Feigenbaum graphs at the onset of chaos

We analyze the properties of networks obtained from the trajectories of unimodal maps at the transi- tion to chaos via the horizontal visibility (HV) algorithm. We find that the network degrees fluctuate at all scales with amplitude that increases as the size of the network grows, and can be described by a spectrum of graph-theoretical generalized Lyapunov exponents. We further define an entropy growth rate that describes the amount of information created along paths in network space, and find that such en- tropy growth rate coincides with the spectrum of generalized graph-theoretical exponents, constituting a set of Pesin-like identities for the network.

Detecting periodicity with horizontal visibility graphs

The horizontal visibility algorithm was recently introduced as a mapping between time series and networks. The challenge lies in characterizing the structure of time series (and the processes that generated those series) using the powerful tools of graph theory. Recent works have shown that the visibility graphs inherit several degrees of correlations from their associated series, and therefore such graph theoretical characterization is in principle possible. However, both the mathematical grounding of this promising theory and its applications are in its infancy. Following this line, here we address the question of detecting hidden periodicity in series polluted with a certain amount of noise. We first put forward some generic properties of horizontal visibility graphs which allow us to define a (graph theoretical) noise reduction filter. Accordingly, we evaluate its performance for the task of calculating the period of noisy periodic signals, and compare our results with standard time domain (autocorrelation) methods. Finally, potentials, limitations and applications are discussed.

The Phase Space as a New Representation of the Dynamical Behaviour of Temperature and Enthalpy in a Reefer monitored with a Multidistributed Sensors Network

The study of temperature gradients in cold stores and containers is a critical issue in the food industry for the quality assurance of products during transport, as well as forminimizing losses. The objective of this work is to develop a new methodology of data analysis based on phase space graphs of temperature and enthalpy, collected by means of multidistributed, low cost and autonomous wireless sensors and loggers. A transoceanic refrigerated transport of lemons in a reefer container ship from Montevideo (Uruguay) to Cartagena (Spain) was monitored with a network of 39 semi-passive TurboTag RFID loggers and 13 i-button loggers. Transport included intermodal transit from transoceanic to short shipping vessels and a truck trip. Data analysis is carried out using qualitative phase diagrams computed on the basis of Takens?Ruelle reconstruction of attractors. Fruit stress is quantified in terms of the phase diagram area which characterizes the cyclic behaviour of temperature. Areas within the enthalpy phase diagram computed for the short sea shipping transport were 5 times higher than those computed for the long sea shipping, with coefficients of variation above 100% for both periods. This new methodology for data analysis highlights the significant heterogeneity of thermohygrometric conditions at different locations in the container.

Minimal strong digraphs

We introduce adequate concepts of expansion of a digraph to obtain a sequential construction of minimal strong digraphs. We obtain a characterization of the class of minimal strong digraphs whose expansion preserves the property of minimality. We prove that every minimal strong digraph of order nmayor que=2 is the expansion of a minimal strong digraph of order n-1 and we give sequentially generative procedures for the constructive characterization of the classes of minimal strong digraphs. Finally we describe algorithms to compute unlabeled minimal strong digraphs and their isospectral classes.

Horizontal visibility graphs generated by type-I intermittency

The type-I intermittency route to (or out of) chaos is investigated within the horizontal visibility (HV) graph theory. For that purpose, we address the trajectories generated by unimodal maps close to an inverse tangent bifurcation and construct their associatedHVgraphs.We showhowthe alternation of laminar episodes and chaotic bursts imprints a fingerprint in the resulting graph structure. Accordingly, we derive a phenomenological theory that predicts quantitative values for several network parameters. In particular, we predict that the characteristic power-law scaling of the mean length of laminar trend sizes is fully inherited by the variance of the graph degree distribution, in good agreement with the numerics. We also report numerical evidence on how the characteristic power-law scaling of the Lyapunov exponent as a function of the distance to the tangent bifurcation is inherited in the graph by an analogous scaling of block entropy functionals defined on the graph. Furthermore, we are able to recast the full set of HV graphs generated by intermittent dynamics into a renormalization-group framework, where the fixed points of its graph-theoretical renormalization-group flow account for the different types of dynamics.We also establish that the nontrivial fixed point of this flow coincides with the tangency condition and that the corresponding invariant graph exhibits extremal entropic properties.

