diff --git a/downloads-generation/models_class1/hyperparameters.yaml b/downloads-generation/models_class1/hyperparameters.yaml index 7984d8822de137f69a07e2fcc260339b8984a71e..c6c2c2b6424cb3f61341bdbb9e6689afdb75b909 100644 --- a/downloads-generation/models_class1/hyperparameters.yaml +++ b/downloads-generation/models_class1/hyperparameters.yaml @@ -42,7 +42,7 @@ "activation": "relu", "output_activation": "sigmoid", "layer_sizes": [ - 32 + 16 ], "dense_layer_l1_regularization": 0.001, "batch_normalization": false, diff --git a/downloads-generation/models_class1_experiments1/hyperparameters-0local.yaml b/downloads-generation/models_class1_experiments1/hyperparameters-0local.yaml index bab321573a211027629dff1c9880f9b61dbc0170..f36ec334679c3f7ce2ade82c1456bccc0262b820 100644 --- a/downloads-generation/models_class1_experiments1/hyperparameters-0local.yaml +++ b/downloads-generation/models_class1_experiments1/hyperparameters-0local.yaml @@ -36,7 +36,7 @@ "activation": "relu", "output_activation": "sigmoid", "layer_sizes": [ - 32 + 16 ], "dense_layer_l1_regularization": 0.001, "batch_normalization": false, diff --git a/downloads-generation/models_class1_experiments1/hyperparameters-0local_noL1.yaml b/downloads-generation/models_class1_experiments1/hyperparameters-0local_noL1.yaml index 62d506372eeabd6f066e6554fb76d55ebd7d0290..b7b5fe7a023dc061a7ff724cd064299724ff305d 100644 --- a/downloads-generation/models_class1_experiments1/hyperparameters-0local_noL1.yaml +++ b/downloads-generation/models_class1_experiments1/hyperparameters-0local_noL1.yaml @@ -36,7 +36,7 @@ "activation": "relu", "output_activation": "sigmoid", "layer_sizes": [ - 32 + 16 ], "dense_layer_l1_regularization": 0.0, "batch_normalization": false, diff --git a/downloads-generation/models_class1_experiments1/hyperparameters-2local.yaml b/downloads-generation/models_class1_experiments1/hyperparameters-2local.yaml index 128355604a568fcf791e31d348d9a53f11ee5c14..7f7427c632e31ba98955cab39d9e0f9474e35cf5 100644 --- a/downloads-generation/models_class1_experiments1/hyperparameters-2local.yaml +++ b/downloads-generation/models_class1_experiments1/hyperparameters-2local.yaml @@ -46,7 +46,7 @@ "activation": "relu", "output_activation": "sigmoid", "layer_sizes": [ - 32 + 16 ], "dense_layer_l1_regularization": 0.001, "batch_normalization": false, diff --git a/downloads-generation/models_class1_experiments1/hyperparameters-dense16.yaml b/downloads-generation/models_class1_experiments1/hyperparameters-dense32.yaml similarity index 99% rename from downloads-generation/models_class1_experiments1/hyperparameters-dense16.yaml rename to downloads-generation/models_class1_experiments1/hyperparameters-dense32.yaml index b7e4ee4400db4b15cf863da0b0456bc75f4b665f..97fe80ed0b18cbc74b84f88af1cce29adcfe0d04 100644 --- a/downloads-generation/models_class1_experiments1/hyperparameters-dense16.yaml +++ b/downloads-generation/models_class1_experiments1/hyperparameters-dense32.yaml @@ -41,7 +41,7 @@ "activation": "relu", "output_activation": "sigmoid", "layer_sizes": [ - 16 + 32 ], "dense_layer_l1_regularization": 0.001, "batch_normalization": false, diff --git a/downloads-generation/models_class1_experiments1/hyperparameters-dense64.yaml b/downloads-generation/models_class1_experiments1/hyperparameters-dense64.yaml index c63c399d22913e7ae9c1efb744d18c75ce5bf6b9..33fcfd301c4d61dca79b597afb6089f594a92c63 100644 --- a/downloads-generation/models_class1_experiments1/hyperparameters-dense64.yaml +++ b/downloads-generation/models_class1_experiments1/hyperparameters-dense64.yaml @@ -41,7 +41,7 @@ "activation": "relu", "output_activation": "sigmoid", "layer_sizes": [ - 64 + 64 ], "dense_layer_l1_regularization": 0.001, "batch_normalization": false, diff --git a/downloads-generation/models_class1_experiments1/hyperparameters-dense8.yaml b/downloads-generation/models_class1_experiments1/hyperparameters-dense8.yaml new file