High-Quality Hypergraph Partitioning

This dissertation focuses on computing high-quality solutions for the NP-hard balanced hypergraph partitioning problem: Given a hypergraph and an integer $k$, partition its vertex set into $k$ disjoint blocks of bounded size, while minimizing an objective function over the hyperedges. Here, we consider the two most commonly used objectives: the cut-net metric and the connectivity metric. Since the problem is computationally intractable, heuristics are used in practice - the most prominent being the three-phase multi-level paradigm: During coarsening, the hypergraph is successively contracted to obtain a hierarchy of smaller instances. After applying an initial partitioning algorithm to the smallest hypergraph, contraction is undone and, at each level, refinement algorithms try to improve the current solution. With this work, we give a brief overview of the field and present several algorithmic improvements to the multi-level paradigm. Instead of using a logarithmic number of levels like traditional algorithms, we present two coarsening algorithms that create a hierarchy of (nearly) $n$ levels, where $n$ is the number of vertices. This makes consecutive levels as similar as possible and provides many opportunities for refinement algorithms to improve the partition. This approach is made feasible in practice by tailoring all algorithms and data structures to the $n$-level paradigm, and developing lazy-evaluation techniques, caching mechanisms and early stopping criteria to speed up the partitioning process. Furthermore, we propose a sparsification algorithm based on locality-sensitive hashing that improves the running time for hypergraphs with large hyperedges, and show that incorporating global information about the community structure into the coarsening process improves quality. Moreover, we present a portfolio-based initial partitioning approach, and propose three refinement algorithms. Two are based on the Fiduccia-Mattheyses (FM) heuristic, but perform a highly localized search at each level. While one is designed for two-way partitioning, the other is the first FM-style algorithm that can be efficiently employed in the multi-level setting to directly improve $k$-way partitions. The third algorithm uses max-flow computations on pairs of blocks to refine $k$-way partitions. Finally, we present the first memetic multi-level hypergraph partitioning algorithm for an extensive exploration of the global solution space. All contributions are made available through our open-source framework KaHyPar. In a comprehensive experimental study, we compare KaHyPar with hMETIS, PaToH, Mondriaan, Zoltan-AlgD, and HYPE on a wide range of hypergraphs from several application areas. Our results indicate that KaHyPar, already without the memetic component, computes better solutions than all competing algorithms for both the cut-net and the connectivity metric, while being faster than Zoltan-AlgD and equally fast as hMETIS. Moreover, KaHyPar compares favorably with the current best graph partitioning system KaFFPa - both in terms of solution quality and running time

Hypergraph Partitioning in the Cloud

The thesis investigates the partitioning and load balancing problem which has many applications in High Performance Computing (HPC). The application to be partitioned is described with a graph or hypergraph. The latter is of greater interest as hypergraphs, compared to graphs, have a more general structure and can be used to model more complex relationships between groups of objects such as non-symmetric dependencies. Optimal graph and hypergraph partitioning is known to be NP-Hard but good polynomial time heuristic algorithms have been proposed. In this thesis, we propose two multi-level hypergraph partitioning algorithms. The algorithms are based on rough set clustering techniques. The first algorithm, which is a serial algorithm, obtains high quality partitionings and improves the partitioning cut by up to 71\% compared to the state-of-the-art serial hypergraph partitioning algorithms. Furthermore, the capacity of serial algorithms is limited due to the rapid growth of problem sizes of distributed applications. Consequently, we also propose a parallel hypergraph partitioning algorithm. Considering the generality of the hypergraph model, designing a parallel algorithm is difficult and the available parallel hypergraph algorithms offer less scalability compared to their graph counterparts. The issue is twofold: the parallel algorithm and the complexity of the hypergraph structure. Our parallel algorithm provides a trade-off between global and local vertex clustering decisions. By employing novel techniques and approaches, our algorithm achieves better scalability than the state-of-the-art parallel hypergraph partitioner in the Zoltan tool on a set of benchmarks, especially ones with irregular structure. Furthermore, recent advances in cloud computing and the services they provide have led to a trend in moving HPC and large scale distributed applications into the cloud. Despite its advantages, some aspects of the cloud, such as limited network resources, present a challenge to running communication-intensive applications and make them non-scalable in the cloud. While hypergraph partitioning is proposed as a solution for decreasing the communication overhead within parallel distributed applications, it can also offer advantages for running these applications in the cloud. The partitioning is usually done as a pre-processing step before running the parallel application. As parallel hypergraph partitioning itself is a communication-intensive operation, running it in the cloud is hard and suffers from poor scalability. The thesis also investigates the scalability of parallel hypergraph partitioning algorithms in the cloud, the challenges they present, and proposes solutions to improve the cost/performance ratio for running the partitioning problem in the cloud. Our algorithms are implemented as a new hypergraph partitioning package within Zoltan. It is an open source Linux-based toolkit for parallel partitioning, load balancing and data-management designed at Sandia National Labs. The algorithms are known as FEHG and PFEHG algorithms