Quasiperiodic graphs at the onset of chaos

We examine the connectivity fluctuations across networks obtained when the horizontal visibility (HV) algorithm is used on trajectories generated by nonlinear circle maps at the quasiperiodic transition to chaos. The resultant HV graph is highly anomalous as the degrees fluctuate at all scales with amplitude that increases with the size of the network. We determine families of Pesin-like identities between entropy growth rates and generalized graph-theoretical Lyapunov exponents. An irrational winding number with pure periodic continued fraction characterizes each family. We illustrate our results for the so-called golden, silver, and bronze numbers

Mapping Dynamics into Graphs. The Visibility Algorithm

Si no tenemos en cuenta posibles procesos subyacentes con significado físico, químico, económico, etc., podemos considerar una serie temporal como un mero conjunto ordenado de valores y jugar con él algún inocente juego matemático como transformar dicho conjunto en otro objeto con la ayuda de una operación matemática para ver qué sucede: qué propiedades del conjunto original se conservan, cuáles se transforman y cómo, qué podemos decir de alguna de las dos representaciones matemáticas del objeto con sólo atender a la otra... Este ejercicio sería de cierto interés matemático por sí solo. Ocurre, además, que las series temporales son un método universal de extraer información de sistemas dinámicos en cualquier campo de la ciencia. Esto hace ganar un inesperado interés práctico al juego matemático anteriormente descrito, ya que abre la posibilidad de analizar las series temporales (vistas ahora como evolución temporal de procesos dinámicos) desde una nueva perspectiva. Hemos para esto de asumir la hipótesis de que la información codificada en la serie original se conserva de algún modo en la transformación (al menos una parte de ella). El interés resulta completo cuando la nueva representación del objeto pertencece a un campo de la matemáticas relativamente maduro, en el cual la información codificada en dicha representación puede ser descodificada y procesada de manera efectiva. ABSTRACT Disregarding any underlying process (and therefore any physical, chemical, economical or whichever meaning of its mere numeric values), we can consider a time series just as an ordered set of values and play the naive mathematical game of turning this set into a different mathematical object with the aids of an abstract mapping, and see what happens: which properties of the original set are conserved, which are transformed and how, what can we say about one of the mathematical representations just by looking at the other... This exercise is of mathematical interest by itself. In addition, it turns out that time series or signals is a universal method of extracting information from dynamical systems in any field of science. Therefore, the preceding mathematical game gains some unexpected practical interest as it opens the possibility of analyzing a time series (i.e. the outcome of a dynamical process) from an alternative angle. Of course, the information stored in the original time series should be somehow conserved in the mapping. The motivation is completed when the new representation belongs to a relatively mature mathematical field, where information encoded in such a representation can be effectively disentangled and processed. This is, in a nutshell, a first motivation to map time series into networks.

Self-organizing cultured neural networks: Image analysis techniques for longitudinal tracking and modeling of the underlying network structure

