Investigating Smart Sampling as a population initialization method for Differential Evolution in continuous problems

Recently, researches have shown that the performance of metaheuristics can be affected by population initialization. Opposition-based Differential Evolution (ODE), Quasi-Oppositional Differential Evolution (QODE), and Uniform-Quasi-Opposition Differential Evolution (UQODE) are three state-of-the-art methods that improve the performance of the Differential Evolution algorithm based on population initialization and different search strategies. In a different approach to achieve similar results, this paper presents a technique to discover promising regions in a continuous search-space of an optimization problem. Using machine-learning techniques, the algorithm named Smart Sampling (SS) finds regions with high possibility of containing a global optimum. Next, a metaheuristic can be initialized inside each region to find that optimum. SS and DE were combined (originating the SSDE algorithm) to evaluate our approach, and experiments were conducted in the same set of benchmark functions used by ODE, QODE and UQODE authors. Results have shown that the total number of function evaluations required by DE to reach the global optimum can be significantly reduced and that the success rate improves if SS is employed first. Such results are also in consonance with results from the literature, stating the importance of an adequate starting population. Moreover, SS presents better efficacy to find initial populations of superior quality when compared to the other three algorithms that employ oppositional learning. Finally and most important, the SS performance in finding promising regions is independent of the employed metaheuristic with which SS is combined, making SS suitable to improve the performance of a large variety of optimization techniques. (C) 2012 Elsevier Inc. All rights reserved.

A decaying factor accounts for contained activity in neuronal networks with no need of hierarchical or modular organization

The mechanisms responsible for containing activity in systems represented by networks are crucial in various phenomena, for example, in diseases such as epilepsy that affect the neuronal networks and for information dissemination in social networks. The first models to account for contained activity included triggering and inhibition processes, but they cannot be applied to social networks where inhibition is clearly absent. A recent model showed that contained activity can be achieved with no need of inhibition processes provided that the network is subdivided into modules (communities). In this paper, we introduce a new concept inspired in the Hebbian theory, through which containment of activity is achieved by incorporating a dynamics based on a decaying activity in a random walk mechanism preferential to the node activity. Upon selecting the decay coefficient within a proper range, we observed sustained activity in all the networks tested, namely, random, Barabasi-Albert and geographical networks. The generality of this finding was confirmed by showing that modularity is no longer needed if the dynamics based on the integrate-and-fire dynamics incorporated the decay factor. Taken together, these results provide a proof of principle that persistent, restrained network activation might occur in the absence of any particular topological structure. This may be the reason why neuronal activity does not spread out to the entire neuronal network, even when no special topological organization exists.

Decisions on Temporal Sampling Protocol Influence the Detection of Ecological Patterns

Within-site variability in species detectability is a problem common to many biodiversity assessments and can strongly bias the results. Such variability can be caused by many factors, including simple counting inaccuracies, which can be solved by increasing sample size, or by temporal changes in species behavior, meaning that the way the temporal sampling protocol is designed is also very important. Here we use the example of mist-netted tropical birds to determine how design decisions in the temporal sampling protocol can alter the data collected and how these changes might affect the detection of ecological patterns, such as the species-area relationship (SAR). Using data from almost 3400 birds captured from 21,000 net-hours at 31 sites in the Brazilian Atlantic Forest, we found that the magnitude of ecological trends remained fairly stable, but the probability of detecting statistically significant ecological patterns varied depending on sampling effort, time of day and season in which sampling was conducted. For example, more species were detected in the wet season, but the SAR was strongest in the dry season. We found that the temporal distribution of sampling effort was more important than its total amount, discovering that similar ecological results could have been obtained with one-third of the total effort, as long as each site had been equally sampled over 2 yr. We discuss that projects with the same sampling effort and spatial design, but with different temporal sampling protocol are likely to report different ecological patterns, which may ultimately lead to inappropriate conservation strategies.

