34,187 research outputs found

    Simple, compact and robust approximate string dictionary

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    This paper is concerned with practical implementations of approximate string dictionaries that allow edit errors. In this problem, we have as input a dictionary DD of dd strings of total length nn over an alphabet of size σ\sigma. Given a bound kk and a pattern xx of length mm, a query has to return all the strings of the dictionary which are at edit distance at most kk from xx, where the edit distance between two strings xx and yy is defined as the minimum-cost sequence of edit operations that transform xx into yy. The cost of a sequence of operations is defined as the sum of the costs of the operations involved in the sequence. In this paper, we assume that each of these operations has unit cost and consider only three operations: deletion of one character, insertion of one character and substitution of a character by another. We present a practical implementation of the data structure we recently proposed and which works only for one error. We extend the scheme to 2≤k<m2\leq k<m. Our implementation has many desirable properties: it has a very fast and space-efficient building algorithm. The dictionary data structure is compact and has fast and robust query time. Finally our data structure is simple to implement as it only uses basic techniques from the literature, mainly hashing (linear probing and hash signatures) and succinct data structures (bitvectors supporting rank queries).Comment: Accepted to a journal (19 pages, 2 figures

    HYDRA: Hybrid Deep Magnetic Resonance Fingerprinting

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    Purpose: Magnetic resonance fingerprinting (MRF) methods typically rely on dictio-nary matching to map the temporal MRF signals to quantitative tissue parameters. Such approaches suffer from inherent discretization errors, as well as high computational complexity as the dictionary size grows. To alleviate these issues, we propose a HYbrid Deep magnetic ResonAnce fingerprinting approach, referred to as HYDRA. Methods: HYDRA involves two stages: a model-based signature restoration phase and a learning-based parameter restoration phase. Signal restoration is implemented using low-rank based de-aliasing techniques while parameter restoration is performed using a deep nonlocal residual convolutional neural network. The designed network is trained on synthesized MRF data simulated with the Bloch equations and fast imaging with steady state precession (FISP) sequences. In test mode, it takes a temporal MRF signal as input and produces the corresponding tissue parameters. Results: We validated our approach on both synthetic data and anatomical data generated from a healthy subject. The results demonstrate that, in contrast to conventional dictionary-matching based MRF techniques, our approach significantly improves inference speed by eliminating the time-consuming dictionary matching operation, and alleviates discretization errors by outputting continuous-valued parameters. We further avoid the need to store a large dictionary, thus reducing memory requirements. Conclusions: Our approach demonstrates advantages in terms of inference speed, accuracy and storage requirements over competing MRF method

    A new problem in string searching

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    We describe a substring search problem that arises in group presentation simplification processes. We suggest a two-level searching model: skip and match levels. We give two timestamp algorithms which skip searching parts of the text where there are no matches at all and prove their correctness. At the match level, we consider Harrison signature, Karp-Rabin fingerprint, Bloom filter and automata based matching algorithms and present experimental performance figures.Comment: To appear in Proceedings Fifth Annual International Symposium on Algorithms and Computation (ISAAC'94), Lecture Notes in Computer Scienc
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