best val_rmse 0.0269

config.json

@@ -0,0 +1,453 @@
+{
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+  "comet_ai_key": null,
+  "context_observations": {
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+    "max_past": 5,
+    "min_past": 3,
+    "past_time_ratio": 0.1,
+    "split_past_future": false,
+    "type": "pk_peak_half_life"
+  },
+  "debug_test": true,
+  "dosing": {
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+      2.0
+    ],
+    "logdose_std_range": [
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+      0.5
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+    "num_individuals": 10,
+    "route_options": [
+      "oral",
+      "iv"
+    ],
+    "route_weights": [
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+      0.2
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+    "same_route": true,
+    "time": 0.0
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+  "experiment_dir": "/home/cesarali/Pharma/sim_priors_pk/results/comet/uai/c17af585ff204840866b0ee41c2ed2ad",
+  "experiment_indentifier": null,
+  "experiment_name": "uai",
+  "experiment_type": "nodepk",
+  "hf_model_card_path": [
+    "hf_model_cards",
+    "AICME-PK_Readme.md"
+  ],
+  "hf_model_name": "AICMEPK_test",
+  "hugging_face_token": null,
+  "meta_study": {
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+      0.001
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+      5
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+      "Drug_B",
+      "Drug_C"
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+      0.6
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+    "num_individuals_range": [
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+      10
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+    "num_peripherals_range": [
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+    "rel_ruv_range": [
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+    "solver_method": "rk4",
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+    "time_start": 0.0,
+    "time_stop": 16.0
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+    "keep_tempfile": false,
+    "log_and_max": false,
+    "log_and_z": false,
+    "log_transform": false,
+    "n_of_databatches": null,
+    "n_of_permutations": 3,
+    "n_of_target_individuals": 1,
+    "normalize_by_max": true,
+    "normalize_time": true,
+    "recreate_tempfile": false,
+    "sample_size_for_generative_evaluation": null,
+    "sample_size_for_generative_evaluation_end_of_training": 500,
+    "sample_size_for_generative_evaluation_val": 10,
+    "store_in_tempfile": false,
+    "tempfile_path": [
+      "preprocessed",
+      "simulated_ou_as_rates"
+    ],
+    "test_empirical_datasets": [
+      "cesarali/Indometacin",
+      "cesarali/Theophylline"
+    ],
+    "test_size": 64,
+    "tqdm_progress": false,
+    "train_size": 256,
+    "val_size": 64,
+    "z_score_normalization": false
+  },
+  "model_type": "node_pk",
+  "my_results_path": null,
+  "name_str": "AICMEPK",
+  "network": {
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+    "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",
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+    "drift_activation": "Tanh",
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+    "dropout": 0.1,
+    "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": 4,
+    "input_encoding_hidden_dim": 128,
+    "kl_weight": 1.0,
+    "loss_name": "log_nll",
+    "node_step": true,
+    "norm": "layer",
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+    "prediction_latent_deterministic": false,
+    "prediction_only": false,
+    "reconstruction_only": false,
+    "rnn_decoder_number_of_layers": 4,
+    "rnn_individual_encoder_number_of_layers": 4,
+    "scale_dosing_amounts": true,
+    "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": true,
+    "use_kl_i_np": true,
+    "use_kl_init": true,
+    "use_kl_s": true,
+    "use_self_attention": true,
+    "use_time_deltas": true,
+    "z_i_latent_dim": 256,
+    "z_s_latent_dim": 128,
+    "zi_latent_dim": 256
+  },
+  "run_index": 0,
+  "tags": [
+    "UAI-Rebutal-2026",
+    "AICME-T-PK"
+  ],
+  "target_observations": {
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+    "drop_time_zero_observations": true,
+    "empirical_number_of_obs": 2,
+    "fixed_grid_start_index": 0,
+    "generative_bias": false,
+    "max_num_obs": 15,
+    "max_past": 5,
+    "min_past": 3,
+    "past_time_ratio": 0.1,
+    "split_past_future": true,
+    "type": "pk_peak_half_life"
+  },
+  "tracking": {
+    "best": {
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+        "step": null,
+        "value": 0.026932690292596817
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+    "meta": {}
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+  "train": {
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+    "batch_size": 64,
+    "betas": [
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+      0.999
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+    "callbacks_scheduler": {
+      "checkpoint_used_in_end": [
+        "end",
+        "log_rmse"
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+      "include_end": true,
+      "keep_temp_files": false,
