best val_rmse 0.3957

config.json

@@ -0,0 +1,273 @@
+{
+  "best_val_loss": 0.395673006772995,
+  "comet_ai_key": null,
+  "context_observations": {
+    "add_rem": true,
+    "max_num_obs": 15,
+    "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": {
+    "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": "/work/ojedamarin/Projects/Pharma/Results/comet/context-vae-pk/f768565b2eb7409498e517dc08d3d827",
+  "experiment_indentifier": null,
+  "experiment_name": "context-vae-pk",
+  "hf_model_card_path": [
+    "hf_model_cards",
+    "CVAE-PK_Readme.md"
+  ],
+  "hf_model_name": "CVAE_cluster_debug",
+  "hugging_face_token": null,
+  "meta_study": {
+    "V_tmag_range": [
+      0.001,
+      0.001
+    ],
+    "V_tscl_range": [
+      1,
+      5
+    ],
+    "drug_id_options": [
+      "Drug_A",
+      "Drug_B",
+      "Drug_C"
+    ],
+    "k_1p_tmag_range": [
+      0.01,
+      0.02
+    ],
+    "k_1p_tscl_range": [
+      1,
+      5
+    ],
+    "k_a_tmag_range": [
+      0.01,
+      0.02
+    ],
+    "k_a_tscl_range": [
+      1,
+      5
+    ],
+    "k_e_tmag_range": [
+      0.01,
+      0.02
+    ],
+    "k_e_tscl_range": [
+      1,
+      5
+    ],
+    "k_p1_tmag_range": [
+      0.01,
+      0.02
+    ],
+    "k_p1_tscl_range": [
+      1,
+      5
+    ],
+    "log_V_mean_range": [
+      2,
+      8
+    ],
+    "log_V_std_range": [
+      0.2,
+      0.6
+    ],
+    "log_k_1p_mean_range": [
+      -4,
+      0
+    ],
+    "log_k_1p_std_range": [
+      0.2,
+      0.6
+    ],
+    "log_k_a_mean_range": [
+      -1,
+      2
+    ],
+    "log_k_a_std_range": [
+      0.2,
+      0.6
+    ],
+    "log_k_e_mean_range": [
+      -5,
+      0
+    ],
+    "log_k_e_std_range": [
+      0.2,
+      0.6
+    ],
+    "log_k_p1_mean_range": [
+      -4,
+      -1
+    ],
+    "log_k_p1_std_range": [
+      0.2,
+      0.6
+    ],
+    "num_individuals_range": [
+      5,
+      10
+    ],
+    "num_peripherals_range": [
+      1,
+      3
+    ],
+    "rel_ruv_range": [
+      0.001,
+      0.01
+    ],
+    "solver_method": "rk4",
+    "time_num_steps": 100,
+    "time_start": 0.0,
+    "time_stop": 16.0
+  },
+  "mix_data": {
+    "evaluate_prediction_steps_past": 5,
+    "keep_tempfile": false,
+    "log_transform": false,
+    "n_of_databatches": null,
+    "n_of_permutations": 3,
+    "n_of_target_individuals": 1,
+    "normalize_by_max": true,
+    "normalize_time": true,
+    "pretraining_epochs": 4800,
+    "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": 256,
+    "tqdm_progress": false,
+    "train_size": 1024,
+    "val_protocol": "simulated",
+    "val_size": 256,
+    "z_score_normalization": false
+  },
+  "model_type": "node_pk",
+  "my_results_path": "/work/ojedamarin/Projects/Pharma/Results/",
+  "name_str": "ContextVAEPK",
+  "network": {
+    "activation": "ReLU",
+    "aggregator_num_heads": 8,
+    "aggregator_type": "mean",
+    "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": 2,
+    "dropout": 0.1,
+    "encoder_rnn_hidden_dim": 256,
+    "exclusive_node_step": true,
+    "individual_encoder_name": "RNNContextEncoder",
+    "individual_encoder_number_of_heads": 4,
+    "init_hidden_num_layers": 2,
+    "input_encoding_hidden_dim": 128,
+    "kl_weight": 1.0,
+    "loss_name": "log_nll",
+    "node_step": true,
+    "norm": "layer",
+    "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": 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": 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": [
+    "SIM_PRIOR",
+    "ContextVAE",
+    "NodePK"
+  ],
+  "target_observations": {
+    "add_rem": true,
+    "max_num_obs": 15,
+    "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"
+  },
+  "train": {
+    "amsgrad": false,
+    "batch_size": 128,
+    "betas": [
+      0.9,
+      0.999
+    ],
+    "epochs": 100,
+    "eps": 1e-08,
+    "eval_empirical_every_pct": 0.5,
+    "gradient_clip_val": 1.0,
+    "learning_rate": 0.0001,
+    "log_image_every_epoch": 30,
+    "log_interval": 1,
+    "log_vcp": false,
+    "num_batch_plot": 1,
+    "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": 0.5,
+    "weight_decay": 0.0001
+  },
+  "transformers_version": "4.52.4",
+  "upload_to_hf_hub": false,
+  "verbose": false
+}

pytorch_model.bin

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:0a60676629d33d943d6f938a15502d6eb014698a7fcb5e7807c76ee2ede1a0e3
+size 38746519