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.

Multiple paths extraction in images using a constrained expanded trellis

Single shortest path extraction algorithms have been used in a number of areas such as network flow and image analysis. In image analysis, shortest path techniques can be used for object boundary detection, crack detection, or stereo disparity estimation. Sometimes one needs to find multiple paths as opposed to a single path in a network or an image where the paths must satisfy certain constraints. In this paper, we propose a new algorithm to extract multiple paths simultaneously within an image using a constrained expanded trellis (CET) for feature extraction and object segmentation. We also give a number of application examples for our multiple paths extraction algorithm.

Approximate processing of massive continuous quantile queries over high-speed data streams

Quantile computation has many applications including data mining and financial data analysis. It has been shown that an is an element of-approximate summary can be maintained so that, given a quantile query d (phi, is an element of), the data item at rank [phi N] may be approximately obtained within the rank error precision is an element of N over all N data items in a data stream or in a sliding window. However, scalable online processing of massive continuous quantile queries with different phi and is an element of poses a new challenge because the summary is continuously updated with new arrivals of data items. In this paper, first we aim to dramatically reduce the number of distinct query results by grouping a set of different queries into a cluster so that they can be processed virtually as a single query while the precision requirements from users can be retained. Second, we aim to minimize the total query processing costs. Efficient algorithms are developed to minimize the total number of times for reprocessing clusters and to produce the minimum number of clusters, respectively. The techniques are extended to maintain near-optimal clustering when queries are registered and removed in an arbitrary fashion against whole data streams or sliding windows. In addition to theoretical analysis, our performance study indicates that the proposed techniques are indeed scalable with respect to the number of input queries as well as the number of items and the item arrival rate in a data stream.

Coloring random graphs and maximizing local diversity

We study a variation of the graph coloring problem on random graphs of finite average connectivity. Given the number of colors, we aim to maximize the number of different colors at neighboring vertices (i.e. one edge distance) of any vertex. Two efficient algorithms, belief propagation and Walksat are adapted to carry out this task. We present experimental results based on two types of random graphs for different system sizes and identify the critical value of the connectivity for the algorithms to find a perfect solution. The problem and the suggested algorithms have practical relevance since various applications, such as distributed storage, can be mapped onto this problem.

The Knowledge: Its Presentation and Role in Recognition Systems

The concept of knowledge is the central one used when solving the various problems of data mining and pattern recognition in finite spaces of Boolean or multi-valued attributes. A special form of knowledge representation, called implicative regularities, is proposed for applying in two powerful tools of modern logic: the inductive inference and the deductive inference. The first one is used for extracting the knowledge from the data. The second is applied when the knowledge is used for calculation of the goal attribute values. A set of efficient algorithms was developed for that, dealing with Boolean functions and finite predicates represented by logical vectors and matrices.

On the Recursive Estimation of the Location and of the Size of the Mode of a Probability Density

2000 Mathematics Subject Classification: 62G07, 62L20.

Scaling geospatial searches in large spatial databases

Modern geographical databases, which are at the core of geographic information systems (GIS), store a rich set of aspatial attributes in addition to geographic data. Typically, aspatial information comes in textual and numeric format. Retrieving information constrained on spatial and aspatial data from geodatabases provides GIS users the ability to perform more interesting spatial analyses, and for applications to support composite location-aware searches; for example, in a real estate database: “Find the nearest homes for sale to my current location that have backyard and whose prices are between $50,000 and $80,000”. Efficient processing of such queries require combined indexing strategies of multiple types of data. Existing spatial query engines commonly apply a two-filter approach (spatial filter followed by nonspatial filter, or viceversa), which can incur large performance overheads. On the other hand, more recently, the amount of geolocation data has grown rapidly in databases due in part to advances in geolocation technologies (e.g., GPS-enabled smartphones) that allow users to associate location data to objects or events. The latter poses potential data ingestion challenges of large data volumes for practical GIS databases. In this dissertation, we first show how indexing spatial data with R-trees (a typical data pre-processing task) can be scaled in MapReduce—a widely-adopted parallel programming model for data intensive problems. The evaluation of our algorithms in a Hadoop cluster showed close to linear scalability in building R-tree indexes. Subsequently, we develop efficient algorithms for processing spatial queries with aspatial conditions. Novel techniques for simultaneously indexing spatial with textual and numeric data are developed to that end. Experimental evaluations with real-world, large spatial datasets measured query response times within the sub-second range for most cases, and up to a few seconds for a small number of cases, which is reasonable for interactive applications. Overall, the previous results show that the MapReduce parallel model is suitable for indexing tasks in spatial databases, and the adequate combination of spatial and aspatial attribute indexes can attain acceptable response times for interactive spatial queries with constraints on aspatial data.

