File size: 5,057 Bytes
6412b04 |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 |
{
"best_val_loss": 0.017609668895602226,
"comet_ai_key": null,
"context_observations": {
"add_rem": true,
"max_num_obs": 15,
"max_past": 5,
"min_past": 3,
"obs_dataset": "/home/ojedamarin/Projects/Pharma/generative_pk/data/preprocessed/lenuzza/Lenuzza2016.csv",
"past_time_ratio": 0.1,
"split_past_future": false,
"type": "pk_peak_half_life"
},
"debug_test": false,
"dosing": {
"logdose_mean_range": [
-2.0,
2.0
],
"logdose_std_range": [
0.1,
0.5
],
"num_individuals": 10,
"route_options": [
"oral",
"oral"
],
"route_weights": [
0.8,
0.2
],
"same_route": true,
"time": 0.0
},
"experiment_dir": "/work/ojedamarin/Projects/Pharma/Results/comet/context-vae-pk/733ef42f1ee349b0af05c2e706ea15b5",
"experiment_indentifier": null,
"experiment_name": "context-vae-pk",
"hf_model_card_path": [
"hf_model_cards",
"CVAE-PK_Readme.md"
],
"hf_model_name": "PredictionPK_cluster",
"hugging_face_token": null,
"meta_study": {
"band_scale_range": [
0.05,
1.0
],
"baseline_range": [
0.6,
1.4
],
"decay_rate_range": [
0.001,
0.2
],
"drug_id_options": [
"DummyDrug"
],
"num_individuals": 20,
"num_individuals_range": [
16,
16
],
"num_peripherals_range": [
1,
3
],
"p1": 0.0,
"simple_mode": true,
"solver_method": "dummy",
"time_num_steps": 40,
"time_start": 0.0,
"time_stop": 24.0
},
"mix_data": {
"evaluate_prediction_steps_past": 5,
"keep_tempfile": false,
"log_transform": false,
"n_of_databatches": null,
"n_of_permutations": 3,
"n_of_target_individuals": 1,
"normalize_by_max": true,
"normalize_time": true,
"pretraining_epochs": 4800,
"pretraining_protocol": "none",
"recreate_tempfile": false,
"split_seed": 42,
"split_strategy": "study",
"store_in_tempfile": false,
"tempfile_path": [
"preprocessed",
"simulated_ou_as_rates"
],
"test_empirical_datasets": [
"cesarali/Indometacin"
],
"test_protocol": "simulated",
"test_size": 640,
"tqdm_progress": false,
"train_size": 2560,
"val_protocol": "simulated",
"val_size": 640,
"z_score_normalization": false
},
"model_type": "node_pk",
"my_results_path": "/work/ojedamarin/Projects/Pharma/Results/",
"name_str": "ContextVAEPK",
"network": {
"activation": "ReLU",
"aggregator_num_heads": 8,
"aggregator_type": "mean",
"combine_latent_mode": "mlp",
"cov_proj_dim": 16,
"decoder_attention_layers": 2,
"decoder_hidden_dim": 512,
"decoder_name": "TransformerDecoder",
"decoder_num_layers": 4,
"decoder_rnn_hidden_dim": 256,
"drift_activation": "Tanh",
"drift_num_layers": 2,
"dropout": 0.1,
"encoder_rnn_hidden_dim": 256,
"exclusive_node_step": true,
"ignore_logvar": true,
"individual_encoder_name": "RNNContextEncoder",
"individual_encoder_number_of_heads": 4,
"init_hidden_num_layers": 2,
"input_encoding_hidden_dim": 128,
"kl_weight": 1.0,
"loss_name": "log_nll",
"node_step": true,
"norm": "layer",
"output_head_num_layers": 3,
"prediction_latent_deterministic": false,
"prediction_only": false,
"reconstruction_only": false,
"rnn_decoder_number_of_layers": 4,
"rnn_individual_encoder_number_of_layers": 4,
"study_latent_deterministic": false,
"time_obs_encoder_hidden_dim": 256,
"time_obs_encoder_output_dim": 256,
"use_attention": true,
"use_invariance_loss": true,
"use_kl_i": true,
"use_kl_i_np": true,
"use_kl_init": true,
"use_kl_s": true,
"use_self_attention": true,
"use_time_deltas": true,
"zi_latent_dim": 256
},
"run_index": 0,
"tags": [
"SIM_PRIOR",
"ContextVAE",
"NodePK"
],
"target_observations": {
"add_rem": true,
"max_num_obs": 15,
"max_past": 5,
"min_past": 3,
"obs_dataset": "/home/ojedamarin/Projects/Pharma/generative_pk/data/preprocessed/lenuzza/Lenuzza2016.csv",
"past_time_ratio": 0.1,
"split_past_future": false,
"type": "pk_peak_half_life"
},
"train": {
"amsgrad": false,
"batch_size": 128,
"betas": [
0.9,
0.999
],
"epochs": 1000,
"eps": 1e-08,
"gradient_clip_val": 1.0,
"learning_rate": 0.0001,
"log_empirical_evaluation_pct": 0.1,
"log_image_every_epoch_pct": 0.1,
"log_interval": 1,
"log_prediction_in_val": true,
"log_reconstruction_in_val": true,
"log_vcp": false,
"num_batch_plot": 1,
"num_workers": 8,
"optimizer_name": "AdamW",
"persistent_workers": true,
"scheduler_name": "CosineAnnealingLR",
"scheduler_params": {
"T_max": 1000,
"eta_min": 5e-05,
"last_epoch": -1
},
"shuffle_val": true,
"weight_decay": 0.0001
},
"transformers_version": "4.52.4",
"upload_to_hf_hub": false,
"verbose": false
}
|