Parallel String Matching with Multi Core Processors-A Comparative Study for Gene Sequences

The increase in huge amount of data is seen clearly in present days because of requirement for storing more information. To extract certain data from this large database is a very difficult task, including text processing, information retrieval, text mining, pattern recognition and DNA sequencing. So we need concurrent events and high performance computing models for extracting the data. This will create a challenge to the researchers. One of the solutions is parallel algorithms for string matching on computing models. In this we implemented parallel string matching with JAVA Multi threading with multi core processing, and performed a comparative study on Knuth Morris Pratt, Boyer Moore and Brute force string matching algorithms. For testing our system we take a gene sequence which consists of lacks of records. From the test results it is shown that the multicore processing is better compared to lower versions. Finally this proposed parallel string matching with multicore processing is better compared to other sequential approaches

TAPER: query-aware, partition-enhancement for large, heterogenous, graphs

Graph partitioning has long been seen as a viable approach to address Graph DBMS scalability. A partitioning, however, may introduce extra query processing latency unless it is sensitive to a specific query workload, and optimised to minimise inter-partition traversals for that workload. Additionally, it should also be possible to incrementally adjust the partitioning in reaction to changes in the graph topology, the query workload, or both. Because of their complexity, current partitioning algorithms fall short of one or both of these requirements, as they are designed for offline use and as one-off operations. The TAPER system aims to address both requirements, whilst leveraging existing partitioning algorithms. TAPER takes any given initial partitioning as a starting point, and iteratively adjusts it by swapping chosen vertices across partitions, heuristically reducing the probability of inter-partition traversals for a given pattern matching queries workload. Iterations are inexpensive thanks to time and space optimisations in the underlying support data structures. We evaluate TAPER on two different large test graphs and over realistic query workloads. Our results indicate that, given a hash-based partitioning, TAPER reduces the number of inter-partition traversals by around 80%; given an unweighted METIS partitioning, by around 30%. These reductions are achieved within 8 iterations and with the additional advantage of being workload-aware and usable online.Comment: 12 pages, 11 figures, unpublishe

Scalable NIDS via Negative Pattern Matching and Exclusive Pattern Matching

In this paper, we identify the unique challenges in deploying parallelism on TCAM-based pattern matching for Network Intrusion Detection Systems (NIDSes). We resolve two critical issues when designing scalable parallelism specifically for pattern matching modules: 1) how to enable fine-grained parallelism in pursuit of effective load balancing and desirable speedup simultaneously; and 2) how to reconcile the tension between parallel processing speedup and prohibitive TCAM power consumption. To this end, we first propose the novel concept of Negative Pattern Matching to partition flows, by which the number of TCAM lookups can be significantly reduced, and the resulting (fine-grained) flow segments can be inspected in parallel without incurring false negatives. Then we propose the notion of Exclusive Pattern Matching to divide the entire pattern set into multiple subsets which can later be matched against selectively and independently without affecting the correctness. We show that Exclusive Pattern Matching enables the adoption of smaller and faster TCAM blocks and improves both the pattern matching speed and scalability. Finally, our theoretical and experimental results validate that the above two concepts are inherently complementary, enabling our integrated scheme to provide performance gain in any scenario (with either clean or dirty traffic).Department of ComputingRefereed conference pape

EAGLE—A Scalable Query Processing Engine for Linked Sensor Data

Recently, many approaches have been proposed to manage sensor data using semantic web technologies for effective heterogeneous data integration. However, our empirical observations revealed that these solutions primarily focused on semantic relationships and unfortunately paid less attention to spatio–temporal correlations. Most semantic approaches do not have spatio–temporal support. Some of them have attempted to provide full spatio–temporal support, but have poor performance for complex spatio–temporal aggregate queries. In addition, while the volume of sensor data is rapidly growing, the challenge of querying and managing the massive volumes of data generated by sensing devices still remains unsolved. In this article, we introduce EAGLE, a spatio–temporal query engine for querying sensor data based on the linked data model. The ultimate goal of EAGLE is to provide an elastic and scalable system which allows fast searching and analysis with respect to the relationships of space, time and semantics in sensor data. We also extend SPARQL with a set of new query operators in order to support spatio–temporal computing in the linked sensor data context.EC/H2020/732679/EU/ACTivating InnoVative IoT smart living environments for AGEing well/ACTIVAGEEC/H2020/661180/EU/A Scalable and Elastic Platform for Near-Realtime Analytics for The Graph of Everything/SMARTE