Validação de heterogeneidade estrutural em dados de Crio-ME por comitês de agrupadores

Orientadores: Fernando José Von Zuben, Rodrigo Villares PortugalDissertação (mestrado) - Universidade Estadual de Campinas, Faculdade de Engenharia Elétrica e de ComputaçãoResumo: Análise de Partículas Isoladas é uma técnica que permite o estudo da estrutura tridimensional de proteínas e outros complexos macromoleculares de interesse biológico. Seus dados primários consistem em imagens de microscopia eletrônica de transmissão de múltiplas cópias da molécula em orientações aleatórias. Tais imagens são bastante ruidosas devido à baixa dose de elétrons utilizada. Reconstruções 3D podem ser obtidas combinando-se muitas imagens de partículas em orientações similares e estimando seus ângulos relativos. Entretanto, estados conformacionais heterogêneos frequentemente coexistem na amostra, porque os complexos moleculares podem ser flexíveis e também interagir com outras partículas. Heterogeneidade representa um desafio na reconstrução de modelos 3D confiáveis e degrada a resolução dos mesmos. Entre os algoritmos mais populares usados para classificação estrutural estão o agrupamento por k-médias, agrupamento hierárquico, mapas autoorganizáveis e estimadores de máxima verossimilhança. Tais abordagens estão geralmente entrelaçadas à reconstrução dos modelos 3D. No entanto, trabalhos recentes indicam ser possível inferir informações a respeito da estrutura das moléculas diretamente do conjunto de projeções 2D. Dentre estas descobertas, está a relação entre a variabilidade estrutural e manifolds em um espaço de atributos multidimensional. Esta dissertação investiga se um comitê de algoritmos de não-supervisionados é capaz de separar tais "manifolds conformacionais". Métodos de "consenso" tendem a fornecer classificação mais precisa e podem alcançar performance satisfatória em uma ampla gama de conjuntos de dados, se comparados a algoritmos individuais. Nós investigamos o comportamento de seis algoritmos de agrupamento, tanto individualmente quanto combinados em comitês, para a tarefa de classificação de heterogeneidade conformacional. A abordagem proposta foi testada em conjuntos sintéticos e reais contendo misturas de imagens de projeção da proteína Mm-cpn nos estados "aberto" e "fechado". Demonstra-se que comitês de agrupadores podem fornecer informações úteis na validação de particionamentos estruturais independetemente de algoritmos de reconstrução 3DAbstract: Single Particle Analysis is a technique that allows the study of the three-dimensional structure of proteins and other macromolecular assemblies of biological interest. Its primary data consists of transmission electron microscopy images from multiple copies of the molecule in random orientations. Such images are very noisy due to the low electron dose employed. Reconstruction of the macromolecule can be obtained by averaging many images of particles in similar orientations and estimating their relative angles. However, heterogeneous conformational states often co-exist in the sample, because the molecular complexes can be flexible and may also interact with other particles. Heterogeneity poses a challenge to the reconstruction of reliable 3D models and degrades their resolution. Among the most popular algorithms used for structural classification are k-means clustering, hierarchical clustering, self-organizing maps and maximum-likelihood estimators. Such approaches are usually interlaced with the reconstructions of the 3D models. Nevertheless, recent works indicate that it is possible to infer information about the structure of the molecules directly from the dataset of 2D projections. Among these findings is the relationship between structural variability and manifolds in a multidimensional feature space. This dissertation investigates whether an ensemble of unsupervised classification algorithms is able to separate these "conformational manifolds". Ensemble or "consensus" methods tend to provide more accurate classification and may achieve satisfactory performance across a wide range of datasets, when compared with individual algorithms. We investigate the behavior of six clustering algorithms both individually and combined in ensembles for the task of structural heterogeneity classification. The approach was tested on synthetic and real datasets containing a mixture of images from the Mm-cpn chaperonin in the "open" and "closed" states. It is shown that cluster ensembles can provide useful information in validating the structural partitionings independently of 3D reconstruction methodsMestradoEngenharia de ComputaçãoMestre em Engenharia Elétric

