors and Circuits

Bipolar junction transistors (BJTs) have been at the core of linear electronics from its beginnings. Although their properties can be well represented transport model equations, design and analysis approaches have, to a good extent, been limited to using current-equispaced horizontal and parallel isolines of the characteristic surface. Here, we resort to the geometrical structure imposed on BJTs behavior by the Early effect and voltage as a means to derive a simple, intuitive and more complete respective model that, though excluding cut-off and saturation regimes, can simplify the design and characterization of BJTs and respective circuits, including integrated devices. The approach involves using a beam of isolines converging at the Early voltage as the model of a BJT. The angles of the isolines, another important aspect of BJTs, are experimentally verified often to vary almost in linear fashion with the base current, endowing the proposed Early model with an intrinsic geometric nature. An experimental-numerical methodology is suggested for the Early model estimation, and applied to 12 real-world small signal NPN BJTs. Interesting results are obtained, including the identification of diverse Early voltage values for different BJT types and the observation, for the considered BJTs, of the almost linear variation of the isoline angles with the input current. A case example of transfer function estimation, as well as total harmonic distortion analysis, are also provided in order to illustrate the potential of the proposed methodology for approximating, under certain circumstances, the operation of the common emitter configuration. The proposed model also has good potential as a didactic aid in physics and electronics programs, complementing the currently adopted modeling approaches.

physics.ins-det↗

arXiv2013

A systematic comparison of supervised classifiers

Pattern recognition techniques have been employed in a myriad of industrial, medical, commercial and academic applications. To tackle such a diversity of data, many techniques have been devised. However, despite the long tradition of pattern recognition research, there is no technique that yields the best classification in all scenarios. Therefore, the consideration of as many as possible techniques presents itself as an fundamental practice in applications aiming at high accuracy. Typical works comparing methods either emphasize the performance of a given algorithm in validation tests or systematically compare various algorithms, assuming that the practical use of these methods is done by experts. In many occasions, however, researchers have to deal with their practical classification tasks without an in-depth knowledge about the underlying mechanisms behind parameters. Actually, the adequate choice of classifiers and parameters alike in such practical circumstances constitutes a long-standing problem and is the subject of the current paper. We carried out a study on the performance of nine well-known classifiers implemented by the Weka framework and compared the dependence of the accuracy with their configuration parameter configurations. The analysis of performance with default parameters revealed that the k-nearest neighbors method exceeds by a large margin the other methods when high dimensional datasets are considered. When other configuration of parameters were allowed, we found that it is possible to improve the quality of SVM in more than 20% even if parameters are set randomly. Taken together, the investigation conducted in this paper suggests that, apart from the SVM implementation, Weka's default configuration of parameters provides an performance close the one achieved with the optimal configuration.

cs.LG↗

arXiv2012

Good practices for a literature survey are not followed by authors while preparing scientific manuscripts

The number of citations received by authors in scientific journals has become a major parameter to assess individual researchers and the journals themselves through the impact factor. A fair assessment therefore requires that the criteria for selecting references in a given manuscript should be unbiased with respect to the authors or the journals cited. In this paper, we advocate that authors should follow two mandatory principles to select papers (later reflected in the list of references) while studying the literature for a given research: i) consider similarity of content with the topics investigated, lest very related work should be reproduced or ignored; ii) perform a systematic search over the network of citations including seminal or very related papers. We use formalisms of complex networks for two datasets of papers from the arXiv repository to show that neither of these two criteria is fulfilled in practice.

physics.soc-ph↗

arXiv2012

Prominent effect of soil network heterogeneity on microbial invasion

Using a network representation for real soil samples and mathematical models for microbial spread, we show that the structural heterogeneity of the soil habitat may have a very significant influence on the size of microbial invasions of the soil pore space. In particular, neglecting the soil structural heterogeneity may lead to a substantial underestimation of microbial invasion. Such effects are explained in terms of a crucial interplay between heterogeneity in microbial spread and heterogeneity in the topology of soil networks. The main influence of network topology on invasion is linked to the existence of long channels in soil networks that may act as bridges for transmission of microorganisms between distant parts of soil.

q-bio.PE↗

arXiv2012

Epidemics in Networks of Spatially Correlated Three-dimensional Root Branching Structures

Using digitized images of the three-dimensional, branching structures for root systems of bean seedlings, together with analytical and numerical methods that map a common 'SIR' epidemiological model onto the bond percolation problem, we show how the spatially-correlated branching structures of plant roots affect transmission efficiencies, and hence the invasion criterion, for a soil-borne pathogen as it spreads through ensembles of morphologically complex hosts. We conclude that the inherent heterogeneities in transmissibilities arising from correlations in the degrees of overlap between neighbouring plants, render a population of root systems less susceptible to epidemic invasion than a corresponding homogeneous system. Several components of morphological complexity are analysed that contribute to disorder and heterogeneities in transmissibility of infection. Anisotropy in root shape is shown to increase resilience to epidemic invasion, while increasing the degree of branching enhances the spread of epidemics in the population of roots. Some extension of the methods for other epidemiological systems are discussed.

