manual notebook push from load_and_push.ipynb
Browse files- config.json +423 -0
- pytorch_model.bin +3 -0
config.json
ADDED
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@@ -0,0 +1,423 @@
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| 1 |
+
{
|
| 2 |
+
"best_val_loss": Infinity,
|
| 3 |
+
"comet_ai_key": null,
|
| 4 |
+
"context_observations": {
|
| 5 |
+
"add_rem": true,
|
| 6 |
+
"drop_time_zero_observations": false,
|
| 7 |
+
"empirical_number_of_obs": false,
|
| 8 |
+
"generative_bias": false,
|
| 9 |
+
"max_num_obs": 15,
|
| 10 |
+
"max_past": 5,
|
| 11 |
+
"min_past": 3,
|
| 12 |
+
"past_time_ratio": 0.1,
|
| 13 |
+
"split_past_future": false,
|
| 14 |
+
"type": "pk_peak_half_life"
|
| 15 |
+
},
|
| 16 |
+
"debug_test": false,
|
| 17 |
+
"dosing": {
|
| 18 |
+
"logdose_mean_range": [
|
| 19 |
+
-2.0,
|
| 20 |
+
2.0
|
| 21 |
+
],
|
| 22 |
+
"logdose_std_range": [
|
| 23 |
+
0.1,
|
| 24 |
+
0.5
|
| 25 |
+
],
|
| 26 |
+
"num_individuals": 10,
|
| 27 |
+
"route_options": [
|
| 28 |
+
"oral",
|
| 29 |
+
"iv"
|
| 30 |
+
],
|
| 31 |
+
"route_weights": [
|
| 32 |
+
0.8,
|
| 33 |
+
0.2
|
| 34 |
+
],
|
| 35 |
+
"same_route": true,
|
| 36 |
+
"time": 0.0
|
| 37 |
+
},
|
| 38 |
+
"experiment_dir": "/work/ojedamarin/Projects/Pharma/Results/comet/uai/7195d8f55b5d4684a766a69d5a736d28",
|
| 39 |
+
"experiment_indentifier": null,
|
| 40 |
+
"experiment_name": "uai",
|
| 41 |
+
"experiment_type": "nodepk",
|
| 42 |
+
"hf_model_card_path": [
|
| 43 |
+
"hf_model_cards",
|
| 44 |
+
"AICME-PK_Readme.md"
|
| 45 |
+
],
|
| 46 |
+
"hf_model_name": "AICMEPK_cluster",
|
| 47 |
+
"hugging_face_token": null,
|
| 48 |
+
"meta_study": {
|
| 49 |
+
"V_tmag_range": [
|
| 50 |
+
0.001,
|
| 51 |
+
0.001
|
| 52 |
+
],
|
| 53 |
+
"V_tscl_range": [
|
| 54 |
+
1,
|
| 55 |
+
5
|
| 56 |
+
],
|
| 57 |
+
"drug_id_options": [
|
| 58 |
+
"Drug_A",
|
| 59 |
+
"Drug_B",
|
| 60 |
+
"Drug_C"
|
| 61 |
+
],
|
| 62 |
+
"k_1p_tmag_range": [
|
| 63 |
+
0.01,
|
| 64 |
+
0.02
|
| 65 |
+
],
|
| 66 |
+
"k_1p_tscl_range": [
|
| 67 |
+
1,
|
| 68 |
+
5
|
| 69 |
+
],
|
| 70 |
+
"k_a_tmag_range": [
|
| 71 |
+
0.01,
|
| 72 |
+
0.02
|
| 73 |
+
],
|
| 74 |
+
"k_a_tscl_range": [
|
| 75 |
+
1,
|
| 76 |
+
5
|
| 77 |
+
],
|
| 78 |
+
"k_e_tmag_range": [
|
| 79 |
+
0.01,
|
| 80 |
+
0.02
|
| 81 |
+
],
|
| 82 |
+
"k_e_tscl_range": [
|
| 83 |
+
1,
|
| 84 |
+
5
|
| 85 |
+
],
|
| 86 |
+
"k_p1_tmag_range": [
|
| 87 |
+
0.01,
|
| 88 |
+
0.02
|
| 89 |
+
],
|
| 90 |
+
"k_p1_tscl_range": [
|
| 91 |
+
1,
|
| 92 |
+
5
|
| 93 |
+
],
|
| 94 |
+
"log_V_mean_range": [
|
| 95 |
+
2,
|
| 96 |
+
8
|
| 97 |
+
],
|
| 98 |
+
"log_V_std_range": [
|
| 99 |
+
0.2,
|
| 100 |
+
0.6
|
| 101 |
+
],
|
| 102 |
+
"log_k_1p_mean_range": [
|
| 103 |
+
-4,
|
| 104 |
+
0
|
| 105 |
+
],
|
| 106 |
+
"log_k_1p_std_range": [
|
| 107 |
+
0.2,
|
| 108 |
+
0.6
|
| 109 |
+
],
|
| 110 |
+
"log_k_a_mean_range": [
|
| 111 |
+
-1,
|
| 112 |
+
2
|
| 113 |
+
],
|
| 114 |
+
"log_k_a_std_range": [
|
| 115 |
+
0.2,
|
| 116 |
+
0.6
|
| 117 |
+
],
|
| 118 |
+
"log_k_e_mean_range": [
|
| 119 |
+
-5,
|
| 120 |
+
0
|
| 121 |
+
],
|
| 122 |
+
"log_k_e_std_range": [
|
| 123 |
+
0.2,
|
| 124 |
+
0.6
|
| 125 |
+
],
|
| 126 |
+
"log_k_p1_mean_range": [
|
| 127 |
+
-4,
|
| 128 |
+
-1
|
| 129 |
+
],
|
| 130 |
+
"log_k_p1_std_range": [
|
| 131 |
+
0.2,
|
| 132 |
+
0.6
|
| 133 |
+
],
|
| 134 |
+
"num_individuals_range": [
|
| 135 |
+
5,
|
| 136 |
+
10
|
| 137 |
+
],
|
| 138 |
+
"num_peripherals_range": [
|
| 139 |
+
1,
|
| 140 |
+
3
|
| 141 |
+
],
|
| 142 |
+
"rel_ruv_range": [
|
| 143 |
+
0.001,
|
| 144 |
+
0.01
|
| 145 |
+
],
|
| 146 |
+
"solver_method": "rk4",
|
| 147 |
+
"time_num_steps": 100,
|
| 148 |
+
"time_start": 0.0,
|
| 149 |
+
"time_stop": 16.0
|
| 150 |
+
},
|
| 151 |
+
"mix_data": {
|
| 152 |
+
"evaluate_prediction_steps_past": 5,
|
| 153 |
+
"keep_tempfile": false,
|
| 154 |
+
"log_and_max": false,
|
| 155 |
+
"log_and_z": false,
|
| 156 |
+
"log_transform": false,
|
| 157 |
+
"n_of_databatches": null,
|
| 158 |
+
"n_of_permutations": 3,
|
| 159 |
+
"n_of_target_individuals": 1,
|
| 160 |
+
"normalize_by_max": true,
|
| 161 |
+
"normalize_time": true,
|
| 162 |
+
"recreate_tempfile": false,
|
| 163 |
+
"sample_size_for_generative_evaluation": null,
|
| 164 |
+
"sample_size_for_generative_evaluation_end_of_training": 500,
|
| 165 |
+
"sample_size_for_generative_evaluation_val": 10,
|
| 166 |
+
"store_in_tempfile": false,
|
| 167 |
+
"tempfile_path": [
|
| 168 |
+
"preprocessed",
|
| 169 |
+
"simulated_ou_as_rates"
|
| 170 |
+
],
|
| 171 |
+
"test_empirical_datasets": [
|
| 172 |
+
"cesarali/lenuzza-2016",
|
| 173 |
+
"cesarali/Indometacin",
|
| 174 |
+
"cesarali/Theophylline"
|
| 175 |
+
],
|
| 176 |
+
"test_size": 64,
|
| 177 |
+
"tqdm_progress": false,
|
| 178 |
+
"train_size": 12800,
|
| 179 |
+
"val_size": 256,
|
| 180 |
+
"z_score_normalization": false
|
| 181 |
+
},
|
| 182 |
+
"model_type": "node_pk",
|
| 183 |
+
