Efficient Indexing for Structured and Unstructured Data

The collection of digital data is growing at an exponential rate. Data originates from wide range of data sources such as text feeds, biological sequencers, internet traffic over routers, through sensors and many other sources. To mine intelligent information from these sources, users have to query the data. Indexing techniques aim to reduce the query time by preprocessing the data. Diversity of data sources in real world makes it imperative to develop application specific indexing solutions based on the data to be queried. Data can be structured i.e., relational tables or unstructured i.e., free text. Moreover, increasingly many applications need to seamlessly analyze both kinds of data making data integration a central issue. Integrating text with structured data needs to account for missing values, errors in the data etc. Probabilistic models have been proposed recently for this purpose. These models are also useful for applications where uncertainty is inherent in data e.g. sensor networks. This dissertation aims to propose efficient indexing solutions for several problems that lie at the intersection of database and information retrieval such as joining ranked inputs, full-text documents searching etc. Other well-known problems of ranked retrieval and pattern matching are also studied under probabilistic settings. For each problem, the worst-case theoretical bounds of the proposed solutions are established and/or their practicality is demonstrated by thorough experimentation

Scalable String and Suffix Sorting: Algorithms, Techniques, and Tools

This dissertation focuses on two fundamental sorting problems: string sorting and suffix sorting. The first part considers parallel string sorting on shared-memory multi-core machines, the second part external memory suffix sorting using the induced sorting principle, and the third part distributed external memory suffix sorting with a new distributed algorithmic big data framework named Thrill.Comment: 396 pages, dissertation, Karlsruher Instituts f\"ur Technologie (2018). arXiv admin note: text overlap with arXiv:1101.3448 by other author

ENABLING TECHNIQUES FOR EXPRESSIVE FLOW FIELD VISUALIZATION AND EXPLORATION

Flow visualization plays an important role in many scientific and engineering disciplines such as climate modeling, turbulent combustion, and automobile design. The most common method for flow visualization is to display integral flow lines such as streamlines computed from particle tracing. Effective streamline visualization should capture flow patterns and display them with appropriate density, so that critical flow information can be visually acquired. In this dissertation, we present several approaches that facilitate expressive flow field visualization and exploration. First, we design a unified information-theoretic framework to model streamline selection and viewpoint selection as symmetric problems. Two interrelated information channels are constructed between a pool of candidate streamlines and a set of sample viewpoints. Based on these information channels, we define streamline information and viewpoint information to select best streamlines and viewpoints, respectively. Second, we present a focus+context framework to magnify small features and reduce occlusion around them while compacting the context region in a full view. This framework parititions the volume into blocks and deforms them to guide streamline repositioning. The desired deformation is formulated into energy terms and achieved by minimizing the energy function. Third, measuring the similarity of integral curves is fundamental to many tasks such as feature detection, pattern querying, streamline clustering and hierarchical exploration. We introduce FlowString that extracts shape invariant features from streamlines to form an alphabet of characters, and encodes each streamline into a string. The similarity of two streamline segments then becomes a specially designed edit distance between two strings. Leveraging the suffix tree, FlowString provides a string-based method for exploratory streamline analysis and visualization. A universal alphabet is learned from multiple data sets to capture basic flow patterns that exist in a variety of flow fields. This allows easy comparison and efficient query across data sets. Fourth, for exploration of vascular data sets, which contain a series of vector fields together with multiple scalar fields, we design a web-based approach for users to investigate the relationship among different properties guided by histograms. The vessel structure is mapped from the 3D volume space to a 2D graph, which allow more efficient interaction and effective visualization on websites. A segmentation scheme is proposed to divide the vessel structure based on a user specified property to further explore the distribution of that property over space

Lightweight Massively Parallel Suffix Array Construction

The suffix array is an array of sorted suffixes in lexicographic order, where each sorted suffix is represented by its starting position in the input string. It is a fundamental data structure that finds various applications in areas such as string processing, text indexing, data compression, computational biology, and many more. Over the last three decades, researchers have proposed a broad spectrum of suffix array construction algorithms (SACAs). However, the majority of SACAs were implemented using sequential and parallel programming models. The maturity of GPU programming opened doors to the development of massively parallel GPU SACAs that outperform the fastest versions of suffix sorting algorithms optimized for the CPU parallel computing. Over the last five years, several GPU SACA approaches were proposed and implemented. They prioritized the running time over lightweight design. In this thesis, we design and implement a lightweight massively parallel SACA on the GPU using the prefix-doubling technique. Our prefix-doubling implementation is memory-efficient and can successfully construct the suffix array for input strings as large as 640 megabytes (MB) on Tesla P100 GPU. On large datasets, our implementation achieves a speedup of 7-16x over the fastest, highly optimized, OpenMP-accelerated suffix array constructor, libdivsufsort, that leverages the CPU shared memory parallelism. The performance of our algorithm relies on several high-performance parallel primitives such as radix sort, conditional filtering, inclusive prefix sum, random memory scattering, and segmented sort. We evaluate the performance of our implementation over a variety of real-world datasets with respect to its runtime, throughput, memory usage, and scalability. We compare our results against libdivsufsort that we run on a Haswell compute node equipped with 24 cores. Our GPU SACA is simple and compact, consisting of less than 300 lines of readable and effective source code. Additionally, we design and implement a fast and lightweight algorithm for checking the correctness of the suffix array

