Multiple graph matching and applications

En aplicaciones de reconocimiento de patrones, los grafos con atributos son en gran medida apropiados. Normalmente, los vértices de los grafos representan partes locales de los objetos i las aristas relaciones entre estas partes locales. No obstante, estas ventajas vienen juntas con un severo inconveniente, la distancia entre dos grafos no puede ser calculada en un tiempo polinómico. Considerando estas características especiales el uso de los prototipos de grafos es necesariamente omnipresente. Las aplicaciones de los prototipos de grafos son extensas, siendo las más habituales clustering, clasificación, reconocimiento de objetos, caracterización de objetos i bases de datos de grafos entre otras. A pesar de la diversidad de aplicaciones de los prototipos de grafos, el objetivo del mismo es equivalente en todas ellas, la representación de un conjunto de grafos. Para construir un prototipo de un grafo todos los elementos del conjunto de enteramiento tienen que ser etiquetados comúnmente. Este etiquetado común consiste en identificar que nodos de que grafos representan el mismo tipo de información en el conjunto de entrenamiento. Una vez este etiquetaje común esta hecho, los atributos locales pueden ser combinados i el prototipo construido. Hasta ahora los algoritmos del estado del arte para calcular este etiquetaje común mancan de efectividad o bases teóricas. En esta tesis, describimos formalmente el problema del etiquetaje global i mostramos una taxonomía de los tipos de algoritmos existentes. Además, proponemos seis nuevos algoritmos para calcular soluciones aproximadas al problema del etiquetaje común. La eficiencia de los algoritmos propuestos es evaluada en diversas bases de datos reales i sintéticas. En la mayoría de experimentos realizados los algoritmos propuestos dan mejores resultados que los existentes en el estado del arte.In pattern recognition, the use of graphs is, to a great extend, appropriate and advantageous. Usually, vertices of the graph represent local parts of an object while edges represent relations between these local parts. However, its advantages come together with a sever drawback, the distance between two graph cannot be optimally computed in polynomial time. Taking into account this special characteristic the use of graph prototypes becomes ubiquitous. The applicability of graphs prototypes is extensive, being the most common applications clustering, classification, object characterization and graph databases to name some. However, the objective of a graph prototype is equivalent to all applications, the representation of a set of graph. To synthesize a prototype all elements of the set must be mutually labeled. This mutual labeling consists in identifying which nodes of which graphs represent the same information in the training set. Once this mutual labeling is done the set can be characterized and combined to create a graph prototype. We call this initial labeling a common labeling. Up to now, all state of the art algorithms to compute a common labeling lack on either performance or theoretical basis. In this thesis, we formally describe the common labeling problem and we give a clear taxonomy of the types of algorithms. Six new algorithms that rely on different techniques are described to compute a suboptimal solution to the common labeling problem. The performance of the proposed algorithms is evaluated using an artificial and several real datasets. In addition, the algorithms have been evaluated on several real applications. These applications include graph databases and group-wise image registration. In most of the tests and applications evaluated the presented algorithms have showed a great improvement in comparison to state of the art applications

Geometric, Feature-based and Graph-based Approaches for the Structural Analysis of Protein Binding Sites : Novel Methods and Computational Analysis

In this thesis, protein binding sites are considered. To enable the extraction of information from the space of protein binding sites, these binding sites must be mapped onto a mathematical space. This can be done by mapping binding sites onto vectors, graphs or point clouds. To finally enable a structure on the mathematical space, a distance measure is required, which is introduced in this thesis. This distance measure eventually can be used to extract information by means of data mining techniques

Spotting Keywords in Offline Handwritten Documents Using Hausdorff Edit Distance

Keyword spotting has become a crucial topic in handwritten document recognition, by enabling content-based retrieval of scanned documents using search terms. With a query keyword, one can search and index the digitized handwriting which in turn facilitates understanding of manuscripts. Common automated techniques address the keyword spotting problem through statistical representations. Structural representations such as graphs apprehend the complex structure of handwriting. However, they are rarely used, particularly for keyword spotting techniques, due to high computational costs. The graph edit distance, a powerful and versatile method for matching any type of labeled graph, has exponential time complexity to calculate the similarities of graphs. Hence, the use of graph edit distance is constrained to small size graphs. The recently developed Hausdorff edit distance algorithm approximates the graph edit distance with quadratic time complexity by efficiently matching local substructures. This dissertation speculates using Hausdorff edit distance could be a promising alternative to other template-based keyword spotting approaches in term of computational time and accuracy. Accordingly, the core contribution of this thesis is investigation and development of a graph-based keyword spotting technique based on the Hausdorff edit distance algorithm. The high representational power of graphs combined with the efficiency of the Hausdorff edit distance for graph matching achieves remarkable speedup as well as accuracy. In a comprehensive experimental evaluation, we demonstrate the solid performance of the proposed graph-based method when compared with state of the art, both, concerning precision and speed. The second contribution of this thesis is a keyword spotting technique which incorporates dynamic time warping and Hausdorff edit distance approaches. The structural representation of graph-based approach combined with statistical geometric features representation compliments each other in order to provide a more accurate system. The proposed system has been extensively evaluated with four types of handwriting graphs and geometric features vectors on benchmark datasets. The experiments demonstrate a performance boost in which outperforms individual systems

