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scladder

  • Installation
  • Tutorials - Synthetic Data
    • Attributes across dimensions
    • Swiss roll - Standard (Non-Linear) Decoder
    • Swiss roll - Linear Decoder
  • Tutorials - scRNA-seq Data
    • Getting Started - High-level API
    • Interpretable Patches - Vu
    • Interpretable Patches - Mascharak
    • Cross-condition Patches - Mascharak
    • Cross-condition Patches - Vu
  • API
    • Workflows API (High-level)
      • ladder.scripts.workflows.BaseWorkflow
      • ladder.scripts.workflows.InterpretableWorkflow
      • ladder.scripts.workflows.CrossConditionWorkflow
    • Functional API (Low-level)
      • ladder.data.builtin_data.get_data
      • ladder.data.real_data.MetadataConverter
      • ladder.data.real_data.AnndataConverter
      • ladder.data.real_data.construct_labels
      • ladder.data.real_data.distrib_dataset
      • ladder.data.real_data.preprocess_anndata
      • ladder.models.scvi_variants.Patches
      • ladder.models.scvi_variants.SCVI
      • ladder.models.scvi_variants.SCANVI
      • ladder.scripts.metrics.get_normalized_profile
      • ladder.scripts.metrics.gen_profile_reproduction
      • ladder.scripts.metrics.get_reproduction_error
      • ladder.scripts.metrics.calc_asw
      • ladder.scripts.metrics.kmeans_ari
      • ladder.scripts.metrics.kmeans_nmi
      • ladder.scripts.metrics.knn_error
      • ladder.scripts.training.get_device
      • ladder.scripts.training.train_pyro
      • ladder.scripts.training.train_pyro_disjoint_param
  • Changelog
  • Contributing guide
  • References
  • Getting Started - High-level API
  • Computational Morphogenomics Group
  • GitHub
  • .md

Tutorials - scRNA-seq Data

Tutorials - scRNA-seq Data#

  • Getting Started - High-level API
  • Interpretable Patches - Vu
    • Formatting The Data
    • Initializing the Interpretable Workflow
    • Observing the Losses
    • Obtaining Latent Embeddings
    • Evaluation of Model Reconstruction
    • Interpretability - Common and Conditional Gene Loadings
    • Bonus
  • Interpretable Patches - Mascharak
    • Formatting The Data
    • Initializing the Interpretable Workflow
    • Observing the Losses
    • Obtaining Latent Embeddings
    • Evaluation of Model Reconstruction
    • Interpretability - Common and Conditional Gene Loadings
    • Bonus
  • Cross-condition Patches - Mascharak
    • Setting up the data
    • Initializing and running the workflow
    • Inspecting representations
  • Cross-condition Patches - Vu
    • Setting up the data
    • Initializing and running the workflow
    • Inspecting representations

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Swiss roll - Linear Decoder

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Getting Started - High-level API

By Computational Morphogenomics Group

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