Statistical mechanics of multi-edge networks

Statistical properties of binary complex networks are well understood and recently many attempts have been made to extend this knowledge to weighted ones. There are, however, subtle yet important considerations to be made regarding the nature of the weights used in this generalization. Weights can be either continuous or discrete magnitudes, and in the latter case, they can additionally have undistinguishable or distinguishable nature. This fact has not been addressed in the literature insofar and has deep implications on the network statistics. In this work we face this problem introducing multiedge networks as graphs where multiple (distinguishable) connections between nodes are considered. We develop a statistical mechanics framework where it is possible to get information about the most relevant observables given a large spectrum of linear and nonlinear constraints including those depending both on the number of multiedges per link and their binary projection. The latter case is particularly interesting as we show that binary projections can be understood from multiedge processes. The implications of these results are important as many real-agent-based problems mapped onto graphs require this treatment for a proper characterization of their collective behavior.

Providing more informative projections of climate change impact on plant distribution in a mountain environment

Summary Due to their conic shape and the reduction of area with increasing elevation, mountain ecosystems were early identified as potentially very sensitive to global warming. Moreover, mountain systems may experience unprecedented rates of warming during the next century, two or three times higher than that records of the 20th century. In this context, species distribution models (SDM) have become important tools for rapid assessment of the impact of accelerated land use and climate change on the distribution plant species. In my study, I developed and tested new predictor variables for species distribution models (SDM), specific to current and future geographic projections of plant species in a mountain system, using the Western Swiss Alps as model region. Since meso- and micro-topography are relevant to explain geographic patterns of plant species in mountain environments, I assessed the effect of scale on predictor variables and geographic projections of SDM. I also developed a methodological framework of space-for-time evaluation to test the robustness of SDM when projected in a future changing climate. Finally, I used a cellular automaton to run dynamic simulations of plant migration under climate change in a mountain landscape, including realistic distance of seed dispersal. Results of future projections for the 21st century were also discussed in perspective of vegetation changes monitored during the 20th century. Overall, I showed in this study that, based on the most severe A1 climate change scenario and realistic dispersal simulations of plant dispersal, species extinctions in the Western Swiss Alps could affect nearly one third (28.5%) of the 284 species modeled by 2100. With the less severe 61 scenario, only 4.6% of species are predicted to become extinct. However, even with B1, 54% (153 species) may still loose more than 80% of their initial surface. Results of monitoring of past vegetation changes suggested that plant species can react quickly to the warmer conditions as far as competition is low However, in subalpine grasslands, competition of already present species is probably important and limit establishment of newly arrived species. Results from future simulations also showed that heavy extinctions of alpine plants may start already in 2040, but the latest in 2080. My study also highlighted the importance of fine scale and regional. assessments of climate change impact on mountain vegetation, using more direct predictor variables. Indeed, predictions at the continental scale may fail to predict local refugees or local extinctions, as well as loss of connectivity between local populations. On the other hand, migrations of low-elevation species to higher altitude may be difficult to predict at the local scale. Résumé La forme conique des montagnes ainsi que la diminution de surface dans les hautes altitudes sont reconnues pour exposer plus sensiblement les écosystèmes de montagne au réchauffement global. En outre, les systèmes de montagne seront sans doute soumis durant le 21ème siècle à un réchauffement deux à trois fois plus rapide que celui mesuré durant le 20ème siècle. Dans ce contexte, les modèles prédictifs de distribution géographique de la végétation se sont imposés comme des outils puissants pour de rapides évaluations de l'impact des changements climatiques et de la transformation du paysage par l'homme sur la végétation. Dans mon étude, j'ai développé de nouvelles variables prédictives pour les modèles de distribution, spécifiques à la projection géographique présente et future des plantes dans un système de montagne, en utilisant les Préalpes vaudoises comme zone d'échantillonnage. La méso- et la microtopographie étant particulièrement adaptées pour expliquer les patrons de distribution géographique des plantes dans un environnement montagneux, j'ai testé les effets d'échelle sur les variables prédictives et sur les projections des modèles de distribution. J'ai aussi développé un cadre méthodologique pour tester la robustesse potentielle des modèles lors de projections pour le futur. Finalement, j'ai utilisé un automate cellulaire pour simuler de manière dynamique la migration future des plantes dans le paysage et dans quatre scénarios de changement climatique pour le 21ème siècle. J'ai intégré dans ces simulations des mécanismes et des distances plus réalistes de dispersion de graines. J'ai pu montrer, avec les simulations les plus réalistes, que près du tiers des 284 espèces considérées (28.5%) pourraient être menacées d'extinction en 2100 dans le cas du plus sévère scénario de changement climatique A1. Pour le moins sévère des scénarios B1, seulement 4.6% des espèces sont menacées d'extinctions, mais 54% (153 espèces) risquent de perdre plus 80% de leur habitat initial. Les résultats de monitoring des changements de végétation dans le passé montrent que les plantes peuvent réagir rapidement au réchauffement climatique si la compétition est faible. Dans les prairies subalpines, les espèces déjà présentes limitent certainement l'arrivée de nouvelles espèces par effet de compétition. Les résultats de simulation pour le futur prédisent le début d'extinctions massives dans les Préalpes à partir de 2040, au plus tard en 2080. Mon travail démontre aussi l'importance d'études régionales à échelle fine pour évaluer l'impact des changements climatiques sur la végétation, en intégrant des variables plus directes. En effet, les études à échelle continentale ne tiennent pas compte des micro-refuges, des extinctions locales ni des pertes de connectivité entre populations locales. Malgré cela, la migration des plantes de basses altitudes reste difficile à prédire à l'échelle locale sans modélisation plus globale.

