AICME-runtime / config.json
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{
"architecture_name": "AICMEPK",
"architectures": [
"PKHubModel"
],
"auto_map": {
"AutoConfig": "configuration_sim_priors_pk.PKHubConfig",
"AutoModel": "modeling_sim_priors_pk.PKHubModel"
},
"builder_config": {
"max_context_individuals": 10,
"max_context_observations": 15,
"max_context_remaining": 15,
"max_target_individuals": 1,
"max_target_observations": 5,
"max_target_remaining": 12
},
"default_task": "generate",
"experiment_config": {
"comet_ai_key": null,
"context_observations": {
"add_rem": true,
"drop_time_zero_observations": false,
"empirical_number_of_obs": false,
"generative_bias": false,
"max_num_obs": 15,
"max_past": 5,
"min_past": 3,
"past_time_ratio": 0.1,
"split_past_future": false,
"type": "pk_peak_half_life"
},
"debug_test": false,
"dosing": {
"logdose_mean_range": [
-2.0,
2.0
],
"logdose_std_range": [
0.1,
0.5
],
"num_individuals": 10,
"route_options": [
"oral",
"iv"
],
"route_weights": [
0.8,
0.2
],
"same_route": true,
"time": 0.0
},
"experiment_dir": "/work/ojedamarin/Projects/Pharma/Results/comet/uai/7195d8f55b5d4684a766a69d5a736d28",
"experiment_indentifier": null,
"experiment_name": "uai",
"experiment_type": "nodepk",
"hf_model_card_path": [
"hf_model_cards",
"AICME-PK_Readme.md"
],
"hf_model_name": "AICMEPK_cluster",
"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_and_max": false,
"log_and_z": false,
"log_transform": false,
"n_of_databatches": null,
"n_of_permutations": 3,
"n_of_target_individuals": 1,
"normalize_by_max": true,
"normalize_time": true,
"recreate_tempfile": false,
"sample_size_for_generative_evaluation": null,
"sample_size_for_generative_evaluation_end_of_training": 500,
"sample_size_for_generative_evaluation_val": 10,
"store_in_tempfile": false,
"tempfile_path": [
"preprocessed",
"simulated_ou_as_rates"
],
"test_empirical_datasets": [
"cesarali/lenuzza-2016",
"cesarali/Indometacin",
"cesarali/Theophylline"
],
"test_size": 64,
"tqdm_progress": false,
"train_size": 12800,
"val_size": 256,
"z_score_normalization": false
},
"my_results_path": "/work/ojedamarin/Projects/Pharma/Results/",
"name_str": "AICMEPK",
"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,
"ignore_logvar": 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,
"scale_dosing_amounts": true,
"study_latent_deterministic": false,
"time_obs_encoder_hidden_dim": 256,
"time_obs_encoder_output_dim": 256,
"use_attention": true,
"use_invariance_loss": false,
"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": 128
},
"run_index": 0,
"tags": [
"AICME",
"AISTATS-2026",
"camera-ready"
],
"target_observations": {
"add_rem": true,
"drop_time_zero_observations": false,
"empirical_number_of_obs": 2,
"generative_bias": false,
"max_num_obs": 15,
"max_past": 5,
"min_past": 3,
"past_time_ratio": 0.1,
"split_past_future": true,
"type": "pk_peak_half_life"
},
"train": {
"amsgrad": false,
"batch_size": 64,
"betas": [
0.9,
0.999
],
"callbacks_scheduler": {
"checkpoint_used_in_end": [
"end",
"best",
"log_rmse"
],
"include_end": true,
"keep_temp_files": false,
"max_samples_per_group": 500,
"percent_step": 0.1,
"skip_sanity_check": true,
"store_samples": true,
"task_during": [
{
"fn_key": "pk.predictive.images",
"log_prefix": "Synthetic",
"n_samples": 1,
"name": "synthetic/predictive_images",
"sample_source": "val_batch",
"save_to_disk": true,
"split": "val",
"task_cfg": {
"label": "Synthetic",
"milestone_stride": 1
}
},
{
"fn_key": "pk.generative.images",
"log_prefix": "Synthetic",
"n_samples": 10,
"name": "synthetic/new_individuals_images",
"sample_source": "val_batch",
"save_to_disk": true,
"split": "val",
"task_cfg": {
"label": "Synthetic",
"milestone_stride": 1
}
},
{
"fn_key": "pk.predictive.metrics",
"log_prefix": "Empirical",
"n_samples": 1,
"name": "empirical/predictive_metrics",
"sample_source": "empirical_set",
"save_to_disk": false,
"split": "empirical_heldout",
"task_cfg": {
"label": "Empirical",
"milestone_stride": 5
}
},
{
"checkpoint_metric": true,
"checkpoint_metric_name": "log_rmse",
"checkpoint_mode": "min",
"fn_key": "pk.empirical.summary",
"log_prefix": "Empirical",
"n_samples": 0,
"name": "empirical/summary",
"sample_source": "val_batch",
"save_to_disk": false,
"split": "val",
"task_cfg": {
"label": "Empirical",
"milestone_stride": 5,
"selected_summary_drugs": [
"paracetamol glucuronide",
"midazolam"
],
"summary_metric": "log_rmse"
}
}
],
"tasks_end": [
{
"fn_key": "pk.predictive.metrics",
"log_prefix": "Empirical",
"n_samples": 1,
"name": "empirical/predictive_metrics",
"sample_source": "empirical_set",
"save_to_disk": false,
"split": "empirical_heldout",
"task_cfg": {
"label": "Empirical"
}
},
{
"fn_key": "pk.predictive.images",
"log_prefix": "Empirical",
"n_samples": 1,
"name": "empirical/predictive_images",
"sample_source": "empirical_set",
"save_to_disk": true,
"split": "empirical_heldout",
"task_cfg": {
"label": "Empirical"
}
},
{
"fn_key": "pk.vpc.npde_pvalues",
"log_prefix": "Empirical",
"n_samples": 500,
"name": "empirical/vpc_npde_pvalues",
"sample_source": "empirical_set",
"save_to_disk": false,
"split": "empirical_no_heldout",
"task_cfg": {
"label": "Empirical"
}
},
{
"fn_key": "pk.vpc.images",
"log_prefix": "Empirical",
"n_samples": 500,
"name": "empirical/vpc_images",
"sample_source": "empirical_set",
"save_to_disk": true,
"split": "empirical_no_heldout",
"task_cfg": {
"label": "Empirical"
}
},
{
"fn_key": "pk.empirical.summary",
"log_prefix": "Empirical",
"n_samples": 0,
"name": "empirical/summary",
"sample_source": "val_batch",
"save_to_disk": false,
"split": "val",
"task_cfg": {
"label": "Empirical",
"selected_summary_drugs": [
"paracetamol glucuronide",
"midazolam"
],
"summary_metric": "log_rmse"
}
}
],
"tasks_validation": []
},
"epochs": 100,
"eps": 1e-08,
"gradient_clip_val": 0.5,
"learning_rate": 0.0001,
"log_interval": 1,
"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
},
"upload_to_hf_hub": true,
"verbose": false
},
"experiment_type": "nodepk",
"io_schema_version": "studyjson-v1",
"model_type": "sim_priors_pk",
"original_repo_id": "cesarali/AICMEPK_cluster",
"runtime_repo_id": "cesarali/AICME-runtime",
"supported_tasks": [
"generate",
"predict"
],
"transformers_version": "4.52.4"
}