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.

Binary metal oxides for composite ultrafiltration membranes

A new ultrafiltration membrane was developed by the incorporation of binary metal oxides inside polyethersulfone. Physico-chemical characterization of the binary metal oxides demonstrated that the presence of Ti in the TiO2?ZrO2 system results in an increase of the size of the oxides, and also their dispersity. The crystalline phases of the synthesized binary metal oxides were identified as srilankite and zirconium titanium oxide. The effect of the addition of ZrO2 can be expressed in terms of the inhibition of crystal growth of anocrystalline TiO2 during the synthesis process. For photocatalytic applications the band gap of the synthesized semiconductors was determined, confirming a gradual increase (blue shift) in the band gap as the amount of Zr loading increases. Distinct distributions of binary metal oxides were found along the permeation axis for the synthesized membranes. Particles with Ti are more uniformly dispersed throughout the membrane cross-section. The physico-chemical characterization of membranes showed a strong correlation between some key membrane properties and the spatial particle distribution in the membrane structure. The proximity of metal oxide fillers to the membrane surface determines the hydrophilicity and porosity of modified membranes. Membranes incorporating binary metal oxides were found to be promising candidates for wastewater treatment by ultrafiltration, considering the observed improvement influx and anti-fouling properties of doped membranes. Multi-run fouling tests of doped membranes confirmed the stability of permeation through membranes embedded with binary TiO2?ZrO2 particles.

Entre: de repente, sin fin, lo innombrable

Etiquetamos para reducir nuestra incertidumbre; clasificamos en base a términos opuestos para poder entender. El universo y el espacio construido en particular, se explican desde una arquitectónica dual: dentro – fuera, arriba – abajo, derecha – izquierda, día – noche, hombre – mujer. Lo que nos diferencia como grupo, raza o género, distinguiendo los modos de vivir, las ideologías y las teorías, es la relación que establecemos entre los términos opuestos: entre lo individual y lo colectivo, lo privado y lo público, la imaginación y la realidad, la identidad y la otredad, el orden y el caos, el deseo y la saciedad. El afán clasificatorio dicotómico de la realidad que la modernidad lleva a su extremo, hiere la vida: la mutua exclusión de los opuestos elimina la distancia, el espacio-tiempo entre ambos, que es donde la vida se sitúa. La concepción dual que rige nuestro conocimiento contamina también la relación entre los arquitectos y la sociedad, siendo la causa del ambiente tóxico que envuelve al habitante que ya no se identifica con los lugares que habita. Puede que sea oportuno pasar del pensamiento binario a una lógica de lo intersticial que abandone la dualidad para instalarse en el Entre; los arquitectos serían mediadores entre el poder y la vida, sintiendo el Entre como el transcurso de la vida y la potencia de interacción: los lugares ambiguos e intermedios, es donde sucede el encuentro entre los términos, entre arquitectos y habitantes, entre la imaginación y la realidad, entre tú y yo. ABSTRACT We label to reduce our uncertainty; we classify based on opposites to understand. The universe and all constructed space in particular, are explained from a dual architecture: inside - out, up - down, right - left, day - night, male - female, black - white. What differentiate us as a group, race, gender, distinguishing the lifestyles, ideologies and theories, is how we draw the relation between the opposites: between the individual and the collective, private and public, imagination and reality , identity and otherness, order and disorder, desire and satiety. The dichotomous classification of reality that modernity carried to its extreme, hurts life: the mutual exclusion of opposites eliminates the distance, the space-time between the two, which is where life is located. The dual conception that governs our knowledge has also contaminated the relationship between architect and society, being the cause of the toxic environment that surrounds the inhabitant who no longer identify himself with the places he inhabit. It may be appropriate pass from binary thinking to a logic of the interstitial which abandon duality to settle in Between; architect then will be the mediator between authorities and life, sensing the Between as a flowing of life a potency of interaction rather than a separation between the extremes; ambiguous, in –between, places are where the encounter between opposites happens, between the architect and the inhabitant, between imagination and reality, between you and me.

Human-computer interaction based on visual hand-gesture recognition using volumetric spatiograms of local binary patterns

A more natural, intuitive, user-friendly, and less intrusive Human–Computer interface for controlling an application by executing hand gestures is presented. For this purpose, a robust vision-based hand-gesture recognition system has been developed, and a new database has been created to test it. The system is divided into three stages: detection, tracking, and recognition. The detection stage searches in every frame of a video sequence potential hand poses using a binary Support Vector Machine classifier and Local Binary Patterns as feature vectors. These detections are employed as input of a tracker to generate a spatio-temporal trajectory of hand poses. Finally, the recognition stage segments a spatio-temporal volume of data using the obtained trajectories, and compute a video descriptor called Volumetric Spatiograms of Local Binary Patterns (VS-LBP), which is delivered to a bank of SVM classifiers to perform the gesture recognition. The VS-LBP is a novel video descriptor that constitutes one of the most important contributions of the paper, which is able to provide much richer spatio-temporal information than other existing approaches in the state of the art with a manageable computational cost. Excellent results have been obtained outperforming other approaches of the state of the art.