Esta tesis estudia la evolución estructural de conjuntos de neuronas como la capacidad de auto-organización desde conjuntos de neuronas separadas hasta que forman una red (clusterizada) compleja. Esta tesis contribuye con el diseño e implementación de un algoritmo no supervisado de segmentación basado en grafos con un coste computacional muy bajo. Este algoritmo proporciona de forma automática la estructura completa de la red a partir de imágenes de cultivos neuronales tomadas con microscopios de fase con una resolución muy alta. La estructura de la red es representada mediante un objeto matemático (matriz) cuyos nodos representan a las neuronas o grupos de neuronas y los enlaces son las conexiones reconstruidas entre ellos. Este algoritmo extrae también otras medidas morfológicas importantes que caracterizan a las neuronas y a las neuritas. A diferencia de otros algoritmos hasta el momento, que necesitan de fluorescencia y técnicas inmunocitoquímicas, el algoritmo propuesto permite el estudio longitudinal de forma no invasiva posibilitando el estudio durante la formación de un cultivo. Además, esta tesis, estudia de forma sistemática un grupo de variables topológicas que garantizan la posibilidad de cuantificar e investigar la progresión de las características principales durante el proceso de auto-organización del cultivo. Nuestros resultados muestran la existencia de un estado concreto correspondiente a redes con configuracin small-world y la emergencia de propiedades a micro- y meso-escala de la estructura de la red. Finalmente, identificamos los procesos físicos principales que guían las transformaciones morfológicas de los cultivos y proponemos un modelo de crecimiento de red que reproduce el comportamiento cuantitativamente de las observaciones experimentales. ABSTRACT The thesis analyzes the morphological evolution of assemblies of living neurons, as they self-organize from collections of separated cells into elaborated, clustered, networks. In particular, it contributes with the design and implementation of a graph-based unsupervised segmentation algorithm, having an associated very low computational cost. The processing automatically retrieves the whole network structure from large scale phase-contrast images taken at high resolution throughout the entire life of a cultured neuronal network. The network structure is represented by a mathematical object (a matrix) in which nodes are identified neurons or neurons clusters, and links are the reconstructed connections between them. The algorithm is also able to extract any other relevant morphological information characterizing neurons and neurites. More importantly, and at variance with other segmentation methods that require fluorescence imaging from immunocyto- chemistry techniques, our measures are non invasive and entitle us to carry out a fully longitudinal analysis during the maturation of a single culture. In turn, a systematic statistical analysis of a group of topological observables grants us the possibility of quantifying and tracking the progression of the main networks characteristics during the self-organization process of the culture. Our results point to the existence of a particular state corresponding to a small-world network configuration, in which several relevant graphs micro- and meso-scale properties emerge. Finally, we identify the main physical processes taking place during the cultures morphological transformations, and embed them into a simplified growth model that quantitatively reproduces the overall set of experimental observations.

Self-organizing cultured neural networks: Image analysis techniques for longitudinal tracking and modeling of the underlying network structure (versión actualizada)

Esta tesis estudia la evolución estructural de conjuntos de neuronas como la capacidad de auto-organización desde conjuntos de neuronas separadas hasta que forman una red (clusterizada) compleja. Esta tesis contribuye con el diseño e implementación de un algoritmo no supervisado de segmentación basado en grafos con un coste computacional muy bajo. Este algoritmo proporciona de forma automática la estructura completa de la red a partir de imágenes de cultivos neuronales tomadas con microscopios de fase con una resolución muy alta. La estructura de la red es representada mediante un objeto matemático (matriz) cuyos nodos representan a las neuronas o grupos de neuronas y los enlaces son las conexiones reconstruidas entre ellos. Este algoritmo extrae también otras medidas morfológicas importantes que caracterizan a las neuronas y a las neuritas. A diferencia de otros algoritmos hasta el momento, que necesitan de fluorescencia y técnicas inmunocitoquímicas, el algoritmo propuesto permite el estudio longitudinal de forma no invasiva posibilitando el estudio durante la formación de un cultivo. Además, esta tesis, estudia de forma sistemática un grupo de variables topológicas que garantizan la posibilidad de cuantificar e investigar la progresión de las características principales durante el proceso de auto-organización del cultivo. Nuestros resultados muestran la existencia de un estado concreto correspondiente a redes con configuracin small-world y la emergencia de propiedades a micro- y meso-escala de la estructura de la red. Finalmente, identificamos los procesos físicos principales que guían las transformaciones morfológicas de los cultivos y proponemos un modelo de crecimiento de red que reproduce el comportamiento cuantitativamente de las observaciones experimentales. ABSTRACT The thesis analyzes the morphological evolution of assemblies of living neurons, as they self-organize from collections of separated cells into elaborated, clustered, networks. In particular, it contributes with the design and implementation of a graph-based unsupervised segmentation algorithm, having an associated very low computational cost. The processing automatically retrieves the whole network structure from large scale phase-contrast images taken at high resolution throughout the entire life of a cultured neuronal network. The network structure is represented by a mathematical object (a matrix) in which nodes are identified neurons or neurons clusters, and links are the reconstructed connections between them. The algorithm is also able to extract any other relevant morphological information characterizing neurons and neurites. More importantly, and at variance with other segmentation methods that require fluorescence imaging from immunocyto- chemistry techniques, our measures are non invasive and entitle us to carry out a fully longitudinal analysis during the maturation of a single culture. In turn, a systematic statistical analysis of a group of topological observables grants us the possibility of quantifying and tracking the progression of the main networks characteristics during the self-organization process of the culture. Our results point to the existence of a particular state corresponding to a small-world network configuration, in which several relevant graphs micro- and meso-scale properties emerge. Finally, we identify the main physical processes taking place during the cultures morphological transformations, and embed them into a simplified growth model that quantitatively reproduces the overall set of experimental observations.