Illusory contours: a window onto the neurophysiology of constructing perception.

Seeing seems effortless, despite the need to segregate and integrate visual information that varies in quality, quantity, and location. The extent to which seeing passively recapitulates the external world is challenged by phenomena such as illusory contours, an example of visual completion whereby borders are perceived despite their physical absence in the image. Instead, visual completion and seeing are increasingly conceived as active processes, dependent on information exchange across neural populations. How this is instantiated in the brain remains controversial. Divergent models emanate from single-unit and population-level electrophysiology, neuroimaging, and neurostimulation studies. We reconcile discrepant findings from different methods and disciplines, and underscore the importance of taking into account spatiotemporal brain dynamics in generating models of brain function and perception.

Aspergillus protein degradation pathways with different secreted protease sets at neutral and acidic pH.

Aspergillus fumigatus grows well at neutral and acidic pH in a medium containing protein as the sole nitrogen source by secreting two different sets of proteases. Neutral pH favors the secretion of neutral and alkaline endoproteases, leucine aminopeptidases (Laps) which are nonspecific monoaminopeptidases, and an X-prolyl dipeptidase (DppIV). Acidic pH environment promotes the secretion of an aspartic endoprotease of pepsin family (Pep1) and tripeptidyl-peptidases of the sedolisin family (SedB and SedD). A novel prolyl peptidase, AfuS28, was found to be secreted in both alkaline and acidic conditions. In previous studies, Laps were shown to degrade peptides from their N-terminus until an X-Pro sequence acts as a stop signal. X-Pro sequences can be then removed by DppIV, which allows Laps access to the following residues. We have shown that at acidic pH Seds degrade large peptides from their N-terminus into tripeptides until Pro in P1 or P'1 position acts as a stop for these exopeptidases. However, X-X-Pro and X-X-X-Pro sequences can be removed by AfuS28 thus allowing Seds further sequential proteolysis. In conclusion, both alkaline and acidic sets of proteases contain exoprotease activity capable of cleaving after proline residues that cannot be removed during sequential digestion by nonspecific exopeptidases.

Iowa population projections, 1980-2000, 1984

Iowa population projections are made for 1980-2000.

Cooperative games with size-truncated information

[Eng] We study the marginal worth vectors and their convex hull, the socalled Weber set, from the original coalitional game and the transformed one, which is called the Weber set of level k. We prove that the core of the original game is included in each of the Weber set of level k, for any k, and that the Weber sets of consecutive levels form a chain if and only if the original game is 0-monotone. Even if the game is not 0-monotone, the intersection of the Weber sets for consecutive levels is always not empty, what is not the case for non-consecutive ones. Spanish education system.

Cooperative games with size-truncated information

[Eng] We study the marginal worth vectors and their convex hull, the socalled Weber set, from the original coalitional game and the transformed one, which is called the Weber set of level k. We prove that the core of the original game is included in each of the Weber set of level k, for any k, and that the Weber sets of consecutive levels form a chain if and only if the original game is 0-monotone. Even if the game is not 0-monotone, the intersection of the Weber sets for consecutive levels is always not empty, what is not the case for non-consecutive ones. Spanish education system.

Sierpinski curve Julia sets for quadratic rational maps

We investigate under which dynamical conditions the Julia set of a quadratic rational map is a Sierpiński curve.

Approximate polytope ensemble for one-class classification

In this work, a new one-class classification ensemble strategy called approximate polytope ensemble is presented. The main contribution of the paper is threefold. First, the geometrical concept of convex hull is used to define the boundary of the target class defining the problem. Expansions and contractions of this geometrical structure are introduced in order to avoid over-fitting. Second, the decision whether a point belongs to the convex hull model in high dimensional spaces is approximated by means of random projections and an ensemble decision process. Finally, a tiling strategy is proposed in order to model non-convex structures. Experimental results show that the proposed strategy is significantly better than state of the art one-class classification methods on over 200 datasets.