Why Are Women With Cervical Cancer Not Being Diagnosed in Preinvasive Phase? An Analysis of Risk Factors Using a Hierarchical Model

Objective: To assess the risk factors for delayed diagnosis of uterine cervical lesions. Materials and Methods: This is a case-control study that recruited 178 women at 2 Brazilian hospitals. The cases (n = 74) were composed of women with a late diagnosis of a lesion in the uterine cervix (invasive carcinoma in any stage). The controls (n = 104) were composed of women with cervical lesions diagnosed early on (low-or high-grade intraepithelial lesions). The analysis was performed by means of logistic regression model using a hierarchical model. The socioeconomic and demographic variables were included at level I (distal). Level II (intermediate) included the personal and family antecedents and knowledge about the Papanicolaou test and human papillomavirus. Level III (proximal) encompassed the variables relating to individuals' care for their own health, gynecologic symptoms, and variables relating to access to the health care system. Results: The risk factors for late diagnosis of uterine cervical lesions were age older than 40 years (odds ratio [OR] = 10.4; 95% confidence interval [CI], 2.3-48.4), not knowing the difference between the Papanicolaou test and gynecological pelvic examinations (OR, = 2.5; 95% CI, 1.3-4.9), not thinking that the Papanicolaou test was important (odds ratio [OR], 4.2; 95% CI, 1.3-13.4), and abnormal vaginal bleeding (OR, 15.0; 95% CI, 6.5-35.0). Previous treatment for sexually transmissible disease was a protective factor (OR, 0.3; 95% CI, 0.1-0.8) for delayed diagnosis. Conclusions: Deficiencies in cervical cancer prevention programs in developing countries are not simply a matter of better provision and coverage of Papanicolaou tests. The misconception about the Papanicolaou test is a serious educational problem, as demonstrated by the present study.

Use of passive diffusion sampling method for defining NO2 concentrations gradient in São Paulo, Brazil

Abstract Background Air pollution in São Paulo is constantly being measured by the State of Sao Paulo Environmental Agency, however there is no information on the variation between places with different traffic densities. This study was intended to identify a gradient of exposure to traffic-related air pollution within different areas in São Paulo to provide information for future epidemiological studies. Methods We measured NO2 using Palmes' diffusion tubes in 36 sites on streets chosen to be representative of different road types and traffic densities in São Paulo in two one-week periods (July and August 2000). In each study period, two tubes were installed in each site, and two additional tubes were installed in 10 control sites. Results Average NO2 concentrations were related to traffic density, observed on the spot, to number of vehicles counted, and to traffic density strata defined by the city Traffic Engineering Company (CET). Average NO2concentrations were 63μg/m3 and 49μg/m3 in the first and second periods, respectively. Dividing the sites by the observed traffic density, we found: heavy traffic (n = 17): 64μg/m3 (95% CI: 59μg/m3 – 68μg/m3); local traffic (n = 16): 48μg/m3 (95% CI: 44μg/m3 – 52μg/m3) (p < 0.001). Conclusion The differences in NO2 levels between heavy and local traffic sites are large enough to suggest the use of a more refined classification of exposure in epidemiological studies in the city. Number of vehicles counted, traffic density observed on the spot and traffic density strata defined by the CET might be used as a proxy for traffic exposure in São Paulo when more accurate measurements are not available.

Annealed Ising model on hierarchical structures: a transfer matrix approach.

Spin systems in the presence of disorder are described by two sets of degrees of freedom, associated with orientational (spin) and disorder variables, which may be characterized by two distinct relaxation times. Disordered spin models have been mostly investigated in the quenched regime, which is the usual situation in solid state physics, and in which the relaxation time of the disorder variables is much larger than the typical measurement times. In this quenched regime, disorder variables are fixed, and only the orientational variables are duly thermalized. Recent studies in the context of lattice statistical models for the phase diagrams of nematic liquid-crystalline systems have stimulated the interest of going beyond the quenched regime. The phase diagrams predicted by these calculations for a simple Maier-Saupe model turn out to be qualitative different from the quenched case if the two sets of degrees of freedom are allowed to reach thermal equilibrium during the experimental time, which is known as the fully annealed regime. In this work, we develop a transfer matrix formalism to investigate annealed disordered Ising models on two hierarchical structures, the diamond hierarchical lattice (DHL) and the Apollonian network (AN). The calculations follow the same steps used for the analysis of simple uniform systems, which amounts to deriving proper recurrence maps for the thermodynamic and magnetic variables in terms of the generations of the construction of the hierarchical structures. In this context, we may consider different kinds of disorder, and different types of ferromagnetic and anti-ferromagnetic interactions. In the present work, we analyze the effects of dilution, which are produced by the removal of some magnetic ions. The system is treated in a “grand canonical" ensemble. The introduction of two extra fields, related to the concentration of two different types of particles, leads to higher-rank transfer matrices as compared with the formalism for the usual uniform models. Preliminary calculations on a DHL indicate that there is a phase transition for a wide range of dilution concentrations. Ising spin systems on the AN are known to be ferromagnetically ordered at all temperatures; in the presence of dilution, however, there are indications of a disordered (paramagnetic) phase at low concentrations of magnetic ions.

