Mercurial > repos > goeckslab > pycaret_predict

annotate base_model_trainer.py @ 14:7d78a6afc958 draft default tip

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planemo upload for repository https://github.com/goeckslab/gleam commit 1ffd143e57fa952ee9dd84fc141771520aea0791
author goeckslab
date Wed, 26 Nov 2025 17:49:50 +0000
parents f07850192bc2
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 (
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14 add_hr_to_html,
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15 add_plot_to_html,
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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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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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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
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45 self.best_model = None
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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(
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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
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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"
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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 )
8
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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 )
8
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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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diff changeset
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 "n_jobs",
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179 ]:
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180 val = getattr(self, attr, None)
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181 if val is not None:
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182 self.setup_params[attr] = val
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183 if getattr(self, "cross_validation_folds", None) is not None:
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184 self.setup_params["fold"] = self.cross_validation_folds
0
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185 LOG.info(self.setup_params)
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186
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187 if self.task_type == "classification":
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188 from pycaret.classification import ClassificationExperiment
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189
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190 self.exp = ClassificationExperiment()
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191 elif self.task_type == "regression":
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192 from pycaret.regression import RegressionExperiment
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193
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194 self.exp = RegressionExperiment()
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195 else:
10
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196 raise ValueError(
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197 "task_type must be 'classification' or 'regression'"
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198 )
6
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199
0
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200 self.exp.setup(self.data, **self.setup_params)
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diff changeset
201 self.setup_params.update(self.user_kwargs)
0
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202
13
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diff changeset
203 def _normalize_metric(self, m: str) -> str:
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204 if not m:
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205 return "R2" if self.task_type == "regression" else "Accuracy"
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206 m_low = str(m).strip().lower()
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207 alias = {
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208 "auc": "AUC", "roc_auc": "AUC", "roc-auc": "AUC",
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209 "accuracy": "Accuracy",
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210 "precision": "Precision",
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211 "recall": "Recall",
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212 "f1": "F1",
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213 "kappa": "Kappa",
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214 "logloss": "Log Loss", "log_loss": "Log Loss",
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215 "pr_auc": "PR-AUC-Weighted", "prauc": "PR-AUC-Weighted",
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216 "r2": "R2",
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217 "mae": "MAE",
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218 "mse": "MSE",
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219 "rmse": "RMSE",
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220 "rmsle": "RMSLE",
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221 "mape": "MAPE",
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222 }
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223 return alias.get(m_low, m)
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224
0
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225 def train_model(self):
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226 LOG.info("Training and selecting the best model")
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227 if self.task_type == "classification":
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228 self.exp.add_metric(
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229 id="PR-AUC-Weighted",
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230 name="PR-AUC-Weighted",
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231 target="pred_proba",
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232 score_func=average_precision_score,
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233 average="weighted",
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234 )
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235 # Build arguments for compare_models()
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236 compare_kwargs = {}
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237 if getattr(self, "models", None):
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238 compare_kwargs["include"] = self.models
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239
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240 # Respect explicit cross-validation flag
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241 if getattr(self, "cross_validation", None) is not None:
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242 compare_kwargs["cross_validation"] = self.cross_validation
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243
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244 # Respect explicit fold count
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245 if getattr(self, "cross_validation_folds", None) is not None:
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246 compare_kwargs["fold"] = self.cross_validation_folds
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247
13
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248 chosen_metric = self._normalize_metric(getattr(self, "best_model_metric", None))
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249 if chosen_metric:
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250 compare_kwargs["sort"] = chosen_metric
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251 self.chosen_metric_label = chosen_metric
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252 try:
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253 setattr(self.exp, "_fold_metric", chosen_metric)
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254 except Exception as e:
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255 LOG.warning(f"Failed to set '_fold_metric' to '{chosen_metric}': {e}", exc_info=True)
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256
8
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257 LOG.info(f"compare_models kwargs: {compare_kwargs}")
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258 self.best_model = self.exp.compare_models(**compare_kwargs)
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259 self.results = self.exp.pull()
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260 if getattr(self, "tune_model", False):
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261 LOG.info("Tuning hyperparameters of the best model")
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262 self.best_model = self.exp.tune_model(self.best_model)
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263 self.tuning_results = self.exp.pull()
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264
0
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265 if self.task_type == "classification":
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266 self.results.rename(columns={"AUC": "ROC-AUC"}, inplace=True)
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267
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268 prob_thresh = getattr(self, "probability_threshold", None)
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269 if self.task_type == "classification" and (
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270 prob_thresh is not None
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271 ):
