abaco package

Submodules

• abaco.ABaCo module
  • BatchDiscriminator
    • BatchDiscriminator.forward()
    • BatchDiscriminator.loss()
  • ConditionalEnsembleVAE
    • ConditionalEnsembleVAE.elbo()
    • ConditionalEnsembleVAE.forward()
    • ConditionalEnsembleVAE.get_posterior()
    • ConditionalEnsembleVAE.kl_div_loss()
    • ConditionalEnsembleVAE.log_prob()
    • ConditionalEnsembleVAE.pca_posterior()
    • ConditionalEnsembleVAE.pca_prior()
    • ConditionalEnsembleVAE.sample()
  • ConditionalVAE
    • ConditionalVAE.elbo()
    • ConditionalVAE.forward()
    • ConditionalVAE.get_posterior()
    • ConditionalVAE.kl_div_loss()
    • ConditionalVAE.log_prob()
    • ConditionalVAE.pca_posterior()
    • ConditionalVAE.pca_prior()
    • ConditionalVAE.sample()
  • DMDecoder
    • DMDecoder.forward()
  • DirichletMultinomial
    • DirichletMultinomial.arg_constraints
    • DirichletMultinomial.has_rsample
    • DirichletMultinomial.log_prob()
    • DirichletMultinomial.sample()
  • MixtureOfGaussians
    • MixtureOfGaussians.arg_constraints
    • MixtureOfGaussians.entropy()
    • MixtureOfGaussians.has_rsample
    • MixtureOfGaussians.log_prob()
    • MixtureOfGaussians.mean
    • MixtureOfGaussians.rsample()
    • MixtureOfGaussians.sample()
    • MixtureOfGaussians.variance()
  • MoCPEncoder
    • MoCPEncoder.encode()
    • MoCPEncoder.forward()
  • MoCPPrior
    • MoCPPrior.cluster_loss()
    • MoCPPrior.forward()
  • MoGEncoder
    • MoGEncoder.det_encode()
    • MoGEncoder.encode()
    • MoGEncoder.forward()
    • MoGEncoder.monte_carlo_encode()
  • MoGPrior
    • MoGPrior.forward()
  • NBDecoder
    • NBDecoder.forward()
  • NormalEncoder
    • NormalEncoder.det_encode()
    • NormalEncoder.encode()
    • NormalEncoder.forward()
    • NormalEncoder.monte_carlo_encode()
  • NormalPrior
    • NormalPrior.forward()
  • SupervisedContrastiveLoss
    • SupervisedContrastiveLoss.forward()
  • VAE
    • VAE.decode()
    • VAE.encode()
    • VAE.get_posterior()
    • VAE.kl_divergence()
    • VAE.pca_posterior()
  • VMMPrior
    • VMMPrior.cluster_loss()
    • VMMPrior.forward()
    • VMMPrior.sample_from_dataloader()
  • VampPriorMixtureConditionalEnsembleVAE
    • VampPriorMixtureConditionalEnsembleVAE.forward()
    • VampPriorMixtureConditionalEnsembleVAE.get_posterior()
    • VampPriorMixtureConditionalEnsembleVAE.get_prior()
    • VampPriorMixtureConditionalEnsembleVAE.log_prob()
    • VampPriorMixtureConditionalEnsembleVAE.pca_posterior()
    • VampPriorMixtureConditionalEnsembleVAE.pca_prior()
    • VampPriorMixtureConditionalEnsembleVAE.sample()
    • VampPriorMixtureConditionalEnsembleVAE.sample_from_dataloader()
  • VampPriorMixtureConditionalVAE
    • VampPriorMixtureConditionalVAE.forward()
    • VampPriorMixtureConditionalVAE.get_posterior()
    • VampPriorMixtureConditionalVAE.get_prior()
    • VampPriorMixtureConditionalVAE.log_prob()
    • VampPriorMixtureConditionalVAE.pca_posterior()
    • VampPriorMixtureConditionalVAE.pca_prior()
    • VampPriorMixtureConditionalVAE.sample()
    • VampPriorMixtureConditionalVAE.sample_from_dataloader()
  • ZIDM
    • ZIDM.arg_constraints
    • ZIDM.has_rsample
    • ZIDM.log_prob()
    • ZIDM.sample()
  • ZIDMDecoder
    • ZIDMDecoder.forward()
  • ZINB
    • ZINB.arg_constraints
    • ZINB.has_rsample
    • ZINB.log_prob()
    • ZINB.sample()
  • ZINBDecoder
    • ZINBDecoder.forward()
  • abaco_recon()
  • abaco_recon_ensemble()
  • abaco_run()
  • abaco_run_ensemble()
  • adversarial_loss()
  • contour_plot()
  • kl_mog_mog()
  • kl_zinb_zinb()
  • log_normal_diag()
  • metaABaCo
    • metaABaCo.batch_correct()
    • metaABaCo.batch_mask()
    • metaABaCo.correct()
    • metaABaCo.fit()
    • metaABaCo.plot_pca_posterior()
    • metaABaCo.train_vae()
  • new_pre_train_abaco()
  • pre_train_abaco()
  • pre_train_abaco_ensemble()
  • train_abaco()
  • train_abaco_ensemble()
• abaco.batch_correction module
• abaco.dataloader module
  • ABaCoDataLoader()
  • DataPreprocess()
  • DataReverseTransform()
  • DataTransform()
  • class_to_int()
  • one_hot_encoding()
• abaco.metrics module
• abaco.plots module
• abaco.utils module
  • assert_nonempty_keys()
  • assert_nonempty_vals()
  • assert_path()
  • create_folder()
  • df_joiner()
  • generate_log_filename()
  • get_args()
  • get_basename()
  • get_logger()
  • get_time()
  • init_log()
  • normalize_url()