Hierarchical multi-label classification using local neural networks

Hierarchical multi-label classification is a complex classification task where the classes involved in the problem are hierarchically structured and each example may simultaneously belong to more than one class in each hierarchical level. In this paper, we extend our previous works, where we investigated a new local-based classification method that incrementally trains a multi-layer perceptron for each level of the classification hierarchy. Predictions made by a neural network in a given level are used as inputs to the neural network responsible for the prediction in the next level. We compare the proposed method with one state-of-the-art decision-tree induction method and two decision-tree induction methods, using several hierarchical multi-label classification datasets. We perform a thorough experimental analysis, showing that our method obtains competitive results to a robust global method regarding both precision and recall evaluation measures.

Isocyanates and Amines – Sampling and Analytical Procedures

This thesis covers sampling and analytical procedures for isocyanates (R-NCO) and amines (R-NH2), two kinds of chemicals frequently used in association with the polymeric material polyurethane (PUR). Exposure to isocyanates may result in respiratory disorders and dermal sensitisation, and they are one of the main causes of occupational asthma. Several of the aromatic diamines associated with PUR production are classified as suspected carcinogens. Hence, the presence of these chemicals in different exposure situations must be monitored. In the context of determining isocyanates in air, the methodologies included derivatisation with the reagent di-n-butylamine (DBA) upon collection and subsequent determination using liquid chromatography (LC) and mass spectrometric detection (MS). A user-friendly solvent-free sampler for collection of airborne isocyanates was developed as an alternative to a more cumbersome impinger-filter sampling technique. The combination of the DBA reagent together with MS detection techniques revealed several new exposure situations for isocyanates, such as isocyanic acid during thermal degradation of PUR and urea-based resins. Further, a method for characterising isocyanates in technical products used in the production of PUR was developed. This enabled determination of isocyanates in air for which pure analytical standards are missing. Tandem MS (MS/MS) determination of isocyanates in air below 10-6 of the threshold limit values was achieved. As for the determination of amines, the analytical methods included derivatisation into pentafluoropropionic amide or ethyl carbamate ester derivatives and subsequent MS analysis. Several amines in biological fluids, as markers of exposure for either the amines themselves or the corresponding isocyanates, were determined by LC-MS/MS at amol level. In aqueous extraction solutions of flexible PUR foam products, toluene diamine and related compounds were found. In conclusion, this thesis demonstrates the usefulness of well characterised analytical procedures and techniques for determination of hazardous compounds. Without reliable and robust methodologies there is a risk that exposure levels will be underestimated or, even worse, that relevant compounds will be completely missed.

A simple strategy for defining polynomial spline spaces over hierarchical T-meses

[EN]We present a new strategy for constructing spline spaces over hierarchical T-meshes with quad- and octree subdivision scheme. The proposed technique includes some simple rules for inferring local knot vectors to define C 2 -continuous cubic tensor product spline blending functions. Our conjecture is that these rules allow to obtain, for a given T-mesh, a set of linearly independent spline functions with the property that spaces spanned by nested T-meshes are also nested, and therefore, the functions can reproduce cubic polynomials. In order to span spaces with these properties applying the proposed rules, the T-mesh should fulfill the only requirement of being a 0- balanced mesh...

