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Search.setIndex({"alltitles": {"API and Modules": [[0, null]], "Adaptive Affinities": [[0, "adaptive-affinities"]], "Added": [[57, "added"], [57, "id2"], [57, "id5"], [57, "id8"]], "Advanced Features": [[49, "advanced-features"]], "Affinities": [[0, "affinities"], [10, "affinities"], [49, "affinities"], [58, "affinities"]], "Affinity": [[51, null]], "AffinityMatcher": [[12, null], [52, null]], "Base Classes": [[0, "base-classes"]], "Base structure": [[58, "base-structure"]], "Basics": [[10, "basics"]], "Benchmarks": [[49, "benchmarks"]], "Bibliography": [[55, null]], "COSNE": [[13, null]], "Changed": [[57, "changed"], [57, "id3"], [57, "id6"], [57, "id9"]], "Computation times": [[2, null], [9, null], [11, null], [50, null]], "Compute the TSNE embedding": [[6, "compute-the-tsne-embedding"]], "Computing TSNE and COSNE on SNARE-seq data": [[7, "computing-tsne-and-cosne-on-snare-seq-data"]], "Contributing": [[56, null]], "Core Base Classes": [[0, "core-base-classes"]], "DRModule": [[14, null], [53, null]], "DataLoader for Streaming Data": [[58, "dataloader-for-streaming-data"]], "Dimensionality Reduction Methods": [[0, "dimensionality-reduction-methods"], [58, "dimensionality-reduction-methods"]], "Documentation": [[57, "documentation"]], "DoublyStochasticQuadraticAffinity": [[15, null]], "Entropic Affinities can adapt to varying noise levels": [[1, null]], "Entropic affinity (adaptive bandwidth)": [[1, "entropic-affinity-adaptive-bandwidth"]], "EntropicAffinity": [[16, null]], "Evaluation Metrics": [[0, "evaluation-metrics"], [49, "evaluation-metrics"]], "ExactIncrementalPCA": [[17, null]], "Examples": [[49, "examples"]], "Examples using Affinity:": [[51, "examples-using-affinity"]], "Examples using AffinityMatcher:": [[12, "examples-using-affinitymatcher"], [52, "examples-using-affinitymatcher"]], "Examples using COSNE:": [[13, "examples-using-cosne"]], "Examples using DRModule:": [[14, "examples-using-drmodule"], [53, "examples-using-drmodule"]], "Examples using EntropicAffinity:": [[16, "examples-using-entropicaffinity"], [58, "examples-using-entropicaffinity"]], "Examples using IncrementalPCA:": [[18, "examples-using-incrementalpca"]], "Examples using LogAffinity:": [[54, "examples-using-logaffinity"]], "Examples using NegativeSamplingNeighborEmbedding:": [[23, "examples-using-negativesamplingneighborembedding"]], "Examples using NeighborEmbedding:": [[24, "examples-using-neighborembedding"]], "Examples using NormalizedGaussianAffinity:": [[25, "examples-using-normalizedgaussianaffinity"]], "Examples using PCA:": [[29, "examples-using-pca"]], "Examples using SNE:": [[32, "examples-using-sne"]], "Examples using SparseNeighborEmbedding:": [[35, "examples-using-sparseneighborembedding"]], "Examples using TSNE:": [[37, "examples-using-tsne"]], "Examples using UMAP:": [[39, "examples-using-umap"]], "Examples using UMAPAffinity:": [[40, "examples-using-umapaffinity"]], "Finding Help": [[49, "finding-help"]], "Fixed": [[57, "fixed"], [57, "id4"], [57, "id7"]], "GPU Support": [[58, "gpu-support"]], "Gallery": [[10, null]], "General Formulation of Dimensionality Reduction": [[58, "general-formulation-of-dimensionality-reduction"]], "Getting Started": [[49, "getting-started"]], "Handling the quadratic cost via sparsity or symbolic tensors": [[58, "handling-the-quadratic-cost-via-sparsity-or-symbolic-tensors"]], "Incremental PCA on GPU": [[8, null]], "IncrementalPCA": [[18, null]], "InfoTSNE": [[19, null]], "Installation": [[49, "installation"]], "Installation