• SPLIB

  • Referenced in 9 articles [sw22038]
  • matrix must be in a specific data structure: compressed sparse row. This stores the nonzero...
  • DYNAMIC

  • Referenced in 5 articles [sw32484]
  • framework of dynamic data structures for string processing. In this paper we present DYNAMIC ... open-source C++ library implementing dynamic compressed data structures for string manipulation. Our framework includes ... searchable partial sums, succinct/gap-encoded bitvectors, and entropy/run-length compressed strings and FM indexes. We prove close ... that algorithms making use of dynamic compressed data structures can be up to three orders...
  • CMPGRD

  • Referenced in 102 articles [sw24156]
  • composite grid output and data structure is also presented. Some techniques for solving elliptic ... shown. Applications to the solution of the compressible Navier-Stokes equations are discussed. Numerical accuracy...
  • Edgebreaker

  • Referenced in 53 articles [sw04117]
  • Edgebreaker is a simple technique for compressing three-dimensional triangle meshes. We introduce here ... terms of a simple data structure, which we call the Corner Table. It represents ... less than 2 bits per triangle. It compresses vertex locations using Touma and Gottsman...
  • TuckerMPI

  • Referenced in 2 articles [sw27856]
  • Decomposition. Our goal is compression of massive-scale grid-structured data, such as the multi ... package for compressing distributed data. The approach is based on treating the data ... rank approximation of the original tensor-structured data. Compression efficiency is achieved by detecting latent ... global structure within the data, which we contrast to most compression methods that are focused...
  • RNACompress

  • Referenced in 2 articles [sw35325]
  • grammar-based model to compress RNA sequences and their secondary structures. The main goals ... robust and effective way for RNA structural data compression; (2) design a suitable model ... informational complexity of the structural data based on compression. Our extensive tests have shown that ... better compression ratio compared with other sequence-specific or common text-specific compression algorithms, such...
  • PTrie

  • Referenced in 3 articles [sw35790]
  • PTrie: data structure for compressing and storing sets via prefix sharing. Sets and their efficient ... sets are used as the basic data structure for storing (encodings of) states during ... arbitrary length. The PTrie data structure distinguishes itself by compressing the stored elements while sharing ... efficient implementation of the PTrie data structure under the GPL version 3 license, so that...
  • Gudhi

  • Referenced in 30 articles [sw08777]
  • tree is an efficient and flexible data structure for representing general (filtered) simplicial complexes ... persistent cohomology algorithm, implemented with a compressed annotation matrix. Persistent cohomology is the dual...
  • CFDLIB

  • Referenced in 3 articles [sw36271]
  • collection of hydrocodes using a common data structure and a common numerical method, for problems ... multi-species, multi-field, compressible flow. The data structure is multi-block, with...
  • DenseZDD

  • Referenced in 3 articles [sw32975]
  • this article, we propose a succinct data structure of zero-suppressed binary decision diagrams (ZDDs ... information retrieval, information integration, and data mining. However, to support rich manipulation of sets ... introduces a new succinct data structure, called DenseZDD, for further compressing a ZDD when ... show that the sizes of our data structures are three times smaller than those...
  • Mayfly

  • Referenced in 2 articles [sw09233]
  • interfaces to efficient array-based data structures such as compressed matrices, graphs, heaps, and trees...
  • DSJM

  • Referenced in 6 articles [sw12532]
  • employs cache-friendly array-based sparse data structures. The pattern graph remains invariant ... sided, full column, and column-segments compression algorithms.The DSJM implements a greedy partitioning algorithm after...
  • GPU-PLWAH

  • Referenced in 1 article [sw12717]
  • PLWAH algorithm for compressing bitmaps Bitmap indexes are data structures applied to indexing attributes ... efficiently processed. Hence, various techniques of compressing bitmap indexes have been proposed. A compression technique...
  • khmer

  • Referenced in 0 articles [sw17093]
  • probabilistic k-mer counting data structure, a compressible De Bruijn graph representation, De Bruijn graph...
  • BEETL

  • Referenced in 5 articles [sw23284]
  • sequence collections by direct comparison of compressed text indexes. Popular sequence alignment tools such ... reference genome to an indexing data structure based on the Burrows-Wheeler Transform (BWT), from...
  • SplitMEM

  • Referenced in 1 article [sw30182]
  • individuals together. A compressed de Bruijn graph is a sophisticated data structure for representing ... segments, simple single-nucleotide polymorphisms and complex structural variations far beyond what can be represented ... deep topological relationships between suffix trees and compressed de Bruijn graphs and introduce an algorithm...
  • SELL_C_sigma

  • Referenced in 11 articles [sw11232]
  • used most efficiently if there is no structure in the sparsity pattern of the matrix ... Sliced ELLPACK, as a SIMD-friendly data format which combines long-standing ideas from general ... compared to established formats like compressed row storage and ELLPACK and show its suitability...
  • libcds

  • Referenced in 2 articles [sw23211]
  • Library. libcds implements low-level succinct data structures such as bitmaps, sequences, permutations ... goal is to provide a set of structures that form the building block of most ... near future we are planning to add compression algorithms and support for succinct trees...
  • treex

  • Referenced in 2 articles [sw32686]
  • their vertices. The package provides a data structure for rooted trees as well ... functionalities: (i) Random generation algorithms; (ii) DAG compression for ordered or not, labeled...
  • GtEncseq

  • Referenced in 1 article [sw37847]
  • GtEncseq, a compressed biosequence representation with many features. The GtEncseq ... portable software component providing an efficient data structure for storing multiple biological sequences of variable...