File size: 5,963 Bytes
5d3611e d988837 2e30329 5d3611e 1908739 5d3611e efc37c1 5098ed4 48dfff1 efc37c1 5d3611e d988837 2e30329 5d3611e 2e30329 5d3611e 2e30329 1908739 5d3611e b5b56c8 1908739 b5b56c8 5d3611e 1908739 5d3611e b5b56c8 1908739 b5b56c8 5d3611e 1908739 5d3611e b5b56c8 1908739 b5b56c8 5d3611e 1908739 5d3611e b5b56c8 1908739 b5b56c8 5d3611e 1908739 5d3611e b5b56c8 1908739 b5b56c8 5d3611e 1908739 5d3611e 1908739 5d3611e 1908739 5d3611e 1908739 5d3611e 1908739 5d3611e 1908739 5d3611e 1908739 5d3611e 1908739 5d3611e 1908739 5d3611e 1908739 5d3611e 1908739 5d3611e b5b56c8 1908739 b5b56c8 5d3611e 49eb670 5d3611e 7ec3f5f 5d3611e 4e9bbc7 5d3611e d005bb3 49eb670 5d3611e a4e021c cfa320d cc5fdda 5d3611e a4e021c 5d3611e 2e30329 5d3611e 1908739 5d3611e cfa320d 5d3611e 1908739 d988837 efc37c1 1908739 5d3611e efc37c1 5d3611e 1908739 5d3611e 1908739 5d3611e efc37c1 5d3611e efc37c1 d988837 ffbd724 1908739 d988837 1908739 5d3611e ffbd724 1908739 5d3611e 9bf58dc 5d3611e 662bd1e 5d3611e d988837 5d3611e d005bb3 5d3611e b5b56c8 5d3611e bd5c853 6d7ee58 5d3611e |
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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 |
{
"best_val_loss": 0.09732607007026672,
"comet_ai_key": null,
"context_observations": {
"add_rem": true,
"divide_in_past_and_future": false,
"empirical_number_of_obs": false,
"max_num_obs": 15,
"min_num_of_past_context": 3,
"num_of_past_context": 5,
"obs_dataset": "/home/cesarali/Pharma/generative_pk/data/preprocessed/lenuzza/Lenuzza2016.csv",
"obs_type": "observations_pk_peak_halflife",
"past_time_ratio": 0.1
},
"debug_test": true,
"dosing": {
"logdose_mean_range": [
-2.0,
2.0
],
"logdose_std_range": [
0.1,
0.5
],
"num_individuals": 10,
"route_options": [
"oral",
"iv"
],
"route_weights": [
0.8,
0.2
],
"same_route": true,
"time": 0.0
},
"experiment_dir": "/home/cesarali/Pharma/generative_pk/results/comet/node_pk_compartments/25090ec430a14b26ba2171f866e18670",
"experiment_indentifier": null,
"experiment_name": "node_pk_compartments",
"hf_model_card_path": [
"hf_model_cards",
"NP-PK_Readme.md"
],
"hf_model_name": "NeuralProcessPK_development",
"hugging_face_token": null,
"meta_study": {
"V_tmag_range": [
0.001,
0.01
],
"V_tscl_range": [
1.0,
5.0
],
"drug_id_options": [
"Drug_A",
"Drug_B",
"Drug_C"
],
"k_1p_tmag_range": [
0.01,
0.1
],
"k_1p_tscl_range": [
1.0,
5.0
],
"k_a_tmag_range": [
0.01,
0.1
],
"k_a_tscl_range": [
1.0,
5.0
],
"k_e_tmag_range": [
0.01,
0.1
],
"k_e_tscl_range": [
1.0,
5.0
],
"k_p1_tmag_range": [
0.01,
0.1
],
"k_p1_tscl_range": [
1.0,
5.0
],
"log_V_mean_range": [
-1.5,
1.5
],
"log_V_std_range": [
0.1,
0.5
],
"log_k_1p_mean_range": [
-1.5,
1.5
],
"log_k_1p_std_range": [
0.1,
0.5
],
"log_k_a_mean_range": [
-1.5,
1.5
],
"log_k_a_std_range": [
0.1,
0.5
],
"log_k_e_mean_range": [