from Source": [[49, "installation-from-source"]], "KernelPCA": [[20, null]], "Key Features": [[49, "key-features"]], "LargeVis": [[21, null]], "Load the SNARE-seq dataset (gene expression) with cell type labels": [[4, "load-the-snare-seq-dataset-gene-expression-with-cell-type-labels"], [7, "load-the-snare-seq-dataset-gene-expression-with-cell-type-labels"]], "Load toy images": [[5, "load-toy-images"], [6, "load-toy-images"]], "LogAffinity": [[54, null]], "MAGICAffinity": [[22, null]], "Methods": [[49, "methods"]], "Multi-GPU distributed training": [[58, "multi-gpu-distributed-training"]], "NegativeSamplingNeighborEmbedding": [[23, null]], "Neighbor Embedding": [[0, "neighbor-embedding"], [49, "neighbor-embedding"], [58, "neighbor-embedding"]], "Neighbor Embedding Base Classes": [[0, "neighbor-embedding-base-classes"]], "Neighbor Embedding on genomics & equivalent affinity matcher formulation": [[4, null]], "NeighborEmbedding": [[24, null]], "New contributor tips": [[56, "new-contributor-tips"]], "NormalizedGaussianAffinity": [[25, null]], "NormalizedStudentAffinity": [[26, null]], "On the efficiency of using the torchdr API rather than AffinityMatcher directly": [[4, "on-the-efficiency-of-using-the-torchdr-api-rather-than-affinitymatcher-directly"]], "Other Normalized Affinities": [[0, "other-normalized-affinities"]], "Other various affinities": [[58, "other-various-affinities"]], "Overview": [[58, "overview"]], "PACMAP": [[27, null]], "PACMAPAffinity": [[28, null]], "PCA": [[29, null]], "PCA via AffinityMatcher": [[5, "pca-via-affinitymatcher"]], "PCA via SVD": [[5, "pca-via-svd"]], "PCA via SVD and via AffinityMatcher": [[5, null]], "PHATE": [[30, null]], "PHATEAffinity": [[31, null]], "PR Checklist": [[56, "pr-checklist"]], "PR Tutorial": [[56, "pr-tutorial"]], "Plot the TSNE embedding": [[6, "plot-the-tsne-embedding"]], "Plot the dataset": [[6, "plot-the-dataset"]], "Plot the different embeddings": [[4, "plot-the-different-embeddings"]], "Release Notes": [[57, "release-notes"]], "Releases": [[57, null]], "Removed": [[57, "removed"], [57, "id10"]], "Row-normalised Gaussian affinity with constant bandwidth": [[1, "row-normalised-gaussian-affinity-with-constant-bandwidth"]], "Run neighbor embedding methods": [[4, "run-neighbor-embedding-methods"]], "SNE": [[32, null]], "Scalability & Backends": [[58, "scalability-backends"]], "See the impact of perplexity": [[6, "see-the-impact-of-perplexity"]], "SelfTuningAffinity": [[33, null]], "Single vs Multi-GPU UMAPAffinity Comparison": [[3, null]], "SinkhornAffinity": [[34, null]], "SparseNeighborEmbedding": [[35, null]], "Spectral Embedding": [[49, "spectral-embedding"]], "Spectral Methods": [[0, "spectral-methods"], [58, "spectral-methods"]], "Spotlight on affinities based on entropic projections": [[58, "spotlight-on-affinities-based-on-entropic-projections"]], "SymmetricEntropicAffinity": [[36, null]], "TSNE": [[37, null]], "TSNE embedding of the swiss roll dataset": [[6, null]], "TSNE vs COSNE : Euclidean vs Hyperbolic": [[7, null]], "TSNEkhorn": [[38, null]], "Table of Contents": [[58, "table-of-contents"]], "Torch Dimensionality Reduction": [[49, null]], "UMAP": [[39, null]], "UMAPAffinity": [[40, null]], "User Guide": [[58, null]], "Using AffinityMatcher": [[4, "using-affinitymatcher"]], "Utils": [[0, "utils"]], "Version 0.1 (2024-09-17)": [[57, "version-0-1-2024-09-17"]], "Version 0.2 (2025-02-07)": [[57, 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