Mercurial > repos > goeckslab > pycaret_compare

annotate base_model_trainer.py @ 4:4aa511539199 draft default tip

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planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit cf47efb521b91a9cb44ae5c5ade860627f9b9030
author goeckslab
date Tue, 03 Jun 2025 19:31:16 +0000
parents 02f7746e7772
children
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915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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1 import base64
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
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2 import logging
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
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3 import os
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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4 import tempfile
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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6 import h5py
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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7 import joblib
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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8 import numpy as np
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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9 import pandas as pd
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4aa511539199 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit cf47efb521b91a9cb44ae5c5ade860627f9b9030
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10 from feature_importance import FeatureImportanceAnalyzer
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11 from sklearn.metrics import average_precision_score
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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12 from utils import get_html_closing, get_html_template
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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14 logging.basicConfig(level=logging.DEBUG)
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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15 LOG = logging.getLogger(__name__)
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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18 class BaseModelTrainer:
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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20 def __init__(
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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21 self,
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22 input_file,
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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23 target_col,
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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24 output_dir,
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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25 task_type,
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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26 random_seed,
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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27 test_file=None,
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4aa511539199 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit cf47efb521b91a9cb44ae5c5ade860627f9b9030
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28 **kwargs):
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915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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29 self.exp = None # This will be set in the subclass
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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30 self.input_file = input_file
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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31 self.target_col = target_col
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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32 self.output_dir = output_dir
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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33 self.task_type = task_type
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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34 self.random_seed = random_seed
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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35 self.data = None
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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36 self.target = None
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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37 self.best_model = None
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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38 self.results = None
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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39 self.features_name = None
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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40 self.plots = {}
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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41 self.expaliner = None
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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42 self.plots_explainer_html = None
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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43 self.trees = []
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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44 for key, value in kwargs.items():
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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45 setattr(self, key, value)
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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46 self.setup_params = {}
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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47 self.test_file = test_file
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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48 self.test_data = None
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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49
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50 LOG.info(f"Model kwargs: {self.__dict__}")
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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52 def load_data(self):
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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53 LOG.info(f"Loading data from {self.input_file}")
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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54 self.data = pd.read_csv(self.input_file, sep=None, engine='python')
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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55 self.data.columns = self.data.columns.str.replace('.', '_')
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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56
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57 numeric_cols = self.data.select_dtypes(include=['number']).columns
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58 non_numeric_cols = self.data.select_dtypes(exclude=['number']).columns
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59
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60 self.data[numeric_cols] = self.data[numeric_cols].apply(
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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61 pd.to_numeric, errors='coerce')
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62
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63 if len(non_numeric_cols) > 0:
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64 LOG.info(f"Non-numeric columns found: {non_numeric_cols.tolist()}")
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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65
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66 names = self.data.columns.to_list()
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67 target_index = int(self.target_col) - 1
0
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68 self.target = names[target_index]
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69 self.features_name = [name
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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70 for i, name in enumerate(names)
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71 if i != target_index]
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72 if hasattr(self, 'missing_value_strategy'):
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73 if self.missing_value_strategy == 'mean':
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74 self.data = self.data.fillna(
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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75 self.data.mean(numeric_only=True))
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76 elif self.missing_value_strategy == 'median':
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77 self.data = self.data.fillna(
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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78 self.data.median(numeric_only=True))
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79 elif self.missing_value_strategy == 'drop':
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80 self.data = self.data.dropna()
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81 else:
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82 # Default strategy if not specified
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83 self.data = self.data.fillna(self.data.median(numeric_only=True))
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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84
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85 if self.test_file:
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86 LOG.info(f"Loading test data from {self.test_file}")
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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87 self.test_data = pd.read_csv(
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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88 self.test_file, sep=None, engine='python')
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89 self.test_data = self.test_data[numeric_cols].apply(
