best val_rmse 1.5406

config.json

@@ -1,204 +1,202 @@
 {
-  "best_val_loss": 0.04928312823176384,
+  "best_val_loss": 1.5405571460723877,
+  "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
+    "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": true,
   "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",
+      "oral"
+    ],
+    "route_weights": [
+      0.8,
+      0.2
+    ],
+    "same_route": true,
     "time": 0.0
   },
-  "experiment_dir": null,
+  "experiment_dir": "/home/cesarali/Pharma/sim_priors_pk/results/comet/node-pk/da4b251a530446a9822c849497403e3d",
   "experiment_indentifier": null,
-  "experiment_name": "node_pk_compartments",
+  "experiment_name": "node-pk",
   "hf_model_card_path": [
-    "hf_model_card",
-    "CVAE_Readme.md"
+    "hf_model_cards",
+    "NODE-PK_Readme.md"
   ],
   "hf_model_name": "NodePK_test",
   "hugging_face_token": null,
   "meta_study": {
-    "V_tmag_range": [
-      0.01,
-      0.1
-    ],
-    "drug_id_options": [
-      "Drug_A",
-      "Drug_B",
-      "Drug_C"
-    ],
-    "k_1p_tmag_range": [
-      0.01,
-      0.1
+    "band_scale_range": [
+      0.05,
+      1.0
     ],
-    "k_a_tmag_range": [
-      0.01,
-      0.1
+    "baseline_range": [
+      0.6,
+      1.4
     ],
-    "k_e_tmag_range": [
-      0.01,
-      0.1
-    ],
-    "k_p1_tmag_range": [
-      0.01,
-      0.1
-    ],
-    "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
+    "decay_rate_range": [
+      0.001,
+      0.2
     ],
-    "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
+    "drug_id_options": [
+      "DummyDrug"
     ],
+    "num_individuals": 20,
     "num_individuals_range": [
-      10,
-      10
+      16,
+      16
     ],
     "num_peripherals_range": [
       1,
       3
     ],
-    "solver_method": "rk4",
-    "time_num_steps": 100,
+    "p1": 1.0,
+    "simple_mode": true,
+    "solver_method": "dummy",
+    "time_num_steps": 40,
     "time_start": 0.0,
-    "time_stop": 10.0
+    "time_stop": 24.0
   },
   "mix_data": {
     "evaluate_prediction_steps_past": 5,
+    "keep_tempfile": false,
     "log_transform": false,
-    "n_of_databatches": 3,
+    "n_of_databatches": null,
+    "n_of_permutations": 3,
     "n_of_target_individuals": 1,
     "normalize_by_max": true,
     "normalize_time": true,
-    "pretraining_dataset_path": [
-      "preprocessed",
-      "lenuzza",
-      "Lenuzza2016.csv"
-    ],
-    "pretraining_epochs": 90,
+    "pretraining_epochs": 800,
     "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/lenuzza-2016",
+      "cesarali/Indometacin"
+    ],
     "test_protocol": "simulated",
-    "test_size": 5,
-    "train_size": 100,
+    "test_size": 64,
+    "tqdm_progress": false,
+    "train_size": 320,
     "val_protocol": "simulated",
-    "val_size": 5,
+    "val_size": 64,
     "z_score_normalization": false
   },
   "model_type": "node_pk",
   "my_results_path": null,
-  "name_str": "ContextVAENodePK",
+  "name_str": "PredictionPK",
   "network": {
     "activation": "ReLU",
     "aggregator_num_heads": 8,
     "aggregator_type": "attention",
-    "decoder_hidden_dim": 128,
-    "decoder_name": "RNNDecoder",
-    "decoder_num_layers": 2,
-    "decoder_rnn_hidden_dim": 200,
+    "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": 3,
+    "drift_num_layers": 2,
     "dropout": 0.1,
-    "encoder_rnn_hidden_dim": 200,
+    "encoder_rnn_hidden_dim": 256,
     "exclusive_node_step": false,
+    "ignore_logvar": true,
     "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",
+    "kl_weight": 1.0,
+    "loss_name": "log_nll",
     "node_step": true,
     "norm": "layer",
-    "output_head_num_layers": 2,
+    "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": 2,
-    "time_obs_encoder_hidden_dim": 128,
-    "time_obs_encoder_output_dim": 128,
+    "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,
-    "zi_latent_dim": 200
+    "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": [
-    "snode-pk",
-    "C-0"
+    "SIM_PRIOR",
+    "PredictionPK"
   ],
   "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
+    "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": true,
+    "type": "pk_peak_half_life"
   },
   "train": {
     "amsgrad": false,
-    "batch_size": 8,
+    "batch_size": 32,
     "betas": [
       0.9,
       0.999
     ],
-    "epochs": 4,
+    "epochs": 10,
     "eps": 1e-08,
+    "eval_empirical_every_pct": 2.0,
     "gradient_clip_val": 1.0,
     "learning_rate": 0.0001,
-    "log_image_every_epoch": 2,
+    "log_image_every_epoch": 10,
     "log_interval": 1,
+    "log_vcp": false,
     "num_batch_plot": 1,
-    "num_workers": 3,
+    "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,
+    "val_empirical_every_pct_epochs": 2.0,
     "weight_decay": 0.0001
   },
   "transformers_version": "4.52.4",
-  "upload_to_hf_hub": true,
+  "upload_to_hf_hub": false,
   "verbose": false
 }

pytorch_model.bin

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:483d93d5dde79d04807c5c7458a588c17583cbc139c66bde614a460b1a040fe2
-size 10564425
+oid sha256:ced5e31de3a96fc6377d701ddede4645dbece6ad65258252edd766694fd59c70
+size 39270535