Exploiting Latent Features of Text and Graphs

As the size and scope of online data continues to grow, new machine learning techniques become necessary to best capitalize on the wealth of available information. However, the models that help convert data into knowledge require nontrivial processes to make sense of large collections of text and massive online graphs. In both scenarios, modern machine learning pipelines produce embeddings --- semantically rich vectors of latent features --- to convert human constructs for machine understanding. In this dissertation we focus on information available within biomedical science, including human-written abstracts of scientific papers, as well as machine-generated graphs of biomedical entity relationships. We present the Moliere system, and our method for identifying new discoveries through the use of natural language processing and graph mining algorithms. We propose heuristically-based ranking criteria to augment Moliere, and leverage this ranking to identify a new gene-treatment target for HIV-associated Neurodegenerative Disorders. We additionally focus on the latent features of graphs, and propose a new bipartite graph embedding technique. Using our graph embedding, we advance the state-of-the-art in hypergraph partitioning quality. Having newfound intuition of graph embeddings, we present Agatha, a deep-learning approach to hypothesis generation. This system learns a data-driven ranking criteria derived from the embeddings of our large proposed biomedical semantic graph. To produce human-readable results, we additionally propose CBAG, a technique for conditional biomedical abstract generation

Wearable Sensors Applied in Movement Analysis

Recent advances in electronics have led to sensors whose sizes and weights are such that they can be placed on living systems without impairing their natural motion and habits. They may be worn on the body as accessories or as part of the clothing and enable personalized mobile information processing. Wearable sensors open the way for a nonintrusive and continuous monitoring of body orientation, movements, and various physiological parameters during motor activities in real-life settings. Thus, they may become crucial tools not only for researchers, but also for clinicians, as they have the potential to improve diagnosis, better monitor disease development and thereby individualize treatment. Wearable sensors should obviously go unnoticed for the people wearing them and be intuitive in their installation. They should come with wireless connectivity and low-power consumption. Moreover, the electronics system should be self-calibrating and deliver correct information that is easy to interpret. Cross-platform interfaces that provide secure data storage and easy data analysis and visualization are needed.This book contains a selection of research papers presenting new results addressing the above challenges

Robustness, Heterogeneity and Structure Capturing for Graph Representation Learning and its Application

Graph neural networks (GNNs) are potent methods for graph representation learn- ing (GRL), which extract knowledge from complicated (graph) structured data in various real-world scenarios. However, GRL still faces many challenges. Firstly GNN-based node classification may deteriorate substantially by overlooking the pos- sibility of noisy data in graph structures, as models wrongly process the relation among nodes in the input graphs as the ground truth. Secondly, nodes and edges have different types in the real-world and it is essential to capture this heterogeneity in graph representation learning. Next, relations among nodes are not restricted to pairwise relations and it is necessary to capture the complex relations accordingly. Finally, the absence of structural encodings, such as positional information, deterio- rates the performance of GNNs. This thesis proposes novel methods to address the aforementioned problems: 1. Bayesian Graph Attention Network (BGAT): Developed for situations with scarce data, this method addresses the influence of spurious edges. Incor- porating Bayesian principles into the graph attention mechanism enhances robustness, leading to competitive performance against benchmarks (Chapter 3). 2. Neighbour Contrastive Heterogeneous Graph Attention Network (NC-HGAT): By enhancing a cutting-edge self-supervised heterogeneous graph neural net- work model (HGAT) with neighbour contrastive learning, this method ad- dresses heterogeneity and uncertainty simultaneously. Extra attention to edge relations in heterogeneous graphs also aids in subsequent classification tasks (Chapter 4). 3. A novel ensemble learning framework is introduced for predicting stock price movements. It adeptly captures both group-level and pairwise relations, lead- ing to notable advancements over the existing state-of-the-art. The integration of hypergraph and graph models, coupled with the utilisation of auxiliary data via GNNs before recurrent neural network (RNN), provides a deeper under- standing of long-term dependencies between similar entities in multivariate time series analysis (Chapter 5). 4. A novel framework for graph structure learning is introduced, segmenting graphs into distinct patches. By harnessing the capabilities of transformers and integrating other position encoding techniques, this approach robustly capture intricate structural information within a graph. This results in a more comprehensive understanding of its underlying patterns (Chapter 6)