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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90 pd.to_numeric, errors='coerce')
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91 self.test_data.columns = self.test_data.columns.str.replace(
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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92 '.', '_'
4
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93 )
0
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94
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95 def setup_pycaret(self):
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96 LOG.info("Initializing PyCaret")
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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97 self.setup_params = {
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
98 'target': self.target,
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
99 'session_id': self.random_seed,
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
100 'html': True,
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
101 'log_experiment': False,
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
102 'system_log': False,
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
103 'index': False,
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
104 }
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
105
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
106 if self.test_data is not None:
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
107 self.setup_params['test_data'] = self.test_data
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
108
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
109 if hasattr(self, 'train_size') and self.train_size is not None \
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
110 and self.test_data is None:
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
111 self.setup_params['train_size'] = self.train_size
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
112
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
113 if hasattr(self, 'normalize') and self.normalize is not None:
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
114 self.setup_params['normalize'] = self.normalize
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
115
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
116 if hasattr(self, 'feature_selection') and \
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
117 self.feature_selection is not None:
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
118 self.setup_params['feature_selection'] = self.feature_selection
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
119
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
120 if hasattr(self, 'cross_validation') and \
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
121 self.cross_validation is not None \
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
122 and self.cross_validation is False:
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
123 self.setup_params['cross_validation'] = self.cross_validation
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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parents:
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124
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
125 if hasattr(self, 'cross_validation') and \
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
126 self.cross_validation is not None:
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
127 if hasattr(self, 'cross_validation_folds'):
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
128 self.setup_params['fold'] = self.cross_validation_folds
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
129
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goeckslab
parents:
diff changeset
130 if hasattr(self, 'remove_outliers') and \
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
131 self.remove_outliers is not None:
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
132 self.setup_params['remove_outliers'] = self.remove_outliers
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
133
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
134 if hasattr(self, 'remove_multicollinearity') and \
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
135 self.remove_multicollinearity is not None:
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
136 self.setup_params['remove_multicollinearity'] = \
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
137 self.remove_multicollinearity
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
138
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
139 if hasattr(self, 'polynomial_features') and \
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
140 self.polynomial_features is not None:
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
141 self.setup_params['polynomial_features'] = self.polynomial_features
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
142
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
143 if hasattr(self, 'fix_imbalance') and \
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
144 self.fix_imbalance is not None:
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
145 self.setup_params['fix_imbalance'] = self.fix_imbalance
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
146
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
147 LOG.info(self.setup_params)
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
148 self.exp.setup(self.data, **self.setup_params)
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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parents:
diff changeset
149
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
150 def train_model(self):
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
151 LOG.info("Training and selecting the best model")
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
152 if self.task_type == "classification":
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
153 average_displayed = "Weighted"
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
154 self.exp.add_metric(id=f'PR-AUC-{average_displayed}',
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
155 name=f'PR-AUC-{average_displayed}',
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
156 target='pred_proba',
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
157 score_func=average_precision_score,
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
158 average='weighted'
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
159 )
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
160
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
161 if hasattr(self, 'models') and self.models is not None:
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
162 self.best_model = self.exp.compare_models(
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
163 include=self.models)
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
164 else:
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
165 self.best_model = self.exp.compare_models()
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
166 self.results = self.exp.pull()
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
167 if self.task_type == "classification":
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
168 self.results.rename(columns={'AUC': 'ROC-AUC'}, inplace=True)
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
169
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
170 _ = self.exp.predict_model(self.best_model)
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
171 self.test_result_df = self.exp.pull()
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
172 if self.task_type == "classification":
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
173 self.test_result_df.rename(
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
174 columns={'AUC': 'ROC-AUC'}, inplace=True)
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
175
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
176 def save_model(self):
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
177 hdf5_model_path = "pycaret_model.h5"
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
178 with h5py.File(hdf5_model_path, 'w') as f:
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
179 with tempfile.NamedTemporaryFile(delete=False) as temp_file:
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
180 joblib.dump(self.best_model, temp_file.name)
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
181 temp_file.seek(0)
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
182 model_bytes = temp_file.read()
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
183 f.create_dataset('model', data=np.void(model_bytes))
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
184
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
185 def generate_plots(self):
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
186 raise NotImplementedError("Subclasses should implement this method")
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
187
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
188 def encode_image_to_base64(self, img_path):
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
189 with open(img_path, 'rb') as img_file:
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
190 return base64.b64encode(img_file.read()).decode('utf-8')
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
191
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
192 def save_html_report(self):
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
193 LOG.info("Saving HTML report")
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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194
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195 model_name = type(self.best_model).__name__
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196 excluded_params = ['html', 'log_experiment', 'system_log', 'test_data']
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197 filtered_setup_params = {
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198 k: v
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199 for k, v in self.setup_params.items() if k not in excluded_params
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200 }
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201 setup_params_table = pd.DataFrame(
4
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202 list(filtered_setup_params.items()), columns=['Parameter', 'Value']
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203 )
0
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204
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205 best_model_params = pd.DataFrame(
