Mercurial > repos > goeckslab > pycaret_predict

annotate base_model_trainer.py @ 10:e2a6fed32d54 draft default tip

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planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
author goeckslab
date Fri, 01 Aug 2025 14:02:26 +0000
parents c6c1f8777aae
children
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1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
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1 import base64
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
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2 import logging
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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3 import tempfile
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4 from pathlib import Path
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6 import h5py
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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7 import joblib
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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8 import numpy as np
1f20fe57fdee 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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10 from feature_help_modal import get_feature_metrics_help_modal
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11 from feature_importance import FeatureImportanceAnalyzer
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12 from sklearn.metrics import average_precision_score
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13 from utils import (
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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14 add_hr_to_html,
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15 add_plot_to_html,
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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16 build_tabbed_html,
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17 encode_image_to_base64,
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18 get_html_closing,
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19 get_html_template,
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20 )
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1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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22 logging.basicConfig(level=logging.DEBUG)
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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23 LOG = logging.getLogger(__name__)
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1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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26 class BaseModelTrainer:
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27 def __init__(
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28 self,
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29 input_file,
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30 target_col,
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31 output_dir,
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32 task_type,
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33 random_seed,
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34 test_file=None,
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35 **kwargs,
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36 ):
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37 self.exp = None
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1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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38 self.input_file = input_file
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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39 self.target_col = target_col
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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40 self.output_dir = output_dir
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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41 self.task_type = task_type
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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42 self.random_seed = random_seed
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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43 self.data = None
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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44 self.target = None
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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45 self.best_model = None
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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46 self.results = None
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47 self.tuning_results = None
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48 self.features_name = None
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49 self.plots = {}
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50 self.explainer_plots = {}
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51 self.plots_explainer_html = None
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52 self.trees = []
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53 self.user_kwargs = kwargs.copy()
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54 for key, value in self.user_kwargs.items():
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55 setattr(self, key, value)
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56 self.setup_params = {}
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57 self.test_file = test_file
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58 self.test_data = None
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59
6
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60 if not self.output_dir:
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61 raise ValueError(
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62 "output_dir must be specified and not None"
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63 )
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64
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65 # Warn about irrelevant kwargs for the task type
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66 if self.task_type == "regression" and (
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67 "probability_threshold" in self.user_kwargs
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68 ):
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69 LOG.warning(
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70 "probability_threshold is ignored for regression tasks."
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71 )
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72
0
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73 LOG.info(f"Model kwargs: {self.__dict__}")
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74
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75 def load_data(self):
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76 LOG.info(f"Loading data from {self.input_file}")
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77 self.data = pd.read_csv(
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
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78 self.input_file, sep=None, engine="python"
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79 )
6
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80 self.data.columns = self.data.columns.str.replace(".", "_")
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81
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82 names = self.data.columns.to_list()
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83 LOG.info(f"Original dataset columns: {names}")
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84
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85 target_index = int(self.target_col) - 1
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86 num_cols = len(names)
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87 if target_index < 0 or target_index >= num_cols:
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88 raise ValueError(
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89 f"Target column number {self.target_col} is invalid. "
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90 f"Please select a number between 1 and {num_cols}."
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91 )
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92
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93 self.target = names[target_index]
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94
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95 # Conditional drop: only if 'prediction_label' exists and is not
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96 # the target
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
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97 if "prediction_label" in self.data.columns and (
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98 self.data.columns[target_index] != "prediction_label"
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
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99 ):
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100 LOG.info(
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101 "Dropping 'prediction_label' column as it's not the target."
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102 )
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103 self.data = self.data.drop(columns=["prediction_label"])
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104 else:
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105 if self.target == "prediction_label":
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106 LOG.warning(
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107 "Using 'prediction_label' as target column. "
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108 "This may not be intended if it's a previous prediction."