Soundscape quality analysis by fuzzy logic: A field study in Cordoba, Argentina

This research studies urban soundscapes through the comparative analysis of twelve public open spaces in the city of Córdoba (Argentina), taken as case studies. The work aims to examine selection of indicators and assessment tools intended to characterize soundscape quality. The field study was carried out through surveys and acoustic and psychoacoustic indicators, that are used together to objectively describe the sound quality of urban spaces. The study shows that, while there is a relationship of these indicators with the sound quality of the spaces, this is not linear. Their relative importance or influence depends on the interrelations occurring between the parameters studied. A model analyzing and correlating the parameters with the sound quality, based on the postulates of fuzzy logic, was applied as a tool of analysis, and it was seen to achieve a very close approximation to the subjective or perceptual response of the inhabitants. This close match between the model results and the perceptual response of the users confirms the fuzzy model as an effective tool for the study, not only of soundscapes, but also for those situations in which objective parameters must be related to the perceptual response of users.

On the classification of binary shifts of finite commutant index

We provide a complete classification up to conjugacy of the binary shifts of finite commutant index on the hyperfinite II1, factor. There is a natural correspondence between the conjugacy classes of these shifts and polynomials over GF(2) satisfying a certain duality condition.

Small molecule developmental screens reveal the logic and timing of vertebrate development

Much has been learned about vertebrate development by random mutagenesis followed by phenotypic screening and by targeted gene disruption followed by phenotypic analysis in model organisms. Because the timing of many developmental events is critical, it would be useful to have temporal control over modulation of gene function, a luxury frequently not possible with genetic mutants. Here, we demonstrate that small molecules capable of conditional gene product modulation can be identified through developmental screens in zebrafish. We have identified several small molecules that specifically modulate various aspects of vertebrate ontogeny, including development of the central nervous system, the cardiovascular system, the neural crest, and the ear. Several of the small molecules identified allowed us to dissect the logic of melanocyte and otolith development and to identify critical periods for these events. Small molecules identified in this way offer potential to dissect further these and other developmental processes and to identify novel genes involved in vertebrate development.

Logic gates using high Rydberg states

Connected logic gates can be operated on the levels of one molecule by making use of the special properties of high Rydberg states. Explicit experimental results for the NO molecule are provided as an example. A number of other options, including that of several gates concatenated so as to operate as a full adder, are discussed. Specific properties of high Rydberg states that are used are: their autoionization is delayed so that they can be distinguished from direct multiphoton ionization, during their long life such states also can decay by energy transfer to the molecular core in a way that can be controlled by the judicious application of very weak external electrical fields, and the Rydberg states can be detected by the application of an ionizing electrical field. The combination of two (or three) color photons with and without external weak fields allows the construction of quite elaborate logic circuit diagrams and shows that taking advantage of the different intramolecular dynamics of levels that differ by their excitation enables the compounding of logic operations on one molecular frame.

Extremely sensitive, background-free gene detection using binary probes and beta replicase.

We have developed a specific and sensitive nucleic acid amplification assay that is suitable for routine gene detection. The assay is based on a novel molecular genetic strategy in which two different RNA probes are hybridized to adjacent positions on a target nucleic acid and then ligated to form an amplifiable reporter RNA. The reporter RNA is then replicated up to a hundred billion-fold in a 30-min isothermal reaction that signals the presence of the target. The assay can detect fewer than 100 nucleic acid molecules; it provides quantitative results over a wide range of target concentrations and it employs a universal format that can detect any infectious agent.

Structure-activity relationships derived by machine learning: the use of atoms and their bond connectivities to predict mutagenicity by inductive logic programming.

