scholarly journals A SIMPLE ALPHABET-INDEPENDENT FM-INDEX

2006 ◽  
Vol 17 (06) ◽  
pp. 1365-1384 ◽  
Author(s):  
SZYMON GRABOWSKI ◽  
GONZALO NAVARRO ◽  
RAFAŁ PRZYWARSKI ◽  
ALEJANDRO SALINGER ◽  
VELI MÄKINEN
Keyword(s):  
Data Structures ◽  
Full Text ◽  
Search Time ◽  
Space Time ◽  
Zero Order ◽  
Succinct Data Structures ◽  
Worst Case ◽  
Time Tradeoff ◽  
Burrows Wheeler Transform ◽  
Coding Variants

We design a succinct full-text index based on the idea of Huffman-compressing the text and then applying the Burrows-Wheeler transform over it. The resulting structure can be searched as an FM-index, with the benefit of removing the sharp dependence on the alphabet size, σ, present in that structure. On a text of length n with zero-order entropy H0, our index needs O(n(H0 + 1)) bits of space, without any significant dependence on σ. The average search time for a pattern of length m is O(m(H0 + 1)), under reasonable assumptions. Each position of a text occurrence can be located in worst case time O((H0 + 1) log n), while any text substring of length L can be retrieved in O((H0 + 1)L) average time in addition to the previous worst case time. Our index provides a relevant space/time tradeoff between existing succinct data structures, with the additional interest of being easy to implement. We also explore other coding variants alternative to Huffman and exploit their synchronization properties. Our experimental results on various types of texts show that our indexes are highly competitive in the space/time tradeoff map.

scholarly journals Succinct data structures for Searchable Partial Sums with optimal worst-case performance

2011 ◽  
Vol 412 (39) ◽  
pp. 5176-5186 ◽  
Author(s):  
Wing-Kai Hon ◽  
Kunihiko Sadakane ◽  
Wing-Kin Sung
Keyword(s):  
Data Structures ◽  
Partial Sums ◽  
Succinct Data Structures ◽  
Worst Case

scholarly journals Multi-Tier Heterogeneous Beam Management for Future Indoor FSO Networks

2021 ◽  
Vol 11 (8) ◽  
pp. 3627
Author(s):  
Michael B. Rahaim ◽  
Thomas D. C. Little ◽  
Mona Hella
Keyword(s):  
Management Strategy ◽  
Beam Steering ◽  
Search Time ◽  
Search Space ◽  
Analysis Framework ◽  
Free Space Optical ◽  
Optimization Analysis ◽  
Worst Case ◽  
Available Bandwidth ◽  
Space Optical Communication

To meet the growing demand for wireless capacity, communications in the Terahertz (THz) and optical bands are being broadly explored. Communications within these bands provide massive bandwidth potential along with highly directional beam steering capabilities. While the available bandwidth offers incredible link capacity, the directionality of these technologies offers an even more significant potential for spatial capacity or area spectral efficiency. However, this directionality also implies a challenge related to the network’s ability to quickly establish a connection. In this paper, we introduce a multi-tier heterogeneous (MTH) beamform management strategy that utilizes various wireless technologies in order to quickly acquire a highly directional indoor free space optical communication (FSO) link. The multi-tier design offers the high resolution of indoor FSO while the millimeter-wave (mmWave) system narrows the FSO search space. By narrowing the search space, the system relaxes the requirements of the FSO network in order to assure a practical search time. This paper introduces the necessary components of the proposed beam management strategy and provides a foundational analysis framework to demonstrate the relative impact of coverage, resolution, and steering velocity across tiers. Furthermore, an optimization analysis is used to define the top tier resolution that minimizes worst-case search time as a function of lower tier resolution and top tier range.

scholarly journals LevioSAM: Fast lift-over of alternate reference alignments

2021 ◽  
Author(s):  
Taher Mun ◽  
Nae-Chyun Chen ◽  
Ben Langmead
Keyword(s):  
Population Genetics ◽  
Coordinate System ◽  
Data Structures ◽  
Succinct Data Structures ◽  
Reference Coordinate System ◽  
Link Type ◽  
A Chain ◽  
Time Required ◽  
Effective Use

AbstractMotivationAs more population genetics datasets and population-specific references become available, the task of translating (“lifting”) read alignments from one reference coordinate system to another is becoming more common. Existing tools generally require a chain file, whereas VCF files are the more common way to represent variation. Existing tools also do not make effective use of threads, creating a post-alignment bottleneck.ResultsLevioSAM is a tool for lifting SAM/BAM alignments from one reference to another using a VCF file containing population variants. LevioSAM uses succinct data structures and scales efficiently to many threads. When run downstream of a read aligner, levioSAM completes in less than 13% the time required by an aligner when both are run with 16 threads.Availabilityhttps://github.com/alshai/[email protected], [email protected]

scholarly journals Engineering Augmented Suffix Sorting Algorithms

2018 ◽  
Author(s):  
Felipe A. Louza ◽  
Guilherme P. Telles ◽  
Simon Gog
Keyword(s):  
Computer Science ◽  
Full Text ◽  
Suffix Array ◽  
Optimal Time ◽  
Time And Space ◽  
Sorting Algorithms ◽  
Constant Size ◽  
Common Prefix ◽  
Efficient Processing ◽  
Burrows Wheeler Transform

Strings are prevalent in Computer Science and algorithms for their efficient processing are fundamental in various applications. The results introduced in this work contribute with theoretical improvements and practical advances in building full-text indexes. Our first contribution is an in-place algorithm that computes the Burrows-Wheeler transform and the longest common prefix (LCP) array. Our second contribution is the construction of the suffix array augmented with the LCP array in optimal time and space for strings from constant size alphabets. Our third contribution is a set of algorithms to construct full-text indexes for string collections in optimal theoretical bounds. This work is an extended abstract of the Ph.D. thesis of the first author.

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