
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 coexpression 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 protooncogene...

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 opensource 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]
 platformindependent software program designed to infer species trees from incongruent multicopy 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 pointset 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 machinelearning 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...