annotate pycaret_classification.py @ 8:1aed7d47c5ec draft default tip

planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
author goeckslab
date Fri, 25 Jul 2025 19:02:32 +0000
parents ccd798db5abb
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
1 import logging
8
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
2 import types
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
3 from typing import Dict
0
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
4
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
5 from base_model_trainer import BaseModelTrainer
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
6 from dashboard import generate_classifier_explainer_dashboard
8
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
7 from plotly.graph_objects import Figure
0
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
8 from pycaret.classification import ClassificationExperiment
8
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
9 from utils import predict_proba
0
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
10
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
11 LOG = logging.getLogger(__name__)
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
12
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
13
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
14 class ClassificationModelTrainer(BaseModelTrainer):
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
15 def __init__(
8
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
16 self,
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
17 input_file,
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
18 target_col,
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
19 output_dir,
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
20 task_type,
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
21 random_seed,
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
22 test_file=None,
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
23 **kwargs,
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
24 ):
0
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
25 super().__init__(
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
26 input_file,
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
27 target_col,
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
28 output_dir,
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
29 task_type,
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
30 random_seed,
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
31 test_file,
8
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
32 **kwargs,
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
33 )
0
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
34 self.exp = ClassificationExperiment()
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
35
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
36 def save_dashboard(self):
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
37 LOG.info("Saving explainer dashboard")
8
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
38 dashboard = generate_classifier_explainer_dashboard(self.exp, self.best_model)
0
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
39 dashboard.save_html("dashboard.html")
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
40
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
41 def generate_plots(self):
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
42 LOG.info("Generating and saving plots")
2
0314dad38aaa planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit ff6d674ecc83db933153b797ef4dbde17f07b10e
goeckslab
parents: 0
diff changeset
43
0314dad38aaa planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit ff6d674ecc83db933153b797ef4dbde17f07b10e
goeckslab
parents: 0
diff changeset
44 if not hasattr(self.best_model, "predict_proba"):
0314dad38aaa planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit ff6d674ecc83db933153b797ef4dbde17f07b10e
goeckslab
parents: 0
diff changeset
45 self.best_model.predict_proba = types.MethodType(
8
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
46 predict_proba, self.best_model
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
47 )
2
0314dad38aaa planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit ff6d674ecc83db933153b797ef4dbde17f07b10e
goeckslab
parents: 0
diff changeset
48 LOG.warning(
8
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
49 f"The model {type(self.best_model).__name__} does not support `predict_proba`. Applying monkey patch."
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
50 )
2
0314dad38aaa planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit ff6d674ecc83db933153b797ef4dbde17f07b10e
goeckslab
parents: 0
diff changeset
51
8
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
52 plots = [
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
53 'confusion_matrix',
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
54 'auc',
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
55 'threshold',
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
56 'pr',
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
57 'error',
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
58 'class_report',
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
59 'learning',
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
60 'calibration',
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
61 'vc',
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
62 'dimension',
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
63 'manifold',
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
64 'rfe',
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
65 'feature',
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
66 'feature_all',
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
67 ]
0
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
68 for plot_name in plots:
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
69 try:
8
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
70 if plot_name == "threshold":
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
71 plot_path = self.exp.plot_model(
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
72 self.best_model,
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
73 plot=plot_name,
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
74 save=True,
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
75 plot_kwargs={"binary": True, "percentage": True},
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
76 )
0
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
77 self.plots[plot_name] = plot_path
8
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
78 elif plot_name == "auc" and not self.exp.is_multiclass:
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
79 plot_path = self.exp.plot_model(
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
80 self.best_model,
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
81 plot=plot_name,
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
82 save=True,
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
83 plot_kwargs={
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
84 "micro": False,
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
85 "macro": False,
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
86 "per_class": False,
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
87 "binary": True,
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
88 },
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
89 )
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
90 self.plots[plot_name] = plot_path
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
91 else:
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
92 plot_path = self.exp.plot_model(
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
93 self.best_model, plot=plot_name, save=True
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
94 )
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
95 self.plots[plot_name] = plot_path
0
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
96 except Exception as e:
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
97 LOG.error(f"Error generating plot {plot_name}: {e}")
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
98 continue
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
99
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
100 def generate_plots_explainer(self):
8
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
101 from explainerdashboard import ClassifierExplainer
0
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
102
8
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
103 LOG.info("Generating explainer plots")
0
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
104
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
105 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
106 y_test = self.exp.y_test_transformed
8
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
107 explainer = ClassifierExplainer(self.best_model, X_test, y_test)
0
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
108
8
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
109 # a dict to hold the raw Figure objects or callables
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
110 self.explainer_plots: Dict[str, Figure] = {}
0
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
111
8
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
112 # these go into the Test tab
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
113 for key, fn in [
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
114 ("roc_auc", explainer.plot_roc_auc),
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
115 ("pr_auc", explainer.plot_pr_auc),
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
116 ("lift_curve", explainer.plot_lift_curve),
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
117 ("confusion_matrix", explainer.plot_confusion_matrix),
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
118 ("threshold", explainer.plot_precision), # Percentage vs probability
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
119 ("cumulative_precision", explainer.plot_cumulative_precision),
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
120 ]:
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
121 try:
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
122 self.explainer_plots[key] = fn()
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
123 except Exception as e:
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
124 LOG.error(f"Error generating explainer plot {key}: {e}")
0
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
125
8
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
126 # mean SHAP importances
0
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
127 try:
8
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
128 self.explainer_plots["shap_mean"] = explainer.plot_importances()
0
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
129 except Exception as e:
8
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
130 LOG.warning(f"Could not generate shap_mean: {e}")
0
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
131
8
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
132 # permutation importances
0
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
133 try:
8
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
134 self.explainer_plots["shap_perm"] = lambda: explainer.plot_importances(
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
135 kind="permutation"
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
136 )
0
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
137 except Exception as e:
8
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
138 LOG.warning(f"Could not generate shap_perm: {e}")
0
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
139
8
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
140 # PDPs for each feature (appended last)
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
141 valid_feats = []
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
142 for feat in self.features_name:
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
143 if feat in explainer.X.columns or feat in explainer.onehot_cols:
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
144 valid_feats.append(feat)
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
145 else:
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
146 LOG.warning(f"Skipping PDP for feature {feat!r}: not found in explainer data")
0
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
147
8
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
148 for feat in valid_feats:
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
149 # wrap each PDP call to catch any unexpected AssertionErrors
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
150 def make_pdp_plotter(f):
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
151 def _plot():
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
152 try:
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
153 return explainer.plot_pdp(f)
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
154 except AssertionError as ae:
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
155 LOG.warning(f"PDP AssertionError for {f!r}: {ae}")
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
156 return None
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
157 except Exception as e:
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
158 LOG.error(f"Unexpected error plotting PDP for {f!r}: {e}")
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
159 return None
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
160 return _plot
0
1f20fe57fdee planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff changeset
161
8
1aed7d47c5ec planemo upload for repository https://github.com/goeckslab/gleam commit 8112548ac44b7a4769093d76c722c8fcdeaaef54
goeckslab
parents: 3
diff changeset
162 self.explainer_plots[f"pdp__{feat}"] = make_pdp_plotter(feat)