Graph-Based Approaches to Protein StructureComparison - From Local to Global Similarity

The comparative analysis of protein structure data is a central aspect of structural bioinformatics. Drawing upon structural information allows the inference of function for unknown proteins even in cases where no apparent homology can be found on the sequence level. Regarding the function of an enzyme, the overall fold topology might less important than the specific structural conformation of the catalytic site or the surface region of a protein, where the interaction with other molecules, such as binding partners, substrates and ligands occurs. Thus, a comparison of these regions is especially interesting for functional inference, since structural constraints imposed by the demands of the catalyzed biochemical function make them more likely to exhibit structural similarity. Moreover, the comparative analysis of protein binding sites is of special interest in pharmaceutical chemistry, in order to predict cross-reactivities and gain a deeper understanding of the catalysis mechanism. From an algorithmic point of view, the comparison of structured data, or, more generally, complex objects, can be attempted based on different methodological principles. Global methods aim at comparing structures as a whole, while local methods transfer the problem to multiple comparisons of local substructures. In the context of protein structure analysis, it is not a priori clear, which strategy is more suitable. In this thesis, several conceptually different algorithmic approaches have been developed, based on local, global and semi-global strategies, for the task of comparing protein structure data, more specifically protein binding pockets. The use of graphs for the modeling of protein structure data has a long standing tradition in structural bioinformatics. Recently, graphs have been used to model the geometric constraints of protein binding sites. The algorithms developed in this thesis are based on this modeling concept, hence, from a computer scientist's point of view, they can also be regarded as global, local and semi-global approaches to graph comparison. The developed algorithms were mainly designed on the premise to allow for a more approximate comparison of protein binding sites, in order to account for the molecular flexibility of the protein structures. A main motivation was to allow for the detection of more remote similarities, which are not apparent by using more rigid methods. Subsequently, the developed approaches were applied to different problems typically encountered in the field of structural bioinformatics in order to assess and compare their performance and suitability for different problems. Each of the approaches developed during this work was capable of improving upon the performance of existing methods in the field. Another major aspect in the experiments was the question, which methodological concept, local, global or a combination of both, offers the most benefits for the specific task of protein binding site comparison, a question that is addressed throughout this thesis

Social Network Data Management

With the increasing usage of online social networks and the semantic web's graph structured RDF framework, and the rising adoption of networks in various fields from biology to social science, there is a rapidly growing need for indexing, querying, and analyzing massive graph structured data. Facebook has amassed over 500 million users creating huge volumes of highly connected data. Governments have made RDF datasets containing billions of triples available to the public. In the life sciences, researches have started to connect disparate data sets of research results into one giant network of valuable information. Clearly, networks are becoming increasingly popular and growing rapidly in size, requiring scalable solutions for network data management. This thesis focuses on the following aspects of network data management. We present a hierarchical index structure for external memory storage of network data that aims to maximize data locality. We propose efficient algorithms to answer subgraph matching queries against network databases and discuss effective pruning strategies to improve performance. We show how adaptive cost models can speed up subgraph matching query answering by assigning budgets to index retrieval operations and adjusting the query plan while executing. We develop a cloud oriented social network database, COSI, which handles massive network datasets too large for a single computer by partitioning the data across multiple machines and achieving high performance query answering through asynchronous parallelization and cluster-aware heuristics. Tracking multiple standing queries against a social network database is much faster with our novel multi-view maintenance algorithm, which exploits common substructures between queries. To capture uncertainty inherent in social network querying, we define probabilistic subgraph matching queries over deterministic graph data and propose algorithms to answer them efficiently. Finally, we introduce a general relational machine learning framework and rule-based language, Probabilistic Soft Logic, to learn from and probabilistically reason about social network data and describe applications to information integration and information fusion