Rapid analysis of DNA sequences is important in preventing the evolution of different viruses and bacteria during an early phase, early diagnosis of genetic predispositions to certain diseases (cancer, cardiovascular diseases), and in DNA forensics. However, real-world DNA sequences may comprise several Gigabytes and the process of DNA analysis demands adequate computational resources to be completed within a reasonable time. In this paper we present a scalable approach for parallel DNA analysis that is based on Finite Automata, and which is suitable for analyzing very large DNA segments. We evaluate our approach for real-world DNA segments of mouse (2.7GB), cat (2.4GB), dog (2.4GB), chicken (1GB), human (3.2GB) and turkey (0.2GB). Experimental results on a dual-socket shared-memory system with 24 physical cores show speed-ups of up to 17.6x. Our approach is up to 3x faster than a pattern-based parallel approach that uses the RE2 library.
Existing approaches use both hardware and software to accelerate the process of regular expression matching. In comparison to hardware based state machines, which are faster, less flexible and more expensive, software based acceleration techniques are flexible in terms of updating or adding new patterns @cite_29 .
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2046801051 1990473086 1762798876 1990240966
Current text pattern-matching tools are based on regular expressions. However, pure regular expressions have proven too weak a formalism for the task: many interesting patterns either are difficult to describe or cannot be described by regular expressions. Moreover, the inherent non-determinism of regular expressions does not fit the need to capture specific parts of a match. Motivated by these reasons, most scripting languages nowadays use pattern-matching tools that extend the original regular-expression formalism with a set of ad hoc features, such as greedy repetitions, lazy repetitions, possessive repetitions, ‘longest-match rule,’ lookahead, etc. These ad hoc extensions bring their own set of problems, such as lack of a formal foundation and complex implementations. In this paper, we propose the use of Parsing Expression Grammars (PEGs) as a basis for pattern matching. Following this proposal, we present LPEG, a pattern-matching tool based on PEGs for the Lua scripting language. LPEG unifies the ease of use of pattern-matching tools with the full expressive power of PEGs. Because of this expressive power, it can avoid the myriad of ad hoc constructions present in several current pattern-matching tools. We also present a Parsing Machine that allows a small and efficient implementation of PEGs for pattern matching. Copyright © 2008 John Wiley & Sons, Ltd. Conventionally, regular expression matching (REM) has been performed by sequentially comparing the regular expression (regex) to the input stream, which can be slow due to excessive backtracking (smith:acsac06). Alternatively, the regex can be converted to a deterministic finite automaton (DFA) for efficient matching, which however may require an extremely large state transition table (STT) due to exponential state explosion (meyer:swat71, yu:ancs06). We propose the segmented regex-NFA (SR-NFA) architecture, where the regex is first compiled into modular nondeterministic finite automata (NFA), then partitioned, optimized, and matched efficiently on modern multi-core processors. SR-NFA offers attack-resilient multi-gigabit per second matching throughput, does not suffer from either backtracking or state explosion, and can be rapidly constructed. For regex sets that construct a DFA with moderate state explosion, i.e., on average 200k states in the STT, the proposed SR-NFA is 367k times faster to construct and update and use 23k times less memory than the DFA approach. Running on an 8-core 2.6 GHz Opteron platform, our prototype achieves 2.2 Gbps average matching throughput for regex sets with up to 4,000 SR-NFA states per regex set. We introduce a novel matching algorithm, called DeepMatching, to compute dense correspondences between images. DeepMatching relies on a hierarchical, multi-layer, correlational architecture designed for matching images and was inspired by deep convolutional approaches. The proposed matching algorithm can handle non-rigid deformations and repetitive textures and efficiently determines dense correspondences in the presence of significant changes between images. We evaluate the performance of DeepMatching, in comparison with state-of-the-art matching algorithms, on the Mikolajczyk ( A comparison of affine region detectors, 2005), the MPI-Sintel ( A naturalistic open source movie for optical flow evaluation, 2012) and the Kitti ( Vision meets robotics: The KITTI dataset, 2013) datasets. DeepMatching outperforms the state-of-the-art algorithms and shows excellent results in particular for repetitive textures. We also apply DeepMatching to the computation of optical flow, called DeepFlow, by integrating it in the large displacement optical flow (LDOF) approach of Brox and Malik (Large displacement optical flow: descriptor matching in variational motion estimation, 2011). Additional robustness to large displacements and complex motion is obtained thanks to our matching approach. DeepFlow obtains competitive performance on public benchmarks for optical flow estimation. The efficient processing of large collections of patterns expressed as Boolean expressions over event streams plays a central role in major data intensive applications ranging from user-centric processing and personalization to real-time data analysis. On the one hand, emerging user-centric applications, including computational advertising and selective information dissemination, demand determining and presenting to an end-user the relevant content as it is published. On the other hand, applications in real-time data analysis, including push-based multi-query optimization, computational finance and intrusion detection, demand meeting stringent subsecond processing requirements and providing high-frequency event processing. We achieve these event processing requirements by exploiting the shift towards multi-core architectures by proposing novel adaptive parallel compressed event matching algorithm (A-PCM) and online event stream re-ordering technique (OSR) that unleash an unprecedented degree of parallelism amenable for highly parallel event processing. In our comprehensive evaluation, we demonstrate the efficiency of our proposed techniques. We show that the adaptive parallel compressed event matching algorithm can sustain an event rate of up to 233,863 events second while state-of-the-art sequential event matching algorithms sustains only 36 events second when processing up to five million Boolean expressions.