q-bio.PE↗

arXiv2009

An entropy-based approach to automatic image segmentation of satellite images

An entropy-based image segmentation approach is introduced and applied to color images obtained from Google Earth. Segmentation refers to the process of partitioning a digital image in order to locate different objects and regions of interest. The application to satellite images paves the way to automated monitoring of ecological catastrophes, urban growth, agricultural activity, maritime pollution, climate changing and general surveillance. Regions representing aquatic, rural and urban areas are identified and the accuracy of the proposed segmentation methodology is evaluated. The comparison with gray level images revealed that the color information is fundamental to obtain an accurate segmentation.

physics.comp-ph↗

arXiv2009

Knowledge Acquisition by Networks of Interacting Agents in the Presence of Observation Errors

In this work we investigate knowledge acquisition as performed by multiple agents interacting as they infer, under the presence of observation errors, respective models of a complex system. We focus the specific case in which, at each time step, each agent takes into account its current observation as well as the average of the models of its neighbors. The agents are connected by a network of interaction of Erdős-Renyi or Barabasi-Albert type. First we investigate situations in which one of the agents has a different probability of observation error (higher or lower). It is shown that the influence of this special agent over the quality of the models inferred by the rest of the network can be substantial, varying linearly with the respective degree of the agent with different estimation error. In case the degree of this agent is taken as a respective fitness parameter, the effect of the different estimation error is even more pronounced, becoming superlinear. To complement our analysis, we provide the analytical solution of the overall behavior of the system. We also investigate the knowledge acquisition dynamic when the agents are grouped into communities. We verify that the inclusion of edges between agents (within a community) having higher probability of observation error promotes the loss of quality in the estimation of the agents in the other communities.

physics.soc-ph↗

arXiv2008

Technical Report - Automatic Contour Extraction from 2D Neuron Images

This work describes a novel methodology for automatic contour extraction from 2D images of 3D neurons (e.g. camera lucida images and other types of 2D microscopy). Most contour-based shape analysis methods can not be used to characterize such cells because of overlaps between neuronal processes. The proposed framework is specifically aimed at the problem of contour following even in presence of multiple overlaps. First, the input image is preprocessed in order to obtain an 8-connected skeleton with one-pixel-wide branches, as well as a set of critical regions (i.e., bifurcations and crossings). Next, for each subtree, the tracking stage iteratively labels all valid pixel of branches, up to a critical region, where it determines the suitable direction to proceed. Finally, the labeled skeleton segments are followed in order to yield the parametric contour of the neuronal shape under analysis. The reported system was successfully tested with respect to several images and the results from a set of three neuron images are presented here, each pertaining to a different class, i.e. alpha, delta and epsilon ganglion cells, containing a total of 34 crossings. The algorithms successfully got across all these overlaps. The method has also been found to exhibit robustness even for images with close parallel segments. The proposed method is robust and may be implemented in an efficient manner. The introduction of this approach should pave the way for more systematic application of contour-based shape analysis methods in neuronal morphology.

cs.CV↗

arXiv2008

Sensitivity of complex networks measurements

Complex networks obtained from the real-world networks are often characterized by incompleteness and noise, consequences of limited sampling as well as artifacts in the acquisition process. Because the characterization, analysis and modeling of complex systems underlain by complex networks are critically affected by the quality of the respective initial structures, it becomes imperative to devise methodologies for identifying and quantifying the effect of such sampling problems on the characterization of complex networks. Given that several measurements need to be applied in order to achieve a comprehensive characterization of complex networks, it is important to investigate the effect of incompleteness and noise on such quantifications. In this article we report such a study, involving 8 different measurements applied on 6 different complex networks models. We evaluate the sensitiveness of the measurements to perturbations in the topology of the network considering the relative entropy. Three particularly important types of progressive perturbations to the network are considered: edge suppression, addition and rewiring. The conclusions have important practical consequences including the fact that scale-free structures are more robust to perturbations. The measurements allowing the best balance of stability (smaller sensitivity to perturbations) and discriminability (separation between different network topologies) were also identified.

physics.soc-ph↗

arXiv2007

Seeking the best Internet Model

The models of the Internet reported in the literature are mainly aimed at reproducing the scale-free structure, the high clustering coefficient and the small world effects found in the real Internet, while other important properties (e.g. related to centrality and hierarchical measurements) are not considered. For a better characterization and modeling of such network, a larger number of topological properties must be considered. In this work, we present a sound multivariate statistical approach, including feature spaces and multivariate statistical analysis (especially canonical projections), in order to characterize several Internet models while considering a larger set of relevant measurements. We apply such a methodology to determine, among nine complex networks models, which are those most compatible with the real Internet data (on the autonomous systems level) considering a set of 21 network measurements. We conclude that none of the considered models can reproduce the Internet topology with high accuracy.

