config.json

{
  "best_val_loss": 112.03976440429688,
  "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": true,
    "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": "/home/cesarali/Pharma/sim_priors_pk/results/comet/node-pk/cea66083fce0481299ee7ff454760258",
  "experiment_indentifier": null,
  "experiment_name": "node-pk",
  "hf_model_card_path": [
    "hf_model_cards",
    "NODE-PK_Readme.md"
  ],
  "hf_model_name": "NodePK_test",
  "hugging_face_token": null,
  "meta_study": {
    "band_scale_range": [
      0.05,
      1.0
    ],
    "baseline_range": [
      0.6,
      1.4
    ],
    "decay_rate_range": [
      0.001,
      0.2
    ],
    "drug_id_options": [
      "DummyDrug"
    ],
    "num_individuals": 20,
    "num_individuals_range": [
      16,
      16
    ],
    "num_peripherals_range": [
      1,
      3
    ],
    "p1": 1.0,
    "simple_mode": true,
    "solver_method": "dummy",
    "time_num_steps": 40,
    "time_start": 0.0,
    "time_stop": 24.0
  },
  "mix_data": {
    "evaluate_prediction_steps_past": 5,
    "keep_tempfile": false,
    "log_transform": false,
    "n_of_databatches": null,
    "n_of_permutations": 1,
    "n_of_target_individuals": 1,
    "normalize_by_max": true,
    "normalize_time": true,
    "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/Indometacin"
    ],
    "test_protocol": "simulated",
    "test_size": 64,
    "tqdm_progress": false,
    "train_size": 320,
    "val_protocol": "simulated",
    "val_size": 64,
    "z_score_normalization": false
  },
  "model_type": "node_pk",
  "my_results_path": null,
  "name_str": "PredictionPK",
  "network": {
    "activation": "ReLU",
    "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",
    "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": 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",
    "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",
    "PredictionPK"
  ],
  "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": true,
    "type": "pk_peak_half_life"
  },
  "train": {
    "amsgrad": false,
    "batch_size": 32,
    "betas": [
      0.9,
      0.999
    ],
    "epochs": 20,
    "eps": 1e-08,
    "gradient_clip_val": 1.0,
    "learning_rate": 0.0001,
    "log_empirical_evaluation_pct": 0.2,
    "log_image_every_epoch_pct": 0.2,
    "log_interval": 1,
    "log_prediction_in_val": true,
    "log_reconstruction_in_val": true,
    "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,
    "weight_decay": 0.0001
  },
  "transformers_version": "4.52.4",
  "upload_to_hf_hub": false,
  "verbose": false
}