cesarali/StudyNodePK_development

1{2  "best_val_loss": 0.045754145830869675,3  "comet_ai_key": null,4  "context_observations": {5    "add_rem": true,6    "divide_in_past_and_future": false,7    "empirical_number_of_obs": false,8    "max_num_obs": 15,9    "min_num_of_past_context": 3,10    "num_of_past_context": 5,11    "obs_dataset": "/home/cesarali/Pharma/generative_pk/data/preprocessed/lenuzza/Lenuzza2016.csv",12    "obs_type": "observations_pk_peak_halflife",13    "past_time_ratio": 0.114  },15  "dosing": {16    "dose": 1.0,17    "route": "oral",18    "time": 0.019  },20  "experiment_dir": null,21  "experiment_indentifier": null,22  "experiment_name": "node_pk_compartments",23  "hf_model_card_path": [24    "hf_model_cards",25    "SNODE-PK_Readme.md"26  ],27  "hf_model_name": "StudyNodePK_development",28  "hugging_face_token": null,29  "meta_study": {30    "V_tmag_range": [31      0.01,32      0.133    ],34    "drug_id_options": [35      "Drug_A",36      "Drug_B",37      "Drug_C"38    ],39    "k_1p_tmag_range": [40      0.01,41      0.142    ],43    "k_a_tmag_range": [44      0.01,45      0.146    ],47    "k_e_tmag_range": [48      0.01,49      0.150    ],51    "k_p1_tmag_range": [52      0.01,53      0.154    ],55    "log_V_mean_range": [56      -1.5,57      1.558    ],59    "log_V_std_range": [60      0.1,61      0.562    ],63    "log_k_1p_mean_range": [64      -1.5,65      1.566    ],67    "log_k_1p_std_range": [68      0.1,69      0.570    ],71    "log_k_a_mean_range": [72      -1.5,73      1.574    ],75    "log_k_a_std_range": [76      0.1,77      0.578    ],79    "log_k_e_mean_range": [80      -1.5,81      1.582    ],83    "log_k_e_std_range": [84      0.1,85      0.586    ],87    "log_k_p1_mean_range": [88      -1.5,89      1.590    ],91    "log_k_p1_std_range": [92      0.1,93      0.594    ],95    "num_individuals_range": [96      10,97      1098    ],99    "num_peripherals_range": [100      1,101      3102    ],103    "solver_method": "rk4",104    "time_num_steps": 100,105    "time_start": 0.0,106    "time_stop": 10.0107  },108  "mix_data": {109    "evaluate_prediction_steps_past": 5,110    "log_transform": false,111    "n_of_databatches": 3,112    "n_of_target_individuals": 1,113    "normalize_by_max": true,114    "normalize_time": true,115    "pretraining_dataset_path": [116      "preprocessed",117      "lenuzza",118      "Lenuzza2016.csv"119    ],120    "pretraining_epochs": 90,121    "pretraining_protocol": "none",122    "split_seed": 42,123    "split_strategy": "study",124    "test_protocol": "simulated",125    "test_size": 5,126    "train_size": 100,127    "val_protocol": "simulated",128    "val_size": 5,129    "z_score_normalization": false130  },131  "model_type": "node_pk",132  "my_results_path": null,133  "name_str": "SNodePK",134  "network": {135    "activation": "ReLU",136    "aggregator_num_heads": 8,137    "aggregator_type": "attention",138    "cov_proj_dim": 16,139    "decoder_hidden_dim": 128,140    "decoder_name": "TransformerDecoder",141    "decoder_num_layers": 2,142    "decoder_rnn_hidden_dim": 200,143    "drift_activation": "Tanh",144    "drift_num_layers": 3,145    "dropout": 0.1,146    "encoder_rnn_hidden_dim": 200,147    "exclusive_node_step": false,148    "individual_encoder_name": "RNNContextEncoder",149    "individual_encoder_number_of_heads": 4,150    "init_hidden_num_layers": 2,151    "input_encoding_hidden_dim": 128,152    "loss_name": "nll",153    "node_step": true,154    "norm": "layer",155    "output_head_num_layers": 2,156    "rnn_decoder_number_of_layers": 4,157    "rnn_individual_encoder_number_of_layers": 2,158    "time_obs_encoder_hidden_dim": 128,159    "time_obs_encoder_output_dim": 128,160    "use_attention": true,161    "use_covariance": false,162    "zi_latent_dim": 200163  },164  "run_index": 0,165  "tags": [166    "snode-pk",167    "S-0"168  ],169  "target_observations": {170    "add_rem": true,171    "divide_in_past_and_future": true,172    "empirical_number_of_obs": false,173    "max_num_obs": 14,174    "min_num_of_past_context": 3,175    "num_of_past_context": 4,176    "obs_dataset": "/home/cesarali/Pharma/generative_pk/data/preprocessed/lenuzza/Lenuzza2016.csv",177    "obs_type": "observations_pk_peak_halflife",178    "past_time_ratio": 0.1179  },180  "train": {181    "amsgrad": false,182    "batch_size": 8,183    "betas": [184      0.9,185      0.999186    ],187    "epochs": 5,188    "eps": 1e-08,189    "gradient_clip_val": 1.0,190    "learning_rate": 0.0001,191    "log_image_every_epoch": 2,192    "log_interval": 1,193    "log_vcp": true,194    "num_batch_plot": 1,195    "num_workers": 3,196    "optimizer_name": "AdamW",197    "scheduler_name": "CosineAnnealingLR",198    "scheduler_params": {199      "T_max": 1000,200      "eta_min": 5e-05,201      "last_epoch": -1202    },203    "weight_decay": 0.0001204  },205  "transformers_version": "4.52.4",206  "upload_to_hf_hub": false,207  "verbose": false208}209