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272 _ = self.exp.predict_model(
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273 self.best_model, probability_threshold=prob_thresh
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274 )
9
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275 else:
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276 _ = self.exp.predict_model(self.best_model)
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277
0
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278 self.test_result_df = self.exp.pull()
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279 if self.task_type == "classification":
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280 self.test_result_df.rename(
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281 columns={"AUC": "ROC-AUC"}, inplace=True
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282 )
0
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283
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284 def save_model(self):
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285 hdf5_path = Path(self.output_dir) / "pycaret_model.h5"
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286 with h5py.File(hdf5_path, "w") as f:
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287 with tempfile.NamedTemporaryFile(delete=False) as tmp:
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288 joblib.dump(self.best_model, tmp.name)
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289 tmp.seek(0)
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290 model_bytes = tmp.read()
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291 f.create_dataset("model", data=np.void(model_bytes))
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292
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293 def generate_plots(self):
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294 LOG.info("Generating PyCaret diagnostic pltos")
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295
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296 # choose the right plots based on task type
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297 if self.task_type == "classification":
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298 plot_names = [
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299 "learning",
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300 "vc",
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301 "calibration",
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302 "dimension",
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303 "manifold",
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diff changeset
304 "rfe",
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diff changeset
305 "threshold",
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diff changeset
306 "percentage_above_below",
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diff changeset
307 "class_report",
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diff changeset
308 "pr_auc",
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diff changeset
309 "roc_auc",
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diff changeset
310 ]
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diff changeset
311 else:
10
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312 plot_names = ["residuals", "vc", "parameter", "error",
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diff changeset
313 "learning"]
8
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diff changeset
314 for name in plot_names:
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315 try:
10
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316 ax = self.exp.plot_model(
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317 self.best_model, plot=name, save=False
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318 )
8
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319 out_path = Path(self.output_dir) / f"plot_{name}.png"
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320 fig = ax.get_figure()
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321 fig.savefig(out_path, bbox_inches="tight")
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322 self.plots[name] = str(out_path)
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323 except Exception as e:
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324 LOG.warning(f"Could not generate {name} plot: {e}")
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325
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326 def encode_image_to_base64(self, img_path: str) -> str:
6
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327 with open(img_path, "rb") as img_file:
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328 return base64.b64encode(img_file.read()).decode("utf-8")
0
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329
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330 def save_html_report(self):
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331 LOG.info("Saving HTML report")
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332
8
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333 # 1) Determine best model name
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334 try:
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335 best_model_name = str(self.results.iloc[0]["Model"])
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336 except Exception:
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337 best_model_name = type(self.best_model).__name__
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338 LOG.info(f"Best model determined as: {best_model_name}")
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339
10
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340 # 2) Compute training sample count
8
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341 try:
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342 n_train = self.exp.X_train.shape[0]
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343 except Exception:
10
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344 n_train = getattr(
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345 self.exp, "X_train_transformed", pd.DataFrame()
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346 ).shape[0]
8
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347 total_rows = self.data.shape[0]
6
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348
8
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diff changeset
349 # 3) Build setup parameters table
9
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350 all_params = self.setup_params.copy()
10
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diff changeset
351 if self.task_type == "classification" and (
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diff changeset
352 hasattr(self, "probability_threshold")
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diff changeset
353 ):
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
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diff changeset
354 all_params["probability_threshold"] = (
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
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diff changeset
355 self.probability_threshold
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diff changeset
356 )
8
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
357 display_keys = [
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diff changeset
358 "Target",
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
359 "Session ID",
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
360 "Train Size",
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
361 "Normalize",
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
362 "Feature Selection",
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
363 "Cross Validation",
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
364 "Cross Validation Folds",
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
365 "Remove Outliers",
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
366 "Remove Multicollinearity",
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
367 "Polynomial Features",
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diff changeset
368 "Fix Imbalance",
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
369 "Models",
9
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diff changeset
370 "Probability Threshold",
8
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diff changeset
371 ]
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
372 setup_rows = []
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diff changeset
373 for key in display_keys:
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diff changeset
374 pk = key.lower().replace(" ", "_")
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
375 v = all_params.get(pk)
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
376 if key == "Train Size":
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diff changeset
377 frac = (
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
378 float(v)
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
379 if v is not None
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diff changeset
380 else (n_train / total_rows if total_rows else 0)
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
381 )
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
382 dv = f"{frac:.2f} ({n_train} rows)"
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
383 elif key in {
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
384 "Normalize",
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
385 "Feature Selection",
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
386 "Cross Validation",
