Efficient main memory-based XML stream processing

Applications that process XML documents as files or streams are naturally main-memory based. This makes main memory the bottleneck for scalability. This doctoral thesis addresses this problem and presents a toolkit for effective buffer management in main memory-based XML stream processors. XML document projection is an established technique for reducing the buffer requirements of main memory-based XML processors, where only data relevant to query evaluation is loaded into main memory buffers. We present a novel implementation of this task, where we use string matching algorithms designed for efficient keyword search in flat strings to navigate in tree-structured data. We then introduce an extension of the XQuery language, called FluX, that supports event-based query processing. Purely event-based queries of this language can be executed on streaming XML data in a very direct way. We develop an algorithm to efficiently rewrite XQueries into FluX. This algorithm is capable of exploiting order constraints derived from schemata to reduce the amount of buffering in query evaluation. During streaming query evaluation, we continuously purge buffers from data that is no longer relevant. By combining static query analysis with a dynamic analysis of the buffer contents, we effectively reduce the size of memory buffers. We have confirmed the efficacy of these techniques by extensive experiments and by publication at international venues. To compare our contributions to related work in a systematic manner, we contribute an abstract framework for XML stream processing. This framework allows us to gain a greater-picture view over the factors influencing the main memory consumption.Anwendungen, die XML-Dokumente als Dateien oder Ströme verarbeiten, sind natürlicherweise hauptspeicherbasiert. Für die Skalierbarkeit wird der Hauptspeicher damit zu einem Engpass. Diese Doktorarbeit widmet sich diesem Problem, zu dessen Lösung sie Werkzeuge für eine effektive Pufferverwaltung in hauptspeicherbasierten Prozessoren für XML-Datenströme vorstellt. Die Projektion von XML-Dokumenten ist eine etablierte Methode, um den Pufferverbrauch von hauptspeicherbasierten XML-Prozessoren zu reduzieren. Dabei werden nur jene Daten in den Hauptspeicherpuffer geladen, die für die Anfrageauswertung auch relevant sind. Wir präsentieren eine neue Implementierung dieser Aufgabe, wobei wir Algorithmen zur effizienten Suche in flachen Zeichenketten einsetzen, um in baumartig strukturierten Daten zu navigieren. Danach stellen wir eine Erweiterung der XQuery-Sprache vor, genannt FluX, welche eine ereignisbasierte Anfragebearbeitung erlaubt. Anfragen, die nur ereignisbasierte Konstrukte benutzen, können direkt über XML-Datenströmen ausgewertet werden. Dazu entwickeln wir einen Algorithmus, mit dessen Hilfe sich XQuery-Anfragen effizient in FluX übersetzen lassen. Dieser benutzt Ordnungsinformationen aus Datenschemata, womit das Puffern in der Anfragebearbeitung reduziert werden kann. Während der Verarbeitung des Datenstroms bereinigen wir laufend den Hauptspeicherpuffer von solchen Daten, die nicht länger relevant sind. Eine nachhaltige Reduzierung der Größe von Hauptspeicherpuffern gelingt durch die Kombination der statischen Anfrageanalyse mit einer dynamischen Analyse der Pufferinhalte. Die Effektivität dieser Puffermanagement-Techniken erfährt ihre Bestätigung in umfangreichen Experimenten und internationalen Publikationen. Für einen systematischen Vergleich unserer Beiträge mit der aktuellen Literatur entwickeln wir ein abstraktes System zur Modellierung von Prozessoren zur XML-Stromverarbeitung. So können wir die spezifischen Faktoren herausgreifen, die den Hauptspeicherverbrauch beeinflussen

Algorithms for XML filtering

In a publish-subscribe system based on XML filtering, the subscriber profiles are usually specified by filters written in the XPath language. The system processes the stream of XML documents and delivers to subscribers a notification or the content of those documents that match the filters. The number of interested subscribers and their stored profiles can be very large, thousands or even millions. In this case, the scalability of the system is critical. In this thesis, we develop several algorithms for XML filtering with linear XPath expressions. The algorithms are based on a backtracking Aho-Corasick pattern-matching automaton (PMA) built from "keywords" extracted from the filters, where a keyword is a maximal substring consisting only of XML element names. The output function of the PMA indicates which keyword occurrences of which filter are recognized at a given state. Our best results have been obtained by using a dynamically changing output function, which is dynamically updated during the processing of the input document. We have conducted an extensive performance study in which we compared our filtering algorithms with YFilter and the lazy DFA, two well-known automata-based filtering methods. With a non-recursive XML data set, PMA-based filtering is tens of times more efficient than YFilter and also significantly more efficient than the lazy DFA. With a slightly recursive data set PMA-based filtering has the same performance as the lazy DFA and it is significantly more efficient than YFilter. We have also developed an optimization method called filter pruning. This method improves the performance of filtering by utilizing knowledge about the XML document type definition (DTD) to simplify the filters. The optimization algorithm takes as input a DTD and a set of linear XPath filters and produces a set of pruned linear XPath filters that contain as few wildcards and descendant operators as possible. With a non-recursive data set and with a slightly recursive data set the filter-pruning method yielded a tenfold increase in the filtering speed of the PMA-based algorithms and a hundredfold increase with YFilter and the lazy DFA. Filter pruning can also increase the filtering speed in the case of highly recursive data sets

