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  • Installation
  • Tutorials
    • Quickstart
    • Interpreting Latent Gene Space
    • Hyperparameter Tuning
    • GPU Training with Sinkhorn
    • Computational Speed-ups
    • GGML Method Overview
  • API
    • Core functions: ggml_ot
      • ggml_ot.train
      • ggml_ot.train_emd2
      • ggml_ot.train_sinkhorn
      • ggml_ot.tune
      • ggml_ot.test
      • ggml_ot.train_test
      • ggml_ot.from_anndata
      • ggml_ot.from_numpy
    • Dataset classes: .data
      • ggml_ot.data.AnnData_TripletDataset
      • ggml_ot.data.TripletDataset
      • ggml_ot.data.load_cellxgene
      • ggml_ot.data.from_synth
      • ggml_ot.data.from_synth_gmm
    • Plotting: .pl
      • ggml_ot.pl.clustermap
      • ggml_ot.pl.embedding
      • ggml_ot.pl.clustermap_embedding
      • ggml_ot.pl.table
      • ggml_ot.pl.confusion_matrix
      • ggml_ot.pl.contour_hyperparams
      • ggml_ot.pl.scatter_subspace
      • ggml_ot.pl.scatter_3d
      • ggml_ot.pl.ellipse_overlay
      • ggml_ot.pl.panel_subspaces
      • ggml_ot.pl.plot_gmm_panel
      • ggml_ot.pl.panel_synth_dataset
    • Analysis tools: .gene
      • ggml_ot.gene.ranking
      • ggml_ot.gene.enrichment
      • ggml_ot.gene.top_ranked
    • Settings: .settings
      • ggml_ot.settings
    • GMM API: .gmm
      • ggml_ot.train_gmm
      • ggml_ot.gmm.fit_gmm
  • Contributor’s Guide
    • Issues and Planning
    • Development Setup
    • Documentation
    • Testing
    • Pull Requests & Releases
  • References
  • .md

API

API#

import ggml_ot

This API documentation details functions, modules and classes, describing what they do and what parameters are available. For learning how to use ggml_ot in general, see the tutorials.

  • Core functions: ggml_ot
    • Training & hyperparameter tuning
    • Cross-validation
    • Setup dataset
  • Dataset classes: .data
    • TripletDataset
    • CELLxGENE interface
    • Generate synthetic data
  • Plotting: .pl
    • Patient-level plots
    • Evaluation
    • Subspace / GMM
  • Analysis tools: .gene
    • Rank genes in Loadings/Components
    • Gene Enrichment per Loadings/Components
  • Settings: .settings
    • Settings object
  • GMM API: .gmm
    • GMM-aware training
    • Dataset GMM fitting

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GGML Method Overview

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Core functions: ggml_ot

By Damin Kuehn