Mercurial > repos > goeckslab > pycaret_predict
annotate feature_importance.py @ 8:1aed7d47c5ec draft default tip
planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
author | goeckslab |
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date | Fri, 25 Jul 2025 19:02:32 +0000 |
parents | f4cb41f458fd |
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rev | line source |
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1f20fe57fdee
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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1 import base64 |
1f20fe57fdee
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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2 import logging |
1f20fe57fdee
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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3 import os |
1f20fe57fdee
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
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4 |
1f20fe57fdee
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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5 import matplotlib.pyplot as plt |
1f20fe57fdee
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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6 import pandas as pd |
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a32ff7201629
planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
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7 import shap |
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1f20fe57fdee
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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8 from pycaret.classification import ClassificationExperiment |
1f20fe57fdee
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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9 from pycaret.regression import RegressionExperiment |
1f20fe57fdee
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
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10 |
1f20fe57fdee
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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11 logging.basicConfig(level=logging.DEBUG) |
1f20fe57fdee
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
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12 LOG = logging.getLogger(__name__) |
1f20fe57fdee
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
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13 |
1f20fe57fdee
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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14 |
1f20fe57fdee
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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15 class FeatureImportanceAnalyzer: |
1f20fe57fdee
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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16 def __init__( |
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1aed7d47c5ec
planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents:
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17 self, |
1aed7d47c5ec
planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents:
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18 task_type, |
1aed7d47c5ec
planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents:
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19 output_dir, |
1aed7d47c5ec
planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents:
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20 data_path=None, |
1aed7d47c5ec
planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents:
7
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21 data=None, |
1aed7d47c5ec
planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents:
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22 target_col=None, |
1aed7d47c5ec
planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents:
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23 exp=None, |
1aed7d47c5ec
planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents:
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24 best_model=None, |
1aed7d47c5ec
planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents:
7
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25 ): |
0
1f20fe57fdee
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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26 |
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a32ff7201629
planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
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27 self.task_type = task_type |
a32ff7201629
planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
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28 self.output_dir = output_dir |
a32ff7201629
planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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parents:
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29 self.exp = exp |
a32ff7201629
planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
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30 self.best_model = best_model |
a32ff7201629
planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
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31 |
a32ff7201629
planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
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32 if exp is not None: |
a32ff7201629
planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
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33 # Assume all configs (data, target) are in exp |
a32ff7201629
planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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parents:
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34 self.data = exp.dataset.copy() |
a32ff7201629
planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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parents:
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35 self.target = exp.target_param |
a32ff7201629
planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
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36 LOG.info("Using provided experiment object") |
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1f20fe57fdee
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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37 else: |
6
a32ff7201629
planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
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38 if data is not None: |
a32ff7201629
planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
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39 self.data = data |
a32ff7201629
planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
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40 LOG.info("Data loaded from memory") |
a32ff7201629
planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
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41 else: |
a32ff7201629
planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
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42 self.target_col = target_col |
a32ff7201629
planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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43 self.data = pd.read_csv(data_path, sep=None, engine='python') |
a32ff7201629
planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
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44 self.data.columns = self.data.columns.str.replace('.', '_') |
a32ff7201629
planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
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45 self.data = self.data.fillna(self.data.median(numeric_only=True)) |
a32ff7201629
planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
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46 self.target = self.data.columns[int(target_col) - 1] |
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1aed7d47c5ec
planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents:
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47 self.exp = ( |
1aed7d47c5ec
planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents:
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48 ClassificationExperiment() |
1aed7d47c5ec
planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents:
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49 if task_type == "classification" |
1aed7d47c5ec
planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents:
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50 else RegressionExperiment() |
1aed7d47c5ec
planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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parents:
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51 ) |
6
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planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
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52 |
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planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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parents:
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53 self.plots = {} |
1f20fe57fdee
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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54 |
1f20fe57fdee
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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55 def setup_pycaret(self): |
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planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
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56 if self.exp is not None and hasattr(self.exp, 'is_setup') and self.exp.is_setup: |
a32ff7201629
planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
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57 LOG.info("Experiment already set up. Skipping PyCaret setup.") |
a32ff7201629
planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
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58 return |
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1f20fe57fdee
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
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59 LOG.info("Initializing PyCaret") |
1f20fe57fdee
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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60 setup_params = { |
1f20fe57fdee
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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61 'target': self.target, |
1f20fe57fdee
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
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62 'session_id': 123, |
1f20fe57fdee
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
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63 'html': True, |
1f20fe57fdee
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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64 'log_experiment': False, |
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1aed7d47c5ec
planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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65 'system_log': False, |
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1f20fe57fdee
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
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66 } |
1f20fe57fdee
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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67 self.exp.setup(self.data, **setup_params) |
1f20fe57fdee
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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68 |
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planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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parents:
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69 def save_tree_importance(self): |
a32ff7201629
planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
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70 model = self.best_model or self.exp.get_config('best_model') |
a32ff7201629
planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
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71 processed_features = self.exp.get_config('X_transformed').columns |
a32ff7201629
planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
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72 |
a32ff7201629
planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
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73 # Try feature_importances_ or coef_ if available |
a32ff7201629
planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
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74 importances = None |
a32ff7201629
planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
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75 model_type = model.__class__.__name__ |
a32ff7201629
planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
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76 self.tree_model_name = model_type # Store the model name for reporting |
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planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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77 |
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planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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78 if hasattr(model, 'feature_importances_'): |
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planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
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79 importances = model.feature_importances_ |
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1aed7d47c5ec
planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents:
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80 elif hasattr(model, 'coef_'): |
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a32ff7201629
planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
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81 # For linear models, flatten coef_ and take abs (importance as magnitude) |
a32ff7201629
planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
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82 importances = abs(model.coef_).flatten() |
a32ff7201629
planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
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83 else: |
a32ff7201629
planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
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84 # Neither attribute exists; skip the plot |
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planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents:
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85 LOG.warning( |
1aed7d47c5ec
planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents:
7
diff
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86 f"Model {model_type} does not have feature_importances_ or coef_ attribute. Skipping feature importance plot." |
1aed7d47c5ec
planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents:
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87 ) |
6
a32ff7201629
planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
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88 self.tree_model_name = None # No plot generated |
a32ff7201629
planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
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89 return |
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90 |
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91 # Defensive: handle mismatch in number of features |
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92 if len(importances) != len(processed_features): |
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93 LOG.warning( |
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94 f"Number of importances ({len(importances)}) does not match number of features ({len(processed_features)}). Skipping plot." |
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95 ) |
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96 self.tree_model_name = None |
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97 return |
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98 |
8
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99 feature_importances = pd.DataFrame( |
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100 {'Feature': processed_features, 'Importance': importances} |
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101 ).sort_values(by='Importance', ascending=False) |
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102 plt.figure(figsize=(10, 6)) |
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103 plt.barh(feature_importances['Feature'], feature_importances['Importance']) |
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104 plt.xlabel('Importance') |
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105 plt.title(f'Feature Importance ({model_type})') |
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106 plot_path = os.path.join(self.output_dir, 'tree_importance.png') |
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107 plt.savefig(plot_path) |
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108 plt.close() |
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109 self.plots['tree_importance'] = plot_path |
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110 |
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111 def save_shap_values(self): |
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112 |
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113 model = self.best_model or self.exp.get_config("best_model") |
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114 |
8
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115 X_data = None |
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116 for key in ("X_test_transformed", "X_train_transformed"): |