Alarm flood reduction using multiple data sources

The introduction of distributed control systems in the process industry has increased the number of alarms per operator exponentially. Modern plants present a high level of interconnectivity due to steam recirculation, heat integration and the complex control systems installed in the plant. When there is a disturbance in the plant it spreads through its material, energy and information connections affecting the process variables on the path. The alarms associated to these process variables are triggered. The alarm messages may overload the operator in the control room, who will not be able to properly investigate each one of these alarms. This undesired situation is called an “alarm flood”. In such situations the operator might not be able to keep the plant within safe operation. The aim of this thesis is to reduce alarm flood periods in process plants. Consequential alarms coming from the same process abnormality are isolated and a causal alarm suggestion is given. The causal alarm in an alarm flood is the alarm associated to the asset originating the disturbance that caused the flood. Multiple information sources are used: an alarm log containing all past alarms messages, process data and a topology model of the plant. The alarm flood reduction is achieved with a combination of alarm log analysis, process data root-cause analysis and connectivity analysis. The research findings are implemented in a software tool that guides the user through the different steps of the method. Finally the applicability of the method is proved with an industrial case study

An adaptive multi-scene correlation algorithm

Digital scene matching algorithms have been used in both military and commercial image processing systems for years. The trend toward using multiple sensors in military imaging systems has generated anew interest in real time techniques to accomplish sensor fusion tasks such as field of view alignment. This thesis analyzes methods presently in use and introduces a novel algorithm that improves scene correlation performance. The focus of the new technique is in the segmentation area, where significant features are extracted from background and clutter. These performance improvements are especially helpful when the scene contains excessive noise and or lacks detail, a trouble spot for standard correlation systems. The restrictions imposed on the system design include implementations possible for real time processing and a minimum of hardware and power consumption. Simulations of the algorithms programmed for an image processing board by an IBM personal computer are discussed

Fast index based algorithms and software for matching position specific scoring matrices

BACKGROUND: In biological sequence analysis, position specific scoring matrices (PSSMs) are widely used to represent sequence motifs in nucleotide as well as amino acid sequences. Searching with PSSMs in complete genomes or large sequence databases is a common, but computationally expensive task. RESULTS: We present a new non-heuristic algorithm, called ESAsearch, to efficiently find matches of PSSMs in large databases. Our approach preprocesses the search space, e.g., a complete genome or a set of protein sequences, and builds an enhanced suffix array that is stored on file. This allows the searching of a database with a PSSM in sublinear expected time. Since ESAsearch benefits from small alphabets, we present a variant operating on sequences recoded according to a reduced alphabet. We also address the problem of non-comparable PSSM-scores by developing a method which allows the efficient computation of a matrix similarity threshold for a PSSM, given an E-value or a p-value. Our method is based on dynamic programming and, in contrast to other methods, it employs lazy evaluation of the dynamic programming matrix. We evaluated algorithm ESAsearch with nucleotide PSSMs and with amino acid PSSMs. Compared to the best previous methods, ESAsearch shows speedups of a factor between 17 and 275 for nucleotide PSSMs, and speedups up to factor 1.8 for amino acid PSSMs. Comparisons with the most widely used programs even show speedups by a factor of at least 3.8. Alphabet reduction yields an additional speedup factor of 2 on amino acid sequences compared to results achieved with the 20 symbol standard alphabet. The lazy evaluation method is also much faster than previous methods, with speedups of a factor between 3 and 330. CONCLUSION: Our analysis of ESAsearch reveals sublinear runtime in the expected case, and linear runtime in the worst case for sequences not shorter than | [Formula: see text] |(m )+ m - 1, where m is the length of the PSSM and [Formula: see text] a finite alphabet. In practice, ESAsearch shows superior performance over the most widely used programs, especially for DNA sequences. The new algorithm for accurate on-the-fly calculations of thresholds has the potential to replace formerly used approximation approaches. Beyond the algorithmic contributions, we provide a robust, well documented, and easy to use software package, implementing the ideas and algorithms presented in this manuscript

Confidentiality-Preserving Publish/Subscribe: A Survey

Publish/subscribe (pub/sub) is an attractive communication paradigm for large-scale distributed applications running across multiple administrative domains. Pub/sub allows event-based information dissemination based on constraints on the nature of the data rather than on pre-established communication channels. It is a natural fit for deployment in untrusted environments such as public clouds linking applications across multiple sites. However, pub/sub in untrusted environments lead to major confidentiality concerns stemming from the content-centric nature of the communications. This survey classifies and analyzes different approaches to confidentiality preservation for pub/sub, from applications of trust and access control models to novel encryption techniques. It provides an overview of the current challenges posed by confidentiality concerns and points to future research directions in this promising field

Citation recommendation: approaches and datasets

Citation recommendation describes the task of recommending citations for a given text. Due to the overload of published scientific works in recent years on the one hand, and the need to cite the most appropriate publications when writing scientific texts on the other hand, citation recommendation has emerged as an important research topic. In recent years, several approaches and evaluation data sets have been presented. However, to the best of our knowledge, no literature survey has been conducted explicitly on citation recommendation. In this article, we give a thorough introduction to automatic citation recommendation research. We then present an overview of the approaches and data sets for citation recommendation and identify differences and commonalities using various dimensions. Last but not least, we shed light on the evaluation methods and outline general challenges in the evaluation and how to meet them. We restrict ourselves to citation recommendation for scientific publications, as this document type has been studied the most in this area. However, many of the observations and discussions included in this survey are also applicable to other types of text, such as news articles and encyclopedic articles