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109 )
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110
10
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111 numeric_cols = self.data.select_dtypes(
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112 include=["number"]
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113 ).columns
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114 non_numeric_cols = self.data.select_dtypes(
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115 exclude=["number"]
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116 ).columns
0
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117 self.data[numeric_cols] = self.data[numeric_cols].apply(
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118 pd.to_numeric, errors="coerce"
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119 )
0
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120 if len(non_numeric_cols) > 0:
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121 LOG.info(
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122 f"Non-numeric columns found: {non_numeric_cols.tolist()}"
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123 )
0
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124
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125 # Update names after possible drop
0
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126 names = self.data.columns.to_list()
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127 LOG.info(f"Dataset columns after processing: {names}")
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128
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129 self.features_name = [n for n in names if n != self.target]
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130
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131 if getattr(self, "missing_value_strategy", None):
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diff changeset
132 strat = self.missing_value_strategy
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133 if strat == "mean":
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134 self.data = self.data.fillna(
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135 self.data.mean(numeric_only=True)
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136 )
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137 elif strat == "median":
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138 self.data = self.data.fillna(
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139 self.data.median(numeric_only=True)
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140 )
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141 elif strat == "drop":
0
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142 self.data = self.data.dropna()
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143 else:
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144 self.data = self.data.fillna(
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145 self.data.median(numeric_only=True)
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146 )
0
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147
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148 if self.test_file:
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149 LOG.info(f"Loading test data from {self.test_file}")
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150 df_test = pd.read_csv(
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151 self.test_file, sep=None, engine="python"
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152 )
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153 df_test.columns = df_test.columns.str.replace(".", "_")
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154 self.test_data = df_test
0
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155
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156 def setup_pycaret(self):
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157 LOG.info("Initializing PyCaret")
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158 self.setup_params = {
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159 "target": self.target,
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160 "session_id": self.random_seed,
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161 "html": True,
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162 "log_experiment": False,
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163 "system_log": False,
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164 "index": False,
0
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165 }
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166 if self.test_data is not None:
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167 self.setup_params["test_data"] = self.test_data
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168 for attr in [
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169 "train_size",
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170 "normalize",
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171 "feature_selection",
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172 "remove_outliers",
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173 "remove_multicollinearity",
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174 "polynomial_features",
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175 "feature_interaction",
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176 "feature_ratio",
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177 "fix_imbalance",
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178 ]:
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179 val = getattr(self, attr, None)
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180 if val is not None:
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181 self.setup_params[attr] = val
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182 if getattr(self, "cross_validation_folds", None) is not None:
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183 self.setup_params["fold"] = self.cross_validation_folds
0
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184 LOG.info(self.setup_params)
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185
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186 if self.task_type == "classification":
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187 from pycaret.classification import ClassificationExperiment
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188
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189 self.exp = ClassificationExperiment()
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190 elif self.task_type == "regression":
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191 from pycaret.regression import RegressionExperiment
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192
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193 self.exp = RegressionExperiment()
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194 else:
10
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195 raise ValueError(
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196 "task_type must be 'classification' or 'regression'"
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197 )
6
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198
0
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199 self.exp.setup(self.data, **self.setup_params)
8
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200 self.setup_params.update(self.user_kwargs)
0
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201
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202 def train_model(self):
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203 LOG.info("Training and selecting the best model")
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204 if self.task_type == "classification":
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205 self.exp.add_metric(
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206 id="PR-AUC-Weighted",
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207 name="PR-AUC-Weighted",
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208 target="pred_proba",
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209 score_func=average_precision_score,
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210 average="weighted",
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211 )
8
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212 # Build arguments for compare_models()
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213 compare_kwargs = {}
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214 if getattr(self, "models", None):
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215 compare_kwargs["include"] = self.models
