|
{ |
|
"best_val_loss": 0.045754145830869675, |
|
"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 |
|
}, |
|
"dosing": { |
|
"dose": 1.0, |
|
"route": "oral", |
|
"time": 0.0 |
|
}, |
|
"experiment_dir": null, |
|
"experiment_indentifier": null, |
|
"experiment_name": "node_pk_compartments", |
|
"hf_model_card_path": [ |
|
"hf_model_cards", |
|
"SNODE-PK_Readme.md" |
|
], |
|
"hf_model_name": "StudyNodePK_development", |
|
"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 |
|
], |
|
"k_a_tmag_range": [ |
|
0.01, |
|
0.1 |
|
], |
|
"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 |
|
], |
|
"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 |
|
], |
|
"num_individuals_range": [ |
|
10, |
|
10 |
|
], |
|
"num_peripherals_range": [ |
|
1, |
|
3 |
|
], |
|
"solver_method": "rk4", |
|
"time_num_steps": 100, |
|
"time_start": 0.0, |
|
"time_stop": 10.0 |
|
}, |
|
"mix_data": { |
|
"evaluate_prediction_steps_past": 5, |
|
"log_transform": false, |
|
"n_of_databatches": 3, |
|
"n_of_target_individuals": 1, |
|
"normalize_by_max": true, |
|
"normalize_time": true, |
|
"pretraining_dataset_path": [ |
|
"preprocessed", |
|
"lenuzza", |
|
"Lenuzza2016.csv" |
|
], |
|
"pretraining_epochs": 90, |
|
"pretraining_protocol": "none", |
|
"split_seed": 42, |
|
"split_strategy": "study", |
|
"test_protocol": "simulated", |
|
"test_size": 5, |
|
"train_size": 100, |
|
"val_protocol": "simulated", |
|
"val_size": 5, |
|
"z_score_normalization": false |
|
}, |
|
"model_type": "node_pk", |
|
"my_results_path": null, |
|
"name_str": "SNodePK", |
|
"network": { |
|
"activation": "ReLU", |
|
"aggregator_num_heads": 8, |
|
"aggregator_type": "attention", |
|
"cov_proj_dim": 16, |
|
"decoder_hidden_dim": 128, |
|
"decoder_name": "TransformerDecoder", |
|
"decoder_num_layers": 2, |
|
"decoder_rnn_hidden_dim": 200, |
|
"drift_activation": "Tanh", |
|
"drift_num_layers": 3, |
|
"dropout": 0.1, |
|
"encoder_rnn_hidden_dim": 200, |
|
"exclusive_node_step": false, |
|
"individual_encoder_name": "RNNContextEncoder", |
|
"individual_encoder_number_of_heads": 4, |
|
"init_hidden_num_layers": 2, |
|
"input_encoding_hidden_dim": 128, |
|
"loss_name": "nll", |
|
"node_step": true, |
|
"norm": "layer", |
|
"output_head_num_layers": 2, |
|
"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, |
|
"use_attention": true, |
|
"use_covariance": false, |
|
"zi_latent_dim": 200 |
|
}, |
|
"run_index": 0, |
|
"tags": [ |
|
"snode-pk", |
|
"S-0" |
|
], |
|
"target_observations": { |
|
"add_rem": true, |
|
"divide_in_past_and_future": true, |
|
"empirical_number_of_obs": false, |
|
"max_num_obs": 14, |
|
"min_num_of_past_context": 3, |
|
"num_of_past_context": 4, |
|
"obs_dataset": "/home/cesarali/Pharma/generative_pk/data/preprocessed/lenuzza/Lenuzza2016.csv", |
|
"obs_type": "observations_pk_peak_halflife", |
|
"past_time_ratio": 0.1 |
|
}, |
|
"train": { |
|
"amsgrad": false, |
|
"batch_size": 8, |
|
"betas": [ |
|
0.9, |
|
0.999 |
|
], |
|
"epochs": 5, |
|
"eps": 1e-08, |
|
"gradient_clip_val": 1.0, |
|
"learning_rate": 0.0001, |
|
"log_image_every_epoch": 2, |
|
"log_interval": 1, |
|
"log_vcp": true, |
|
"num_batch_plot": 1, |
|
"num_workers": 3, |
|
"optimizer_name": "AdamW", |
|
"scheduler_name": "CosineAnnealingLR", |
|
"scheduler_params": { |
|
"T_max": 1000, |
|
"eta_min": 5e-05, |
|
"last_epoch": -1 |
|
}, |
|
"weight_decay": 0.0001 |
|
}, |
|
"transformers_version": "4.52.4", |
|
"upload_to_hf_hub": false, |
|
"verbose": false |
|
} |
|
|