Strong Connectivity in Directed Hypergraphs and its Application to the Atomic Decomposition of Ontologies

Los hipergrafos dirigidos se han empleado en problemas relacionados con lógica proposicional, bases de datos relacionales, linguística computacional y aprendizaje automático. Los hipergrafos dirigidos han sido también utilizados como alternativa a los grafos (bipartitos) dirigidos para facilitar el estudio de las interacciones entre componentes de sistemas complejos que no pueden ser fácilmente modelados usando exclusivamente relaciones binarias. En este contexto, este tipo de representación es conocida como hiper-redes. Un hipergrafo dirigido es una generalización de un grafo dirigido especialmente adecuado para la representación de relaciones de muchos a muchos. Mientras que una arista en un grafo dirigido define una relación entre dos de sus nodos, una hiperarista en un hipergrafo dirigido define una relación entre dos conjuntos de sus nodos. La conexión fuerte es una relación de equivalencia que divide el conjunto de nodos de un hipergrafo dirigido en particiones y cada partición define una clase de equivalencia conocida como componente fuertemente conexo. El estudio de los componentes fuertemente conexos de un hipergrafo dirigido puede ayudar a conseguir una mejor comprensión de la estructura de este tipo de hipergrafos cuando su tamaño es considerable. En el caso de grafo dirigidos, existen algoritmos muy eficientes para el cálculo de los componentes fuertemente conexos en grafos de gran tamaño. Gracias a estos algoritmos, se ha podido averiguar que la estructura de la WWW tiene forma de “pajarita”, donde más del 70% del los nodos están distribuidos en tres grandes conjuntos y uno de ellos es un componente fuertemente conexo. Este tipo de estructura ha sido también observada en redes complejas en otras áreas como la biología. Estudios de naturaleza similar no han podido ser realizados en hipergrafos dirigidos porque no existe algoritmos capaces de calcular los componentes fuertemente conexos de este tipo de hipergrafos. En esta tesis doctoral, hemos investigado como calcular los componentes fuertemente conexos de un hipergrafo dirigido. En concreto, hemos desarrollado dos algoritmos para este problema y hemos determinado que son correctos y cuál es su complejidad computacional. Ambos algoritmos han sido evaluados empíricamente para comparar sus tiempos de ejecución. Para la evaluación, hemos producido una selección de hipergrafos dirigidos generados de forma aleatoria inspirados en modelos muy conocidos de grafos aleatorios como Erdos-Renyi, Newman-Watts-Strogatz and Barabasi-Albert. Varias optimizaciones para ambos algoritmos han sido implementadas y analizadas en la tesis. En concreto, colapsar los componentes fuertemente conexos del grafo dirigido que se puede construir eliminando ciertas hiperaristas complejas del hipergrafo dirigido original, mejora notablemente los tiempos de ejecucion de los algoritmos para varios de los hipergrafos utilizados en la evaluación. Aparte de los ejemplos de aplicación mencionados anteriormente, los hipergrafos dirigidos han sido también empleados en el área de representación de conocimiento. En concreto, este tipo de hipergrafos se han usado para el cálculo de módulos de ontologías. Una ontología puede ser definida como un conjunto de axiomas que especifican formalmente un conjunto de símbolos y sus relaciones, mientras que un modulo puede ser entendido como un subconjunto de axiomas de la ontología que recoge todo el conocimiento que almacena la ontología sobre un conjunto especifico de símbolos y sus relaciones. En la tesis nos hemos centrado solamente en módulos que han sido calculados usando la técnica de localidad sintáctica. Debido a que las ontologías pueden ser muy grandes, el cálculo de módulos puede facilitar las tareas de re-utilización y mantenimiento de dichas ontologías. Sin embargo, analizar todos los posibles módulos de una ontología es, en general, muy costoso porque el numero de módulos crece de forma exponencial con respecto al número de símbolos y de axiomas de la ontología. Afortunadamente, los axiomas de una ontología pueden ser divididos en particiones conocidas como átomos. Cada átomo representa un conjunto máximo de axiomas que siempre aparecen juntos en un modulo. La decomposición atómica de una ontología es definida como un grafo dirigido de tal forma que cada nodo del grafo corresponde con un átomo y cada arista define una dependencia entre una pareja de átomos. En esta tesis introducimos el concepto de“axiom dependency hypergraph” que generaliza el concepto de descomposición atómica de una ontología. Un modulo en una ontología correspondería con un componente conexo en este tipo de hipergrafos y un átomo de una ontología con un componente fuertemente conexo. Hemos adaptado la implementación de nuestros algoritmos para que funcionen también con axiom dependency hypergraphs y poder de esa forma calcular los átomos de una ontología. Para demostrar la viabilidad de esta idea, hemos incorporado nuestros algoritmos en una aplicación que hemos desarrollado para la extracción de módulos y la descomposición atómica de ontologías. A la aplicación la hemos llamado