Search results for "Longest common subsequence problem"
showing 5 items of 5 documents
Real-time recognition of personal routes using instance-based learning
2011
Predicting routes is a critical enabler for many new location-based applications and services, such as warning drivers about congestion- or accident-risky areas. Hybrid vehicles can also utilize the route prediction for optimizing their charging and discharging phases. In this paper, a new lightweight route recognition approach using instance-based learning is introduced. In this approach, the current route is compared in real-time against the route instances observed in past, and the most similar route is selected. In order to assess the similarity between the routes, a similarity measure based on the longest common subsequence (LCSS) is employed, and an algorithm for incrementally evaluat…
XLCS: A New Bit-Parallel Longest Common Subsequence Algorithm on Xeon Phi Clusters
2019
Finding the longest common subsequence (LCS) of two strings is a classical problem in bioinformatics. A basic approach to solve this problem is based on dynamic programming. As the biological sequence databases are growing continuously, bit-parallel sequence comparison algorithms are becoming increasingly important. In this paper, we present XLCS, a new parallel implementation to accelerate the LCS algorithm on Xeon Phi clusters by performing bit-wise operations. We have designed an asynchronous IO framework to improve the data transfer efficiency. To make full use of the computing resources of Xeon Phi clusters, we use three levels of parallelism: node-level, thread-level and vector-level.…
A basic analysis toolkit for biological sequences
2007
This paper presents a software library, nicknamed BATS, for some basic sequence analysis tasks. Namely, local alignments, via approximate string matching, and global alignments, via longest common subsequence and alignments with affine and concave gap cost functions. Moreover, it also supports filtering operations to select strings from a set and establish their statistical significance, via z-score computation. None of the algorithms is new, but although they are generally regarded as fundamental for sequence analysis, they have not been implemented in a single and consistent software package, as we do here. Therefore, our main contribution is to fill this gap between algorithmic theory an…
Longest Common Subsequence from Fragments via Sparse Dynamic Programming
1998
Sparse Dynamic Programming has emerged as an essential tool for the design of efficient algorithms for optimization problems coming from such diverse areas as Computer Science, Computational Biology and Speech Recognition [7,11,15]. We provide a new Sparse Dynamic Programming technique that extends the Hunt-Szymanski [2,9,8] paradigm for the computation of the Longest Common Subsequence (LCS) and apply it to solve the LCS from Fragments problem: given a pair of strings X and Y (of length n and m, resp.) and a set M of matching substrings of X and Y, find the longest common subsequence based only on the symbol correspondences induced by the substrings. This problem arises in an application t…
Sparse Dynamic Programming for Longest Common Subsequence from Fragments
2002
Sparse Dynamic Programming has emerged as an essential tool for the design of efficient algorithms for optimization problems coming from such diverse areas as computer science, computational biology, and speech recognition. We provide a new sparse dynamic programming technique that extends the Hunt?Szymanski paradigm for the computation of the longest common subsequence (LCS) and apply it to solve the LCS from Fragments problem: given a pair of strings X and Y (of length n and m, respectively) and a set M of matching substrings of X and Y, find the longest common subsequence based only on the symbol correspondences induced by the substrings. This problem arises in an application to analysis…