Solving satisfiability, *implication, and equivalence problems in database systems

Satisfiability, implication and equivalence problems are important and widely-encountered database problems that need to be efficiently and effectively solved. We provide a comprehensive and systematic study of these problems. We consider three popular types of arithmetic inequalities, (X op C), (X op Y), and (X op Y + C), where X and Y are attributes, C is a constant of the domain of X, and op $\in\ \{{<},\ {\le},\ {=},\ {\not=},\ {>},\ {\ge}\}.$ These inequalities are most frequently used in a database system, since the first type of inequalities represents $\theta$-join, the second type represents selection, and the third type is popular in deductive databases. We study the problems under the integer domain and the real domain, as well as under two different operator sets.^ Our results show that solutions under different domains and/or different operator sets are quite different. In this dissertation, we either report the first necessary and sufficient conditions as well as their efficient algorithms with complexity analysis, or provide improved algorithms. ^

Processing the Intracardiac Electrogram for Atrial Fibrillation Ablation

Atrial fibrillation (AF) is a major global health issue as it is the most prevalent sustained supraventricular arrhythmia. Catheter-based ablation of some parts of the atria is considered an effective treatment of AF. The main objective of this research is to analyze atrial intracardiac electrograms (IEGMs) and extract insightful information for the ablation therapy. Throughout this thesis we propose several computationally efficient algorithms that take streams of IEGMs from different atrial sites as the input signals, sequentially analyze them in various domains (e.g., time and frequency), and create color-coded three-dimensional map of the atria to be used in the ablation therapy.

A Finite Element to Perform 3D Shakedown Analysis for Limited Kinematic Hardening Materials

The use of the Design by Analysis (DBA) route is a modern trend in pressure vessel and piping international codes in mechanical engineering. However, to apply the DBA to structures under variable mechanical and thermal loads, it is necessary to assure that the plastic collapse modes, alternate plasticity and incremental collapse (with instantaneous plastic collapse as a particular case), be precluded. The tool available to achieve this target is the shakedown theory. Unfortunately, the practical numerical applications of the shakedown theory result in very large nonlinear optimization problems with nonlinear constraints. Precise, robust and efficient algorithms and finite elements to solve this problem in finite dimension has been a more recent achievements. However, to solve real problems in an industrial level, it is necessary also to consider more realistic material properties as well as to accomplish 3D analysis. Limited kinematic hardening, is a typical property of the usual steels and it should be considered in realistic applications. In this paper, a new finite element with internal thermodynamical variables to model kinematic hardening materials is developed and tested. This element is a mixed ten nodes tetrahedron and through an appropriate change of variables is possible to embed it in a shakedown analysis software developed by Zouain and co-workers for elastic ideally-plastic materials, and then use it to perform 3D shakedown analysis in cases with limited kinematic hardening materials

The Influence of Limited Kinematic Hardening in Shakedown Analysis

The use of the Design by Analysis concept is a trend in modern pressure vessel and piping calculations. DBA flexibility allow us to deal with unexpected configurations detected at in-service inspections. It is also important, in life extension calculations, when deviations of the original standard hypotesis adopted initially in Design by Formula, can happen. To apply the DBA to structures under variable mechanic and thermal loads, it is necessary that, alternate plasticity and incremental collapse (with instantaneous plastic collapse as a particular case), be precluded. These are two basic failure modes considered by ASME or European Standards in DBA. The shakedown theory is the tool available to achieve this goal. In order to apply it, is necessary only the range of the variable loads and the material properties. Precise, robust and efficient algorithms to solve the very large nonlinear optimization problems generated in numerical applications of the shakedown theory is a recent achievement. Zouain and co-workers developed one of these algorithms for elastic ideally-plastic materials. But, it is necessary to consider more realistic material properties in real practical applications. This paper shows an enhancement of this algorithm to dealing with limited kinematic hardening, a typical property of the usual steels. This is done using internal thermodynamic variables. A discrete algorithm is obtained using a plane stress, mixed finite element, with internal variable. An example, a beam encased in an end, under constant axial force and variable moment is presented to show the importance of considering the limited kinematic hardening in a shakedown analysis.

Colocated multiple-input multiple-output radars for smart mobility

In recent years, radars have been used in many applications such as precision agriculture and advanced driver assistant systems. Optimal techniques for the estimation of the number of targets and of their coordinates require solving multidimensional optimization problems entailing huge computational efforts. This has motivated the development of sub-optimal estimation techniques able to achieve good accuracy at a manageable computational cost. Another technical issue in advanced driver assistant systems is the tracking of multiple targets. Even if various filtering techniques have been developed, new efficient and robust algorithms for target tracking can be devised exploiting a probabilistic approach, based on the use of the factor graph and the sum-product algorithm. The two contributions provided by this dissertation are the investigation of the filtering and smoothing problems from a factor graph perspective and the development of efficient algorithms for two and three-dimensional radar imaging. Concerning the first contribution, a new factor graph for filtering is derived and the sum-product rule is applied to this graphical model; this allows to interpret known algorithms and to develop new filtering techniques. Then, a general method, based on graphical modelling, is proposed to derive filtering algorithms that involve a network of interconnected Bayesian filters. Finally, the proposed graphical approach is exploited to devise a new smoothing algorithm. Numerical results for dynamic systems evidence that our algorithms can achieve a better complexity-accuracy tradeoff and tracking capability than other techniques in the literature. Regarding radar imaging, various algorithms are developed for frequency modulated continuous wave radars; these algorithms rely on novel and efficient methods for the detection and estimation of multiple superimposed tones in noise. The accuracy achieved in the presence of multiple closely spaced targets is assessed on the basis of both synthetically generated data and of the measurements acquired through two commercial multiple-input multiple-output radars.