Stellar Relics of the hierarchical assembly of the Galaxy

This PhD Thesis is part of a long-term wide research project, carried out by the "Osservatorio Astronomico di Bologna (INAF-OABO)", that has as primary goal the comprehension and reconstruction of formation mechanism of galaxies and their evolution history. There is now substantial evidence, both from theoretical and observational point of view, in favor of the hypothesis that the halo of our Galaxy has been at least partially, built up by the progressive accretion of small fragments, similar in nature to the present day dwarf galaxies of the Local Group. In this context, the photometric and spectroscopic study of systems which populate the halo of our Galaxy (i.e. dwarf spheroidal galaxy, tidal streams, massive globular cluster, etc) permits to discover, not only the origin and behaviour of these systems, but also the structure of our Galactic halo, combined with its formation history. In fact, the study of the population of these objects and also of their chemical compositions, age, metallicities and velocity dispersion, permit us not only an improvement in the understanding of the mechanisms that govern the Galactic formation, but also a valid indirect test for cosmological model itself. Specifically, in this Thesis we provided a complete characterization of the tidal Stream of the Sagittarius dwarf spheroidal galaxy, that is the most striking example of the process of tidal disruption and accretion of a dwarf satellite in to our Galaxy. Using Red Clump stars, extracted from the catalogue of the Sloan Digital Sky Survey (SDSS) we obtained an estimate of the distance, the depth along the line of sight and of the number density for each detected portion of the Stream (and more in general for each detected structure along our line of sight). Moreover comparing the relative number (i.e. the ratio) of Blue Horizontal Branch stars and Red Clump stars (the two features are tracers of different age/different metallicity populations) in the main body of the galaxy and in the Stream, in order to verify the presence of an age-metallicity gradient along the Stream. We also report the detection of a population of Red Clump stars probably associated with the recently discovered Bootes III stellar system. Finally, we also present the results of a survey of radial velocities over a wide region, extending from r ~ 10' out to r ~ 80' within the massive star cluster Omega Centauri. The survey was performed with FLAMES@VLT, to study the velocity dispersion profile in the outer regions of this stellar system. All the results presented in this Thesis, have already been published in refeered journals.

Computational investigations of ion conduction mechanisms using enhanced sampling methods

Proper ion channels’ functioning is a prerequisite for a normal cell and disorders involving ion channels, or channelopathies, underlie many human diseases. Long QT syndromes (LQTS) for example may arise from the malfunctioning of hERG channel, caused either by the binding of drugs or mutations in HERG gene. In the first part of this thesis I present a framework to investigate the mechanism of ion conduction through hERG channel. The free energy profile governing the elementary steps of ion translocation in the pore was computed by means of umbrella sampling simulations. Compared to previous studies, we detected a different dynamic behavior: according to our data hERG is more likely to mediate a conduction mechanism which has been referred to as “single-vacancy-like” by Roux and coworkers (2001), rather then a “knock-on” mechanism. The same protocol was applied to a model of hERG presenting the Gly628Ser mutation, found to be cause of congenital LQTS. The results provided interesting insights about the reason of the malfunctioning of the mutant channel. Since they have critical functions in viruses’ life cycle, viral ion channels, such as M2 proton channel, are considered attractive targets for antiviral therapy. A deep knowledge of the mechanisms that the virus employs to survive in the host cell is of primary importance in the identification of new antiviral strategies. In the second part of this thesis I shed light on the role that M2 plays in the control of electrical potential inside the virus, being the charge equilibration a condition required to allow proton influx. The ion conduction through M2 was simulated using metadynamics technique. Based on our results we suggest that a potential anion-mediated cation-proton exchange, as well as a direct anion-proton exchange could both contribute to explain the activity of the M2 channel.

A novel map-matching procedure for low-sampling GPS data with applications to traffic flow analysis

An extensive sample (2%) of private vehicles in Italy are equipped with a GPS device that periodically measures their position and dynamical state for insurance purposes. Having access to this type of data allows to develop theoretical and practical applications of great interest: the real-time reconstruction of traffic state in a certain region, the development of accurate models of vehicle dynamics, the study of the cognitive dynamics of drivers. In order for these applications to be possible, we first need to develop the ability to reconstruct the paths taken by vehicles on the road network from the raw GPS data. In fact, these data are affected by positioning errors and they are often very distanced from each other (~2 Km). For these reasons, the task of path identification is not straightforward. This thesis describes the approach we followed to reliably identify vehicle paths from this kind of low-sampling data. The problem of matching data with roads is solved with a bayesian approach of maximum likelihood. While the identification of the path taken between two consecutive GPS measures is performed with a specifically developed optimal routing algorithm, based on A* algorithm. The procedure was applied on an off-line urban data sample and proved to be robust and accurate. Future developments will extend the procedure to real-time execution and nation-wide coverage.

