best val_rmse 0.0940

config.json

@@ -1,5 +1,5 @@
 {
-  "best_val_loss": 0.07117409259080887,
+  "best_val_loss": 0.09400381147861481,
   "comet_ai_key": null,
   "context_observations": {
     "add_rem": true,
@@ -12,12 +12,13 @@
     "obs_type": "observations_pk_peak_halflife",
     "past_time_ratio": 0.1
   },
+  "debug_test": true,
   "dosing": {
     "dose": 1.0,
     "route": "oral",
     "time": 0.0
   },
-  "experiment_dir": "/home/cesarali/Pharma/generative_pk/results/comet/node_pk_compartments/faf07144e8404dd0948c02a400b7fdc5",
+  "experiment_dir": "/home/cesarali/Pharma/generative_pk/results/comet/node_pk_compartments/03fcdd3ddee246ab9f79683ec0e45ff6",
   "experiment_indentifier": null,
   "experiment_name": "node_pk_compartments",
   "hf_model_card_path": [
@@ -28,8 +29,12 @@
   "hugging_face_token": null,
   "meta_study": {
     "V_tmag_range": [
-      0.01,
-      0.1
+      0.001,
+      0.01
+    ],
+    "V_tscl_range": [
+      1.0,
+      5.0
     ],
     "drug_id_options": [
       "Drug_A",
@@ -40,18 +45,34 @@
       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
@@ -100,6 +121,10 @@
       1,
       3
     ],
+    "rel_ruv_range": [
+      0.02,
+      0.1
+    ],
     "solver_method": "rk4",
     "time_num_steps": 100,
     "time_start": 0.0,
@@ -107,6 +132,7 @@
   },
   "mix_data": {
     "evaluate_prediction_steps_past": 5,
+    "keep_tempfile": true,
     "log_transform": false,
     "n_of_databatches": 3,
     "n_of_target_individuals": 1,
@@ -119,12 +145,18 @@
     ],
     "pretraining_epochs": 90,
     "pretraining_protocol": "none",
+    "recreate_tempfile": true,
     "return_split_versions": false,
     "split_seed": 42,
     "split_strategy": "study",
+    "store_in_tempfile": true,
+    "tempfile_path": [
+      "preprocessed",
+      "simulated_ou_as_rates"
+    ],
     "test_protocol": "simulated",
     "test_size": 5,
-    "train_size": 100,
+    "train_size": 10,
     "val_protocol": "simulated",
     "val_size": 5,
     "z_score_normalization": false
@@ -136,6 +168,7 @@
     "activation": "ReLU",
     "aggregator_num_heads": 8,
     "aggregator_type": "attention",
+    "combine_latent_mode": "mlp",
     "cov_proj_dim": 16,
     "decoder_attention_layers": 2,
     "decoder_hidden_dim": 128,
@@ -190,6 +223,7 @@
     ],
     "epochs": 3,
     "eps": 1e-08,
+    "eval_empirical_every_pct": 0.25,
     "gradient_clip_val": 1.0,
     "learning_rate": 0.0001,
     "log_image_every_epoch": 2,
@@ -198,12 +232,14 @@
     "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,
     "weight_decay": 0.0001
   },
   "transformers_version": "4.52.4",

pytorch_model.bin

@@ -1,3 +1,3 @@
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+oid sha256:ed063614b164310518f6c2e79abf21e2835f621650b6a47001654c320d303d00
 size 4910617