mode 100644 index 0000000000000000000000000000000000000000..d6933e198c41641e313d7a21d79de2a0368ba8f8 --- /dev/null +++ b/downloads-generation/models_class1_experiments1/hyperparameters-dense8.yaml @@ -0,0 +1,49 @@ +[{ +########################################## +# ENSEMBLE SIZE +########################################## +"n_models": 8, + +########################################## +# OPTIMIZATION +########################################## +"max_epochs": 500, +"patience": 10, +"early_stopping": true, +"validation_split": 0.2, + +########################################## +# RANDOM NEGATIVE PEPTIDES +########################################## +"random_negative_rate": 0.0, +"random_negative_constant": 25, +"random_negative_affinity_min": 20000.0, +"random_negative_affinity_max": 50000.0, + +########################################## +# PEPTIDE REPRESENTATION +########################################## +# One of "one-hot", "embedding", or "BLOSUM62". +"peptide_amino_acid_encoding": "BLOSUM62", +"use_embedding": false, # maintained for backward compatability +"kmer_size": 15, + +########################################## +# NEURAL NETWORK ARCHITECTURE +########################################## +"locally_connected_layers": [ + { + "filters": 8, + "activation": "tanh", + "kernel_size": 3 + } +], +"activation": "relu", +"output_activation": "sigmoid", +"layer_sizes": [ + 8 +], +"dense_layer_l1_regularization": 0.001, +"batch_normalization": false, +"dropout_probability": 0.0, +}] diff --git a/downloads-generation/models_class1_experiments1/hyperparameters-embedding.yaml b/downloads-generation/models_class1_experiments1/hyperparameters-embedding.yaml index 40062bd5193b7d12be8da902445d6c8e48ccf49f..a4c8d0b1253c4768749ff9caec3a13f8377d781b 100644 --- a/downloads-generation/models_class1_experiments1/hyperparameters-embedding.yaml +++ b/downloads-generation/models_class1_experiments1/hyperparameters-embedding.yaml @@ -42,7 +42,7 @@ "activation": "relu", "output_activation": "sigmoid", "layer_sizes": [ - 32 + 16 ], "dense_layer_l1_regularization": 0.001, "batch_normalization": false, diff --git a/downloads-generation/models_class1_experiments1/hyperparameters-noL1.yaml b/downloads-generation/models_class1_experiments1/hyperparameters-noL1.yaml index 5b046c9a6a19007a9533d5b7a77b498aa1448cff..4b02779d24a466a71ddc5965e8917c36d630e03c 100644 --- a/downloads-generation/models_class1_experiments1/hyperparameters-noL1.yaml +++ b/downloads-generation/models_class1_experiments1/hyperparameters-noL1.yaml @@ -41,7 +41,7 @@ "activation": "relu", "output_activation": "sigmoid", "layer_sizes": [ - 32 + 16 ], "dense_layer_l1_regularization": 0.0, "batch_normalization": false, diff --git a/downloads-generation/models_class1_experiments1/hyperparameters-onehot.yaml b/downloads-generation/models_class1_experiments1/hyperparameters-onehot.yaml index 1742093d1436027bd2441e070f9490f17773da33..aade715e55a6c2cc5483a1b6c76efd617a8b039b 100644 --- a/downloads-generation/models_class1_experiments1/hyperparameters-onehot.yaml +++ b/downloads-generation/models_class1_experiments1/hyperparameters-onehot.yaml @@ -41,7 +41,7 @@ "activation": "relu", "output_activation": "sigmoid", "layer_sizes": [ - 32 + 16 ], "dense_layer_l1_regularization": 0.001, "batch_normalization": false, diff --git a/downloads-generation/models_class1_experiments1/hyperparameters-widelocal.yaml b/downloads-generation/models_class1_experiments1/hyperparameters-widelocal.yaml index cfde02c23f8e7d4ef24eec444c37b4929e23dd9d..62c4707c0b38fafc06bcbdc36a39940c688aaa95 100644 --- a/downloads-generation/models_class1_experiments1/hyperparameters-widelocal.yaml +++ b/downloads-generation/models_class1_experiments1/hyperparameters-widelocal.yaml @@ -42,7 +42,7 @@ "activation": "relu", "output_activation": "sigmoid", "layer_sizes": [ - 32 + 16 ], "dense_layer_l1_regularization": 0.001, "batch_normalization": false,