Indexing Metric Spaces for Exact Similarity Search

With the continued digitalization of societal processes, we are seeing an explosion in available data. This is referred to as big data. In a research setting, three aspects of the data are often viewed as the main sources of challenges when attempting to enable value creation from big data: volume, velocity and variety. Many studies address volume or velocity, while much fewer studies concern the variety. Metric space is ideal for addressing variety because it can accommodate any type of data as long as its associated distance notion satisfies the triangle inequality. To accelerate search in metric space, a collection of indexing techniques for metric data have been proposed. However, existing surveys each offers only a narrow coverage, and no comprehensive empirical study of those techniques exists. We offer a survey of all the existing metric indexes that can support exact similarity search, by i) summarizing all the existing partitioning, pruning and validation techniques used for metric indexes, ii) providing the time and storage complexity analysis on the index construction, and iii) report on a comprehensive empirical comparison of their similarity query processing performance. Here, empirical comparisons are used to evaluate the index performance during search as it is hard to see the complexity analysis differences on the similarity query processing and the query performance depends on the pruning and validation abilities related to the data distribution. This article aims at revealing different strengths and weaknesses of different indexing techniques in order to offer guidance on selecting an appropriate indexing technique for a given setting, and directing the future research for metric indexes

CliqueStream: an efficient and fault-resilient live streaming network on a clustered peer-to-peer overlay

Several overlay-based live multimedia streaming platforms have been proposed in the recent peer-to-peer streaming literature. In most of the cases, the overlay neighbors are chosen randomly for robustness of the overlay. However, this causes nodes that are distant in terms of proximity in the underlying physical network to become neighbors, and thus data travels unnecessary distances before reaching the destination. For efficiency of bulk data transmission like multimedia streaming, the overlay neighborhood should resemble the proximity in the underlying network. In this paper, we exploit the proximity and redundancy properties of a recently proposed clique-based clustered overlay network, named eQuus, to build efficient as well as robust overlays for multimedia stream dissemination. To combine the efficiency of content pushing over tree structured overlays and the robustness of data-driven mesh overlays, higher capacity stable nodes are organized in tree structure to carry the long haul traffic and less stable nodes with intermittent presence are organized in localized meshes. The overlay construction and fault-recovery procedures are explained in details. Simulation study demonstrates the good locality properties of the platform. The outage time and control overhead induced by the failure recovery mechanism are minimal as demonstrated by the analysis.Comment: 10 page

R-Forest for Approximate Nearest Neighbor Queries in High Dimensional Space

Searching high dimensional space has been a challenge and an area of intense research for many years. The dimensionality curse has rendered most existing index methods all but useless causing people to research other techniques. In my dissertation I will try to resurrect one of the best known index structures, R-Tree, which most have given up on as a viable method of answering high dimensional queries. I have pointed out the various advantages of R-Tree as a method for answering approximate nearest neighbor queries, and the advantages of locality sensitive hashing and locality sensitive B-Tree, which are the most successful methods today. I started by looking at improving the maintenance of R-Tree by the use of bulk loading and insertion. I proposed and implemented a new method that bulk loads the index which was an improvement of standard method. I then turned my attention to nearest neighbor queries, which is a much more challenging problem especially in high dimensional space. Initially I developed a set of heuristics, easily implemented in R-Tree, which improved the efficiency of high dimensional approximate nearest neighbor queries. To further refine my method I took another approach, by developing a new model, known as R-Forest, which takes advantage of space partitioning while still using R-Tree as its index structure. With this new approach I was able to implement new heuristics and can show that R-Forest, comprised of a set of R-Trees, is a viable solution tohigh dimensional approximate nearest neighbor queries when compared to established methods

Computational strategies for dissecting the high-dimensional complexity of adaptive immune repertoires

The adaptive immune system recognizes antigens via an immense array of antigen-binding antibodies and T-cell receptors, the immune repertoire. The interrogation of immune repertoires is of high relevance for understanding the adaptive immune response in disease and infection (e.g., autoimmunity, cancer, HIV). Adaptive immune receptor repertoire sequencing (AIRR-seq) has driven the quantitative and molecular-level profiling of immune repertoires thereby revealing the high-dimensional complexity of the immune receptor sequence landscape. Several methods for the computational and statistical analysis of large-scale AIRR-seq data have been developed to resolve immune repertoire complexity in order to understand the dynamics of adaptive immunity. Here, we review the current research on (i) diversity, (ii) clustering and network, (iii) phylogenetic and (iv) machine learning methods applied to dissect, quantify and compare the architecture, evolution, and specificity of immune repertoires. We summarize outstanding questions in computational immunology and propose future directions for systems immunology towards coupling AIRR-seq with the computational discovery of immunotherapeutics, vaccines, and immunodiagnostics.Comment: 27 pages, 2 figure

An Efficient Algorithm for Bulk-Loading xBR+ -trees

A major part of the interface to a database is made up of the queries that can be addressed to this database and answered (processed) in an efficient way, contributing to the quality of the developed software. Efficiently processed spatial queries constitute a fundamental part of the interface to spatial databases due to the wide area of applications that may address such queries, like geographical information systems (GIS), location-based services, computer visualization, automated mapping, facilities management, etc. Another important capability of the interface to a spatial database is to offer the creation of efficient index structures to speed up spatial query processing. The xBR + -tree is a balanced disk-resident quadtree-based index structure for point data, which is very efficient for processing such queries. Bulk-loading refers to the process of creating an index from scratch, when the dataset to be indexed is available beforehand, instead of creating the index gradually (and more slowly), when the dataset elements are inserted one-by-one. In this paper, we present an algorithm for bulk-loading xBR + -trees for big datasets residing on disk, using a limited amount of main memory. The resulting tree is not only built fast, but exhibits high performance in processing a broad range of spatial queries, where one or two datasets are involved. To justify these characteristics, using real and artificial datasets of various cardinalities, first, we present an experimental comparison of this algorithm vs. a previous version of the same algorithm and STR, a popular algorithm of bulk-loading R-trees, regarding tree creation time and the characteristics of the trees created, and second, we experimentally compare the query efficiency of bulk-loaded xBR + -trees vs. bulk-loaded R-trees, regarding I/O and execution time. Thus, this paper contributes to the implementation of spatial database interfaces and the efficient storage organization for big spatial data management