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216
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217 # Respect explicit cross-validation flag
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218 if getattr(self, "cross_validation", None) is not None:
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219 compare_kwargs["cross_validation"] = self.cross_validation
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220
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221 # Respect explicit fold count
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222 if getattr(self, "cross_validation_folds", None) is not None:
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223 compare_kwargs["fold"] = self.cross_validation_folds
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224
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225 LOG.info(f"compare_models kwargs: {compare_kwargs}")
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226 self.best_model = self.exp.compare_models(**compare_kwargs)
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227 self.results = self.exp.pull()
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228 if getattr(self, "tune_model", False):
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229 LOG.info("Tuning hyperparameters of the best model")
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230 self.best_model = self.exp.tune_model(self.best_model)
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231 self.tuning_results = self.exp.pull()
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232
0
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233 if self.task_type == "classification":
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234 self.results.rename(columns={"AUC": "ROC-AUC"}, inplace=True)
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235
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236 prob_thresh = getattr(self, "probability_threshold", None)
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237 if self.task_type == "classification" and (
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238 prob_thresh is not None
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239 ):
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240 _ = self.exp.predict_model(
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241 self.best_model, probability_threshold=prob_thresh
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242 )
9
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243 else:
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244 _ = self.exp.predict_model(self.best_model)
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245
0
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246 self.test_result_df = self.exp.pull()
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247 if self.task_type == "classification":
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248 self.test_result_df.rename(
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249 columns={"AUC": "ROC-AUC"}, inplace=True
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250 )
0
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251
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252 def save_model(self):
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253 hdf5_path = Path(self.output_dir) / "pycaret_model.h5"
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254 with h5py.File(hdf5_path, "w") as f:
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255 with tempfile.NamedTemporaryFile(delete=False) as tmp:
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256 joblib.dump(self.best_model, tmp.name)
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257 tmp.seek(0)
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258 model_bytes = tmp.read()
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259 f.create_dataset("model", data=np.void(model_bytes))
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260
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261 def generate_plots(self):
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262 LOG.info("Generating PyCaret diagnostic pltos")
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263
10
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264 # choose the right plots based on task type
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265 if self.task_type == "classification":
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266 plot_names = [
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267 "learning",
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268 "vc",
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269 "calibration",
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270 "dimension",
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diff changeset
271 "manifold",
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272 "rfe",
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273 "threshold",
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274 "percentage_above_below",
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275 "class_report",
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276 "pr_auc",
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277 "roc_auc",
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diff changeset
278 ]
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279 else:
10
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280 plot_names = ["residuals", "vc", "parameter", "error",
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281 "learning"]
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diff changeset
282 for name in plot_names:
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283 try:
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284 ax = self.exp.plot_model(
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285 self.best_model, plot=name, save=False
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diff changeset
286 )
8
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diff changeset
287 out_path = Path(self.output_dir) / f"plot_{name}.png"
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diff changeset
288 fig = ax.get_figure()
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diff changeset
289 fig.savefig(out_path, bbox_inches="tight")
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diff changeset
290 self.plots[name] = str(out_path)
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diff changeset
291 except Exception as e:
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diff changeset
292 LOG.warning(f"Could not generate {name} plot: {e}")
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diff changeset
293
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294 def encode_image_to_base64(self, img_path: str) -> str:
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295 with open(img_path, "rb") as img_file:
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296 return base64.b64encode(img_file.read()).decode("utf-8")
0
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297
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298 def save_html_report(self):
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299 LOG.info("Saving HTML report")
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300
8
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diff changeset
301 # 1) Determine best model name
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302 try:
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303 best_model_name = str(self.results.iloc[0]["Model"])
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304 except Exception:
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305 best_model_name = type(self.best_model).__name__
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306 LOG.info(f"Best model determined as: {best_model_name}")
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307
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308 # 2) Compute training sample count
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309 try:
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310 n_train = self.exp.X_train.shape[0]
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311 except Exception:
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312 n_train = getattr(
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313 self.exp, "X_train_transformed", pd.DataFrame()
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314 ).shape[0]
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315 total_rows = self.data.shape[0]
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316
8
