Conference Paper

A survey of longest common subsequence algorithms

Dept. of Comput. Sci., Turku Univ.;
DOI: 10.1109/SPIRE.2000.878178 Conference: String Processing and Information Retrieval, 2000. SPIRE 2000. Proceedings. Seventh International Symposium on
Source: IEEE Xplore

ABSTRACT The aim of this paper is to give a comprehensive comparison of well-known longest common subsequence algorithms (for two input strings) and study their behaviour in various application environments. The performance of the methods depends heavily on the properties of the problem instance as well as the supporting data structures used in the implementation. We want to make also a clear distinction between methods that determine the actual lcs and those calculating only its length, since the execution time and more importantly, the space demand depends crucially on the type of the task. To our knowledge, this is the first time this kind of survey has been done. Due to the page limits, the paper gives only a coarse overview of the performance of the algorithms; more detailed studies are reported elsewhere

1 Bookmark
 · 
446 Views
  • [Show abstract] [Hide abstract]
    ABSTRACT: Supernode transformation is a technique to decrease the communication overhead by partitioning and scheduling a loop nest to a multi-processor system. This is achieved by grouping a number of iterations in a perfectly nested loop with regular dependences as a $supernode$ supernode . Previous work has been focusing on finding the optimal supernode size and shape as well as an optimal execution schedule for multi-processor systems with unbounded resources. This paper emphasizes on the actual implementation strategies of supernode transformations on multi-core systems with limited resources. Using an example, the longest common subsequence (LCS) problem, we present and compare three different multithreading implementations. A formula for the total execution time of each method is presented. The techniques are benchmarked on a 12-core and a 4-core machine. On the 12-core machine our first technique, which yields increased data locality, speeds up the unaltered sequential loop nest 16.7 times. Combining this technique with skewing the loop by changing the linear schedule scores a 42.6 speedup. A more sophisticated method that executes entire rows of the loop nest in one thread scores a 59.5 speedup. Concepts presented and discussed in this paper on the LCS problem serve as basic foundation for implementations at regular dependence algorithms.
    International Journal of Parallel Programming 04/2014; · 0.40 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: A new data hiding method via collaboratively-written articles with forged revision history records on collaborative writing platforms is proposed. The hidden message is camouflaged as a stego-document consisting of a stego-article and a revision history created through a simulated process of collaborative writing. The revisions are forged using a database constructed by mining word sequences used in real cases from an English Wikipedia XML dump. Four characteristics of article revisions are identified and utilized to embed secret messages, including the author of each revision, the number of corrected word sequences, the content of the corrected word sequences, and the word sequences replacing the corrected ones. Related problems arising in utilizing these characteristics for data hiding are identified and solved skillfully, resulting in an effective multiway method for hiding secret messages into the revision history. To create more realistic revisions, Huffman coding based on the word sequence frequencies collected from Wikipedia is applied to encode the word sequences. Good experimental results show the feasibility of the proposed method.
    ACM Transactions on Multimedia Computing, Communications, and Applications (TOMCCAP). 02/2014; 10(2).
  • [Show abstract] [Hide abstract]
    ABSTRACT: Competing workloads on a shared storage system cause I/O resource contention and application performance vagaries. This problem is already evident in today's HPC storage systems and is likely to become acute at exascale. We need more interaction between application I/O requirements and system software tools to help alleviate the I/O bottleneck, moving towards I/O-aware job scheduling. However, this requires rich techniques to capture application I/O characteristics, which remain evasive in production systems. Traditionally, I/O characteristics have been obtained using client-side tracing tools, with drawbacks such as non-trivial instrumentation/development costs, large trace traffic, and inconsistent adoption. We present a novel approach, I/O Signature Identifier (IOSI), to characterize the I/O behavior of data-intensive applications. IOSI extracts signatures from noisy, zero-overhead server-side I/O throughput logs that are already collected on today's supercomputers, without interfering with the compiling/execution of applications. We evaluated IOSI using the Spider storage system at Oak Ridge National Laboratory, the S3D turbulence application (running on 18,000 Titan nodes), and benchmark-based pseudo-applications. Through our experiments we confirmed that IOSI effectively extracts an application's I/O signature despite significant server-side noise. Compared to client-side tracing tools, IOSI is transparent, interface-agnostic, and incurs no overhead. Compared to alternative data alignment techniques (e.g., dynamic time warping), it offers higher signature accuracy and shorter processing time.
    Proceedings of the 12th USENIX conference on File and Storage Technologies; 02/2014

Full-text

View
56 Downloads
Available from