best val_rmse 0.2959
Browse files- config.json +212 -0
- pytorch_model.bin +3 -0
config.json
ADDED
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| 1 |
+
{
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| 2 |
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"best_val_loss": 0.29585859179496765,
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| 3 |
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"comet_ai_key": null,
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| 4 |
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"context_observations": {
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| 5 |
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"add_rem": true,
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| 6 |
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"divide_in_past_and_future": false,
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| 7 |
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"empirical_number_of_obs": false,
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| 8 |
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"max_num_obs": 15,
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| 9 |
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"min_num_of_past_context": 3,
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| 10 |
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"num_of_past_context": 5,
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| 11 |
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"obs_dataset": "/home/cesarali/Pharma/generative_pk/data/preprocessed/lenuzza/Lenuzza2016.csv",
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| 12 |
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"obs_type": "observations_pk_peak_halflife",
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| 13 |
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"past_time_ratio": 0.1
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| 14 |
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},
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| 15 |
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"dosing": {
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| 16 |
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"dose": 1.0,
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| 17 |
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"route": "oral",
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| 18 |
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"time": 0.0
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| 19 |
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},
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| 20 |
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"experiment_dir": null,
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| 21 |
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"experiment_indentifier": null,
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| 22 |
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"experiment_name": "node_pk_compartments",
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| 23 |
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"hf_model_card_path": [
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"hf_model_cards",
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| 25 |
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"NP-PK_Readme.md"
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| 26 |
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],
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| 27 |
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"hf_model_name": "NeuralProcessPK_development",
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| 28 |
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"hugging_face_token": null,
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| 29 |
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"meta_study": {
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| 30 |
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"V_tmag_range": [
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| 31 |
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0.01,
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| 32 |
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0.1
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| 33 |
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],
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| 34 |
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"drug_id_options": [
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"Drug_A",
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| 36 |
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"Drug_B",
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| 37 |
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"Drug_C"
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| 38 |
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],
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| 39 |
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"k_1p_tmag_range": [
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| 40 |
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0.01,
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| 41 |
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0.1
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| 42 |
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],
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| 43 |
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"k_a_tmag_range": [
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| 44 |
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0.01,
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| 45 |
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0.1
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],
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| 47 |
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"k_e_tmag_range": [
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0.01,
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| 49 |
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0.1
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| 50 |
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],
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| 51 |
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"k_p1_tmag_range": [
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| 52 |
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0.01,
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| 53 |
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0.1
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| 54 |
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],
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"log_V_mean_range": [
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| 56 |
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-1.5,
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| 57 |
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1.5
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| 58 |
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],
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| 59 |
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"log_V_std_range": [
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| 60 |
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0.1,
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| 61 |
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0.5
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],
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| 63 |
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"log_k_1p_mean_range": [
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| 64 |
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-1.5,
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| 65 |
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1.5
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| 66 |
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],
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| 67 |
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"log_k_1p_std_range": [
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| 68 |
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0.1,
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| 69 |
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0.5
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| 70 |
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],
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| 71 |
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"log_k_a_mean_range": [
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| 72 |
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-1.5,
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| 73 |
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1.5
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| 74 |
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],
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| 75 |
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"log_k_a_std_range": [
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| 76 |
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0.1,
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| 77 |
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0.5
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| 78 |
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],
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| 79 |
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"log_k_e_mean_range": [
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| 80 |
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-1.5,
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| 81 |
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1.5
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],
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| 83 |
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"log_k_e_std_range": [
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| 84 |
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0.1,
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| 85 |
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0.5
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| 86 |
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],
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| 87 |
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"log_k_p1_mean_range": [
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-1.5,
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| 89 |
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1.5
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| 90 |
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],
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| 91 |
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"log_k_p1_std_range": [
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| 92 |
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0.1,
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| 93 |
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0.5
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],
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| 95 |
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"num_individuals_range": [
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10,
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| 97 |
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10
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],
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"num_peripherals_range": [
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| 100 |
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1,
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| 101 |
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3
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| 102 |
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],
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| 103 |
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"solver_method": "rk4",
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| 104 |
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"time_num_steps": 100,
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| 105 |
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"time_start": 0.0,
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| 106 |
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"time_stop": 10.0
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| 107 |
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},
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| 108 |
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"mix_data": {
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| 109 |
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"evaluate_prediction_steps_past": 5,
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| 110 |
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"log_transform": false,
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| 111 |
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"n_of_databatches": 10,
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| 112 |
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"n_of_target_individuals": 1,
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| 113 |
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"normalize_by_max": true,
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| 114 |
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"normalize_time": true,
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| 115 |