Stream Processing using Grammars and Regular Expressions

In this dissertation we study regular expression based parsing and the use of grammatical specifications for the synthesis of fast, streaming string-processing programs. In the first part we develop two linear-time algorithms for regular expression based parsing with Perl-style greedy disambiguation. The first algorithm operates in two passes in a semi-streaming fashion, using a constant amount of working memory and an auxiliary tape storage which is written in the first pass and consumed by the second. The second algorithm is a single-pass and optimally streaming algorithm which outputs as much of the parse tree as is semantically possible based on the input prefix read so far, and resorts to buffering as many symbols as is required to resolve the next choice. Optimality is obtained by performing a PSPACE-complete pre-analysis on the regular expression. In the second part we present Kleenex, a language for expressing high-performance streaming string processing programs as regular grammars with embedded semantic actions, and its compilation to streaming string transducers with worst-case linear-time performance. Its underlying theory is based on transducer decomposition into oracle and action machines, and a finite-state specialization of the streaming parsing algorithm presented in the first part. In the second part we also develop a new linear-time streaming parsing algorithm for parsing expression grammars (PEG) which generalizes the regular grammars of Kleenex. The algorithm is based on a bottom-up tabulation algorithm reformulated using least fixed points and evaluated using an instance of the chaotic iteration scheme by Cousot and Cousot

On mining complex sequential data by means of FCA and pattern structures

Nowadays data sets are available in very complex and heterogeneous ways. Mining of such data collections is essential to support many real-world applications ranging from healthcare to marketing. In this work, we focus on the analysis of "complex" sequential data by means of interesting sequential patterns. We approach the problem using the elegant mathematical framework of Formal Concept Analysis (FCA) and its extension based on "pattern structures". Pattern structures are used for mining complex data (such as sequences or graphs) and are based on a subsumption operation, which in our case is defined with respect to the partial order on sequences. We show how pattern structures along with projections (i.e., a data reduction of sequential structures), are able to enumerate more meaningful patterns and increase the computing efficiency of the approach. Finally, we show the applicability of the presented method for discovering and analyzing interesting patient patterns from a French healthcare data set on cancer. The quantitative and qualitative results (with annotations and analysis from a physician) are reported in this use case which is the main motivation for this work. Keywords: data mining; formal concept analysis; pattern structures; projections; sequences; sequential data.Comment: An accepted publication in International Journal of General Systems. The paper is created in the wake of the conference on Concept Lattice and their Applications (CLA'2013). 27 pages, 9 figures, 3 table

A computational framework for unsupervised analysis of everyday human activities

In order to make computers proactive and assistive, we must enable them to perceive, learn, and predict what is happening in their surroundings. This presents us with the challenge of formalizing computational models of everyday human activities. For a majority of environments, the structure of the in situ activities is generally not known a priori. This thesis therefore investigates knowledge representations and manipulation techniques that can facilitate learning of such everyday human activities in a minimally supervised manner. A key step towards this end is finding appropriate representations for human activities. We posit that if we chose to describe activities as finite sequences of an appropriate set of events, then the global structure of these activities can be uniquely encoded using their local event sub-sequences. With this perspective at hand, we particularly investigate representations that characterize activities in terms of their fixed and variable length event subsequences. We comparatively analyze these representations in terms of their representational scope, feature cardinality and noise sensitivity. Exploiting such representations, we propose a computational framework to discover the various activity-classes taking place in an environment. We model these activity-classes as maximally similar activity-cliques in a completely connected graph of activities, and describe how to discover them efficiently. Moreover, we propose methods for finding concise characterizations of these discovered activity-classes, both from a holistic as well as a by-parts perspective. Using such characterizations, we present an incremental method to classify a new activity instance to one of the discovered activity-classes, and to automatically detect if it is anomalous with respect to the general characteristics of its membership class. Our results show the efficacy of our framework in a variety of everyday environments.Ph.D.Committee Chair: Aaron Bobick; Committee Member: Charles Isbell; Committee Member: David Hogg; Committee Member: Irfan Essa; Committee Member: James Reh