Dimensionality Reduction / Cytometry Visualization Provenance v4

75 nodes, 133 labeled edges
G Dimensionality reduction / cytometry visualization provenance v4 cluster_legend legend DistanceMatrix distance matrix / dissimilarities (1950) [concept] ClassicalMDS classical MDS / PCoA (1952) [method] DistanceMatrix->ClassicalMDS embeds distances by eigendecomposition MetricMDS metric/nonmetric MDS (1964) [method] DistanceMatrix->MetricMDS optimizes stress from distances Sammon Sammon mapping (1969) [method] ClassicalMDS->Sammon weights preservation of short distances Isomap Isomap (2000) [method] ClassicalMDS->Isomap MDS on graph-geodesic distances PHATE PHATE (2019) [method] MetricMDS->PHATE MDS-style final embedding AgglomerativeClustering agglomerative clustering (1960) [component] SPADE SPADE (2011) [method] AgglomerativeClustering->SPADE clusters density-normalized cells DensityEstimation density estimation / density peaks (1975) [component] XshiftClustering X-shift clustering (2016) [clustering_algorithm] DensityEstimation->XshiftClustering density peaks / ascending paths DensVM DensVM (2018) [cluster_on_embedding] DensityEstimation->DensVM density-peak population finding DensityDownsampling density-normalized downsampling (2011) [component] DensityDownsampling->SPADE rare-cell-preserving downsampling FlowSOMClustering FlowSOM clustering (2015) [clustering_algorithm] EmbedSOM EmbedSOM (2019) [method] FlowSOMClustering->EmbedSOM SOM codebook to nonlinear embedding FlowSOMMSTMap FlowSOM MST / pie-star map (2015) [graph_layout_visualization] FlowSOMClustering->FlowSOMMSTMap visualizes codebook/metaclusters PhenoGraphClustering PhenoGraph clustering (2015) [clustering_algorithm] PhenoGraphGraphMap PhenoGraph graph map (2015) [graph_layout_visualization] PhenoGraphClustering->PhenoGraphGraphMap cluster labels on phenotypic graph VorteXMSTDMT VorteX MST / DMT views (2016) [graph_layout_visualization] XshiftClustering->VorteXMSTDMT tree/graph summaries VorteXFDL VorteX force-directed layout (2016) [graph_layout_visualization] XshiftClustering->VorteXFDL cluster/sample then lay out viSNE viSNE (2013) [method] DensityPartitioning 2-D density partitioning (2014) [component] ACCENSE ACCENSE (2014) [method] DensityPartitioning->ACCENSE density-based partitioning on t-SNE map ClusterX ClusterX (2016) [cluster_on_embedding] DensityPartitioning->ClusterX density partitioning on 2-D map CytosploreHSNE Cytosplore+HSNE (2017) [method] SPADETreeMap SPADE tree map (2011) [graph_layout_visualization] SPADE->SPADETreeMap outputs MST/progression tree map ScaffoldMaps Scaffold maps (2016) [method] SPADETreeMap->FlowSOMMSTMap SPADE-like MST visual grammar KnownLandmarks known landmark populations (2016) [component] KnownLandmarks->ScaffoldMaps anchors map with landmark populations FLOWMAP FLOW-MAP (2020) [graph_layout_visualization] CyTOFConstraints CyTOF measurement constraints (2011) [problem_context] CyTOFConstraints->FlowSOMClustering method motivated/used in high-dimensional cytometry CyTOFConstraints->PhenoGraphClustering method motivated/used in high-dimensional cytometry CyTOFConstraints->XshiftClustering method motivated/used in high-dimensional cytometry CyTOFConstraints->viSNE method motivated/used in high-dimensional cytometry CyTOFConstraints->ACCENSE method motivated/used in high-dimensional cytometry CyTOFConstraints->ClusterX method motivated/used in high-dimensional cytometry CyTOFConstraints->CytosploreHSNE method motivated/used in high-dimensional cytometry CyTOFConstraints->DensVM method motivated/used in high-dimensional cytometry CyTOFConstraints->EmbedSOM method motivated/used in high-dimensional cytometry CyTOFConstraints->SPADE method motivated/used in high-dimensional cytometry CyTOFConstraints->ScaffoldMaps method motivated/used in high-dimensional cytometry