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"pretraining_dataset_path": [
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| 116 |
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"preprocessed",
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| 117 |
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"lenuzza",
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| 118 |
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"Lenuzza2016.csv"
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| 119 |
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],
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| 120 |
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"pretraining_epochs": 90,
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| 121 |
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"pretraining_protocol": "none",
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| 122 |
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"return_split_versions": true,
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| 123 |
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"split_seed": 42,
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| 124 |
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"split_strategy": "study",
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| 125 |
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"test_protocol": "simulated",
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| 126 |
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"test_size": 5,
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| 127 |
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"train_size": 100,
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| 128 |
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"val_protocol": "simulated",
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| 129 |
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"val_size": 5,
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| 130 |
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"z_score_normalization": false
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| 131 |
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},
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| 132 |
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"model_type": "node_pk",
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| 133 |
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"my_results_path": null,
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| 134 |
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"name_str": "NeuralProcessPK",
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| 135 |
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"network": {
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| 136 |
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"activation": "ReLU",
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| 137 |
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"aggregator_num_heads": 2,
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| 138 |
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"aggregator_type": "attention",
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| 139 |
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"cov_proj_dim": 16,
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| 140 |
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"decoder_attention_layers": 2,
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| 141 |
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"decoder_hidden_dim": 32,
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| 142 |
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"decoder_name": "RNNDecoder",
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| 143 |
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"decoder_num_layers": 2,
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| 144 |
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"decoder_rnn_hidden_dim": 20,
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| 145 |
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"drift_activation": "Tanh",
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| 146 |
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"drift_num_layers": 2,
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| 147 |
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"dropout": 0.1,
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| 148 |
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"encoder_rnn_hidden_dim": 20,
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| 149 |
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"exclusive_node_step": false,
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| 150 |
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"individual_encoder_name": "RNNContextEncoder",
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| 151 |
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"individual_encoder_number_of_heads": 4,
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| 152 |
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"init_hidden_num_layers": 2,
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| 153 |
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"input_encoding_hidden_dim": 128,
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| 154 |
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"loss_name": "nll",
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| 155 |
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"node_step": true,
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| 156 |
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"norm": "layer",
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| 157 |
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"output_head_num_layers": 2,
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| 158 |
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"rnn_decoder_number_of_layers": 2,
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| 159 |
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"rnn_individual_encoder_number_of_layers": 2,
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| 160 |
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"time_obs_encoder_hidden_dim": 32,
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| 161 |
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"time_obs_encoder_output_dim": 32,
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| 162 |
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"use_attention": true,
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| 163 |
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"use_kl_i": true,
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| 164 |
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"use_kl_init": true,
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| 165 |
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"use_kl_s": true,
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| 166 |
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"zi_latent_dim": 20
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| 167 |
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},
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| 168 |
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"run_index": 0,
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| 169 |
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"tags": [
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| 170 |
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"np-pk",
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| 171 |
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"N-0"
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| 172 |
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],
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| 173 |
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"target_observations": {
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| 174 |
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"add_rem": true,
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| 175 |
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"divide_in_past_and_future": false,
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| 176 |
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"empirical_number_of_obs": false,
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| 177 |
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"max_num_obs": 15,
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| 178 |
+
"min_num_of_past_context": 3,
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| 179 |
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"num_of_past_context": 5,
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| 180 |
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"obs_dataset": "/home/cesarali/Pharma/generative_pk/data/preprocessed/lenuzza/Lenuzza2016.csv",
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| 181 |
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"obs_type": "observations_pk_peak_halflife",
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| 182 |
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"past_time_ratio": 0.1
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| 183 |
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},
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| 184 |
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"train": {
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| 185 |
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"amsgrad": false,
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| 186 |
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"batch_size": 8,
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| 187 |
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"betas": [
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| 188 |
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0.9,
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| 189 |
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0.999
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| 190 |
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],
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| 191 |
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"epochs": 3,
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| 192 |
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"eps": 1e-08,
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| 193 |
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"gradient_clip_val": 1.0,
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| 194 |
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"learning_rate": 0.0001,
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| 195 |
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"log_image_every_epoch": 2,
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| 196 |
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"log_interval": 1,
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| 197 |
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"log_vcp": false,
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| 198 |
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"num_batch_plot": 1,
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| 199 |
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"num_workers": 3,
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| 200 |
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"optimizer_name": "AdamW",
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| 201 |
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"scheduler_name": "CosineAnnealingLR",
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| 202 |
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"scheduler_params": {
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| 203 |
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"T_max": 1000,
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| 204 |
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"eta_min": 5e-05,
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| 205 |
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"last_epoch": -1
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| 206 |
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},
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| 207 |
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"weight_decay": 0.0001
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| 208 |
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},
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| 209 |
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"transformers_version": "4.52.4",
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| 210 |
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"upload_to_hf_hub": false,
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| 211 |
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"verbose": false
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| 212 |
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}
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pytorch_model.bin
ADDED
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@@ -0,0 +1,3 @@
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| 1 |
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version https://git-lfs.github.com/spec/v1
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| 2 |
+
oid sha256:57c7e518a42a7fed6dee07e1f8db261ab54b03f020e64c594842f54c8e9acdbc
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| 3 |
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size 168701
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