String Searching with Ranking Constraints and Uncertainty

Strings play an important role in many areas of computer science. Searching pattern in a string or string collection is one of the most classic problems. Different variations of this problem such as document retrieval, ranked document retrieval, dictionary matching has been well studied. Enormous growth of internet, large genomic projects, sensor networks, digital libraries necessitates not just efficient algorithms and data structures for the general string indexing, but indexes for texts with fuzzy information and support for queries with different constraints. This dissertation addresses some of these problems and proposes indexing solutions. One such variation is document retrieval query for included and excluded/forbidden patterns, where the objective is to retrieve all the relevant documents that contains the included patterns and does not contain the excluded patterns. We continue the previous work done on this problem and propose more efficient solution. We conjecture that any significant improvement over these results is highly unlikely. We also consider the scenario when the query consists of more than two patterns. The forbidden pattern problem suffers from the drawback that linear space (in words) solutions are unlikely to yield a solution better than O(root(n/occ)) per document reporting time, where n is the total length of the documents and occ is the number of output documents. Continuing this path, we introduce a new variation, namely document retrieval with forbidden extension query, where the forbidden pattern is an extension of the included pattern.We also address the more general top-k version of the problem, which retrieves the top k documents, where the ranking is based on PageRank relevance metric. This problem finds motivation from search applications. It also holds theoretical interest as we show that the hardness of forbidden pattern problem is alleviated in this problem. We achieve linear space and optimal query time for this variation. We also propose succinct indexes for both these problems. Position restricted pattern matching considers the scenario where only part of the text is searched. We propose succinct index for this problem with efficient query time. An important application for this problem stems from searching in genomic sequences, where only part of the gene sequence is searched for interesting patterns. The problem of computing discriminating(resp. generic) words is to report all minimal(resp. maximal) extensions of a query pattern which are contained in at most(resp. at least) a given number of documents. These problems are motivated from applications in computational biology, text mining and automated text classification. We propose succinct indexes for these problems. Strings with uncertainty and fuzzy information play an important role in increasingly many applications. We propose a general framework for indexing uncertain strings such that a deterministic query string can be searched efficiently. String matching becomes a probabilistic event when a string contains uncertainty, i.e. each position of the string can have different probable characters with associated probability of occurrence for each character. Such uncertain strings are prevalent in various applications such as biological sequence data, event monitoring and automatic ECG annotations. We consider two basic problems of string searching, namely substring searching and string listing. We formulate these well known problems for uncertain strings paradigm and propose exact and approximate solution for them. We also discuss a constrained variation of orthogonal range searching. Given a set of points, the task of orthogonal range searching is to build a data structure such that all the points inside a orthogonal query region can be reported. We introduce a new variation, namely shared constraint range searching which naturally arises in constrained pattern matching applications. Shared constraint range searching is a special four sided range reporting query problem where two constraints has sharing among them, effectively reducing the number of independent constraints. For this problem, we propose a linear space index that can match the best known bound for three dimensional dominance reporting problem. We extend our data structure in the external memory model

Clustering-Based Pre-Processing Approaches To Improve Similarity Join Techniques

Research on similarity join techniques is becoming one of the growing practical areas for study, especially with the increasing E-availability of vast amounts of digital data from more and more source systems. This research is focused on pre-processing clustering-based techniques to improve existing similarity join approaches. Identifying and extracting the same real-world entities from different data sources is still a big challenge and a significant task in the digital information era. Dissimilar extracts may indeed represent the same real-world entity because of inconsistent values and naming conventions, incorrect or missing data values, or incomplete information. Therefore discovering efficient and accurate approaches to determine the similarity of data objects or values is of theoretical as well as practical significance. Semantic problems are raised even on the concept of similarity regarding its usage and foundation. Existing similarity join approaches often have a very specific view of similarity measures and pre-defined predicates that represent a narrow focus on the context of similarity for a given scenario. The predicates have been assumed to be a group of clustering [MSW 72] related attributes on the join. To identify those entities for data integration purposes requires a broader view of similarity; for instance a number of generic similarity measures are useful in a given data integration systems. This study focused on string similarity join, namely based on the Levenshtein or edit distance and Q-gram. Proposed effective and efficient pre-processing clustering-based techniques were the focus of this study to identify clustering related predicates based on either attribute value or data value that improve existing similarity join techniques in enterprise data integration scenarios

Toward Entity-Aware Search

As the Web has evolved into a data-rich repository, with the standard "page view," current search engines are becoming increasingly inadequate for a wide range of query tasks. While we often search for various data "entities" (e.g., phone number, paper PDF, date), today's engines only take us indirectly to pages. In my Ph.D. study, we focus on a novel type of Web search that is aware of data entities inside pages, a significant departure from traditional document retrieval. We study the various essential aspects of supporting entity-aware Web search. To begin with, we tackle the core challenge of ranking entities, by distilling its underlying conceptual model Impression Model and developing a probabilistic ranking framework, EntityRank, that is able to seamlessly integrate both local and global information in ranking. We also report a prototype system built to show the initial promise of the proposal. Then, we aim at distilling and abstracting the essential computation requirements of entity search. From the dual views of reasoning--entity as input and entity as output, we propose a dual-inversion framework, with two indexing and partition schemes, towards efficient and scalable query processing. Further, to recognize more entity instances, we study the problem of entity synonym discovery through mining query log data. The results we obtained so far have shown clear promise of entity-aware search, in its usefulness, effectiveness, efficiency and scalability