Efficient Node Proximity and Node Significance Computations in Graphs

abstract: Node proximity measures are commonly used for quantifying how nearby or otherwise related to two or more nodes in a graph are. Node significance measures are mainly used to find how much nodes are important in a graph. The measures of node proximity/significance have been highly effective in many predictions and applications. Despite their effectiveness, however, there are various shortcomings. One such shortcoming is a scalability problem due to their high computation costs on large size graphs and another problem on the measures is low accuracy when the significance of node and its degree in the graph are not related. The other problem is that their effectiveness is less when information for a graph is uncertain. For an uncertain graph, they require exponential computation costs to calculate ranking scores with considering all possible worlds. In this thesis, I first introduce Locality-sensitive, Re-use promoting, approximate Personalized PageRank (LR-PPR) which is an approximate personalized PageRank calculating node rankings for the locality information for seeds without calculating the entire graph and reusing the precomputed locality information for different locality combinations. For the identification of locality information, I present Impact Neighborhood Indexing (INI) to find impact neighborhoods with nodes' fingerprints propagation on the network. For the accuracy challenge, I introduce Degree Decoupled PageRank (D2PR) technique to improve the effectiveness of PageRank based knowledge discovery, especially considering the significance of neighbors and degree of a given node. To tackle the uncertain challenge, I introduce Uncertain Personalized PageRank (UPPR) to approximately compute personalized PageRank values on uncertainties of edge existence and Interval Personalized PageRank with Integration (IPPR-I) and Interval Personalized PageRank with Mean (IPPR-M) to compute ranking scores for the case when uncertainty exists on edge weights as interval values.Dissertation/ThesisDoctoral Dissertation Computer Science 201

GraphX: Unifying Data-Parallel and Graph-Parallel Analytics

From social networks to language modeling, the growing scale and importance of graph data has driven the development of numerous new graph-parallel systems (e.g., Pregel, GraphLab). By restricting the computation that can be expressed and introducing new techniques to partition and distribute the graph, these systems can efficiently execute iterative graph algorithms orders of magnitude faster than more general data-parallel systems. However, the same restrictions that enable the performance gains also make it difficult to express many of the important stages in a typical graph-analytics pipeline: constructing the graph, modifying its structure, or expressing computation that spans multiple graphs. As a consequence, existing graph analytics pipelines compose graph-parallel and data-parallel systems using external storage systems, leading to extensive data movement and complicated programming model. To address these challenges we introduce GraphX, a distributed graph computation framework that unifies graph-parallel and data-parallel computation. GraphX provides a small, core set of graph-parallel operators expressive enough to implement the Pregel and PowerGraph abstractions, yet simple enough to be cast in relational algebra. GraphX uses a collection of query optimization techniques such as automatic join rewrites to efficiently implement these graph-parallel operators. We evaluate GraphX on real-world graphs and workloads and demonstrate that GraphX achieves comparable performance as specialized graph computation systems, while outperforming them in end-to-end graph pipelines. Moreover, GraphX achieves a balance between expressiveness, performance, and ease of use

NOTES2: Networks-of-Traces for Epidemic Spread Simulations

Decision making and intervention against infectious diseases require analysis of large volumes of data, including demographic data, contact networks, agespecific contact rates, mobility networks, and healthcare and control intervention data and models. In this paper, we present our Networks-Of-Traces for Epidemic Spread Simulations (NOTES2) model and system which aim at assisting experts and helping them explore existing simulation trace data sets. NOTES2 supports analysis and indexing of simulation data sets as well as parameter and feature analysis, including identification of unknown dependencies across the input parameters and output variables spanning the different layers of the observation and simulation data

Deep Shape Matching

We cast shape matching as metric learning with convolutional networks. We break the end-to-end process of image representation into two parts. Firstly, well established efficient methods are chosen to turn the images into edge maps. Secondly, the network is trained with edge maps of landmark images, which are automatically obtained by a structure-from-motion pipeline. The learned representation is evaluated on a range of different tasks, providing improvements on challenging cases of domain generalization, generic sketch-based image retrieval or its fine-grained counterpart. In contrast to other methods that learn a different model per task, object category, or domain, we use the same network throughout all our experiments, achieving state-of-the-art results in multiple benchmarks.Comment: ECCV 201

Modeling Network Populations via Graph Distances

This article introduces a new class of models for multiple networks. The core idea is to parametrize a distribution on labelled graphs in terms of a Fréchet mean graph (which depends on a user-specified choice of metric or graph distance) and a parameter that controls the concentration of this distribution about its mean. Entropy is the natural parameter for such control, varying from a point mass concentrated on the Fréchet mean itself to a uniform distribution over all graphs on a given vertex set. We provide a hierarchical Bayesian approach for exploiting this construction, along with straightforward strategies for sampling from the resultant posterior distribution. We conclude by demonstrating the efficacy of our approach via simulation studies and two multiple-network data analysis examples: one drawn from systems biology and the other from neuroscience

Computational pan-genomics: status, promises and challenges

International audienceMany disciplines, from human genetics and oncology to plant breeding, microbiology and virology, commonly face the challenge of analyzing rapidly increasing numbers of genomes. In case of Homo sapiens, the number of sequenced genomes will approach hundreds of thousands in the next few years. Simply scaling up established bioinformatics pipelines will not be sufficient for leveraging the full potential of such rich genomic data sets. Instead, novel, qualitatively different computational methods and paradigms are needed. We will witness the rapid extension of computational pan-genomics, a new sub-area of research in computational biology. In this article, we generalize existing definitions and understand a pan-genome as any collection of genomic sequences to be analyzed jointly or to be used as a reference. We examine already available approaches to construct and use pan-genomes, discuss the potential benefits of future technologies and methodologies and review open challenges from the vantage point of the above-mentioned biological disciplines. As a prominent example for a computational paradigm shift, we particularly highlight the transition from the representation of reference genomes as strings to representations as graphs. We outline how this and other challenges from different application domains translate into common computational problems, point out relevant bioinformatics techniques and identify open problems in computer science. With this review, we aim to increase awareness that a joint approach to computational pan-genomics can help address many of the problems currently faced in various domains