diff --git a/tutorial/config/data/random_continuous.yaml b/tutorial/config/data/random_continuous.yaml index f72b0f5d..53150799 100755 --- a/tutorial/config/data/random_continuous.yaml +++ b/tutorial/config/data/random_continuous.yaml @@ -5,15 +5,16 @@ defaults: # FEEL FREE TO EDIT BELOW -raw_data_path: data/ # where raw data is stored -interim_data_path: interim_data_cont/ # where intermediate files will be stored -results_path: results_cont/ # where result files will be placed +raw_data_path: data/ # where raw data is stored +interim_data_path: interim_data_cont/ # where intermediate files will be stored +results_path: results_cont/ # where result files will be placed -sample_names: random.continuous.ids # names/IDs of each sample, must appear in the - # other datasets +sample_names: + random.continuous.ids # names/IDs of each sample, must appear in the + # other datasets -categorical_inputs: [] # no categorical inputs +categorical_inputs: [] # no categorical inputs -continuous_inputs: # a list of continuous datasets +continuous_inputs: # a list of continuous datasets - name: random.continuous.proteomics - - name: random.continuous.metagenomics \ No newline at end of file + - name: random.continuous.metagenomics diff --git a/tutorial/config/data/random_small.yaml b/tutorial/config/data/random_small.yaml index e1cc182d..5f1e8d18 100644 --- a/tutorial/config/data/random_small.yaml +++ b/tutorial/config/data/random_small.yaml @@ -5,16 +5,17 @@ defaults: # FEEL FREE TO EDIT BELOW -raw_data_path: data/ # where raw data is stored -interim_data_path: interim_data/ # where intermediate files will be stored -results_path: results/ # where result files will be placed +raw_data_path: data/ # where raw data is stored +interim_data_path: interim_data/ # where intermediate files will be stored +results_path: results/ # where result files will be placed -sample_names: random.small.ids # names/IDs of each sample, must appear in - # the other datasets +sample_names: + random.small.ids # names/IDs of each sample, must appear in + # the other datasets -categorical_inputs: # a list of categorical datasets +categorical_inputs: # a list of categorical datasets - name: random.small.drugs -continuous_inputs: # a list of continuous datasets +continuous_inputs: # a list of continuous datasets - name: random.small.proteomics - name: random.small.metagenomics diff --git a/tutorial/config/experiment/random_continuous.yaml b/tutorial/config/experiment/random_continuous.yaml index 91014c04..fb0e7142 100644 --- a/tutorial/config/experiment/random_continuous.yaml +++ b/tutorial/config/experiment/random_continuous.yaml @@ -2,4 +2,4 @@ defaults: - override /data: random_continuous - - override /task: random_continuous__id_assoc_ttest \ No newline at end of file + - override /task: random_continuous__id_assoc_ttest diff --git a/tutorial/config/experiment/random_continuous__tune.yaml b/tutorial/config/experiment/random_continuous__tune.yaml index d9e96a9f..bf4d91fc 100644 --- a/tutorial/config/experiment/random_continuous__tune.yaml +++ b/tutorial/config/experiment/random_continuous__tune.yaml @@ -18,5 +18,5 @@ hydra: params: task.batch_size: 10 #10, 20 task.model.num_hidden: "[250]" - task.model.num_latent: 100, 200, 220 - task.training_loop.num_epochs: 200 \ No newline at end of file + task.model.num_latent: 100, 200, 220 + task.training_loop.num_epochs: 200 diff --git a/tutorial/config/task/random_continuous__id_assoc_bayes.yaml b/tutorial/config/task/random_continuous__id_assoc_bayes.yaml index 121ba216..6a004992 100644 --- a/tutorial/config/task/random_continuous__id_assoc_bayes.yaml +++ b/tutorial/config/task/random_continuous__id_assoc_bayes.yaml @@ -1,4 +1,3 @@ - defaults: - identify_associations_bayes @@ -6,16 +5,16 @@ batch_size: 10 num_refits: 10 -target_dataset: random.continuous.proteomics +target_dataset: random.continuous.proteomics target_value: plus_std save_refits: True model: num_hidden: - - 100 - num_latent: 50 + - 100 + num_latent: 50 beta: .0001 - dropout: .1 + dropout: .1 training_loop: lr: 1e-4 diff --git a/tutorial/config/task/random_continuous__id_assoc_ks.yaml b/tutorial/config/task/random_continuous__id_assoc_ks.yaml index fed6a9e8..1eb1b3e5 100644 --- a/tutorial/config/task/random_continuous__id_assoc_ks.yaml +++ b/tutorial/config/task/random_continuous__id_assoc_ks.yaml @@ -1,13 +1,12 @@ - defaults: - identify_associations_ks_schema batch_size: 10 -num_refits: 10 +num_refits: 10 sig_threshold: 0.05 -target_dataset: random.continuous.proteomics +target_dataset: random.continuous.proteomics target_value: plus_std save_refits: True @@ -16,7 +15,7 @@ model: continuous_weights: ${weights:${data.continuous_inputs}} num_hidden: - 100 - num_latent: 50 + num_latent: 50 beta: 0.1 dropout: 0.1 cuda: false @@ -38,4 +37,4 @@ training_loop: perturbed_feature_names: - proteomics_3 target_feature_names: - - metagenomics_9 \ No newline at end of file + - metagenomics_9 diff --git a/tutorial/config/task/random_continuous__id_assoc_ttest.yaml b/tutorial/config/task/random_continuous__id_assoc_ttest.yaml index 66ec0dbd..c5ddb34d 100644 --- a/tutorial/config/task/random_continuous__id_assoc_ttest.yaml +++ b/tutorial/config/task/random_continuous__id_assoc_ttest.yaml @@ -3,9 +3,9 @@ defaults: batch_size: 10 -num_refits: 10 +num_refits: 10 -target_dataset: random.continuous.proteomics +target_dataset: random.continuous.proteomics target_value: plus_std save_refits: True @@ -17,8 +17,8 @@ num_latent: model: num_hidden: - - 100 + - 100 training_loop: lr: 1e-4 - num_epochs: 200 \ No newline at end of file + num_epochs: 200 diff --git a/tutorial/config/task/random_continuous__latent.yaml b/tutorial/config/task/random_continuous__latent.yaml index 9cd480e0..ccb9badf 100644 --- a/tutorial/config/task/random_continuous__latent.yaml +++ b/tutorial/config/task/random_continuous__latent.yaml @@ -13,4 +13,4 @@ model: training_loop: lr: 1e-4 - num_epochs: 200 \ No newline at end of file + num_epochs: 200 diff --git a/tutorial/config/task/random_small__id_assoc_bayes.yaml b/tutorial/config/task/random_small__id_assoc_bayes.yaml index 9fdbc980..be596e10 100644 --- a/tutorial/config/task/random_small__id_assoc_bayes.yaml +++ b/tutorial/config/task/random_small__id_assoc_bayes.yaml @@ -1,4 +1,3 @@ - defaults: - identify_associations_bayes diff --git a/tutorial/config/task/random_small__id_assoc_ttest.yaml b/tutorial/config/task/random_small__id_assoc_ttest.yaml index 707d6690..7ad0c65f 100644 --- a/tutorial/config/task/random_small__id_assoc_ttest.yaml +++ b/tutorial/config/task/random_small__id_assoc_ttest.yaml @@ -1,19 +1,18 @@ - defaults: - identify_associations_ttest -batch_size: 10 # number of samples per batch in training loop +batch_size: 10 # number of samples per batch in training loop -num_refits: 5 #10 is the default # number of times to refit (retrain) model +num_refits: 5 # 10 is the default # number of times to refit (retrain) model -target_dataset: random.small.drugs # dataset to perturb -target_value: 1 # value to change to -save_refits: True # whether to save refits to interim folder +target_dataset: random.small.drugs # dataset to perturb +target_value: 1 # value to change to +save_refits: True # whether to save refits to interim folder -model: # model configuration - num_hidden: # list of units in each hidden layer of the VAE encoder/decoder +model: # model configuration + num_hidden: # list of units in each hidden layer of the VAE encoder/decoder - 1000 -training_loop: # training loop configuration - lr: 1e-4 # learning rate - num_epochs: 40 # 40 is the default # number of epochs +training_loop: # training loop configuration + lr: 1e-4 # learning rate + num_epochs: 40 # 40 is the default # number of epochs