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
387 "Remove Outliers",
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
388 "Remove Multicollinearity",
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diff changeset
389 "Polynomial Features",
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diff changeset
390 "Fix Imbalance",
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
391 }:
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
392 dv = bool(v)
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diff changeset
393 elif key == "Cross Validation Folds":
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diff changeset
394 dv = v if v is not None else "None"
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diff changeset
395 elif key == "Models":
10
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diff changeset
396 dv = ", ".join(map(str, v)) if isinstance(
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
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diff changeset
397 v, (list, tuple)
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
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diff changeset
398 ) else "None"
9
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diff changeset
399 elif key == "Probability Threshold":
10
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diff changeset
400 dv = f"{v:.2f}" if v is not None else "0.5"
8
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diff changeset
401 else:
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diff changeset
402 dv = v if v is not None else "None"
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diff changeset
403 setup_rows.append([key, dv])
13
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diff changeset
404 if getattr(self, "chosen_metric_label", None):
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405 setup_rows.append(["Best Model Metric", self.chosen_metric_label])
8
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406
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407 df_setup = pd.DataFrame(setup_rows, columns=["Parameter", "Value"])
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408 df_setup.to_csv(
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409 Path(self.output_dir) / "setup_params.csv", index=False
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410 )
8
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411
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412 # 4) Persist CSVs
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413 self.results.to_csv(
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414 Path(self.output_dir) / "comparison_results.csv",
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415 index=False
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416 )
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417 self.test_result_df.to_csv(
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418 Path(self.output_dir) / "test_results.csv", index=False
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419 )
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420 pd.DataFrame(
10
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421 self.best_model.get_params().items(),
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422 columns=["Parameter", "Value"]
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423 ).to_csv(Path(self.output_dir) / "best_model.csv", index=False)
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424
10
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425 if self.tuning_results is not None:
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426 self.tuning_results.to_csv(
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427 Path(self.output_dir) / "tuning_results.csv",
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428 index=False
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429 )
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430
8
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431 # 5) Header
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432 header = f"<h2>Best Model: {best_model_name}</h2>"
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433
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434 # — Validation Summary & Configuration —
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435 val_df = self.results.copy()
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436 # mapping raw plot keys to user-friendly titles
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437 plot_title_map = {
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438 "learning": "Learning Curve",
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439 "vc": "Validation Curve",
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440 "calibration": "Calibration Curve",
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441 "dimension": "Dimensionality Reduction",
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442 "manifold": "Manifold Learning",
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443 "rfe": "Recursive Feature Elimination",
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444 "threshold": "Threshold Plot",
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445 "percentage_above_below": "Percentage Above vs. Below Cutoff",
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446 "class_report": "Classification Report",
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447 "pr_auc": "Precision-Recall AUC",
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448 "roc_auc": "Receiver Operating Characteristic AUC",
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449 "residuals": "Residuals Distribution",
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450 "error": "Prediction Error Distribution",
0
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451 }
10
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452 val_df.drop(
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453 columns=["TT (Ec)", "TT (Sec)"], errors="ignore", inplace=True
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454 )
8
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455 summary_html = (
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456 header
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457 + "<h2>Train & Validation Summary</h2>"
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458 + '<div class="table-wrapper">'
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459 + val_df.to_html(index=False, classes="table sortable")
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460 + "</div>"
10
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461 )
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462
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diff changeset
463 if self.tuning_results is not None:
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diff changeset
464 tuning_df = self.tuning_results.copy()
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465 tuning_df.drop(
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466 columns=["TT (Sec)"], errors="ignore", inplace=True
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467 )
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468 summary_html += (
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469 f"<h2>{best_model_name}: Tuning Summary</h2>"
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470 + '<div class="table-wrapper">'
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471 + tuning_df.to_html(index=False, classes="table sortable")
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472 + "</div>"
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473 )
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474
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475 summary_html += (
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476 "<h2>Setup Parameters</h2>"
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477 + '<div class="table-wrapper">'
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478 + df_setup.to_html(index=False, classes="table sortable")
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479 + "</div>"
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480 # — Hyperparameters
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481 + "<h2>Best Model Hyperparameters</h2>"
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482 + '<div class="table-wrapper">'
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483 + pd.DataFrame(
10
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484 self.best_model.get_params().items(),
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485 columns=["Parameter", "Value"]
8
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486 ).to_html(index=False, classes="table sortable")
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487 + "</div>"
3
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488 )
0
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489
8
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diff changeset
490 # choose summary plots based on task type
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491 if self.task_type == "classification":
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492 summary_plots = [
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493 "learning",
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diff changeset
494 "vc",
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diff changeset
495 "calibration",
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diff changeset
496 "dimension",
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diff changeset
497 "manifold",
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498 "rfe",
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diff changeset