"my_results_path": "/work/ojedamarin/Projects/Pharma/Results/",
|
| 184 |
+
"name_str": "AICMEPK",
|
| 185 |
+
"network": {
|
| 186 |
+
"activation": "ReLU",
|
| 187 |
+
"aggregator_num_heads": 8,
|
| 188 |
+
"aggregator_type": "mean",
|
| 189 |
+
"combine_latent_mode": "mlp",
|
| 190 |
+
"cov_proj_dim": 16,
|
| 191 |
+
"decoder_attention_layers": 2,
|
| 192 |
+
"decoder_hidden_dim": 512,
|
| 193 |
+
"decoder_name": "TransformerDecoder",
|
| 194 |
+
"decoder_num_layers": 4,
|
| 195 |
+
"decoder_rnn_hidden_dim": 256,
|
| 196 |
+
"drift_activation": "Tanh",
|
| 197 |
+
"drift_num_layers": 2,
|
| 198 |
+
"dropout": 0.1,
|
| 199 |
+
"encoder_rnn_hidden_dim": 256,
|
| 200 |
+
"exclusive_node_step": true,
|
| 201 |
+
"ignore_logvar": true,
|
| 202 |
+
"individual_encoder_name": "RNNContextEncoder",
|
| 203 |
+
"individual_encoder_number_of_heads": 4,
|
| 204 |
+
"init_hidden_num_layers": 2,
|
| 205 |
+
"input_encoding_hidden_dim": 128,
|
| 206 |
+
"kl_weight": 1.0,
|
| 207 |
+
"loss_name": "log_nll",
|
| 208 |
+
"node_step": true,
|
| 209 |
+
"norm": "layer",
|
| 210 |
+
"output_head_num_layers": 3,
|
| 211 |
+
"prediction_latent_deterministic": false,
|
| 212 |
+
"prediction_only": false,
|
| 213 |
+
"reconstruction_only": false,
|
| 214 |
+
"rnn_decoder_number_of_layers": 4,
|
| 215 |
+
"rnn_individual_encoder_number_of_layers": 4,
|
| 216 |
+
"scale_dosing_amounts": true,
|
| 217 |
+
"study_latent_deterministic": false,
|
| 218 |
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|
| 219 |
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|
| 220 |
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|
| 221 |
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|
| 222 |
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|
| 223 |
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|
| 224 |
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|
| 225 |
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|
| 226 |
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|
| 227 |
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|
| 228 |
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|
| 229 |
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|
| 230 |
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|
| 231 |
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"tags": [
|
| 232 |
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"AICME",
|
| 233 |
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"AISTATS-2026",
|
| 234 |
+
"camera-ready"
|
| 235 |
+
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|
| 236 |
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|
| 237 |
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|
| 238 |
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|
| 239 |
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|
| 240 |
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|
| 241 |
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|
| 242 |
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|
| 243 |
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|
| 244 |
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|
| 245 |
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|
| 246 |
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"type": "pk_peak_half_life"
|
| 247 |
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|
| 248 |
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|
| 249 |
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|
| 250 |
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|
| 251 |
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|
| 252 |
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|
| 253 |
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|
| 254 |
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|
| 255 |
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|
| 256 |
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|
| 257 |
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|
| 258 |
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|
| 259 |
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|
| 260 |
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|
| 261 |
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|
| 262 |
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|
| 263 |
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|
| 264 |
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|
| 265 |
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|
| 266 |
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|
| 267 |
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|
| 268 |
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|
| 269 |
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|
| 270 |
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|
| 271 |
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|
| 272 |
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{
|
| 273 |