CyTOFConstraints->SPADETreeMap method motivated/used in high-dimensional cytometry CyTOFConstraints->FlowSOMMSTMap method motivated/used in high-dimensional cytometry CyTOFConstraints->PhenoGraphGraphMap method motivated/used in high-dimensional cytometry CyTOFConstraints->VorteXMSTDMT method motivated/used in high-dimensional cytometry CyTOFConstraints->VorteXFDL method motivated/used in high-dimensional cytometry CyTOFConstraints->FLOWMAP method motivated/used in high-dimensional cytometry CyTOFBenchmark2023 2023 CyTOF DR benchmark (2023) [benchmark] CyTOFConstraints->CyTOFBenchmark2023 motivates CyTOF-specific benchmark Wanderlust Wanderlust (2014) [method] CyTOFConstraints->Wanderlust method motivated/used in high-dimensional cytometry Wishbone Wishbone (2016) [method] CyTOFConstraints->Wishbone method motivated/used in high-dimensional cytometry CytoTree CytoTree (2021) [method] CyTOFConstraints->CytoTree method motivated/used in high-dimensional cytometry Autoencoder autoencoder (1986) [method] SparseAutoencoder sparse autoencoder (2006) [method] Autoencoder->SparseAutoencoder adds sparsity regularization DenoisingAE denoising autoencoder (2008) [method] Autoencoder->DenoisingAE learns to reconstruct clean input VAE variational autoencoder (2013) [method] Autoencoder->VAE probabilistic latent model SAUCIE SAUCIE (2019) [method] SparseAutoencoder->SAUCIE sparse autoencoder for single cells DenoisingAE->SAUCIE denoising/imputation regularization Tybalt Tybalt (2018) [method] VAE->Tybalt VAE expression latent space scVI scVI (2018) [method] VAE->scVI probabilistic single-cell latent model scvis scvis (2017) [method] VAE->scvis deep generative embedding SAUCIE->CyTOFBenchmark2023 benchmarked on CyTOF scvis->CyTOFBenchmark2023 benchmarked on CyTOF ParametricUMAP parametric UMAP (2021) [method] DiffusionMaps Diffusion maps (2006) [method] DiffusionMaps->PHATE diffusion geometry + potential distance DiffusionMaps->CyTOFBenchmark2023 benchmarked on CyTOF DiffusionMaps->Wishbone diffusion components/geometry PHATE->CyTOFBenchmark2023 benchmarked on CyTOF RandomWalkMarkov random walks / finite Markov chains (1906) [component] RandomWalkMarkov->DiffusionMaps diffusion/Markov geometry HSNE HSNE (2016) [method] RandomWalkMarkov->HSNE landmark similarities from Markov chain MST minimum spanning tree (1956) [component] MST->SPADE tree over clusters MST->ScaffoldMaps connects known and discovered clusters MST->SPADETreeMap tree layout over clusters MST->FlowSOMMSTMap MST over SOM nodes MST->VorteXMSTDMT MST/DMT views MST->CytoTree tree-shaped trajectory / pseudotime kNNGraph kNN graph (1970) [component] kNNGraph->PhenoGraphClustering phenotypic kNN graph kNNGraph->XshiftClustering fast kNN density graph kNNGraph->FLOWMAP cell/cluster graph kNNGraph->DiffusionMaps neighborhood graph for diffusion kNNGraph->Isomap constructs geodesic graph LLE Locally Linear Embedding (2000) [method] kNNGraph->LLE local reconstruction neighborhoods LaplacianEigenmaps Laplacian Eigenmaps / spectral embedding (2003) [method] kNNGraph->LaplacianEigenmaps graph Laplacian eigenvectors LargeVis LargeVis (2016) [method] kNNGraph->LargeVis large kNN graph visualization UMAP UMAP (2018) [method] kNNGraph->UMAP fuzzy kNN graph / 1-skeleton kNNGraph->Wanderlust trajectory over nearest-neighbor graph kNNGraph->Wishbone graph-based ordering and branch associations ForceDirected force-directed graph layout (1991) [component] ForceDirected->ScaffoldMaps scaffold graph layout ForceDirected->ScaffoldMaps fixed force / landmark-directed map ForceDirected->PhenoGraphGraphMap spring/force graph visualization ForceDirected->VorteXFDL FDL visualization family ForceDirected->FLOWMAP force-directed trajectory layout ForceAtlas2 ForceAtlas2 (2014) [layout_algorithm] ForceDirected->ForceAtlas2 Gephi continuous force layout