499 "threshold",
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diff changeset
500 "percentage_above_below",
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501 ]
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diff changeset
502 else:
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503 summary_plots = ["learning", "vc", "parameter", "residuals"]
0
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504
8
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diff changeset
505 for name in summary_plots:
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diff changeset
506 if name in self.plots:
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diff changeset
507 summary_html += "<hr>"
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diff changeset
508 b64 = encode_image_to_base64(self.plots[name])
10
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
509 title = plot_title_map.get(
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
510 name, name.replace("_", " ").title()
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
511 )
8
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
512 summary_html += (
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
513 '<div class="plot">'
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
514 f"<h2>{title}</h2>"
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
515 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
516 'style="max-width:90%;max-height:600px;'
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
517 'border:1px solid #ddd;"/>'
8
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
518 "</div>"
6
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 3
diff changeset
519 )
0
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
520
8
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
521 # — Test Summary —
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
522 test_html = (
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
523 header
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
524 + '<div class="table-wrapper">'
10
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
525 + self.test_result_df.to_html(
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
526 index=False, classes="table sortable"
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
527 )
8
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
528 + "</div>"
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
529 )
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
530 if self.task_type == "regression":
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
531 try:
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
532 y_true = (
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
533 pd.Series(self.exp.y_test_transformed)
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
534 .reset_index(drop=True)
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
535 .rename("True")
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
536 )
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
537 y_pred = pd.Series(
10
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
538 self.best_model.predict(
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
539 self.exp.X_test_transformed
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
540 )
8
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
541 ).rename("Predicted")
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
542 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
543 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
544 test_html += (
10
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
545 '<div class="table-wrapper" '
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
546 'style="max-height:400px; overflow-y:auto;">'
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
547 + df_tp.head(50).to_html(
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
548 index=False, classes="table sortable"
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
549 )
8
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
550 + "</div>"
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
551 + add_hr_to_html()
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
552 )
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
553 except Exception as e:
10
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
554 LOG.warning(
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
555 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
556 )
8
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
557
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
558 # 5a) Explainer-substituted plots in order
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
559 if self.task_type == "regression":
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
560 test_order = ["residuals"]
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
561 else:
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
562 test_order = [
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
563 "confusion_matrix",
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
564 "roc_auc",
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
565 "pr_auc",
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
566 "lift_curve",
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
567 "threshold",
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
568 "cumulative_precision",
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
569 ]
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
570 for key in test_order:
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
571 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
572 if fig_or_fn is not None:
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
573 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
574 title = plot_title_map.get(
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
575 key, key.replace("_", " ").title()
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
576 )
8
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
577 test_html += (
10
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
578 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
579 + add_hr_to_html()
8
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
580 )
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
581 # 5b) Remaining PyCaret test plots
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
582 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
583 # classification: include only the small extras, before
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
584 # skipping anything
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
585 if self.task_type == "classification" and (
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
586 name in {
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
587 "threshold",
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
588 "pr_auc",
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
589 "class_report",
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
590 }
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
591 ):
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
592 title = plot_title_map.get(
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
593 name, name.replace("_", " ").title()
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
594 )
8
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
595 b64 = encode_image_to_base64(path)
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
596 test_html += (
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
597 f"<h2>{title}</h2>"
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
598 "<div class='plot'>"
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
599 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
600 "style='max-width:90%;max-height:600px;"
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
601 "border:1px solid #ddd;'/>"
8
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
602 "</div>" + add_hr_to_html()
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
603 )
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
604 continue
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
605
10
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
606 # regression: explicitly include the 'error' plot,
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
607 # before skipping
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
608 if self.task_type == "regression" and (
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
609 name == "error"
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
610 ):
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
611 title = plot_title_map.get(
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
612 "error", "Prediction Error Distribution"
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
613 )
8
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
614 b64 = encode_image_to_base64(path)
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
615 test_html += (
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
616 f"<h2>{title}</h2>"
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
617 "<div class='plot'>"
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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parents: 7
diff changeset
618 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
619 "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
620 "border:1px solid #ddd;'/>"
8
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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parents: 7
diff changeset
621 "</div>" + add_hr_to_html()
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
622 )
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
623 continue
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
624