On the motion planning & control of nonlinear robotic systems

In the last decades, we saw a soaring interest in autonomous robots boosted not only by academia and industry, but also by the ever in- creasing demand from civil users. As a matter of fact, autonomous robots are fast spreading in all aspects of human life, we can see them clean houses, navigate through city traffic, or harvest fruits and vegetables. Almost all commercial drones already exhibit unprecedented and sophisticated skills which makes them suitable for these applications, such as obstacle avoidance, simultaneous localisation and mapping, path planning, visual-inertial odometry, and object tracking. The major limitations of such robotic platforms lie in the limited payload that can carry, in their costs, and in the limited autonomy due to finite battery capability. For this reason researchers start to develop new algorithms able to run even on resource constrained platforms both in terms of computation capabilities and limited types of endowed sensors, focusing especially on very cheap sensors and hardware. The possibility to use a limited number of sensors allowed to scale a lot the UAVs size, while the implementation of new efficient algorithms, performing the same task in lower time, allows for lower autonomy. However, the developed robots are not mature enough to completely operate autonomously without human supervision due to still too big dimensions (especially for aerial vehicles), which make these platforms unsafe for humans, and the high probability of numerical, and decision, errors that robots may make. In this perspective, this thesis aims to review and improve the current state-of-the-art solutions for autonomous navigation from a purely practical point of view. In particular, we deeply focused on the problems of robot control, trajectory planning, environments exploration, and obstacle avoidance.

Data driven regularization models of non-linear ill-posed inverse problems in imaging

Imaging technologies are widely used in application fields such as natural sciences, engineering, medicine, and life sciences. A broad class of imaging problems reduces to solve ill-posed inverse problems (IPs). Traditional strategies to solve these ill-posed IPs rely on variational regularization methods, which are based on minimization of suitable energies, and make use of knowledge about the image formation model (forward operator) and prior knowledge on the solution, but lack in incorporating knowledge directly from data. On the other hand, the more recent learned approaches can easily learn the intricate statistics of images depending on a large set of data, but do not have a systematic method for incorporating prior knowledge about the image formation model. The main purpose of this thesis is to discuss data-driven image reconstruction methods which combine the benefits of these two different reconstruction strategies for the solution of highly nonlinear ill-posed inverse problems. Mathematical formulation and numerical approaches for image IPs, including linear as well as strongly nonlinear problems are described. More specifically we address the Electrical impedance Tomography (EIT) reconstruction problem by unrolling the regularized Gauss-Newton method and integrating the regularization learned by a data-adaptive neural network. Furthermore we investigate the solution of non-linear ill-posed IPs introducing a deep-PnP framework that integrates the graph convolutional denoiser into the proximal Gauss-Newton method with a practical application to the EIT, a recently introduced promising imaging technique. Efficient algorithms are then applied to the solution of the limited electrods problem in EIT, combining compressive sensing techniques and deep learning strategies. Finally, a transformer-based neural network architecture is adapted to restore the noisy solution of the Computed Tomography problem recovered using the filtered back-projection method.

A deep learning model via thermodynamics and condensed matter physics

Deep Learning architectures give brilliant results in a large variety of fields, but a comprehensive theoretical description of their inner functioning is still lacking. In this work, we try to understand the behavior of neural networks by modelling in the frameworks of Thermodynamics and Condensed Matter Physics. We approach neural networks as in a real laboratory and we measure the frequency spectrum and the entropy of the weights of the trained model. The stochasticity of the training occupies a central role in the dynamics of the weights and makes it difficult to assimilate neural networks to simple physical systems. However, the analogy with Thermodynamics and the introduction of a well defined temperature leads us to an interesting result: if we eliminate from a CNN the "hottest" filters, the performance of the model remains the same, whereas, if we eliminate the "coldest" ones, the performance gets drastically worst. This result could be exploited in the realization of a training loop which eliminates the filters that do not contribute to loss reduction. In this way, the computational cost of the training will be lightened and more importantly this would be done by following a physical model. In any case, beside important practical applications, our analysis proves that a new and improved modeling of Deep Learning systems can pave the way to new and more efficient algorithms.