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|
| 274 |
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|
| 275 |
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|
| 276 |
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|
| 277 |
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|
| 278 |
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|
| 279 |
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|
| 280 |
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|
| 281 |
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|
| 282 |
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|
| 283 |
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|
| 284 |
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|
| 285 |
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{
|
| 286 |
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|
| 287 |
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|
| 288 |
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|
| 289 |
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|
| 290 |
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|
| 291 |
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|
| 292 |
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|
| 293 |
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|
| 294 |
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|
| 295 |
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|
| 296 |
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|
| 297 |
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|
| 298 |
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|
| 299 |
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|
| 300 |
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|
| 301 |
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|
| 302 |
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|
| 303 |
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|
| 304 |
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|
| 305 |
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|
| 306 |
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| 307 |
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| 308 |
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|
| 309 |
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|
| 310 |
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|
| 311 |
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{
|
| 312 |
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|
| 313 |
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|
| 314 |
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|
| 315 |
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|
| 316 |
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|
| 317 |
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|
| 318 |
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|
| 319 |
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|
| 320 |
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|
| 321 |
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|
| 322 |
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|
| 323 |
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"label": "Empirical",
|
| 324 |
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|
| 325 |
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"selected_summary_drugs": [
|
| 326 |
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"paracetamol glucuronide",
|
| 327 |
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|
| 328 |
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|
| 329 |
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|
| 330 |
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|
| 331 |
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|
| 332 |
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|
| 333 |
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|
| 334 |
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|
| 335 |
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|
| 336 |
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|
| 337 |
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|
| 338 |
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|
| 339 |
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|
| 340 |
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|
| 341 |
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|
| 342 |
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| 343 |
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| 344 |
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|
| 345 |
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| 346 |
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|
| 348 |
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|
| 349 |
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|
| 350 |
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|
| 351 |
