Mercurial > repos > goeckslab > pycaret_compare
annotate feature_importance.py @ 4:4aa511539199 draft default tip
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit cf47efb521b91a9cb44ae5c5ade860627f9b9030
author | goeckslab |
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date | Tue, 03 Jun 2025 19:31:16 +0000 |
parents | 915447b14520 |
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rev | line source |
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915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff
changeset
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1 import base64 |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff
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2 import logging |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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3 import os |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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4 |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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5 import matplotlib.pyplot as plt |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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6 import pandas as pd |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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7 from pycaret.classification import ClassificationExperiment |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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8 from pycaret.regression import RegressionExperiment |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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9 |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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10 logging.basicConfig(level=logging.DEBUG) |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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11 LOG = logging.getLogger(__name__) |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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12 |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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13 |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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14 class FeatureImportanceAnalyzer: |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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15 def __init__( |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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16 self, |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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17 task_type, |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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18 output_dir, |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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19 data_path=None, |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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20 data=None, |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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21 target_col=None): |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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22 |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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23 if data is not None: |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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24 self.data = data |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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25 LOG.info("Data loaded from memory") |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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26 else: |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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27 self.target_col = target_col |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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28 self.data = pd.read_csv(data_path, sep=None, engine='python') |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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29 self.data.columns = self.data.columns.str.replace('.', '_') |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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30 self.data = self.data.fillna(self.data.median(numeric_only=True)) |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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31 self.task_type = task_type |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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32 self.target = self.data.columns[int(target_col) - 1] |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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33 self.exp = ClassificationExperiment() \ |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff
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34 if task_type == 'classification' \ |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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35 else RegressionExperiment() |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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36 self.plots = {} |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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37 self.output_dir = output_dir |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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38 |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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39 def setup_pycaret(self): |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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40 LOG.info("Initializing PyCaret") |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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41 setup_params = { |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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42 'target': self.target, |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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43 'session_id': 123, |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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44 'html': True, |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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45 'log_experiment': False, |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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46 'system_log': False |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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47 } |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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48 LOG.info(self.task_type) |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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49 LOG.info(self.exp) |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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50 self.exp.setup(self.data, **setup_params) |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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51 |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
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52 # def save_coefficients(self): |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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53 # model = self.exp.create_model('lr') |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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54 # coef_df = pd.DataFrame({ |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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55 # 'Feature': self.data.columns.drop(self.target), |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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56 # 'Coefficient': model.coef_[0] |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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57 # }) |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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58 # coef_html = coef_df.to_html(index=False) |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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59 # return coef_html |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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60 |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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61 def save_tree_importance(self): |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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62 model = self.exp.create_model('rf') |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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63 importances = model.feature_importances_ |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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64 processed_features = self.exp.get_config('X_transformed').columns |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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65 LOG.debug(f"Feature importances: {importances}") |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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66 LOG.debug(f"Features: {processed_features}") |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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67 feature_importances = pd.DataFrame({ |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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68 'Feature': processed_features, |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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69 'Importance': importances |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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70 }).sort_values(by='Importance', ascending=False) |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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71 plt.figure(figsize=(10, 6)) |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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72 plt.barh( |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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73 feature_importances['Feature'], |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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74 feature_importances['Importance']) |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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75 plt.xlabel('Importance') |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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76 plt.title('Feature Importance (Random Forest)') |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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77 plot_path = os.path.join( |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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78 self.output_dir, |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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79 'tree_importance.png') |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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80 plt.savefig(plot_path) |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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81 plt.close() |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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82 self.plots['tree_importance'] = plot_path |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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83 |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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84 def save_shap_values(self): |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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85 model = self.exp.create_model('lightgbm') |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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86 import shap |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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87 explainer = shap.Explainer(model) |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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88 shap_values = explainer.shap_values( |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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89 self.exp.get_config('X_transformed')) |
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90 shap.summary_plot(shap_values, |
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91 self.exp.get_config('X_transformed'), show=False) |
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92 plt.title('Shap (LightGBM)') |
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93 plot_path = os.path.join( |
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94 self.output_dir, 'shap_summary.png') |
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95 plt.savefig(plot_path) |
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96 plt.close() |
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97 self.plots['shap_summary'] = plot_path |
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98 |
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99 def generate_feature_importance(self): |
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100 # coef_html = self.save_coefficients() |
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101 self.save_tree_importance() |
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102 self.save_shap_values() |
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103 |
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104 def encode_image_to_base64(self, img_path): |
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105 with open(img_path, 'rb') as img_file: |
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106 return base64.b64encode(img_file.read()).decode('utf-8') |
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107 |
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108 def generate_html_report(self): |
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109 LOG.info("Generating HTML report") |
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110 |
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111 # Read and encode plot images |
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112 plots_html = "" |
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113 for plot_name, plot_path in self.plots.items(): |
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114 encoded_image = self.encode_image_to_base64(plot_path) |
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115 plots_html += f""" |
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116 <div class="plot" id="{plot_name}"> |
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117 <h2>{'Feature importance analysis from a' |
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118 'trained Random Forest' |
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119 if plot_name == 'tree_importance' |
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120 else 'SHAP Summary from a trained lightgbm'}</h2> |
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121 <h3>{'Use gini impurity for' |
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122 'calculating feature importance for classification' |
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123 'and Variance Reduction for regression' |
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124 if plot_name == 'tree_importance' |
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125 else ''}</h3> |
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126 <img src="data:image/png;base64, |
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127 {encoded_image}" alt="{plot_name}"> |
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128 </div> |
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129 """ |
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130 |
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131 # Generate HTML content with tabs |
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132 html_content = f""" |
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133 <h1>PyCaret Feature Importance Report</h1> |
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134 {plots_html} |
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135 """ |
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136 |
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137 return html_content |
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138 |
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139 def run(self): |
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140 LOG.info("Running feature importance analysis") |
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141 self.setup_pycaret() |
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142 self.generate_feature_importance() |
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143 html_content = self.generate_html_report() |
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144 LOG.info("Feature importance analysis completed") |
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145 return html_content |
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146 |
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147 |
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148 if __name__ == "__main__": |
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149 import argparse |
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150 parser = argparse.ArgumentParser(description="Feature Importance Analysis") |
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151 parser.add_argument( |
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152 "--data_path", type=str, help="Path to the dataset") |
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153 parser.add_argument( |
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154 "--target_col", type=int, |
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155 help="Index of the target column (1-based)") |
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156 parser.add_argument( |
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157 "--task_type", type=str, |
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158 choices=["classification", "regression"], |
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159 help="Task type: classification or regression") |
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160 parser.add_argument( |
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161 "--output_dir", |
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162 type=str, |
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163 help="Directory to save the outputs") |
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164 args = parser.parse_args() |
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165 |
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166 analyzer = FeatureImportanceAnalyzer( |
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167 args.data_path, args.target_col, |
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168 args.task_type, args.output_dir) |
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169 analyzer.run() |