-1.5,
1.5
],
"log_k_e_std_range": [
0.1,
0.5
],
"log_k_p1_mean_range": [
-1.5,
1.5
],
"log_k_p1_std_range": [
0.1,
0.5
],
"num_individuals_range": [
9,
10
],
"num_peripherals_range": [
1,
3
],
"rel_ruv_range": [
0.02,
0.1
],
"solver_method": "rk4",
"time_num_steps": 100,
"time_start": 0.0,
"time_stop": 10.0
},
"mix_data": {
"evaluate_prediction_steps_past": 5,
"keep_tempfile": true,
"log_transform": false,
"n_of_databatches": 3,
"n_of_target_individuals": 1,
"normalize_by_max": true,
"normalize_time": true,
"pretraining_dataset_path": [
"preprocessed",
"lenuzza",
"Lenuzza2016.csv"
],
"pretraining_epochs": 90,
"pretraining_protocol": "none",
"recreate_tempfile": false,
"return_split_versions": true,
"split_seed": 42,
"split_strategy": "study",
"store_in_tempfile": false,
"tempfile_path": [
"preprocessed",
"simulated_ou_as_rates"
],
"test_protocol": "simulated",
"test_size": 5,
"tqdm_progress": false,
"train_size": 1000,
"val_protocol": "simulated",
"val_size": 5,
"z_score_normalization": false
},
"model_type": "node_pk",
"my_results_path": null,
"name_str": "NeuralProcessPK",
"network": {
"activation": "ReLU",
"aggregator_num_heads": 8,
"aggregator_type": "attention",
"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": false,
"individual_encoder_name": "RNNContextEncoder",
"individual_encoder_number_of_heads": 4,
"init_hidden_num_layers": 4,
"input_encoding_hidden_dim": 128,
"loss_name": "nll",
"node_step": true,
"norm": "layer",
"output_head_num_layers": 3,
"prediction_latent_deterministic": true,
"prediction_only": false,
"rnn_decoder_number_of_layers": 4,
"rnn_individual_encoder_number_of_layers": 4,
"study_latent_deterministic": true,
"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,
"zi_latent_dim": 256
},
"run_index": 0,
"tags": [
"np-pk",
"N-0",
"INIT-ISSUE"
],
"target_observations": {
"add_rem": true,
"divide_in_past_and_future": false,
"empirical_number_of_obs": false,
"max_num_obs": 15,
"min_num_of_past_context": 3,
"num_of_past_context": 5,
"obs_dataset": "/home/cesarali/Pharma/generative_pk/data/preprocessed/lenuzza/Lenuzza2016.csv",
"obs_type": "observations_pk_peak_halflife",
"past_time_ratio": 0.1
},
"train": {
"amsgrad": false,
"batch_size": 64,
"betas": [
0.9,
0.999
],
"epochs": 3,
"eps": 1e-08,
"eval_empirical_every_pct": 0.5,
"gradient_clip_val": 1.0,
"learning_rate": 0.0001,
"log_image_every_epoch": 2,
"log_interval": 1,
"log_vcp": false,
"num_batch_plot": 1,
"num_workers": 3,
"optimizer_name": "AdamW",
"persistent_workers": true,
"scheduler_name": "CosineAnnealingLR",
"scheduler_params": {
"T_max": 1000,
"eta_min": 5e-05,
"last_epoch": -1
},
"shuffle_val": true,
"val_empirical_every_pct_epochs": 0.5,
"weight_decay": 0.0001
},
"transformers_version": "4.52.4",
"upload_to_hf_hub": false,
"verbose": false
}
|