Self-Organising Maps and Correlation Analysis as a Tool to Explore Patterns in Excitation-Emission Matrix Data Sets and to Discriminate Dissolved Organic Matter Fluorescence Components

Dissolved organic matter (DOM) is a complex mixture of organic compounds, ubiquitous in marine and freshwater systems. Fluorescence spectroscopy, by means of Excitation-Emission Matrices (EEM), has become an indispensable tool to study DOM sources, transport and fate in aquatic ecosystems. However the statistical treatment of large and heterogeneous EEM data sets still represents an important challenge for biogeochemists. Recently, Self-Organising Maps (SOM) has been proposed as a tool to explore patterns in large EEM data sets. SOM is a pattern recognition method which clusterizes and reduces the dimensionality of input EEMs without relying on any assumption about the data structure. In this paper, we show how SOM, coupled with a correlation analysis of the component planes, can be used both to explore patterns among samples, as well as to identify individual fluorescence components. We analysed a large and heterogeneous EEM data set, including samples from a river catchment collected under a range of hydrological conditions, along a 60-km downstream gradient, and under the influence of different degrees of anthropogenic impact. According to our results, chemical industry effluents appeared to have unique and distinctive spectral characteristics. On the other hand, river samples collected under flash flood conditions showed homogeneous EEM shapes. The correlation analysis of the component planes suggested the presence of four fluorescence components, consistent with DOM components previously described in the literature. A remarkable strength of this methodology was that outlier samples appeared naturally integrated in the analysis. We conclude that SOM coupled with a correlation analysis procedure is a promising tool for studying large and heterogeneous EEM data sets.

A Topological Approach to Fuzzy Sets

This thesis presents a topological approach to studying fuzzy setsby means of modifier operators. Modifier operators are mathematical models, e.g., for hedges, and we present briefly different approaches to studying modifier operators. We are interested in compositional modifier operators, modifiers for short, and these modifiers depend on binary relations. We show that if a modifier depends on a reflexive and transitive binary relation on U, then there exists a unique topology on U such that this modifier is the closure operator in that topology. Also, if U is finite then there exists a lattice isomorphism between the class of all reflexive and transitive relations and the class of all topologies on U. We define topological similarity relation "≈" between L-fuzzy sets in an universe U, and show that the class LU/ ≈ is isomorphic with the class of all topologies on U, if U is finite and L is suitable. We consider finite bitopological spaces as approximation spaces, and we show that lower and upper approximations can be computed by means of α-level sets also in the case of equivalence relations. This means that approximations in the sense of Rough Set Theory can be computed by means of α-level sets. Finally, we present and application to data analysis: we study an approach to detecting dependencies of attributes in data base-like systems, called information systems.

A priori parameterisation of the CERES soil-crop models and tests against several European data sets

Mechanistic soil-crop models have become indispensable tools to investigate the effect of management practices on the productivity or environmental impacts of arable crops. Ideally these models may claim to be universally applicable because they simulate the major processes governing the fate of inputs such as fertiliser nitrogen or pesticides. However, because they deal with complex systems and uncertain phenomena, site-specific calibration is usually a prerequisite to ensure their predictions are realistic. This statement implies that some experimental knowledge on the system to be simulated should be available prior to any modelling attempt, and raises a tremendous limitation to practical applications of models. Because the demand for more general simulation results is high, modellers have nevertheless taken the bold step of extrapolating a model tested within a limited sample of real conditions to a much larger domain. While methodological questions are often disregarded in this extrapolation process, they are specifically addressed in this paper, and in particular the issue of models a priori parameterisation. We thus implemented and tested a standard procedure to parameterize the soil components of a modified version of the CERES models. The procedure converts routinely-available soil properties into functional characteristics by means of pedo-transfer functions. The resulting predictions of soil water and nitrogen dynamics, as well as crop biomass, nitrogen content and leaf area index were compared to observations from trials conducted in five locations across Europe (southern Italy, northern Spain, northern France and northern Germany). In three cases, the model’s performance was judged acceptable when compared to experimental errors on the measurements, based on a test of the model’s root mean squared error (RMSE). Significant deviations between observations and model outputs were however noted in all sites, and could be ascribed to various model routines. In decreasing importance, these were: water balance, the turnover of soil organic matter, and crop N uptake. A better match to field observations could therefore be achieved by visually adjusting related parameters, such as field-capacity water content or the size of soil microbial biomass. As a result, model predictions fell within the measurement errors in all sites for most variables, and the model’s RMSE was within the range of published values for similar tests. We conclude that the proposed a priori method yields acceptable simulations with only a 50% probability, a figure which may be greatly increased through a posteriori calibration. Modellers should thus exercise caution when extrapolating their models to a large sample of pedo-climatic conditions for which they have only limited information.

Cooperative games with size-truncated information

[Eng] We study the marginal worth vectors and their convex hull, the socalled Weber set, from the original coalitional game and the transformed one, which is called the Weber set of level k. We prove that the core of the original game is included in each of the Weber set of level k, for any k, and that the Weber sets of consecutive levels form a chain if and only if the original game is 0-monotone. Even if the game is not 0-monotone, the intersection of the Weber sets for consecutive levels is always not empty, what is not the case for non-consecutive ones. Spanish education system.

Cooperative games with size-truncated information

[Eng] We study the marginal worth vectors and their convex hull, the socalled Weber set, from the original coalitional game and the transformed one, which is called the Weber set of level k. We prove that the core of the original game is included in each of the Weber set of level k, for any k, and that the Weber sets of consecutive levels form a chain if and only if the original game is 0-monotone. Even if the game is not 0-monotone, the intersection of the Weber sets for consecutive levels is always not empty, what is not the case for non-consecutive ones. Spanish education system.