HyS y hemos estudiado sus tiempos de ejecución usando una selección de ontologías muy conocidas del área biomédica, la mayoría disponibles en el portal de Internet NCBO. Los resultados de la evaluación muestran que los tiempos de ejecución de HyS son mucho mejores que las aplicaciones más rápidas conocidas. ABSTRACT Directed hypergraphs are an intuitive modelling formalism that have been used in problems related to propositional logic, relational databases, computational linguistic and machine learning. Directed hypergraphs are also presented as an alternative to directed (bipartite) graphs to facilitate the study of the interactions between components of complex systems that cannot naturally be modelled as binary relations. In this context, they are known as hyper-networks. A directed hypergraph is a generalization of a directed graph suitable for representing many-to-many relationships. While an edge in a directed graph defines a relation between two nodes of the graph, a hyperedge in a directed hypergraph defines a relation between two sets of nodes. Strong-connectivity is an equivalence relation that induces a partition of the set of nodes of a directed hypergraph into strongly-connected components. These components can be collapsed into single nodes. As result, the size of the original hypergraph can significantly be reduced if the strongly-connected components have many nodes. This approach might contribute to better understand how the nodes of a hypergraph are connected, in particular when the hypergraphs are large. In the case of directed graphs, there are efficient algorithms that can be used to compute the strongly-connected components of large graphs. For instance, it has been shown that the macroscopic structure of the World Wide Web can be represented as a “bow-tie” diagram where more than 70% of the nodes are distributed into three large sets and one of these sets is a large strongly-connected component. This particular structure has been also observed in complex networks in other fields such as, e.g., biology. Similar studies cannot be conducted in a directed hypergraph because there does not exist any algorithm for computing the strongly-connected components of the hypergraph. In this thesis, we investigate ways to compute the strongly-connected components of directed hypergraphs. We present two new algorithms and we show their correctness and computational complexity. One of these algorithms is inspired by Tarjan’s algorithm for directed graphs. The second algorithm follows a simple approach to compute the stronglyconnected components. This approach is based on the fact that two nodes of a graph that are strongly-connected can also reach the same nodes. In other words, the connected component of each node is the same. Both algorithms are empirically evaluated to compare their performances. To this end, we have produced a selection of random directed hypergraphs inspired by existent and well-known random graphs models like Erd˝os-Renyi and Newman-Watts-Strogatz. Besides the application examples that we mentioned earlier, directed hypergraphs have also been employed in the field of knowledge representation. In particular, they have been used to compute the modules of an ontology. An ontology is defined as a collection of axioms that provides a formal specification of a set of terms and their relationships; and a module is a subset of an ontology that completely captures the meaning of certain terms as defined in the ontology. In particular, we focus on the modules computed using the notion of syntactic locality. As ontologies can be very large, the computation of modules facilitates the reuse and maintenance of these ontologies. Analysing all modules of an ontology, however, is in general not feasible as the number of modules grows exponentially in the number of terms and axioms of the ontology. Nevertheless, the modules can succinctly be represented using the Atomic Decomposition of an ontology. Using this representation, an ontology can be partitioned into atoms, which are maximal sets of axioms that co-occur in every module. The Atomic Decomposition is then defined as a directed graph such that each node correspond to an atom and each edge represents a dependency relation between two atoms. In this thesis, we introduce the notion of an axiom dependency hypergraph which is a generalization of the atomic decomposition of an ontology. A module in the ontology corresponds to a connected component in the hypergraph, and the atoms of the ontology to the strongly-connected components. We apply our algorithms for directed hypergraphs to axiom dependency hypergraphs and in this manner, we compute the atoms of an ontology. To demonstrate the viability of this approach, we have implemented the algorithms in the application HyS which computes the modules of ontologies and calculate their atomic decomposition. In the thesis, we provide an experimental evaluation of HyS with a selection of large and prominent biomedical ontologies, most of which are available in the NCBO Bioportal. HyS outperforms state-of-the-art implementations in the tasks of extracting modules and computing the atomic decomposition of these ontologies.