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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206 self.best_model.get_params().items(),
4
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207 columns=['Parameter', 'Value']
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208 )
0
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209 best_model_params.to_csv(
4
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210 os.path.join(self.output_dir, "best_model.csv"), index=False
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211 )
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212 self.results.to_csv(
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213 os.path.join(self.output_dir, "comparison_results.csv")
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214 )
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215 self.test_result_df.to_csv(
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216 os.path.join(self.output_dir, "test_results.csv")
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217 )
0
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218
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219 plots_html = ""
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220 length = len(self.plots)
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221 for i, (plot_name, plot_path) in enumerate(self.plots.items()):
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222 encoded_image = self.encode_image_to_base64(plot_path)
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223 plots_html += f"""
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224 <div class="plot">
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225 <h3>{plot_name.capitalize()}</h3>
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226 <img src="data:image/png;base64,{encoded_image}"
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diff changeset
227 alt="{plot_name}">
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228 </div>
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229 """
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230 if i < length - 1:
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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231 plots_html += "<hr>"
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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232
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233 tree_plots = ""
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234 for i, tree in enumerate(self.trees):
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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235 if tree:
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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236 tree_plots += f"""
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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diff changeset
237 <div class="plot">
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238 <h3>Tree {i+1}</h3>
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239 <img src="data:image/png;base64,
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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240 {tree}"
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241 alt="tree {i+1}">
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
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242 </div>
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diff changeset
243 """
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244
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245 analyzer = FeatureImportanceAnalyzer(
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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246 data=self.data,
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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247 target_col=self.target_col,
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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248 task_type=self.task_type,
4
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249 output_dir=self.output_dir,
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250 )
0
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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251 feature_importance_html = analyzer.run()
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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252
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253 html_content = f"""
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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254 {get_html_template()}
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255 <h1>PyCaret Model Training Report</h1>
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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256 <div class="tabs">
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257 <div class="tab" onclick="openTab(event, 'summary')">
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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diff changeset
258 Setup & Best Model</div>
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259 <div class="tab" onclick="openTab(event, 'plots')">
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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260 Best Model Plots</div>
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261 <div class="tab" onclick="openTab(event, 'feature')">
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262 Feature Importance</div>
4
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diff changeset
263 """
3
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diff changeset
264 if self.plots_explainer_html:
02f7746e7772 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit ff6d674ecc83db933153b797ef4dbde17f07b10e
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265 html_content += """
4
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266 <div class="tab" onclick="openTab(event, 'explainer')">
3
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diff changeset
267 Explainer Plots</div>
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diff changeset
268 """
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diff changeset
269 html_content += f"""
0
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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270 </div>
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271 <div id="summary" class="tab-content">
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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272 <h2>Setup Parameters</h2>
4
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273 {setup_params_table.to_html(
4aa511539199 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit cf47efb521b91a9cb44ae5c5ade860627f9b9030
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274 index=False,
4aa511539199 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit cf47efb521b91a9cb44ae5c5ade860627f9b9030
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275 header=True,
4aa511539199 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit cf47efb521b91a9cb44ae5c5ade860627f9b9030
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276 classes='table sortable'
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277 )}
0
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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278 <h5>If you want to know all the experiment setup parameters,
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
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diff changeset
279 please check the PyCaret documentation for
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280 the classification/regression <code>exp</code> function.</h5>
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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281 <h2>Best Model: {model_name}</h2>
4
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diff changeset
282 {best_model_params.to_html(
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diff changeset
283 index=False,
4aa511539199 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit cf47efb521b91a9cb44ae5c5ade860627f9b9030
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284 header=True,
4aa511539199 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit cf47efb521b91a9cb44ae5c5ade860627f9b9030
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285 classes='table sortable'
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diff changeset
286 )}
0
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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287 <h2>Comparison Results on the Cross-Validation Set</h2>
4
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288 {self.results.to_html(index=False, classes='table sortable')}
0
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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289 <h2>Results on the Test Set for the best model</h2>
4
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290 {self.test_result_df.to_html(
4aa511539199 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit cf47efb521b91a9cb44ae5c5ade860627f9b9030
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291 index=False,
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292 classes='table sortable'
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293 )}
0
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294 </div>
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295 <div id="plots" class="tab-content">
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296 <h2>Best Model Plots on the testing set</h2>
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297 {plots_html}
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298 </div>
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299 <div id="feature" class="tab-content">
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300 {feature_importance_html}
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301 </div>
3
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302 """
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303 if self.plots_explainer_html:
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304 html_content += f"""
0
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305 <div id="explainer" class="tab-content">
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306 {self.plots_explainer_html}
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307 {tree_plots}
