best val_rmse 0.0157

config.json

@@ -1,10 +1,10 @@
 {
-  "best_val_loss": 0.02294633910059929,
+  "best_val_loss": 0.01571166329085827,
   "comet_ai_key": null,
   "context_observations": {
     "add_rem": true,
     "divide_in_past_and_future": false,
-    "empirical_number_of_obs": true,
+    "empirical_number_of_obs": false,
     "max_num_obs": 15,
     "min_num_of_past_context": 3,
     "num_of_past_context": 5,
@@ -14,11 +14,23 @@
   },
   "debug_test": "",
   "dosing": {
-    "dose": 1.0,
-    "route": "oral",
+    "logdose_mean_range": [
+      -2.0,
+      2.0
+    ],
+    "logdose_std_range": [
+      0.1,
+      0.5
+    ],
+    "num_individuals": 10,
+    "route_options": [
+      "oral",
+      "iv"
+    ],
+    "same_route": true,
     "time": 0.0
   },
-  "experiment_dir": "/work/ojedamarin/Projects/Pharma/Results/comet/node_pk_compartments/9fdb8ce6a8b64f6d9f01825bec5c1fce",
+  "experiment_dir": "/work/ojedamarin/Projects/Pharma/Results/comet/node_pk_compartments/edf4c9ff9b6f4e7dbf2a67afd2d52fa9",
   "experiment_indentifier": null,
   "experiment_name": "node_pk_compartments",
   "hf_model_card_path": [
@@ -30,11 +42,11 @@
   "meta_study": {
     "V_tmag_range": [
       0.001,
-      0.01
+      0.0099
     ],
     "V_tscl_range": [
-      1.0,
-      5.0
+      1,
+      5
     ],
     "drug_id_options": [
       "Drug_A",
@@ -43,78 +55,78 @@
     ],
     "k_1p_tmag_range": [
       0.01,
-      0.1
+      0.2
     ],
     "k_1p_tscl_range": [
-      1.0,
-      5.0
+      1,
+      5
     ],
     "k_a_tmag_range": [
       0.01,
-      0.1
+      0.2
     ],
     "k_a_tscl_range": [
-      1.0,
-      5.0
+      1,
+      5
     ],
     "k_e_tmag_range": [
       0.01,
-      0.1
+      0.2
     ],
     "k_e_tscl_range": [
-      1.0,
-      5.0
+      1,
+      5
     ],
     "k_p1_tmag_range": [
       0.01,
-      0.1
+      0.2
     ],
     "k_p1_tscl_range": [
-      1.0,
-      5.0
+      1,
+      5
     ],
     "log_V_mean_range": [
-      -1.5,
-      1.5
+      2,
+      8
     ],
     "log_V_std_range": [
-      0.1,
-      0.5
+      0.2,
+      0.6
     ],
     "log_k_1p_mean_range": [
-      -1.5,
-      1.5
+      -4,
+      0
     ],
     "log_k_1p_std_range": [
-      0.1,
-      0.5
+      0.2,
+      0.6
     ],
     "log_k_a_mean_range": [
-      -1.5,
-      1.5
+      -1,
+      2
     ],
     "log_k_a_std_range": [
-      0.1,
-      0.5
+      0.2,
+      0.6
     ],
     "log_k_e_mean_range": [
-      -1.5,
-      1.5
+      -5,
+      0
     ],
     "log_k_e_std_range": [
-      0.1,
-      0.5
+      0.2,
+      0.6
     ],
     "log_k_p1_mean_range": [
-      -1.5,
-      1.5
+      -4,
+      -1
     ],
     "log_k_p1_std_range": [
-      0.1,
-      0.5
+      0.2,
+      0.6
     ],
     "num_individuals_range": [
-      10,
+      6,
       10
     ],
     "num_peripherals_range": [
@@ -122,8 +134,8 @@
       3
     ],
     "rel_ruv_range": [
-      0.02,
-      0.1
+      0.05,
+      0.3
     ],
     "solver_method": "rk4",
     "time_num_steps": 100,
@@ -132,7 +144,7 @@
   },
   "mix_data": {
     "evaluate_prediction_steps_past": 5,
-    "keep_tempfile": true,
+    "keep_tempfile": false,
     "log_transform": false,
     "n_of_databatches": 3,
     "n_of_target_individuals": 1,
@@ -143,23 +155,23 @@
       "lenuzza",
       "Lenuzza2016.csv"
     ],
-    "pretraining_epochs": 2000,
+    "pretraining_epochs": "",
     "pretraining_protocol": "none",
-    "recreate_tempfile": true,
+    "recreate_tempfile": false,
     "return_split_versions": true,
     "split_seed": 42,
     "split_strategy": "study",
-    "store_in_tempfile": true,
+    "store_in_tempfile": false,
     "tempfile_path": [
       "preprocessed",
       "simulated_ou_as_rates"
     ],
     "test_protocol": "simulated",
-    "test_size": 500,
+    "test_size": 128,
     "tqdm_progress": false,
-    "train_size": 10000,
+    "train_size": 1000,
     "val_protocol": "simulated",
-    "val_size": 500,
+    "val_size": 1000,
     "z_score_normalization": false
   },
   "model_type": "node_pk",
@@ -167,9 +179,9 @@
   "name_str": "NeuralProcessPK",
   "network": {
     "activation": "ReLU",
-    "aggregator_num_heads": 4,
+    "aggregator_num_heads": 8,
     "aggregator_type": "attention",
-    "combine_latent_mode": "sum",
+    "combine_latent_mode": "mlp",
     "cov_proj_dim": 16,
     "decoder_attention_layers": 2,
     "decoder_hidden_dim": 512,
@@ -180,29 +192,33 @@
     "drift_num_layers": 2,
     "dropout": 0.1,
     "encoder_rnn_hidden_dim": 256,
-    "exclusive_node_step": true,
+    "exclusive_node_step": false,
     "individual_encoder_name": "RNNContextEncoder",
     "individual_encoder_number_of_heads": 4,
-    "init_hidden_num_layers": 2,
+    "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": false,
+    "prediction_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": false,
-    "use_kl_i_np": false,
+    "use_kl_i": true,
+    "use_kl_i_np": true,
     "use_kl_init": true,
     "use_kl_s": true,
-    "zi_latent_dim": 512
+    "zi_latent_dim": 256
   },
   "run_index": 0,
   "tags": [
+    "META-STUDY",
     "YOLO-0",
     "N-0"
   ],
@@ -224,12 +240,12 @@
       0.9,
       0.999
     ],
-    "epochs": 2500,
+    "epochs": 500,
     "eps": 1e-08,
-    "eval_empirical_every_pct": 0.1,
+    "eval_empirical_every_pct": 0.3,
     "gradient_clip_val": 1.0,
     "learning_rate": 0.0001,
-    "log_image_every_epoch": 25,
+    "log_image_every_epoch": 10,
     "log_interval": 1,
     "log_vcp": false,
     "num_batch_plot": 1,
@@ -243,6 +259,7 @@
       "last_epoch": -1
     },
     "shuffle_val": true,
+    "val_empirical_every_pct_epochs": 0.1,
     "weight_decay": 0.0001
   },
   "transformers_version": "4.52.4",

pytorch_model.bin

@@ -1,3 +1,3 @@
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+size 38753498