Mercurial > repos > goeckslab > pycaret_predict

annotate pycaret_regression.py @ 8:1aed7d47c5ec draft default tip

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planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
author goeckslab
date Fri, 25 Jul 2025 19:02:32 +0000
parents ccd798db5abb
children
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1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
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diff changeset
1 import logging
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
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goeckslab
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3 from base_model_trainer import BaseModelTrainer
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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4 from dashboard import generate_regression_explainer_dashboard
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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5 from pycaret.regression import RegressionExperiment
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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6
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7 LOG = logging.getLogger(__name__)
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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8
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9
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10 class RegressionModelTrainer(BaseModelTrainer):
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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11 def __init__(
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12 self,
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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13 input_file,
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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14 target_col,
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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15 output_dir,
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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16 task_type,
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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17 random_seed,
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
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18 test_file=None,
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19 **kwargs,
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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20 ):
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1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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21 super().__init__(
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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22 input_file,
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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23 target_col,
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24 output_dir,
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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25 task_type,
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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26 random_seed,
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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27 test_file,
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28 **kwargs,
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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29 )
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goeckslab
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30 # The BaseModelTrainer.setup_pycaret will set self.exp appropriately
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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31 # But we reassign here for clarity
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1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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32 self.exp = RegressionExperiment()
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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33
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34 def save_dashboard(self):
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35 LOG.info("Saving explainer dashboard")
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goeckslab
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36 dashboard = generate_regression_explainer_dashboard(self.exp, self.best_model)
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1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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37 dashboard.save_html("dashboard.html")
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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38
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39 def generate_plots(self):
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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40 LOG.info("Generating and saving plots")
8
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41 plots = [
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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42 "residuals",
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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43 "error",
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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44 "cooks",
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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45 "learning",
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
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46 "vc",
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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47 "manifold",
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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48 "rfe",
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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49 "feature",
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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50 "feature_all",
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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51 ]
0
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52 for plot_name in plots:
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53 try:
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54 plot_path = self.exp.plot_model(
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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55 self.best_model, plot=plot_name, save=True
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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56 )
0
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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57 self.plots[plot_name] = plot_path
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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58 except Exception as e:
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59 LOG.error(f"Error generating plot {plot_name}: {e}")
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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60 continue
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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61
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62 def generate_plots_explainer(self):
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63 LOG.info("Generating and saving plots from explainer")
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64
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65 from explainerdashboard import RegressionExplainer
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66
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67 X_test = self.exp.X_test_transformed.copy()
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68 y_test = self.exp.y_test_transformed
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69
2
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70 try:
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71 explainer = RegressionExplainer(self.best_model, X_test, y_test)
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72 except Exception as e:
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73 LOG.error(f"Error creating explainer: {e}")
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74 return
0
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75
8
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76 # --- 1) SHAP mean impact (average absolute SHAP values) ---
0
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77 try:
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78 self.explainer_plots["shap_mean"] = explainer.plot_importances()
0
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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79 except Exception as e:
8
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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80 LOG.error(f"Error generating SHAP mean importance: {e}")
0
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81
8
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82 # --- 2) SHAP permutation importance ---
0
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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83 try:
8
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84 self.explainer_plots["shap_perm"] = explainer.plot_importances_permutation(
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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85 kind="permutation"
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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86 )
0
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87 except Exception as e:
8
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88 LOG.error(f"Error generating SHAP permutation importance: {e}")
0
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89
8
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90 # Pre-filter features so we never call PDP or residual-vs-feature on missing cols
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91 valid_feats = []
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92 for feat in self.features_name:
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93 if feat in explainer.X.columns or feat in explainer.onehot_cols:
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94 valid_feats.append(feat)
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95 else:
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96 LOG.warning(f"Skipping feature {feat!r}: not found in explainer data")
0
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97
8
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98 # --- 3) Partial Dependence Plots (PDPs) per feature ---
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99 for feature in valid_feats:
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100 try:
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101 fig_pdp = explainer.plot_pdp(feature)
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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102 self.explainer_plots[f"pdp__{feature}"] = fig_pdp
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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103 except AssertionError as ae:
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104 LOG.warning(f"PDP AssertionError for {feature!r}: {ae}")
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105 except Exception as e:
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106 LOG.error(f"Error generating PDP for {feature}: {e}")
0
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107
8
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108 # --- 4) Predicted vs Actual plot ---
0
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109 try:
8
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110 self.explainer_plots["predicted_vs_actual"] = explainer.plot_predicted_vs_actual()
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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111 except Exception as e:
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112 LOG.error(f"Error generating Predicted vs Actual plot: {e}")
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113
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114 # --- 5) Global residuals distribution ---
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115 try:
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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116 self.explainer_plots["residuals"] = explainer.plot_residuals()
0
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117 except Exception as e:
8
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118 LOG.error(f"Error generating Residuals plot: {e}")
0
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119
8
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120 # --- 6) Residuals vs each feature ---
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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121 for feature in valid_feats:
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122 try:
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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123 fig_res_vs_feat = explainer.plot_residuals_vs_feature(feature)
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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124 self.explainer_plots[f"residuals_vs_feature__{feature}"] = fig_res_vs_feat
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125 except AssertionError as ae:
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126 LOG.warning(f"Residuals-vs-feature AssertionError for {feature!r}: {ae}")
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127 except Exception as e:
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128 LOG.error(f"Error generating Residuals vs {feature}: {e}")