• PersistenceImages

  • Referenced in 35 articles [sw41418]
  • identify features containing discriminating topological information. Finally, high accuracy inference of parameter values from...
  • ARACNE

  • Referenced in 38 articles [sw17200]
  • eliminate the majority of indirect interactions inferred by co-expression methods. Results: We prove that ... effect of loops in the network topology is negligible, and we show that the algorithm ... presence of numerous loops and complex topologies. We assess ARACNE’s ability to reconstruct transcriptional ... cells demonstrates ARACNE’s ability to infer validated transcriptional targets of the cMYC proto-oncogene...
  • TDAstats

  • Referenced in 3 articles [sw31276]
  • comprehensive toolset for any useR conducting topological data analysis, specifically via the calculation of persistent ... calculating persistent homology; (2) conducting statistical inference on persistent homology calculations; (3) visualizing persistent homology ... statistical inference. The published form of TDAstats can be found in Wadhwa ... test is used for nonparametric statistical inference in topological data analysis, read Robinson & Turner...
  • NETWORKINFERENCE

  • Referenced in 8 articles [sw06744]
  • network inference algorithms by applying them to biologically realistic simulations with known network topology. Here ... network topology and data sampling regime influence the ability of our Bayesian network inference algorithm...
  • spaghetti

  • Referenced in 1 article [sw38778]
  • spaghetti: SPAtial GrapHs: nETworks, Topology, & Inference. Spaghetti is an open-source Python library...
  • GeoLogic

  • Referenced in 1 article [sw33592]
  • logic required by ITPs, allowing to infer topological facts from pictures. We present our system...
  • MulRF

  • Referenced in 3 articles [sw23051]
  • platform-independent software program designed to infer species trees from incongruent multi-copy gene trees ... trees for species tree search. Topological constraints on the inferred species tree. Automated execution...
  • MUSCADET

  • Referenced in 10 articles [sw06859]
  • mathématique Université Paris VI, 1984).} The inference part of MUSCADET is based on natural reduction ... adapted to prove theorems in point-set topology and topological linear spaces. The main ideas...
  • RSVP

  • Referenced in 4 articles [sw03395]
  • models. Two types of errors are considered: topological errors, i.e., aggregate errors, like zero volume ... procedure for inferring local adjacencies of edges. The geometric representation of topologically adjacent edges...
  • NetBenchmark

  • Referenced in 2 articles [sw29311]
  • robustness of network inference algorithms against different simulators, topologies, sample sizes and noise intensities. Conclusions...
  • StarBEAST2

  • Referenced in 1 article [sw29665]
  • StarBEAST2 brings faster species tree inference and accurate estimates of substitution rates. Fully Bayesian multispecies ... inconsistent estimator of species tree topology, a worse estimator of divergence times, and induces spurious ... available data and more accurate inference of species tree topologies, divergence times, and substitution rates...
  • KERNEL

  • Referenced in 2 articles [sw02454]
  • that reflects in its topology the structure of the fuzzy inference model on which...
  • STELLS2

  • Referenced in 2 articles [sw32301]
  • based maximum likelihood inference of species trees from gene tree topologies. STELLS is a program ... also been extended for the inference of population trees from haplotypes...
  • SmoothSketch

  • Referenced in 4 articles [sw09069]
  • inferring a smooth solid shape from its visible contours: completion of hidden contours, topological shape...
  • MergeAlign

  • Referenced in 2 articles [sw24604]
  • substitution. Phylogenetic trees inferred from these MergeAlign alignments have better topological support values, are better...
  • SegNet

  • Referenced in 26 articles [sw27575]
  • architecture of the encoder network is topologically identical to the 13 convolutional layers ... terms of memory and computational time during inference. It is also significantly smaller...
  • GemPy

  • Referenced in 5 articles [sw31288]
  • link to machine-learning and Bayesian inference frameworks and thus a path to stochastic geological ... addition, we provide methods to analyze model topology and to compute gravity fields...
  • FastMe

  • Referenced in 5 articles [sw28027]
  • inference program. FastME provides distance algorithms to infer phylogenies. FastME is based on balanced minimum ... FastME improves over NJ by performing topological moves using fast, sophisticated algorithms. The first version...
  • iGLASS

  • Referenced in 4 articles [sw29611]
  • trees. Several methods have been designed to infer species trees from gene trees while taking ... these methods provide consistent species tree topology estimates under a standard model, most either...
  • AWTY

  • Referenced in 4 articles [sw18698]
  • Monte Carlo (MCMC) convergence in Bayesian phylogenetic inference. The graphics produced by AWTY are designed ... long enough, such that tree topologies are being sampled in proportion to their true posterior...