Quantifying the OH radical by global scale NMHC measurements from the NOAA - ESRL cooperative flask sampling network

Summary PhD Thesis Jan Pollmann: This thesis focuses on global scale measurements of light reactive non-methane hydrocarbon (NMHC), in the volatility range from ethane to toluene with a special focus on ethane, propane, isobutane, butane, isopentane and pentane. Even though they only occur at the ppt level (nmol mol-1) in the remote troposphere these species can yield insight into key atmospheric processes. An analytical method was developed and subsequently evaluated to analyze NMHC from the NOAA – ERSL cooperative air sampling network. Potential analytical interferences through other atmospheric trace gases (water vapor and ozone) were carefully examined. The analytical parameters accuracy and precision were analyzed in detail. It was proven that more than 90% of the data points meet the Global Atmospheric Watch (GAW) data quality objective. Trace gas measurements from 28 measurement stations were used to derive the global atmospheric distribution profile for 4 NMHC (ethane, propane, isobutane, butane). A close comparison of the derived ethane data with previously published reports showed that northern hemispheric ethane background mixing ratio declined by approximately 30% since 1990. No such change was observed for southern hemispheric ethane. The NMHC data and trace gas data supplied by NOAA ESRL were used to estimate local diurnal averaged hydroxyl radical (OH) mixing ratios by variability analysis. Comparison of the variability derived OH with directly measured OH and modeled OH mixing ratios were found in good agreement outside the tropics. Tropical OH was on average two times higher than predicted by the model. Variability analysis was used to assess the effect of chlorine radicals on atmospheric oxidation chemistry. It was found that Cl is probably not of significant relevance on a global scale.

Local Earthquake Tomography by trans-dimensional Monte Carlo Sampling

In this study a new, fully non-linear, approach to Local Earthquake Tomography is presented. Local Earthquakes Tomography (LET) is a non-linear inversion problem that allows the joint determination of earthquakes parameters and velocity structure from arrival times of waves generated by local sources. Since the early developments of seismic tomography several inversion methods have been developed to solve this problem in a linearized way. In the framework of Monte Carlo sampling, we developed a new code based on the Reversible Jump Markov Chain Monte Carlo sampling method (Rj-McMc). It is a trans-dimensional approach in which the number of unknowns, and thus the model parameterization, is treated as one of the unknowns. I show that our new code allows overcoming major limitations of linearized tomography, opening a new perspective in seismic imaging. Synthetic tests demonstrate that our algorithm is able to produce a robust and reliable tomography without the need to make subjective a-priori assumptions about starting models and parameterization. Moreover it provides a more accurate estimate of uncertainties about the model parameters. Therefore, it is very suitable for investigating the velocity structure in regions that lack of accurate a-priori information. Synthetic tests also reveal that the lack of any regularization constraints allows extracting more information from the observed data and that the velocity structure can be detected also in regions where the density of rays is low and standard linearized codes fails. I also present high-resolution Vp and Vp/Vs models in two widespread investigated regions: the Parkfield segment of the San Andreas Fault (California, USA) and the area around the Alto Tiberina fault (Umbria-Marche, Italy). In both the cases, the models obtained with our code show a substantial improvement in the data fit, if compared with the models obtained from the same data set with the linearized inversion codes.

Sampling methods for low-frequency electromagnetic imaging

For the detection of hidden objects by low-frequency electromagnetic imaging the Linear Sampling Method works remarkably well despite the fact that the rigorous mathematical justification is still incomplete. In this work, we give an explanation for this good performance by showing that in the low-frequency limit the measurement operator fulfills the assumptions for the fully justified variant of the Linear Sampling Method, the so-called Factorization Method. We also show how the method has to be modified in the physically relevant case of electromagnetic imaging with divergence-free currents. We present numerical results to illustrate our findings, and to show that similar performance can be expected for the case of conducting objects and layered backgrounds.