ForceDirected->LargeVis graph-layout attraction/repulsion AttractRepel attraction-repulsion neighbor embedding (2020) [framework] ForceDirected->AttractRepel force-directed layout family link CommunityDetection community detection / modularity (2004) [component] CommunityDetection->FlowSOMClustering metaclusters SOM nodes CommunityDetection->PhenoGraphClustering Louvain/modularity communities SharedNeighborJaccard shared-neighbor / Jaccard graph (2015) [component] SharedNeighborJaccard->PhenoGraphClustering Jaccard-weighted SNN graph ForceAtlas2->VorteXFDL Gephi-style FDL implementation ForceAtlas2->FLOWMAP ForceAtlas2 layout backend SQuaDMDS_tSNE SQuaD-MDS/t-SNE hybrid (2023) [method] SQuaDMDS_tSNE->CyTOFBenchmark2023 benchmarked on CyTOF KernelPCA kernel PCA (1998) [method] ZIFA ZIFA (2015) [method] ZIFA->CyTOFBenchmark2023 benchmarked on CyTOF PCA PCA (1901) [method] PCA->CyTOFBenchmark2023 benchmarked on CyTOF PCA->KernelPCA kernelizes linear PCA tSNE t-SNE (2008) [method] PCA->tSNE important initialization / preprocessing LaplacianEigenmaps->UMAP default spectral initialization LaplacianEigenmaps->AttractRepel extreme of attraction-repulsion spectrum SQuaDMDS SQuaD-MDS (2021) [method] SQuaDMDS->CyTOFBenchmark2023 benchmarked on CyTOF SQuaDMDS->SQuaDMDS_tSNE hybrid with t-SNE SNE SNE (2002) [method] SNE->tSNE variation of SNE SNE->HSNE SNE-family probability embedding tSNE->viSNE adapts t-SNE to cytometry tSNE->ACCENSE t-SNE map plus density partition tSNE->ClusterX partitions t-SNE/density map tSNE->DensVM t-SNE plus density peaks tSNE->CyTOFBenchmark2023 benchmarked on CyTOF tSNE->SQuaDMDS_tSNE hybrid with SQuaD-MDS BarnesHutTSNE Barnes-Hut t-SNE (2014) [accelerated_method] tSNE->BarnesHutTSNE accelerates repulsive forces tSNE->HSNE uses t-SNE-style embedding objective tSNE->UMAP shared neighbor-embedding attract/repel family tSNECUDA t-SNE-CUDA (2018) [accelerated_method] tSNE->tSNECUDA GPU acceleration FItSNE FIt-SNE (2019) [accelerated_method] tSNE->FItSNE FFT/interpolation acceleration openTSNE openTSNE (2019) [implementation_method] tSNE->openTSNE modular t-SNE implementation optSNE opt-SNE (2019) [parameterization] tSNE->optSNE automates t-SNE stopping/parameters PaCMAP PaCMAP (2020) [method] tSNE->PaCMAP empirical analysis predecessor tSNE->AttractRepel canonical attraction/repulsion method TriMap TriMap (2018) [method] tSNE->TriMap response to pairwise t-SNE limits BarnesHutTSNE->CyTOFBenchmark2023 benchmarked on CyTOF HSNE->CytosploreHSNE mass cytometry deployment LargeVis->UMAP negative-sampling graph-embedding lineage LargeVis->TriMap response to pairwise LargeVis limits UMAP->FLOWMAP alternative UMAP output backend UMAP->ParametricUMAP neural parametric version UMAP->CyTOFBenchmark2023 benchmarked on CyTOF UMAP->PaCMAP post-UMAP design response UMAP->AttractRepel placed on same attraction/repulsion spectrum UMAP->TriMap benchmark comparator, not parent FItSNE->CyTOFBenchmark2023 benchmarked on CyTOF PaCMAP->CyTOFBenchmark2023 benchmarked on CyTOF PairSampling controlled pair sampling (2020) [component] PairSampling->PaCMAP near/mid/far pair control SOM self-organizing map (1982) [method] SOM->FlowSOMClustering SOM codebook clustering TripletConstraints triplet / ordinal constraints (1960) [component] TripletConstraints->TriMap triplet constraints are core LandmarkHierarchy landmarks / multiscale hierarchy (1995) [component] LandmarkHierarchy->HSNE multiscale landmark hierarchy Wanderlust->Wishbone adds bifurcation SequentialTimeOrdering sequential time ordering (2020) [component] SequentialTimeOrdering->FLOWMAP time-constrained trajectory map TriMap->CyTOFBenchmark2023 benchmarked on CyTOF TriMap->PaCMAP post-TriMap design response legend0 cytometry/CyTOF-specific legend1 general used in CyTOF legend2 single-cell used in CyTOF legend3 general/component