plismbench package

Top level package for plismbench.

Subpackages

• plismbench.engine package
  • Subpackages
    • plismbench.engine.extract package
      • Submodules
  • Submodules
    • plismbench.engine.cli module
    • plismbench.engine.evaluate module
• plismbench.metrics package
  • CosineSimilarity
    • CosineSimilarity.compute_metric()
  • TopkAccuracy
    • TopkAccuracy.compute_metric()
  • Submodules
    • plismbench.metrics.base module
      • BasePlismMetric
    • plismbench.metrics.cosine_similarity module
      • CosineSimilarity
    • plismbench.metrics.retrieval module
      • TopkAccuracy
• plismbench.models package
  • StringEnum
    • StringEnum.choices()
  • FeatureExtractorsEnum
    • FeatureExtractorsEnum.H0_MINI
    • FeatureExtractorsEnum.HOPTIMUS0
    • FeatureExtractorsEnum.KAIKO_VIT_BASE
    • FeatureExtractorsEnum.KAIKO_VIT_LARGE
    • FeatureExtractorsEnum.MIDNIGHT_12K
    • FeatureExtractorsEnum.VIRCHOW
    • FeatureExtractorsEnum.VIRCHOW2
    • FeatureExtractorsEnum.PROVGIGAPATH
    • FeatureExtractorsEnum.CONCH
    • FeatureExtractorsEnum.CONCHV15
    • FeatureExtractorsEnum.UNI
    • FeatureExtractorsEnum.UNI2H
    • FeatureExtractorsEnum.HIBOU_BASE
    • FeatureExtractorsEnum.HIBOU_LARGE
    • FeatureExtractorsEnum.PHIKON
    • FeatureExtractorsEnum.PHIKONV2
    • FeatureExtractorsEnum.GPFM
    • FeatureExtractorsEnum.PLIP
    • FeatureExtractorsEnum.LUNIT_VIT_SMALL_8
    • FeatureExtractorsEnum.DINOV2_VIT_GIANT_IMAGENET
    • FeatureExtractorsEnum.init()
  • Submodules
    • plismbench.models.bioptimus module
      • HOptimus0
      • H0Mini
      • HOptimus1
    • plismbench.models.extractor module
      • Extractor
    • plismbench.models.histai module
      • HibouBase
      • HibouLarge
    • plismbench.models.hkust module
      • GPFM
    • plismbench.models.kaiko_ai module
      • KaikoViTBase
      • KaikoViTLarge
      • Midnight12k
    • plismbench.models.lunit module
      • LunitViTS8
    • plismbench.models.mahmood_lab module
      • UNI
      • UNI2h
      • CONCH
      • CONCHv15
    • plismbench.models.meta module
      • Dinov2ViTGiant
    • plismbench.models.microsoft module
      • ProvGigaPath
    • plismbench.models.owkin module
      • Phikon
      • PhikonV2
    • plismbench.models.paige_ai module
      • Virchow
      • Virchow2
    • plismbench.models.standford module
      • PLIP
    • plismbench.models.utils module
      • PrecisionModule
      • prepare_module()
      • prepare_device()
• plismbench.utils package
  • Submodules
    • plismbench.utils.aggregate module
      • iqr()
      • aggregate_metrics()
      • pad()
      • format_results()
      • get_results()
    • plismbench.utils.core module
      • load_pickle()
      • write_pickle()
      • download_state_dict()
    • plismbench.utils.evaluate module
      • get_tiles_subset_idx()
      • load_features()
      • prepare_features_dataframe()
      • prepare_pairs_dataframe()
    • plismbench.utils.metrics module
      • get_extractor_results()
      • get_results()
      • format_results()
      • rank_results()
      • get_aggregated_results()
      • get_leaderboard_results()
    • plismbench.utils.viz module
      • expand_columns()
      • display_plism_metrics()