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317 # 3) Build setup parameters table
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318 all_params = self.setup_params.copy()
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319 if self.task_type == "classification" and (
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320 hasattr(self, "probability_threshold")
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321 ):
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322 all_params["probability_threshold"] = (
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323 self.probability_threshold
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324 )
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325 display_keys = [
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326 "Target",
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327 "Session ID",
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328 "Train Size",
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329 "Normalize",
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330 "Feature Selection",
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331 "Cross Validation",
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332 "Cross Validation Folds",
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333 "Remove Outliers",
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334 "Remove Multicollinearity",
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335 "Polynomial Features",
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336 "Fix Imbalance",
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337 "Models",
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338 "Probability Threshold",
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339 ]
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340 setup_rows = []
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341 for key in display_keys:
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342 pk = key.lower().replace(" ", "_")
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343 v = all_params.get(pk)
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344 if key == "Train Size":
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345 frac = (
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346 float(v)
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347 if v is not None
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348 else (n_train / total_rows if total_rows else 0)
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349 )
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350 dv = f"{frac:.2f} ({n_train} rows)"
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351 elif key in {
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352 "Normalize",
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353 "Feature Selection",
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354 "Cross Validation",
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355 "Remove Outliers",
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356 "Remove Multicollinearity",
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357 "Polynomial Features",
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358 "Fix Imbalance",
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359 }:
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360 dv = bool(v)
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361 elif key == "Cross Validation Folds":
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362 dv = v if v is not None else "None"
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363 elif key == "Models":
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364 dv = ", ".join(map(str, v)) if isinstance(
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365 v, (list, tuple)
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366 ) else "None"
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367 elif key == "Probability Threshold":
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368 dv = f"{v:.2f}" if v is not None else "0.5"
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369 else:
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370 dv = v if v is not None else "None"
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371 setup_rows.append([key, dv])
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372 if hasattr(self.exp, "_fold_metric"):
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373 setup_rows.append(["best_model_metric", self.exp._fold_metric])
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374
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375 df_setup = pd.DataFrame(setup_rows, columns=["Parameter", "Value"])
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376 df_setup.to_csv(
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377 Path(self.output_dir) / "setup_params.csv", index=False
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378 )
8
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379
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380 # 4) Persist CSVs
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381 self.results.to_csv(
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382 Path(self.output_dir) / "comparison_results.csv",
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383 index=False
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384 )
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385 self.test_result_df.to_csv(
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386 Path(self.output_dir) / "test_results.csv", index=False
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387 )
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388 pd.DataFrame(
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389 self.best_model.get_params().items(),
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390 columns=["Parameter", "Value"]
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391 ).to_csv(Path(self.output_dir) / "best_model.csv", index=False)
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392
10
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393 if self.tuning_results is not None:
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394 self.tuning_results.to_csv(
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395 Path(self.output_dir) / "tuning_results.csv",
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396 index=False
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397 )
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398
8
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diff changeset
399 # 5) Header
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400 header = f"<h2>Best Model: {best_model_name}</h2>"
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diff changeset
401
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402 # — Validation Summary & Configuration —
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403 val_df = self.results.copy()
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404 # mapping raw plot keys to user-friendly titles
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405 plot_title_map = {
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406 "learning": "Learning Curve",
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diff changeset
407 "vc": "Validation Curve",
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diff changeset
408 "calibration": "Calibration Curve",
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diff changeset
409 "dimension": "Dimensionality Reduction",
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diff changeset
410 "manifold": "Manifold Learning",
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diff changeset
411 "rfe": "Recursive Feature Elimination",
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diff changeset
412 "threshold": "Threshold Plot",
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diff changeset
413 "percentage_above_below": "Percentage Above vs. Below Cutoff",
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diff changeset
414 "class_report": "Classification Report",
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415 "pr_auc": "Precision-Recall AUC",
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416 "roc_auc": "Receiver Operating Characteristic AUC",
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417 "residuals": "Residuals Distribution",
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
418 "error": "Prediction Error Distribution",
0
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419 }
10
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420 val_df.drop(
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421 columns=["TT (Ec)", "TT (Sec)"], errors="ignore", inplace=True
