scButterfly.butterfly.Butterfly.construct_model

Butterfly.construct_model(chrom_list, logging_path=None, R_encoder_nlayer=2, A_encoder_nlayer=2, R_decoder_nlayer=2, A_decoder_nlayer=2, R_encoder_dim_list=[256, 128], A_encoder_dim_list=[32, 128], R_decoder_dim_list=[128, 256], A_decoder_dim_list=[128, 32], R_encoder_act_list=[LeakyReLU(negative_slope=0.01), LeakyReLU(negative_slope=0.01)], A_encoder_act_list=[LeakyReLU(negative_slope=0.01), LeakyReLU(negative_slope=0.01)], R_decoder_act_list=[LeakyReLU(negative_slope=0.01), LeakyReLU(negative_slope=0.01)], A_decoder_act_list=[LeakyReLU(negative_slope=0.01), Sigmoid()], translator_embed_dim=128, translator_input_dim_r=128, translator_input_dim_a=128, translator_embed_act_list=[LeakyReLU(negative_slope=0.01), LeakyReLU(negative_slope=0.01), LeakyReLU(negative_slope=0.01)], discriminator_nlayer=1, discriminator_dim_list_R=[128], discriminator_dim_list_A=[128], discriminator_act_list=[Sigmoid()], dropout_rate=0.1, R_noise_rate=0.5, A_noise_rate=0.3)

Main model.

Parameters:

  • chrom_list (list) – list of peaks count for each chromosomes.

  • logging_path (str) – the path for output process logging, if not save, set it None, default None.

  • R_encoder_nlayer (int) – layer counts of RNA encoder, default 2.

  • A_encoder_nlayer (int) – layer counts of ATAC encoder, default 2.

  • R_decoder_nlayer (int) – layer counts of RNA decoder, default 2.

  • A_decoder_nlayer (int) – layer counts of ATAC decoder, default 2.

  • R_encoder_dim_list (list) – dimension list of RNA encoder, length equal to R_encoder_nlayer, default [256, 128].

  • A_encoder_dim_list (list) – dimension list of ATAC encoder, length equal to A_encoder_nlayer, default [32, 128].

  • R_decoder_dim_list (list) – dimension list of RNA decoder, length equal to R_decoder_nlayer, default [128, 256].

  • A_decoder_dim_list (list) – dimension list of ATAC decoder, length equal to A_decoder_nlayer, default [128, 32].

  • R_encoder_act_list (list) – activation list of RNA encoder, length equal to R_encoder_nlayer, default [nn.LeakyReLU(), nn.LeakyReLU()].

  • A_encoder_act_list (list) – activation list of ATAC encoder, length equal to A_encoder_nlayer, default [nn.LeakyReLU(), nn.LeakyReLU()].

  • R_decoder_act_list (list) – activation list of RNA decoder, length equal to R_decoder_nlayer, default [nn.LeakyReLU(), nn.LeakyReLU()].

  • A_decoder_act_list (list) – activation list of ATAC decoder, length equal to A_decoder_nlayer, default [nn.LeakyReLU(), nn.Sigmoid()].

  • translator_embed_dim (int) – dimension of embedding space for translator, default 128.

  • translator_input_dim_r (int) – dimension of input from RNA encoder for translator, default 128.

  • translator_input_dim_a (int) – dimension of input from ATAC encoder for translator, default 128.

  • translator_embed_act_list (list) – activation list for translator, involving [mean_activation, log_var_activation, decoder_activation], default [nn.LeakyReLU(), nn.LeakyReLU(), nn.LeakyReLU()].

  • discriminator_nlayer (int) – layer counts of discriminator, default 1.

  • discriminator_dim_list_R (list) – dimension list of discriminator, length equal to discriminator_nlayer, the first equal to translator_input_dim_R, default [128].

  • discriminator_dim_list_A (list) – dimension list of discriminator, length equal to discriminator_nlayer, the first equal to translator_input_dim_A, default [128].

  • discriminator_act_list (list) – activation list of discriminator, length equal to discriminator_nlayer, default [nn.Sigmoid()].

  • dropout_rate (float) – rate of dropout for network, default 0.1.

  • R_noise_rate (float) – rate of set part of RNA input data to 0, default 0.5.

  • A_noise_rate (float) – rate of set part of ATAC input data to 0, default 0.3.