+      "max_samples_per_group": 500,
+      "percent_step": 0.5,
+      "skip_sanity_check": true,
+      "store_samples": true,
+      "task_during": [
+        {
+          "fn_key": "pk.predictive.images",
+          "log_prefix": "Synthetic",
+          "n_samples": 1,
+          "name": "synthetic/predictive_images",
+          "sample_source": "val_batch",
+          "save_to_disk": true,
+          "split": "val",
+          "task_cfg": {
+            "label": "Synthetic",
+            "milestone_stride": 1
+          }
+        },
+        {
+          "fn_key": "pk.generative.images",
+          "log_prefix": "Synthetic",
+          "n_samples": 10,
+          "name": "synthetic/new_individuals_images",
+          "sample_source": "val_batch",
+          "save_to_disk": true,
+          "split": "val",
+          "task_cfg": {
+            "label": "Synthetic",
+            "milestone_stride": 1
+          }
+        }
+      ],
+      "tasks_end": [
+        {
+          "fn_key": "pk.empirical.predictive.metrics",
+          "log_prefix": "Empirical",
+          "n_samples": 0,
+          "name": "empirical/predictive_metrics",
+          "sample_source": "task_internal",
+          "save_to_disk": false,
+          "split": "empirical_heldout",
+          "task_cfg": {
+            "label": "Empirical",
+            "sample_size": 1,
+            "split": "empirical_heldout"
+          }
+        },
+        {
+          "empirical_name": "cesarali/Indometacin",
+          "fn_key": "pk.predictive.images",
+          "log_prefix": "Empirical",
+          "n_samples": 1,
+          "name": "empirical/predictive_images_repo_0",
+          "sample_source": "empirical_set",
+          "save_to_disk": true,
+          "split": "empirical_heldout",
+          "task_cfg": {
+            "label": "Empirical"
+          }
+        },
+        {
+          "empirical_name": "cesarali/Theophylline",
+          "fn_key": "pk.predictive.images",
+          "log_prefix": "Empirical",
+          "n_samples": 1,
+          "name": "empirical/predictive_images_repo_1",
+          "sample_source": "empirical_set",
+          "save_to_disk": true,
+          "split": "empirical_heldout",
+          "task_cfg": {
+            "label": "Empirical"
+          }
+        },
+        {
+          "empirical_name": "cesarali/Indometacin",
+          "fn_key": "pk.vpc.images",
+          "log_prefix": "Empirical",
+          "n_samples": 10,
+          "name": "empirical/vpc_images_repo_0",
+          "sample_source": "empirical_set",
+          "save_to_disk": true,
+          "split": "empirical_no_heldout",
+          "task_cfg": {
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+          }
+        },
+        {
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+          "fn_key": "pk.vpc.images",
+          "log_prefix": "Empirical",
+          "n_samples": 10,
+          "name": "empirical/vpc_images_repo_1",
+          "sample_source": "empirical_set",
+          "save_to_disk": true,
+          "split": "empirical_no_heldout",
+          "task_cfg": {
+            "label": "Empirical"
+          }
+        },
+        {
+          "empirical_name": "cesarali/Indometacin",
+          "fn_key": "pk.empirical.heldout_generated_classifier",
+          "log_prefix": "Empirical",
+          "n_samples": 0,
+          "name": "empirical/heldout_generated_classifier_repo_0",
+          "sample_source": "task_internal",
+          "save_to_disk": false,
+          "split": "empirical_heldout",
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+              "seed": 0,
+              "show_progress": true,
+              "weight_decay": 0.0001
+            },
+            "empirical_name": "cesarali/Indometacin",
+            "label": "Empirical",
+            "save_details": false,
+            "split": "empirical_heldout"
+          }
+        },
+        {
+          "empirical_name": "cesarali/Theophylline",
+          "fn_key": "pk.empirical.heldout_generated_classifier",
+          "log_prefix": "Empirical",
+          "n_samples": 0,
+          "name": "empirical/heldout_generated_classifier_repo_1",
+          "sample_source": "task_internal",
+          "save_to_disk": false,
+          "split": "empirical_heldout",
+          "task_cfg": {
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+            "empirical_name": "cesarali/Theophylline",
+            "label": "Empirical",
+            "save_details": false,
+            "split": "empirical_heldout"
+          }
+        }
+      ],
+      "tasks_validation": []
+    },
+    "epochs": 5,
+    "eps": 1e-08,
+    "gradient_clip_val": 0.5,
+    "learning_rate": 0.0001,
+    "log_interval": 1,
+    "num_batch_plot": 1,
+    "num_workers": 4,
+    "optimizer_name": "AdamW",
+    "persistent_workers": true,
+    "scheduler_name": "CosineAnnealingLR",
+    "scheduler_params": {
+      "T_max": 1000,
+      "eta_min": 5e-05,
+      "last_epoch": -1
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+    "shuffle_val": true,
+    "weight_decay": 0.0001
+  },
+  "transformers_version": "4.52.4",
+  "upload_to_hf_hub": true,
+  "verbose": false
+}

pytorch_model.bin

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