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ReconEval

  • Installation
  • Overview
  • Tutorials
  • API reference
  • Experiments
    • Reproducibility
    • References
  • GitHub
  • Installation
  • Overview
  • Tutorials
  • API reference
  • Experiments
  • Reproducibility
  • References
  • GitHub

Section Navigation

  • metrics
    • sc_reconstruction.metrics.compute_all_metrics
    • sc_reconstruction.metrics.compute_statistical_metrics
    • sc_reconstruction.metrics.compute_biological_metrics
    • sc_reconstruction.metrics.compute_perturbational_metrics
    • sc_reconstruction.metrics.aggregate_rank_percentile
    • sc_reconstruction.metrics.funky_heatmap
    • sc_reconstruction.metrics.HIGHER_IS_BETTER
    • sc_reconstruction.metrics.metric_r2
    • sc_reconstruction.metrics.metric_mse
    • sc_reconstruction.metrics.metric_energy_distance
    • sc_reconstruction.metrics.metric_cellcycle
    • sc_reconstruction.metrics.metric_pathway
    • sc_reconstruction.metrics.metric_coexpression
    • sc_reconstruction.metrics.metric_deg
    • sc_reconstruction.metrics.metric_cytokine
    • sc_reconstruction.metrics.metric_knn_purity
    • sc_reconstruction.metrics.load_cell_cycle_genes
    • sc_reconstruction.metrics.load_cytokine_dict_from_csv
    • sc_reconstruction.metrics.load_progeny
  • models
    • sc_reconstruction.models.ReconPCA
    • sc_reconstruction.models.ReconAE
    • sc_reconstruction.models.ReconSCVI
    • sc_reconstruction.models.ReconNLSCVI
    • sc_reconstruction.models.ReconMLSCVI
    • sc_reconstruction.models.ReconKNN
    • sc_reconstruction.models.BaseReconstructionModel
    • sc_reconstruction.models.ReconPretrainedStateModel
    • sc_reconstruction.models.ReconPretrainedscGPT
    • sc_reconstruction.models.ReconPretrainedscConcept
    • sc_reconstruction.models.ReconPretrainedscimilarity
  • decoders
    • sc_reconstruction.decoders.ReconMLPDecoder
    • sc_reconstruction.decoders.ReconTransformerDecoder
    • sc_reconstruction.decoders.BaseReconstructionDecoder
  • dataloaders
    • sc_reconstruction.dataloaders.IterDaskDataModule
    • sc_reconstruction.dataloaders.DaskPCADataModule
    • sc_reconstruction.dataloaders.DatasetEpochCallback
  • adapters
    • sc_reconstruction.adapters.FrozenMLPDecoderAdapter
  • utils
    • sc_reconstruction.utils.transform_to_csr
    • sc_reconstruction.utils.get_zarr_attr
    • sc_reconstruction.utils.split_zarr_dataloader
    • sc_reconstruction.utils.filter_genes
    • sc_reconstruction.utils.parse_model_params_from_filename
    • sc_reconstruction.utils.get_model_class_from_name
    • sc_reconstruction.utils.inst_model_from_checkpoint
    • sc_reconstruction.utils.create_model_from_cfg
    • sc_reconstruction.utils.read_csv_pandas_flexible
    • sc_reconstruction.utils.find_model_paths
    • sc_reconstruction.utils.sample_list
  • API reference
  • dataloaders

dataloaders#

LightningDataModules used by the training drivers under experiments/01_end_to_end/. Most users instantiate them via the Hydra configs rather than calling them directly.

  • sc_reconstruction.dataloaders.IterDaskDataModule
  • sc_reconstruction.dataloaders.DaskPCADataModule
  • sc_reconstruction.dataloaders.DatasetEpochCallback

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sc_reconstruction.decoders.BaseReconstructionDecoder

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sc_reconstruction.dataloaders.IterDaskDataModule

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