• CONTEST

  • Referenced in 19 articles [sw12738]
  • test toolbox for MATLAB. Large, sparse networks that describe complex interactions are a common feature ... that capture key properties of real-life networks. These models provide realistic, parametrized matrices ... CONTEST (CONtrollable TEST matrices) is a random network toolbox for MATLAB that implements nine models ... order to create further classes of networks. Other utilities convert the adjacency matrices into real...
  • Graphs

  • Referenced in 104 articles [sw12277]
  • sparse spanners. Related problems are considered for compact routing and distance labeling schemes in networking ... practical significance such as planar graphs and complex networks...
  • ITensor

  • Referenced in 12 articles [sw23286]
  • library for implementing tensor network calculations. See the list of recent papers using ITensor. Features ... number conserving (block-sparse) tensors; same interface as dense tensors; Complex numbers handled lazily...
  • Sparse-Dowker-Nerves

  • Referenced in 1 article [sw34683]
  • Dowker nerves. We propose sparse versions of filtered simplicial complexes used to compute persistent homology ... clouds and of networks. In particular, we extend the Sparse Čech Complex of Cavanna ... common generalization of metric spaces and networks...
  • RAIcode

  • Referenced in 8 articles [sw34283]
  • known networks and natural problems, it demonstrated superiority with respect to computational complexity, run-time ... optimal reinsertion, greedy search, greedy equivalence search, sparse candidate, and max-min hill-climbing algorithms...
  • ADAM

  • Referenced in 8 articles [sw21957]
  • either lack the algorithmic functionality to analyze complex models deterministically or they are inaccessible ... arising in systems biology and randomly generated networks, we found that the algebraic algorithms presented ... systems, namely sparseness and robustness. For a large set of published complex discrete models, ADAM...
  • TIGRESS

  • Referenced in 9 articles [sw23826]
  • BACKGROUND: Inferring the structure of gene regulatory networks (GRN) from a collection of gene expression ... many potential applications, from the elucidation of complex biological processes to the identification of potential ... paper, we formulate GRN inference as a sparse regression problem and investigate the performance ... inference methods in the DREAM5 gene network inference challenge. In particular, TIGRESS was evaluated...
  • Graemlin

  • Referenced in 5 articles [sw29736]
  • sparse interaction networks. Recently, however, new computational techniques have produced hundreds of predicted interaction networks ... networks, we have developed Græmlin, the first algorithm capable of scalable multiple network alignment. Græmlin ... location of conserved network topologies other than protein complexes and metabolic pathways. To assess Græmlin...
  • symPACK

  • Referenced in 1 article [sw16317]
  • eigenvalues. The performance and resource usage of sparse matrix factorizations are critical to time ... same time, network topologies have become increasingly complex, so that modern platforms exhibit a high ... sided communication and dynamic scheduling in implementing sparse Cholesky factorization (symPACK) on large-scale distributed...
  • AlignNemo

  • Referenced in 0 articles [sw34159]
  • AlignNemo, a new algorithm that, given the networks of two organisms, uncovers subnetworks of proteins ... functional complexes proposed in the literature. The algorithm is able to handle sparse interaction data ... step explores the local topology of the networks beyond the proteins directly interacting with ... knowledge. Based on reference datasets of protein complexes, AlignNemo shows better performance than other methods...
  • MCGS

  • Referenced in 2 articles [sw02522]
  • systems (Ax=b) with complex nonsymmetric, very large, and very sparse coefficient matrices ... processor IBM SP2 with multistage network indicate that MCGS is approximately 20% faster than...
  • hebbRNN

  • Referenced in 1 article [sw29194]
  • modeling complex human behaviors such as memory and motor skills using neural networks. However, training ... these networks to produce meaningful behavior has proven difficult. Furthermore, the most common methods ... rule for recurrent neural networks using a delayed and sparse reward signal. On individual trials...
  • RankQA

  • Referenced in 1 article [sw34398]
  • passages are retrieved and, subsequently, a neural network for machine comprehension extracts the likeliest answer ... efficient, data-sparse estimation, it nevertheless outperforms more complex QA systems by a significant margin...
  • TLRank

  • Referenced in 0 articles [sw34495]
  • fold sparse information, the conventional rating data given by users and the social network among ... algorithm has the advantage of low complexity and is shown to be linear with...
  • ADOL-C

  • Referenced in 233 articles [sw00019]
  • ADOL-C: Automatic Differentiation of C/C++. We present...
  • ANSYS

  • Referenced in 655 articles [sw00044]
  • ANSYS offers a comprehensive software suite that spans...
  • BARON

  • Referenced in 311 articles [sw00066]
  • BARON is a computational system for solving nonconvex...
  • CGAL

  • Referenced in 355 articles [sw00118]
  • The goal of the CGAL Open Source Project...
  • CoCoA

  • Referenced in 621 articles [sw00143]
  • CoCoA is a system for Computations in Commutative...
  • Coq

  • Referenced in 1784 articles [sw00161]
  • Coq is a formal proof management system. It...