Design and implementation of an adaptive dashboard and visualization interface for the dynamic optimization and control of Data Centers

Over the last few years, the Data Center market has increased exponentially and this tendency continues today. As a direct consequence of this trend, the industry is pushing the development and implementation of different new technologies that would improve the energy consumption efficiency of data centers. An adaptive dashboard would allow the user to monitor the most important parameters of a data center in real time. For that reason, monitoring companies work with IoT big data filtering tools and cloud computing systems to handle the amounts of data obtained from the sensors placed in a data center.Analyzing the market trends in this field we can affirm that the study of predictive algorithms has become an essential area for competitive IT companies. Complex algorithms are used to forecast risk situations based on historical data and warn the user in case of danger. Considering that several different users will interact with this dashboard from IT experts or maintenance staff to accounting managers, it is vital to personalize it automatically. Following that line of though, the dashboard should only show relevant metrics to the user in different formats like overlapped maps or representative graphs among others. These maps will show all the information needed in a visual and easy-to-evaluate way. To sum up, this dashboard will allow the user to visualize and control a wide range of variables. Monitoring essential factors such as average temperature, gradients or hotspots as well as energy and power consumption and savings by rack or building would allow the client to understand how his equipment is behaving, helping him to optimize the energy consumption and efficiency of the racks. It also would help him to prevent possible damages in the equipment with predictive high-tech algorithms.