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422 )
8
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423 summary_html = (
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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424 header
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425 + "<h2>Train & Validation Summary</h2>"
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diff changeset
426 + '<div class="table-wrapper">'
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
427 + val_df.to_html(index=False, classes="table sortable")
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diff changeset
428 + "</div>"
10
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
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diff changeset
429 )
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
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diff changeset
430
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
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431 if self.tuning_results is not None:
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diff changeset
432 tuning_df = self.tuning_results.copy()
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diff changeset
433 tuning_df.drop(
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
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diff changeset
434 columns=["TT (Sec)"], errors="ignore", inplace=True
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diff changeset
435 )
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
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diff changeset
436 summary_html += (
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
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437 f"<h2>{best_model_name}: Tuning Summary</h2>"
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diff changeset
438 + '<div class="table-wrapper">'
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
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diff changeset
439 + tuning_df.to_html(index=False, classes="table sortable")
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
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diff changeset
440 + "</div>"
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
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diff changeset
441 )
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
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diff changeset
442
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
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443 summary_html += (
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
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444 "<h2>Setup Parameters</h2>"
8
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diff changeset
445 + '<div class="table-wrapper">'
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
446 + df_setup.to_html(index=False, classes="table sortable")
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
447 + "</div>"
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
448 # — Hyperparameters
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diff changeset
449 + "<h2>Best Model Hyperparameters</h2>"
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
450 + '<div class="table-wrapper">'
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
451 + pd.DataFrame(
10
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
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diff changeset
452 self.best_model.get_params().items(),
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
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453 columns=["Parameter", "Value"]
8
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diff changeset
454 ).to_html(index=False, classes="table sortable")
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diff changeset
455 + "</div>"
3
ccd798db5abb planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit cf47efb521b91a9cb44ae5c5ade860627f9b9030
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diff changeset
456 )
0
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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diff changeset
457
8
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
458 # choose summary plots based on task type
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
459 if self.task_type == "classification":
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
460 summary_plots = [
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
461 "learning",
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
462 "vc",
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
463 "calibration",
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
464 "dimension",
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
465 "manifold",
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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parents: 7
diff changeset
466 "rfe",
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
467 "threshold",
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
468 "percentage_above_below",
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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parents: 7
diff changeset
469 ]
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
470 else:
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
471 summary_plots = ["learning", "vc", "parameter", "residuals"]
0
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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diff changeset
472
8
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
473 for name in summary_plots:
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
474 if name in self.plots:
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
475 summary_html += "<hr>"
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
476 b64 = encode_image_to_base64(self.plots[name])
10
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
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diff changeset
477 title = plot_title_map.get(
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
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diff changeset
478 name, name.replace("_", " ").title()
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
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diff changeset
479 )
8
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
480 summary_html += (
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
481 '<div class="plot">'
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
482 f"<h2>{title}</h2>"
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
483 f'<img src="data:image/png;base64,{b64}" '
10
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
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diff changeset
484 'style="max-width:90%;max-height:600px;'
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
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diff changeset
485 'border:1px solid #ddd;"/>'
8
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
486 "</div>"
6
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
487 )
0
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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parents:
diff changeset
488
8
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
489 # — Test Summary —
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
490 test_html = (
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
491 header
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diff changeset
492 + '<div class="table-wrapper">'
10
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
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diff changeset
493 + self.test_result_df.to_html(
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
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diff changeset
494 index=False, classes="table sortable"
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
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diff changeset
495 )
8
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
496 + "</div>"
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
497 )
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
498 if self.task_type == "regression":
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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parents: 7
diff changeset
499 try:
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
500 y_true = (
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
501 pd.Series(self.exp.y_test_transformed)
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
502 .reset_index(drop=True)
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