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| 353 |
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| 354 |
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| 355 |
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| 356 |
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|
| 357 |
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|
| 358 |
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{
|
| 359 |
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|
| 360 |
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|
| 361 |
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|
| 362 |
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|
| 363 |
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| 364 |
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|
| 365 |
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|
| 366 |
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|
| 367 |
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|
| 368 |
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|
| 369 |
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|
| 370 |
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{
|
| 371 |
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|
| 372 |
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|
| 373 |
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|
| 374 |
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"name": "empirical/vpc_images",
|
| 375 |
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|
| 376 |
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|
| 377 |
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|
| 378 |
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|
| 379 |
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|
| 380 |
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|
| 381 |
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|
| 382 |
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{
|
| 383 |
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|
| 384 |
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|
| 385 |
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|
| 386 |
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|
| 387 |
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|
| 388 |
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|
| 389 |
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|
| 390 |
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|
| 391 |
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|
| 392 |
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|
| 393 |
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|
| 394 |
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|
| 395 |
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|
| 396 |
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|
| 397 |
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|
| 398 |
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|
| 399 |
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|
| 400 |
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"tasks_validation": []
|
| 401 |
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},
|
| 402 |
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"epochs": 100,
|
| 403 |
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"eps": 1e-08,
|
| 404 |
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|
| 405 |
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|
| 406 |
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|
| 407 |
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|
| 408 |
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|
| 409 |
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|
| 410 |
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|
| 411 |
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|
| 412 |
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"scheduler_params": {
|
| 413 |
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"T_max": 1000,
|
| 414 |
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"eta_min": 5e-05,
|
| 415 |
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"last_epoch": -1
|
| 416 |
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},
|
| 417 |
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|
| 418 |
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"weight_decay": 0.0001
|
| 419 |
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},
|
| 420 |
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"transformers_version": "4.52.4",
|
| 421 |
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"upload_to_hf_hub": true,
|
| 422 |
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"verbose": false
|
| 423 |
+
}
|
pytorch_model.bin
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:ac19cbf13fa3f6d17207fcd18034a11fdbfa043e90209c0f142527966da323e3
|
| 3 |
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size 37500323
|