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308 </div>
3
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309 """
4
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310 html_content += """
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311 <script>
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312 document.addEventListener("DOMContentLoaded", function() {
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313 var tables = document.querySelectorAll("table.sortable");
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314 tables.forEach(function(table) {
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315 var headers = table.querySelectorAll("th");
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316 headers.forEach(function(header, index) {
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317 header.style.cursor = "pointer";
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318 // Add initial arrow (up) to indicate sortability
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319 header.innerHTML += '<span class="sort-arrow"> ↑</span>';
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320 header.addEventListener("click", function() {
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321 var direction = this.getAttribute(
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322 "data-sort-direction"
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323 ) || "asc";
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324 // Reset arrows in all headers of this table
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325 headers.forEach(function(h) {
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326 var arrow = h.querySelector(".sort-arrow");
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327 if (arrow) arrow.textContent = " ↑";
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328 });
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329 // Set arrow for clicked header
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330 var arrow = this.querySelector(".sort-arrow");
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331 arrow.textContent = direction === "asc" ? " ↓" : " ↑";
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332 sortTable(table, index, direction);
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333 this.setAttribute("data-sort-direction",
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334 direction === "asc" ? "desc" : "asc");
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335 });
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336 });
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337 });
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338 });
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339
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340 function sortTable(table, colNum, direction) {
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341 var tb = table.tBodies[0];
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342 var tr = Array.prototype.slice.call(tb.rows, 0);
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343 var multiplier = direction === "asc" ? 1 : -1;
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344 tr = tr.sort(function(a, b) {
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345 var aText = a.cells[colNum].textContent.trim();
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346 var bText = b.cells[colNum].textContent.trim();
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347 // Remove arrow from text comparison
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348 aText = aText.replace(/[↑↓]/g, '').trim();
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349 bText = bText.replace(/[↑↓]/g, '').trim();
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350 if (!isNaN(aText) && !isNaN(bText)) {
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351 return multiplier * (
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352 parseFloat(aText) - parseFloat(bText)
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353 );
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354 } else {
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355 return multiplier * aText.localeCompare(bText);
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356 }
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357 });
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358 for (var i = 0; i < tr.length; ++i) tb.appendChild(tr[i]);
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359 }
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360 </script>
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361 """
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362 html_content += f"""
4aa511539199 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit cf47efb521b91a9cb44ae5c5ade860627f9b9030
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363 {get_html_closing()}
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364 """
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diff changeset
365 with open(
4aa511539199 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit cf47efb521b91a9cb44ae5c5ade860627f9b9030
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366 os.path.join(self.output_dir, "comparison_result.html"),
4aa511539199 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit cf47efb521b91a9cb44ae5c5ade860627f9b9030
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367 "w"
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368 ) as file:
0
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369 file.write(html_content)
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370
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371 def save_dashboard(self):
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372 raise NotImplementedError("Subclasses should implement this method")
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373
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374 def generate_plots_explainer(self):
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375 raise NotImplementedError("Subclasses should implement this method")
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376
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377 # not working now
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378 def generate_tree_plots(self):
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379 from sklearn.ensemble import RandomForestClassifier, \
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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380 RandomForestRegressor
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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381 from xgboost import XGBClassifier, XGBRegressor
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382 from explainerdashboard.explainers import RandomForestExplainer
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383
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384 LOG.info("Generating tree plots")
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385 X_test = self.exp.X_test_transformed.copy()
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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diff changeset
386 y_test = self.exp.y_test_transformed
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387
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388 is_rf = isinstance(self.best_model, RandomForestClassifier) or \
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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389 isinstance(self.best_model, RandomForestRegressor)
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diff changeset
390
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391 is_xgb = isinstance(self.best_model, XGBClassifier) or \
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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392 isinstance(self.best_model, XGBRegressor)
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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393
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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394 try:
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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395 if is_rf:
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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396 num_trees = self.best_model.n_estimators
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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397 if is_xgb:
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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398 num_trees = len(self.best_model.get_booster().get_dump())
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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399 explainer = RandomForestExplainer(self.best_model, X_test, y_test)
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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400 for i in range(num_trees):
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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401 fig = explainer.decisiontree_encoded(tree_idx=i, index=0)
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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402 LOG.info(f"Tree {i+1}")
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
403 LOG.info(fig)
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
404 self.trees.append(fig)
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
405 except Exception as e:
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
406 LOG.error(f"Error generating tree plots: {e}")
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
407
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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408 def run(self):
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
409 self.load_data()
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
410 self.setup_pycaret()
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
411 self.train_model()
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
412 self.save_model()
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
413 self.generate_plots()
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
414 self.generate_plots_explainer()
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
415 self.generate_tree_plots()
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
416 self.save_html_report()
915447b14520 planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
417 # self.save_dashboard()