Persistent Homology in Sparse Regression and its Application to Brain Morphometry

Sparse systems are usually parameterized by a tuning parameter that determines the sparsity of the system. How to choose the right tuning parameter is a fundamental and difficult problem in learning the sparse system. In this paper, by treating the the tuning parameter as an additional dimension, persistent homological structures over the parameter space is introduced and explored. The structures are then further exploited in speeding up the computation using the proposed soft-thresholding technique. The topological structures are further used as multivariate features in the tensor-based morphometry (TBM) in characterizing white matter alterations in children who have experienced severe early life stress and maltreatment. These analyses reveal that stress-exposed children exhibit more diffuse anatomical organization across the whole white matter region.Comment: submitted to IEEE Transactions on Medical Imagin

LazyFox: Fast and parallelized overlapping community detection in large graphs

The detection of communities in graph datasets provides insight about a graph's underlying structure and is an important tool for various domains such as social sciences, marketing, traffic forecast, and drug discovery. While most existing algorithms provide fast approaches for community detection, their results usually contain strictly separated communities. However, most datasets would semantically allow for or even require overlapping communities that can only be determined at much higher computational cost. We build on an efficient algorithm, Fox, that detects such overlapping communities. Fox measures the closeness of a node to a community by approximating the count of triangles which that node forms with that community. We propose LazyFox, a multi-threaded version of the Fox algorithm, which provides even faster detection without an impact on community quality. This allows for the analyses of significantly larger and more complex datasets. LazyFox enables overlapping community detection on complex graph datasets with millions of nodes and billions of edges in days instead of weeks. As part of this work, LazyFox's implementation was published and is available as a tool under an MIT licence at https://github.com/TimGarrels/LazyFox.Comment: 17 pages, 5 figure

Error-tolerant Graph Matching on Huge Graphs and Learning Strategies on the Edit Costs

Els grafs són estructures de dades abstractes que s'utilitzen per a modelar problemes reals amb dues entitats bàsiques: nodes i arestes. Cada node o vèrtex representa un punt d'interès rellevant d'un problema, i cada aresta representa la relació entre aquests vèrtexs. Els nodes i les arestes podrien incorporar atributs per augmentar la precisió del problema modelat. Degut a aquesta versatilitat, s'han trobat moltes aplicacions en camps com la visió per computador, biomèdics, anàlisi de xarxes, etc. La Distància d'edició de grafs (GED) s'ha convertit en una eina important en el reconeixement de patrons estructurals, ja que permet mesurar la dissimilitud dels grafs. A la primera part d'aquesta tesi es presenta un mètode per generar una parella grafs juntament amb la seva correspondència en un cost computacional lineal. A continuació, se centra en com mesurar la dissimilitud entre dos grafs enormes (més de 10.000 nodes), utilitzant un nou algoritme de aparellament de grafs anomenat Belief Propagation. Té un cost computacional O(d^3.5N). Aquesta tesi també presenta un marc general per aprendre els costos d'edició implicats en els càlculs de la GED automàticament. Després, concretem aquest marc en dos models diferents basats en xarxes neuronals i funcions de densitat de probabilitat. S'ha realitzat una validació pràctica exhaustiva en 14 bases de dades públiques. Aquesta validació mostra que la precisió és major amb els costos d'edició apresos, que amb alguns costos impostos manualment o altres costos apresos automàticament per mètodes anteriors. Finalment proposem una aplicació de l'algoritme Belief propagation utilitzat en la simulació de la mecànica muscular.Los grafos son estructuras de datos abstractos que se utilizan para modelar problemas reales con dos entidades básicas: nodos y aristas. Cada nodo o vértice representa un punto de interés relevante de un problema, y cada arista representa la relación entre estos vértices. Los nodos y las aristas podrían incorporar atributos para aumentar la precisión del problema modelado. Debido a esta versatilidad, se han encontrado muchas aplicaciones en campos como la visión por computador, biomédicos, análisis de redes, etc. La Distancia de edición de grafos (GED) se ha convertido en una herramienta importante en el reconocimiento de patrones estructurales, ya que permite medir la disimilitud de los grafos. En la primera parte de esta tesis se presenta un método para generar una pareja grafos junto con su correspondencia en un coste computacional lineal. A continuación, se centra en cómo medir la disimilitud entre dos grafos enormes (más de 10.000 nodos), utilizando un nuevo algoritmo de emparejamiento de grafos llamado Belief Propagation. Tiene un coste computacional O(d^3.5n). Esta tesis también presenta un marco general para aprender los costos de edición implicados en los cálculos de GED automáticamente. Luego, concretamos este marco en dos modelos diferentes basados en redes neuronales y funciones de densidad de probabilidad. Se ha realizado una validación práctica exhaustiva en 14 bases de datos públicas. Esta validación muestra que la precisión es mayor con los costos de edición aprendidos, que con algunos costos impuestos manualmente u otros costos aprendidos automáticamente por métodos anteriores. Finalmente proponemos una aplicación del algoritmo Belief propagation utilizado en la simulación de la mecánica muscular.Graphs are abstract data structures used to model real problems with two basic entities: nodes and edges. Each node or vertex represents a relevant point of interest of a problem, and each edge represents the relationship between these points. Nodes and edges could be attributed to increase the accuracy of the modeled problem, which means that these attributes could vary from feature vectors to description labels. Due to this versatility, many applications have been found in fields such as computer vision, bio-medics, network analysis, etc. Graph Edit Distance (GED) has become an important tool in structural pattern recognition since it allows to measure the dissimilarity of attributed graphs. The first part presents a method is presented to generate graphs together with an upper and lower bound distance and a correspondence in a linear computational cost. Through this method, the behaviour of the known -or the new- sub-optimal Error-Tolerant graph matching algorithm can be tested against a lower and an upper bound GED on large graphs, even though we do not have the true distance. Next, the present is focused on how to measure the dissimilarity between two huge graphs (more than 10.000 nodes), using a new Error-Tolerant graph matching algorithm called Belief Propagation algorithm. It has a O(d^3.5n) computational cost.This thesis also presents a general framework to learn the edit costs involved in the GED calculations automatically. Then, we concretise this framework in two different models based on neural networks and probability density functions. An exhaustive practical validation on 14 public databases has been performed. This validation shows that the accuracy is higher with the learned edit costs, than with some manually imposed costs or other costs automatically learned by previous methods. Finally we propose an application of the Belief propagation algorithm applied to muscle mechanics

A Neighborhood-preserving Graph Summarization

We introduce in this paper a new summarization method for large graphs. Our summarization approach retains only a user-specified proportion of the neighbors of each node in the graph. Our main aim is to simplify large graphs so that they can be analyzed and processed effectively while preserving as many of the node neighborhood properties as possible. Since many graph algorithms are based on the neighborhood information available for each node, the idea is to produce a smaller graph which can be used to allow these algorithms to handle large graphs and run faster while providing good approximations. Moreover, our compression allows users to control the size of the compressed graph by adjusting the amount of information loss that can be tolerated. The experiments conducted on various real and synthetic graphs show that our compression reduces considerably the size of the graphs. Moreover, we conducted several experiments on the obtained summaries using various graph algorithms and applications, such as node embedding, graph classification and shortest path approximations. The obtained results show interesting trade-offs between the algorithms runtime speed-up and the precision loss.Comment: 17 pages, 10 figure