Multi-Stage Search Architectures for Streaming Documents

The web is becoming more dynamic due to the increasing engagement and contribution of Internet users in the age of social media. A more dynamic web presents new challenges for web search--an important application of Information Retrieval (IR). A stream of new documents constantly flows into the web at a high rate, adding to the old content. In many cases, documents quickly lose their relevance. In these time-sensitive environments, finding relevant content in response to user queries requires a real-time search service; immediate availability of content for search and a fast ranking, which requires an optimized search architecture. These aspects of today's web are at odds with how academic IR researchers have traditionally viewed the web, as a collection of static documents. Moreover, search architectures have received little attention in the IR literature. Therefore, academic IR research, for the most part, does not provide a mechanism to efficiently handle a high-velocity stream of documents, nor does it facilitate real-time ranking. This dissertation addresses the aforementioned shortcomings. We present an efficient mech- anism to index a stream of documents, thereby enabling immediate availability of content. Our indexer works entirely in main memory and provides a mechanism to control inverted list con- tiguity, thereby enabling faster retrieval. Additionally, we consider document ranking with a machine-learned model, dubbed "Learning to Rank" (LTR), and introduce a novel multi-stage search architecture that enables fast retrieval and allows for more design flexibility. The stages of our architecture include candidate generation (top k retrieval), feature extraction, and docu- ment re-ranking. We compare this architecture with a traditional monolithic architecture where candidate generation and feature extraction occur together. As we lay out our architecture, we present optimizations to each stage to facilitate low-latency ranking. These optimizations include a fast approximate top k retrieval algorithm, document vectors for feature extraction, architecture- conscious implementations of tree ensembles for LTR using predication and vectorization, and algorithms to train tree-based LTR models that are fast to evaluate. We also study the efficiency- effectiveness tradeoffs of these techniques, and empirically evaluate our end-to-end architecture on microblog document collections. We show that our techniques improve efficiency without degrading quality

Prospects and limitations of full-text index structures in genome analysis

The combination of incessant advances in sequencing technology producing large amounts of data and innovative bioinformatics approaches, designed to cope with this data flood, has led to new interesting results in the life sciences. Given the magnitude of sequence data to be processed, many bioinformatics tools rely on efficient solutions to a variety of complex string problems. These solutions include fast heuristic algorithms and advanced data structures, generally referred to as index structures. Although the importance of index structures is generally known to the bioinformatics community, the design and potency of these data structures, as well as their properties and limitations, are less understood. Moreover, the last decade has seen a boom in the number of variant index structures featuring complex and diverse memory-time trade-offs. This article brings a comprehensive state-of-the-art overview of the most popular index structures and their recently developed variants. Their features, interrelationships, the trade-offs they impose, but also their practical limitations, are explained and compared

OpenFPM: A scalable environment for particle and particle-mesh codes on parallel computers

Scalable and efficient numerical simulations continue to gain importance, as computation is firmly established tool of discovery, together with theory and experiment. Meanwhile, the performance of computing hardware grows with increasing heterogeneous hardware, enabling simulations of ever more complex models. However, efficiently implementing scalable codes on heterogeneous, distributed hardware systems becomes the bottleneck. This bottleneck can be alleviated by intermediate software layers that provide higher-level abstractions closer to the problem domain, hence allowing the computational scientist to focus on the simulation. Here, we present OpenFPM, an open and scalable framework that provides an abstraction layer for numerical simulations using particles and/or meshes. OpenFPM provides transparent and scalable infrastructure for shared-memory and distributed-memory implementations of particles-only and hybrid particle-mesh simulations of both discrete and continuous models, as well as non-simulation codes. This infrastructure is complemented with frequently used numerical routines, as well as interfaces to third-party libraries. This thesis will present the architecture and design of OpenFPM, detail the underlying abstractions, and benchmark the framework in applications ranging from Smoothed-Particle Hydrodynamics (SPH) to Molecular Dynamics (MD), Discrete Element Methods (DEM), Vortex Methods, stencil codes, high-dimensional Monte Carlo sampling (CMA-ES), and Reaction-Diffusion solvers, comparing it to the current state of the art and existing software frameworks

An implementation of dynamic fully compressed suffix trees

Dissertação apresentada na Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa para obtenção do grau de Mestre em Engenharia InformáticaThis dissertation studies and implements a dynamic fully compressed suffix tree. Suffix trees are important algorithms in stringology and provide optimal solutions for myriads of problems. Suffix trees are used, in bioinformatics to index large volumes of data. For most aplications suffix trees need to be efficient in size and funcionality. Until recently they were very large, suffix trees for the 700 megabyte human genome spawn 40 gigabytes of data. The compressed suffix tree requires less space and the recent static fully compressed suffix tree requires even less space, in fact it requires optimal compressed space. However since it is static it is not suitable for dynamic environments. Chan et. al.[3] proposed the first dynamic compressed suffix tree however the space used for a text of size n is O(n log )bits which is far from the new static solutions. Our goal is to implement a recent proposal by Russo, Arlindo and Navarro[22] that defines a dynamic fully compressed suffix tree and uses only nH0 +O(n log ) bits of space

Memory-Adjustable Navigation Piles with Applications to Sorting and Convex Hulls

We consider space-bounded computations on a random-access machine (RAM) where the input is given on a read-only random-access medium, the output is to be produced to a write-only sequential-access medium, and the available workspace allows random reads and writes but is of limited capacity. The length of the input is $N$ elements, the length of the output is limited by the computation, and the capacity of the workspace is $O(S)$ bits for some predetermined parameter $S$. We present a state-of-the-art priority queue---called an adjustable navigation pile---for this restricted RAM model. Under some reasonable assumptions, our priority queue supports $\mathit{minimum}$ and $\mathit{insert}$ in $O(1)$ worst-case time and $\mathit{extract}$ in $O(N/S + \lg{} S)$ worst-case time for any $S \geq \lg{} N$. We show how to use this data structure to sort $N$ elements and to compute the convex hull of $N$ points in the two-dimensional Euclidean space in $O(N^2/S + N \lg{} S)$ worst-case time for any $S \geq \lg{} N$. Following a known lower bound for the space-time product of any branching program for finding unique elements, both our sorting and convex-hull algorithms are optimal. The adjustable navigation pile has turned out to be useful when designing other space-efficient algorithms, and we expect that it will find its way to yet other applications.Comment: 21 page