On Dynamic Bitvector Implementations

Dönges, Saska; Puglisi, Simon J.; Raman, Rajeev

doi:10.1109/dcc52660.2022.00033

Cited by 4 publications

(3 citation statements)

References 18 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…However, we note a sparsity in the literature for dynamic structures. Relying on a theoretical proposition and an implementation (40–42), we adopted a solution with fast dynamic rank/select operation.…”

Section: Methodsmentioning

confidence: 99%

“…However, we note a sparsity in the literature for dynamic structures. Relying on a theoretical proposition and an implementation (40)(41)(42), we adopted a solution with fast dynamic rank/select operation. A Fenwick tree, an efficient data structure to compute the prefix sums of a dynamic array, is behind our prefix datastructure.…”

Section: Data-structures For K-mer Set Representation Based On Necklacesmentioning

confidence: 99%

See 1 more Smart Citation

Conway-Bromage-Lyndon (CBL): an exact, dynamic representation ofk-mer sets

Martayan,

Cazaux,

Limasset

et al. 2024

Preprint

View full text Add to dashboard Cite

In this paper, we introduce the Conway-Bromage-Lyndon (CBL) structure, a compressed, dynamic and exact method for representing k-mer sets. Originating from Conway and Bromage's concept, CBL innovatively employs the smallest cyclic rotations of k-mers, akin to Lyndon words, to leverage lexicographic redundancies. In order to support dynamic operations and set operations, we propose a dynamic bit vector structure that draws a parallel with Elias-Fano's scheme. This structure is encapsulated in a Rust library, demonstrating a balanced blend of construction efficiency, cache locality, and compression. Our findings suggest that CBL outperforms existing k-mer set methods, particularly in dynamic scenarios. Unique to this work, CBL stands out as the only known exact k-mer structure offering in-place set operations. Its different combined abilities position it as a flexible Swiss knife structure for k-mer set management. Availability: https://github.com/imartayan/CBL.

show abstract

Section: Methodsmentioning

confidence: 99%

Section: Data-structures For K-mer Set Representation Based On Necklacesmentioning

confidence: 99%

Conway-Bromage-Lyndon (CBL): an exact, dynamic representation ofk-mer sets

Martayan,

Cazaux,

Limasset

et al. 2024

Preprint

View full text Add to dashboard Cite

show abstract

“…However, we note a sparsity in the literature for dynamic structures. Relying on a theoretical proposition and an implementation ( Marchini and Vigna 2020 , Pibiri and Kanda 2021 , Dönges et al 2022 ), we adopted a solution with fast dynamic rank/select operation.…”

Section: Methodsmentioning

confidence: 99%

Conway–Bromage–Lyndon (CBL): an exact, dynamic representation of k-mer sets

Martayan,

Cazaux,

Limasset

et al. 2024

Bioinformatics

View full text Add to dashboard Cite

Summary In this article, we introduce the Conway–Bromage–Lyndon (CBL) structure, a compressed, dynamic and exact method for representing k-mer sets. Originating from Conway and Bromage’s concept, CBL innovatively employs the smallest cyclic rotations of k-mers, akin to Lyndon words, to leverage lexicographic redundancies. In order to support dynamic operations and set operations, we propose a dynamic bit vector structure that draws a parallel with Elias-Fano’s scheme. This structure is encapsulated in a Rust library, demonstrating a balanced blend of construction efficiency, cache locality, and compression. Our findings suggest that CBL outperforms existing dynamic k-mer set methods. Unique to this work, CBL stands out as the only known exact k-mer structure offering in-place set operations. Its different combined abilities position it as a flexible Swiss knife structure for k-mer set management. Availability and implementation https://github.com/imartayan/CBL.

show abstract

Adaptive Dynamic Bitvectors

Navarro

2024

Lecture Notes in Computer Science

View full text Add to dashboard Cite

On Dynamic Bitvector Implementations

Cited by 4 publications

References 18 publications

Conway-Bromage-Lyndon (CBL): an exact, dynamic representation ofk-mer sets

Conway-Bromage-Lyndon (CBL): an exact, dynamic representation ofk-mer sets

Conway–Bromage–Lyndon (CBL): an exact, dynamic representation of k-mer sets

Adaptive Dynamic Bitvectors

Contact Info

Product

Resources

About