diff --git a/example/annotations.parquet b/example/annotations.parquet index 35f6ea5e..0a90b8b1 100644 Binary files a/example/annotations.parquet and b/example/annotations.parquet differ diff --git a/example/config.yaml b/example/config.yaml index c6a6a3fb..33ffb03b 100644 --- a/example/config.yaml +++ b/example/config.yaml @@ -158,6 +158,7 @@ training_data: - DeepRipe_plus_MBNL1_parclip - DeepRipe_plus_QKI_parclip - SpliceAI_delta_score + - alphamissense use_common_variants: False use_rare_variants: True rare_embedding: @@ -197,6 +198,7 @@ training_data: - DeepRipe_plus_MBNL1_parclip - DeepRipe_plus_QKI_parclip - SpliceAI_delta_score + - alphamissense thresholds: MAF: "MAF < 1e-2" CADD_PHRED: "CADD_PHRED > 5" @@ -277,6 +279,7 @@ data: - DeepRipe_plus_MBNL1_parclip - DeepRipe_plus_QKI_parclip - SpliceAI_delta_score + - alphamissense gene_file: protein_coding_genes.parquet use_common_variants: False use_rare_variants: True @@ -317,6 +320,7 @@ data: - DeepRipe_plus_MBNL1_parclip - DeepRipe_plus_QKI_parclip - SpliceAI_delta_score + - alphamissense thresholds: MAF: "MAF < 1e-3" CADD_PHRED: "CADD_PHRED > 5" diff --git a/pretrained_models/config.yaml b/pretrained_models/config.yaml index 341196ea..706451f3 100644 --- a/pretrained_models/config.yaml +++ b/pretrained_models/config.yaml @@ -1,24 +1,24 @@ model: - type: DeepSet - model_collection: agg_models - checkpoint: combined_agg.pt - config: - phi_layers: 2 - phi_hidden_dim: 20 - rho_layers: 3 - rho_hidden_dim: 10 - activation: LeakyReLU - pool: max - use_sigmoid: True - metrics: - objective: MSE - objective_mode: min - loss: MSE - all: - MSE: {} - PearsonCorrTorch: {} - MAE: {} - RSquared: {} - optimizer: - type: AdamW - config: {} + checkpoint: combined_agg.pt + config: + activation: LeakyReLU + metrics: + all: + MAE: {} + MSE: {} + PearsonCorrTorch: {} + RSquared: {} + loss: MSE + objective: MSE + objective_mode: min + optimizer: + config: {} + type: AdamW + phi_hidden_dim: 20 + phi_layers: 2 + pool: max + 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b/tests/deeprvat/test_data/training/config.yaml @@ -194,6 +194,7 @@ training_data: - DeepRipe_plus_MBNL1_parclip - DeepRipe_plus_QKI_parclip - SpliceAI_delta_score + - alphamissense use_common_variants: False use_rare_variants: True verbose: True @@ -234,6 +235,7 @@ training_data: - DeepRipe_plus_MBNL1_parclip - DeepRipe_plus_QKI_parclip - SpliceAI_delta_score + - alphamissense thresholds: MAF: "MAF < 1e-2" CADD_PHRED: "CADD_PHRED > 5" @@ -312,6 +314,7 @@ data: - DeepRipe_plus_MBNL1_parclip - DeepRipe_plus_QKI_parclip - SpliceAI_delta_score + - alphamissense gene_file: example/protein_coding_genes.parquet use_common_variants: False use_rare_variants: True @@ -352,6 +355,7 @@ data: - DeepRipe_plus_MBNL1_parclip - DeepRipe_plus_QKI_parclip - SpliceAI_delta_score + - alphamissense thresholds: MAF: "MAF < 1e-3" CADD_PHRED: "CADD_PHRED > 5"