A distributed multi-threaded data partitioner with space-filling curve orders

The problem discussed in this thesis is distributed data partitioning and data re-ordering on many-core architectures. We present extensive literature survey, with examples from various application domains - scientific computing, databases and large-scale graph processing. We propose a low-overhead partitioning framework based on geometry, that can be used to partition multi-dimensional data where the number of dimensions is >=2. The partitioner linearly orders items with good spatial locality. Partial output is stored on each process in the communication group. Space-filling curves are used to permute data - Morton order is the default curve. For dimensions <=3, we have options to generate Hilbert-like curves. Two metrics used to determine partitioning overheads are memory consumption and execution time, although these two factors are dependent on each other. The focus of this thesis is to reduce partitioning overheads as much as possible. We have described several optimizations to this end - incremental adjustments to partitions, careful dynamic memory management and using multi-threading and multi-processing to advantage. The quality of partitions is an important criteria for evaluating a partitioner. We have used graph partitioners as base-implementations against which our partitions are compared. The degree and edge-cuts of our partitions are comparable to graph partitions for regular grids. For irregular meshes, there is still room for improvement. No comparisons have been made for evaluating partitions of datasets without edges. We have deployed these partitions on two large applications - atmosphere simulation in 2D and adaptive mesh refinement in 3D. An adaptive mesh refinement benchmark was built to be part of the framework, which later became a testcase for evaluating partitions and load-balancing schemes. The performance of this benchmark is discussed in detail in the last chapter

Behavioral analysis in cybersecurity using machine learning: a study based on graph representation, class imbalance and temporal dissection

The main goal of this thesis is to improve behavioral cybersecurity analysis using machine learning, exploiting graph structures, temporal dissection, and addressing imbalance problems.This main objective is divided into four specific goals: OBJ1: To study the influence of the temporal resolution on highlighting micro-dynamics in the entity behavior classification problem. In real use cases, time-series information could be not enough for describing the entity behavior classification. For this reason, we plan to exploit graph structures for integrating both structured and unstructured data in a representation of entities and their relationships. In this way, it will be possible to appreciate not only the single temporal communication but the whole behavior of these entities. Nevertheless, entity behaviors evolve over time and therefore, a static graph may not be enoughto describe all these changes. For this reason, we propose to use a temporal dissection for creating temporal subgraphs and therefore, analyze the influence of the temporal resolution on the graph creation and the entity behaviors within. Furthermore, we propose to study how the temporal granularity should be used for highlighting network micro-dynamics and short-term behavioral changes which can be a hint of suspicious activities. OBJ2: To develop novel sampling methods that work with disconnected graphs for addressing imbalanced problems avoiding component topology changes. Graph imbalance problem is a very common and challenging task and traditional graph sampling techniques that work directly on these structures cannot be used without modifying the graph’s intrinsic information or introducing bias. Furthermore, existing techniques have shown to be limited when disconnected graphs are used. For this reason, novel resampling methods for balancing the number of nodes that can be directly applied over disconnected graphs, without altering component topologies, need to be introduced. In particular, we propose to take advantage of the existence of disconnected graphs to detect and replicate the most relevant graph components without changing their topology, while considering traditional data-level strategies for handling the entity behaviors within. OBJ3: To study the usefulness of the generative adversarial networks for addressing the class imbalance problem in cybersecurity applications. Although traditional data-level pre-processing techniques have shown to be effective for addressing class imbalance problems, they have also shown downside effects when highly variable datasets are used, as it happens in cybersecurity. For this reason, new techniques that can exploit the overall data distribution for learning highly variable behaviors should be investigated. In this sense, GANs have shown promising results in the image and video domain, however, their extension to tabular data is not trivial. For this reason, we propose to adapt GANs for working with cybersecurity data and exploit their ability in learning and reproducing the input distribution for addressing the class imbalance problem (as an oversampling technique). Furthermore, since it is not possible to find a unique GAN solution that works for every scenario, we propose to study several GAN architectures with several training configurations to detect which is the best option for a cybersecurity application. OBJ4: To analyze temporal data trends and performance drift for enhancing cyber threat analysis. Temporal dynamics and incoming new data can affect the quality of the predictions compromising the model reliability. This phenomenon makes models get outdated without noticing. In this sense, it is very important to be able to extract more insightful information from the application domain analyzing data trends, learning processes, and performance drifts over time. For this reason, we propose to develop a systematic approach for analyzing how the data quality and their amount affect the learning process. Moreover, in the contextof CTI, we propose to study the relations between temporal performance drifts and the input data distribution for detecting possible model limitations, enhancing cyber threat analysis.Programa de Doctorado en Ciencias y Tecnologías Industriales (RD 99/2011) Industria Zientzietako eta Teknologietako Doktoretza Programa (ED 99/2011