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117 try: |
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118 X_data = self.exp.get_config(key) |
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119 break |
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120 except KeyError: |
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121 continue |
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122 if X_data is None: |
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123 raise RuntimeError( |
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124 "Could not find 'X_test_transformed' or 'X_train_transformed' in the experiment. " |
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125 "Make sure PyCaret setup/compare_models was run with feature_selection=True." |
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126 ) |
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127 |
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128 try: |
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129 used_features = model.booster_.feature_name() |
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130 except Exception: |
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131 used_features = getattr(model, "feature_names_in_", X_data.columns.tolist()) |
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132 X_data = X_data[used_features] |
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133 |
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134 max_bg = min(len(X_data), 100) |
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135 bg = X_data.sample(max_bg, random_state=42) |
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136 |
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137 predict_fn = model.predict_proba if hasattr(model, "predict_proba") else model.predict |
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138 |
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139 explainer = shap.Explainer(predict_fn, bg) |
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140 self.shap_model_name = explainer.__class__.__name__ |
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141 |
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142 shap_values = explainer(X_data) |
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143 |
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144 output_names = getattr(shap_values, "output_names", None) |
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145 if output_names is None and hasattr(model, "classes_"): |
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146 output_names = list(model.classes_) |
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147 if output_names is None: |
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148 n_out = shap_values.values.shape[-1] |
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149 output_names = list(map(str, range(n_out))) |
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150 |
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151 values = shap_values.values |
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152 if values.ndim == 3: |
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153 for j, name in enumerate(output_names): |
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154 safe = name.replace(" ", "_").replace("/", "_") |
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155 out_path = os.path.join(self.output_dir, f"shap_summary_{safe}.png") |
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156 plt.figure() |
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157 shap.plots.beeswarm(shap_values[..., j], show=False) |
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158 plt.title(f"SHAP for {model.__class__.__name__} ⇒ {name}") |
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159 plt.savefig(out_path) |
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160 plt.close() |
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161 self.plots[f"shap_summary_{safe}"] = out_path |
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162 else: |
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163 plt.figure() |
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164 shap.plots.beeswarm(shap_values, show=False) |
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165 plt.title(f"SHAP Summary for {model.__class__.__name__}") |
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166 out_path = os.path.join(self.output_dir, "shap_summary.png") |
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167 plt.savefig(out_path) |
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168 plt.close() |
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169 self.plots["shap_summary"] = out_path |
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170 |
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171 def generate_html_report(self): |
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172 LOG.info("Generating HTML report") |
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173 |
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174 plots_html = "" |
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175 for plot_name, plot_path in self.plots.items(): |
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176 # Special handling for tree importance: skip if no model name (not generated) |
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177 if plot_name == 'tree_importance' and not getattr( |
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178 self, 'tree_model_name', None |
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179 ): |
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180 continue |
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181 encoded_image = self.encode_image_to_base64(plot_path) |
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182 if plot_name == 'tree_importance' and getattr( |
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183 self, 'tree_model_name', None |
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184 ): |
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185 section_title = ( |
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186 f"Feature importance analysis from a trained {self.tree_model_name}" |
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187 ) |
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188 elif plot_name == 'shap_summary': |
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189 section_title = f"SHAP Summary from a trained {getattr(self, 'shap_model_name', 'model')}" |
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190 else: |
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191 section_title = plot_name |
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192 plots_html += f""" |
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193 <div class="plot" id="{plot_name}"> |
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194 <h2>{section_title}</h2> |
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195 <img src="data:image/png;base64,{encoded_image}" alt="{plot_name}"> |
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196 </div> |
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197 """ |
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198 |
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199 html_content = f""" |
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200 {plots_html} |
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201 """ |
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202 |
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203 return html_content |
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204 |
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205 def encode_image_to_base64(self, img_path): |
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206 with open(img_path, 'rb') as img_file: |
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207 return base64.b64encode(img_file.read()).decode('utf-8') |
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208 |
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209 def run(self): |
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210 if ( |
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211 self.exp is None |
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212 or not hasattr(self.exp, 'is_setup') |
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213 or not self.exp.is_setup |
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214 ): |
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215 self.setup_pycaret() |
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216 self.save_tree_importance() |
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217 self.save_shap_values() |
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218 html_content = self.generate_html_report() |
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219 return html_content |