We present a general approach to forming structure-activity relationships (SARs). This approach is based on representing chemical structure by atoms and their bond connectivities in combination with the inductive logic programming (ILP) algorithm PROGOL. Existing SAR methods describe chemical structure by using attributes which are general properties of an object. It is not possible to map chemical structure directly to attribute-based descriptions, as such descriptions have no internal organization. A more natural and general way to describe chemical structure is to use a relational description, where the internal construction of the description maps that of the object described. Our atom and bond connectivities representation is a relational description. ILP algorithms can form SARs with relational descriptions. We have tested the relational approach by investigating the SARs of 230 aromatic and heteroaromatic nitro compounds. These compounds had been split previously into two subsets, 188 compounds that were amenable to regression and 42 that were not. For the 188 compounds, a SAR was found that was as accurate as the best statistical or neural network-generated SARs. The PROGOL SAR has the advantages that it did not need the use of any indicator variables handcrafted by an expert, and the generated rules were easily comprehensible. For the 42 compounds, PROGOL formed a SAR that was significantly (P < 0.025) more accurate than linear regression, quadratic regression, and back-propagation. This SAR is based on an automatically generated structural alert for mutagenicity.

Simultaneous optical and X-ray observations of flares and rotational modulation on the RS CVn binary HR 1099 (V711 Tau) from the MUSICOS 1998 campaign

We present simultaneous and continuous observations of the Hα, Hβ, He I D_3, Na I D_1,D_2 doublet and the Ca II H&K lines for the RS CVn system HR 1099. The spectroscopic observations were obtained during the MUSICOS 1998 campaign involving several observatories and instruments, both echelle and long-slit spectrographs. During this campaign, HR 1099 was observed almost continuously for more than 8 orbits of 2^d.8. Two large optical flares were observed, both showing an increase in the emission of Hα, Ca II H K, Hβ and He I D_3 and a strong filling-in of the Na I D_1, D_2 doublet. Contemporary photometric observations were carried out with the robotic telescopes APT-80 of Catania and Phoenix-25 of Fairborn Observatories. Maps of the distribution of the spotted regions on the photosphere of the binary components were derived using the Maximum Entropy and Tikhonov photometric regularization criteria. Rotational modulation was observed in Hα and He I D_3 in anti-correlation with the photometric light curves. Both flares occurred at the same binary phase (0.85), suggesting that these events took place in the same active region. Simultaneous X-ray observations, performed by ASM on board RXTE, show several flare-like events, some of which correlate well with the observed optical flares. Rotational modulation in the X-ray light curve has been detected with minimum flux when the less active G5 V star was in front. A possible periodicity in the X-ray flare-like events was also found.

Clarity, Light, and Logic : Parallels between Olafur Eliasson’s The weather project and the Gothic Cathedral

This Master’s Research Paper investigates Olafur Eliasson’s The weather project as a case study for the dialogue between Gothic artistic principles and prominent elements of contemporary art. A product of a post-modern mindset, weakened historicity allows us to examine these connections anew; past, present, and future blur and artists (and viewers) have the whole of time from which to gain inspiration and meaning in works of art. I demonstrate similarities through theories on phenomenology; the spatiotemporal relationship between viewer and artwork; the convergence of art and science; and the communal, quasi-liminal experience of pilgrimage. I embrace Eliasson’s belief in the self-reflexive potential of art and the importance of the viewer’s own values, memories, and methods of seeing. This new interpretive layer will hopefully offer a richer experience for future participants of both Gothic cathedrals and environments produced by Studio Olafur Eliasson.

An approach based on Logic Forms and WordNet relationships to Textual Entailment performance

This paper outlines the approach adopted by the PLSI research group at University of Alicante in the PASCAL-2006 second Recognising Textual Entailment challenge. Our system is composed of several components. On the one hand, the first component performs the derivation of the logic forms of the text/hypothesis pairs and, on the other hand, the second component provides us with a similarity score given by the semantic relations between the derived logic forms. In order to obtain this score we apply several measures of similitude and relatedness based on the structure and content of WordNet.

Applying logic forms and statistical methods to CL-SR performance

This paper describes a CL-SR system that employs two different techniques: the first one is based on NLP rules that consist on applying logic forms to the topic processing while the second one basically consists on applying the IR-n statistical search engine to the spoken document collection. The application of logic forms to the topics allows to increase the weight of topic terms according to a set of syntactic rules. Thus, the weights of the topic terms are used by IR-n system in the information retrieval process.

Correlation of the liquid–liquid equilibrium data for specific ternary systems with one or two partially miscible binary subsystems

This paper presents the results of a liquid–liquid equilibrium data correlation for 11 ternary systems which have not been previously fitted using the NRTL model or, when they have, the results presented in the literature are inconsistent with the experimental behavior of the system. These ternary systems include mixtures with one or two partially miscible pairs. During the correlation process, new restrictions were imposed on the values for the NRTL binary parameters to ensure correct prediction of the total or partial miscibility for the binary pairs involved. In addition, topological concepts related to the Gibbs stability test have been applied in order to validate the results in the whole range of compositions.