{ "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" }