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
625 # 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
626 if name in test_order:
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
627 continue
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
628
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
629 # — Feature Importance —
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
630 feature_html = header
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
631
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
632 # 6a) PyCaret’s default feature importances
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
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diff changeset
633 feature_html += FeatureImportanceAnalyzer(
0
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
634 data=self.data,
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
635 target_col=self.target_col,
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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parents:
diff changeset
636 task_type=self.task_type,
3
ccd798db5abb planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit cf47efb521b91a9cb44ae5c5ade860627f9b9030
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diff changeset
637 output_dir=self.output_dir,
6
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
638 exp=self.exp,
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff changeset
639 best_model=self.best_model,
8
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
640 ).run()
0
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
641
8
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
642 # 6b) Explainer SHAP importances
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
643 for key in ["shap_mean", "shap_perm"]:
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
644 fig_or_fn = self.explainer_plots.pop(key, None)
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
645 if fig_or_fn is not None:
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
646 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
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diff changeset
647 # give SHAP plots explicit titles
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
648 title = (
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
649 "Mean Absolute SHAP Value Impact"
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
650 if key == "shap_mean"
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
651 else "Permutation Feature Importance"
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
652 )
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
653 feature_html += (
10
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
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diff changeset
654 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
655 + add_hr_to_html()
8
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
656 )
6
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 3
diff changeset
657
8
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
658 # 6c) PDPs last
10
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
659 pdp_keys = sorted(
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
660 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
661 )
8
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
662 for k in pdp_keys:
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
663 fig_or_fn = self.explainer_plots[k]
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
664 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
665 # extract feature name
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
666 feature = k.split("__", 1)[1]
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
667 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
668 feature_html += (
10
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
669 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
670 + add_hr_to_html()
6
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 3
diff changeset
671 )
8
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
672 # 7) Assemble final HTML (three tabs)
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
673 html = get_html_template()
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
674 html += "<h1>Tabular Learner Model Report</h1>"
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
675 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
676 html += get_feature_metrics_help_modal()
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
677 html += get_html_closing()
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
678
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
679 # 8) Write out
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
680 (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
681 html, encoding="utf-8"
6
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 3
diff changeset
682 )
10
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
683 LOG.info(
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
684 f"HTML report generated at: "
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
685 f"{self.output_dir}/comparison_result.html"
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
parents: 9
diff changeset
686 )
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 save_dashboard(self):
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
689 raise NotImplementedError("Subclasses should implement this method")
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
690
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
691 def generate_plots_explainer(self):
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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parents:
diff changeset
692 raise NotImplementedError("Subclasses should implement this method")
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
693
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
694 def generate_tree_plots(self):
10
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
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diff changeset
695 from sklearn.ensemble import (
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
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diff changeset
696 RandomForestClassifier, RandomForestRegressor
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
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diff changeset
697 )
0
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
698 from xgboost import XGBClassifier, XGBRegressor
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
699 from explainerdashboard.explainers import RandomForestExplainer
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
700
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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parents:
diff changeset
701 LOG.info("Generating tree plots")
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
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parents:
diff changeset
702 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
703 y_test = self.exp.y_test_transformed
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
704
10
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
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parents: 9
diff changeset
705 if isinstance(
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
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diff changeset
706 self.best_model, (RandomForestClassifier, RandomForestRegressor)
e2a6fed32d54 planemo upload for repository https://github.com/goeckslab/gleam commit 47a5977e074223e92e216efa42969a4056516707
goeckslab
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diff changeset
707 ):
8
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
708 n_trees = self.best_model.n_estimators
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
709 elif isinstance(self.best_model, (XGBClassifier, XGBRegressor)):
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
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diff changeset
710 n_trees = len(self.best_model.get_booster().get_dump())
6
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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parents: 3
diff changeset
711 else:
a32ff7201629 planemo upload for repository https://github.com/goeckslab/gleam commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents: 3
diff changeset
712 LOG.warning("Tree plots not supported for this model type.")
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diff changeset
713 return
0
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
714
8
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
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diff changeset
715 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
716 for i in range(n_trees):
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 7
diff changeset
717 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
718 self.trees.append(fig)
0
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
719
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
720 def run(self):
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
721 self.load_data()
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
722 self.setup_pycaret()
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
723 self.train_model()
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
724 self.save_model()
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
725 self.generate_plots()
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
726 self.generate_plots_explainer()
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
727 self.generate_tree_plots()
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
728 self.save_html_report()
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
729 # self.save_dashboard()