503 .rename("True")
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
504 )
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
505 y_pred = pd.Series(
10
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
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diff changeset
506 self.best_model.predict(
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
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diff changeset
507 self.exp.X_test_transformed
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
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diff changeset
508 )
8
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
509 ).rename("Predicted")
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
510 df_tp = pd.concat([y_true, y_pred], axis=1)
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
511 test_html += "<h2>True vs Predicted Values</h2>"
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
512 test_html += (
10
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
513 '<div class="table-wrapper" '
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
514 'style="max-height:400px; overflow-y:auto;">'
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
515 + df_tp.head(50).to_html(
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
516 index=False, classes="table sortable"
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
517 )
8
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
518 + "</div>"
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
519 + add_hr_to_html()
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
520 )
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
521 except Exception as e:
10
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
522 LOG.warning(
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
523 f"Could not generate True vs Predicted table: {e}"
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
524 )
8
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
525
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
526 # 5a) Explainer-substituted plots in order
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
527 if self.task_type == "regression":
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
528 test_order = ["residuals"]
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
529 else:
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
530 test_order = [
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
531 "confusion_matrix",
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
532 "roc_auc",
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
533 "pr_auc",
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
534 "lift_curve",
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
535 "threshold",
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
536 "cumulative_precision",
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
537 ]
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
538 for key in test_order:
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
539 fig_or_fn = self.explainer_plots.pop(key, None)
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
540 if fig_or_fn is not None:
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
541 fig = fig_or_fn() if callable(fig_or_fn) else fig_or_fn
10
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
542 title = plot_title_map.get(
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
543 key, key.replace("_", " ").title()
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
544 )
8
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
545 test_html += (
10
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
546 f"<h2>{title}</h2>" + add_plot_to_html(fig)
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
547 + add_hr_to_html()
8
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
548 )
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
549 # 5b) Remaining PyCaret test plots
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
550 for name, path in self.plots.items():
10
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
551 # classification: include only the small extras, before
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
552 # skipping anything
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
553 if self.task_type == "classification" and (
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
554 name in {
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
555 "threshold",
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
556 "pr_auc",
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
557 "class_report",
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
558 }
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
559 ):
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
560 title = plot_title_map.get(
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
561 name, name.replace("_", " ").title()
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
562 )
8
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
563 b64 = encode_image_to_base64(path)
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
564 test_html += (
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
565 f"<h2>{title}</h2>"
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
566 "<div class='plot'>"
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
567 f"<img src='data:image/png;base64,{b64}' "
10
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
568 "style='max-width:90%;max-height:600px;"
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
569 "border:1px solid #ddd;'/>"
8
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
570 "</div>" + add_hr_to_html()
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
571 )
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
572 continue
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
573
10
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
574 # regression: explicitly include the 'error' plot,
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
575 # before skipping
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
576 if self.task_type == "regression" and (
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
577 name == "error"
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
578 ):
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
579 title = plot_title_map.get(
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
580 "error", "Prediction Error Distribution"
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
581 )
8
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
582 b64 = encode_image_to_base64(path)
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
583 test_html += (
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
584 f"<h2>{title}</h2>"
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
585 "<div class='plot'>"
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
586 f"<img src='data:image/png;base64,{b64}' "
10
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
587 "style='max-width:90%;max-height:600px;"
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
588 "border:1px solid #ddd;'/>"
8
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
589 "</div>" + add_hr_to_html()
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
590 )
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
591 continue
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
592
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
593 # now skip any plots already rendered via test_order
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
594 if name in test_order:
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
595 continue
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
596
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
597 # — Feature Importance —
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
598 feature_html = header
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
599
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
600 # 6a) PyCaret’s default feature importances
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
601 feature_html += FeatureImportanceAnalyzer(
0
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
602 data=self.data,
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
603 target_col=self.target_col,
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
604 task_type=self.task_type,
3
ccd798db5abb planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit cf47efb521b91a9cb44ae5c5ade860627f9b9030
goeckslab
parents: 2
diff changeset
605 output_dir=self.output_dir,
6
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 3
diff changeset
606 exp=self.exp,
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 3
diff changeset
607 best_model=self.best_model,
