cesarali's picture
best val_rmse 0.0458
1211146 verified
{
"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
}