physics.soc-ph↗

arXiv2007

Formation energy and interaction of point defects in two-dimensional colloidal crystals

The manipulation of individual colloidal particles using optical tweezers has allowed vacancies to be created in two-dimensional (2d) colloidal crystals, with unprecedented possibility of real-time monitoring the dynamics of such defects (Nature {\bf 413}, 147 (2001)). In this Letter, we employ molecular dynamics (MD) simulations to calculate the formation energy of single defects and the binding energy between pairs of defects in a 2d colloidal crystal. In the light of our results, experimental observations of vacancies could be explained and then compared to simulation results for the interstitial defects. We see a remarkable similarity between our results for a 2d colloidal crystal and the 2d Wigner crystal (Phys. Rev. Lett. {\bf 86}, 492 (2001)). The results show that the formation energy to create a single interstitial is $12% - 28%$ lower than that of the vacancy. Because the pair binding energies of the defects are strongly attractive for short distances, the ground state should correspond to bound pairs with the interstitial bound pairs being the most probable.

cond-mat.other↗

arXiv2005

On the Importance of Hubs in Hopfield Complex Neuronal Networks under Attack

The organizational principles behind the connectivity of a complex network are known to influence its behavior. In this work we investigate, using the Hopfield model, the influence of the network architecture on the performance for associative recall while the network is under hub and edge attack. We show, by using four different attack strategies, that although the importance of hubs is more definite for Barabási-Albert neuronal networks, the random removal of the same amount of edges as in a hub may imply a greater reduction of memory recall.

cond-mat.dis-nn↗

arXiv2005

Extended morphometric analysis of neuronal cells with Minkowski valuations

Minkowski valuations provide a systematic framework for quantifying different aspects of morphology. In this paper we apply vector- and tensor-valued Minkowski valuations to neuronal cells from the cat's retina in order to describe their morphological structure in a comprehensive way. We introduce the framework of Minkowski valuations, discuss their implementation for neuronal cells and show how they can discriminate between cells of different types.

cond-mat.dis-nn↗

arXiv2005

Non-Maxwellian velocity distribution and anomalous diffusion of {\it in vitro} kidney cells

This manuscript uses a statistical mechanical approach to study the effect of the adhesion, through MOCA protein, on cell locomotion. The MOCA protein regulates cell-cell adhesion, and we explore its potential role in the cell movement. We present a series of statistical descriptions of the motion in order to characterize the cell movement, and found that MOCA affects the statistical scenario of cell locomotion. In particular, we observe that MOCA enhances the tendency of joint motion, inhibits super-diffusion, and decreases overall cell motion. These facts are compatible with the hypothesis that the cells move faster in a less cohesive environment. Furthermore, we observe that velocity distribution tails are longer than those predicted by Maxwell-Boltzmann in all cases studied here, indicating that cell movement is more complex than that of a liquid.

q-bio.CB↗

arXiv2005

On the Potential of the Excluded Volume and Auto-Correlation as Neuromorphometric Descriptors

This work investigates at what degree two neuromorphometric measurements, namely the autocorrelation and the excluded volume of a neuronal cell can influence the characterization and classification of such a type of cells. While the autocorrelation function presents good potential for quantifying the dendrite-dendrite connectivity of cells in mosaic tilings, the excluded volume, i.e. the amount of the surround space which is geometrically not accessible to an axon or dendrite, provides a complementary characterization of the cell connectivity. The potential of such approaches is illustrated with respect to real neuronal cells.

cond-mat.stat-mech↗

arXiv2004

A Field Approach to 3D Gene Expression Pattern Characterization

We present a vector field method for obtaining the spatial organization of 3D patterns of gene expression based on gradients and lines of force obtained by numerical integration. The convergence of these lines of force in local maxima are centers of gene expression, providing a natural and powerful framework to characterize the organization and dynamics of biological structures. We apply this novel methodology to analyze the expression pattern of the Enhanced Green Fluorescent Protein (EGFP) driven by the promoter of light chain myosin II during zebrafish heart formation.

q-bio.GN↗

arXiv2004

Characterizing neuromorphologic alterations with additive shape functionals

The complexity of a neuronal cell shape is known to be related to its function. Specifically, among other indicators, a decreased complexity in the dendritic trees of cortical pyramidal neurons has been associated with mental retardation. In this paper we develop a procedure to address the characterization of morphological changes induced in cultured neurons by over-expressing a gene involved in mental retardation. Measures associated with the multiscale connectivity, an additive image functional, are found to give a reasonable separation criterion between two categories of cells. One category consists of a control group and two transfected groups of neurons, and the other, a class of cat ganglionary cells. The reported framework also identified a trend towards lower complexity in one of the transfected groups. Such results establish the suggested measures as an effective descriptors of cell shape.

q-bio.QM↗