8
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
608 ).run()
0
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
609
8
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
610 # 6b) Explainer SHAP importances
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
611 for key in ["shap_mean", "shap_perm"]:
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
612 fig_or_fn = self.explainer_plots.pop(key, None)
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
613 if fig_or_fn is not None:
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
614 fig = fig_or_fn() if callable(fig_or_fn) else fig_or_fn
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
615 # give SHAP plots explicit titles
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
616 title = (
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
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diff changeset
617 "Mean Absolute SHAP Value Impact"
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
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diff changeset
618 if key == "shap_mean"
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
619 else "Permutation Feature Importance"
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
620 )
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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parents: 7
diff changeset
621 feature_html += (
10
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
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diff changeset
622 f"<h2>{title}</h2>" + add_plot_to_html(fig)
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
623 + add_hr_to_html()
8
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
624 )
6
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 3
diff changeset
625
8
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
626 # 6c) PDPs last
10
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
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diff changeset
627 pdp_keys = sorted(
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
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diff changeset
628 k for k in self.explainer_plots if k.startswith("pdp__")
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
629 )
8
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
630 for k in pdp_keys:
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
631 fig_or_fn = self.explainer_plots[k]
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
632 fig = fig_or_fn() if callable(fig_or_fn) else fig_or_fn
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
633 # extract feature name
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
634 feature = k.split("__", 1)[1]
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
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diff changeset
635 title = f"Partial Dependence for {feature}"
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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parents: 7
diff changeset
636 feature_html += (
10
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
637 f"<h2>{title}</h2>" + add_plot_to_html(fig)
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
638 + add_hr_to_html()
6
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 3
diff changeset
639 )
8
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
640 # 7) Assemble final HTML (three tabs)
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
641 html = get_html_template()
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
642 html += "<h1>Tabular Learner Model Report</h1>"
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
643 html += build_tabbed_html(summary_html, test_html, feature_html)
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
644 html += get_feature_metrics_help_modal()
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
645 html += get_html_closing()
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
646
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
647 # 8) Write out
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
648 (Path(self.output_dir) / "comparison_result.html").write_text(
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
649 html, encoding="utf-8"
6
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 3
diff changeset
650 )
10
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
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diff changeset
651 LOG.info(
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
652 f"HTML report generated at: "
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
653 f"{self.output_dir}/comparison_result.html"
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
654 )
0
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
655
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
656 def save_dashboard(self):
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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parents:
diff changeset
657 raise NotImplementedError("Subclasses should implement this method")
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
658
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
659 def generate_plots_explainer(self):
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
660 raise NotImplementedError("Subclasses should implement this method")
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
661
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
662 def generate_tree_plots(self):
10
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
663 from sklearn.ensemble import (
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
664 RandomForestClassifier, RandomForestRegressor
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
665 )
0
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
666 from xgboost import XGBClassifier, XGBRegressor
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
667 from explainerdashboard.explainers import RandomForestExplainer
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
668
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
669 LOG.info("Generating tree plots")
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
670 X_test = self.exp.X_test_transformed.copy()
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
671 y_test = self.exp.y_test_transformed
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
672
10
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
673 if isinstance(
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
674 self.best_model, (RandomForestClassifier, RandomForestRegressor)
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
675 ):
8
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
676 n_trees = self.best_model.n_estimators
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
677 elif isinstance(self.best_model, (XGBClassifier, XGBRegressor)):
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
678 n_trees = len(self.best_model.get_booster().get_dump())
6
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 3
diff changeset
679 else:
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 3
diff changeset
680 LOG.warning("Tree plots not supported for this model type.")
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 3
diff changeset
681 return
0
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
682
8
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
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diff changeset
683 explainer = RandomForestExplainer(self.best_model, X_test, y_test)
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
684 for i in range(n_trees):
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
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diff changeset
685 fig = explainer.decisiontree_encoded(tree_idx=i, index=0)
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
686 self.trees.append(fig)
0
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
687
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
688 def run(self):
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
689 self.load_data()
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
690 self.setup_pycaret()
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
691 self.train_model()
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
692 self.save_model()
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
693 self.generate_plots()
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
694 self.generate_plots_explainer()
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
695 self.generate_tree_plots()
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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parents:
diff changeset
696 self.save_html_report()
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
697 # self.save_dashboard()