Mercurial > repos > goeckslab > pycaret_compare
annotate pycaret_predict.py @ 4:4aa511539199 draft default tip
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit cf47efb521b91a9cb44ae5c5ade860627f9b9030
author | goeckslab |
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date | Tue, 03 Jun 2025 19:31:16 +0000 |
parents | 915447b14520 |
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rev | line source |
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915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff
changeset
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1 import argparse |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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2 import logging |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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3 import tempfile |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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4 |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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5 import h5py |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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6 import joblib |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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7 import pandas as pd |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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8 from pycaret.classification import ClassificationExperiment |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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9 from pycaret.regression import RegressionExperiment |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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10 from sklearn.metrics import average_precision_score |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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11 from utils import encode_image_to_base64, get_html_closing, get_html_template |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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12 |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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13 LOG = logging.getLogger(__name__) |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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14 |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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15 |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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16 class PyCaretModelEvaluator: |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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17 def __init__(self, model_path, task, target): |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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18 self.model_path = model_path |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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19 self.task = task.lower() |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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20 self.model = self.load_h5_model() |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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21 self.target = target if target != "None" else None |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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22 |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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23 def load_h5_model(self): |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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24 """Load a PyCaret model from an HDF5 file.""" |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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25 with h5py.File(self.model_path, 'r') as f: |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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26 model_bytes = bytes(f['model'][()]) |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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27 with tempfile.NamedTemporaryFile(delete=False) as temp_file: |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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28 temp_file.write(model_bytes) |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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29 temp_file.seek(0) |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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changeset
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30 loaded_model = joblib.load(temp_file.name) |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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31 return loaded_model |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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32 |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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33 def evaluate(self, data_path): |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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34 """Evaluate the model using the specified data.""" |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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35 raise NotImplementedError("Subclasses must implement this method") |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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36 |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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37 |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
diff
changeset
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38 class ClassificationEvaluator(PyCaretModelEvaluator): |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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changeset
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39 def evaluate(self, data_path): |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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40 metrics = None |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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41 plot_paths = {} |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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42 data = pd.read_csv(data_path, engine='python', sep=None) |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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43 if self.target: |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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changeset
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44 exp = ClassificationExperiment() |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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45 names = data.columns.to_list() |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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46 LOG.error(f"Column names: {names}") |
4
4aa511539199
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit cf47efb521b91a9cb44ae5c5ade860627f9b9030
goeckslab
parents:
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47 target_index = int(self.target) - 1 |
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915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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48 target_name = names[target_index] |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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49 exp.setup(data, target=target_name, test_data=data, index=False) |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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changeset
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50 exp.add_metric(id='PR-AUC-Weighted', |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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51 name='PR-AUC-Weighted', |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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52 target='pred_proba', |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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53 score_func=average_precision_score, |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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54 average='weighted') |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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55 predictions = exp.predict_model(self.model) |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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changeset
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56 metrics = exp.pull() |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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57 plots = ['confusion_matrix', 'auc', 'threshold', 'pr', |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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58 'error', 'class_report', 'learning', 'calibration', |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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59 'vc', 'dimension', 'manifold', 'rfe', 'feature', |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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60 'feature_all'] |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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61 for plot_name in plots: |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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62 try: |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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63 if plot_name == 'auc' and not exp.is_multiclass: |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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64 plot_path = exp.plot_model(self.model, |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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65 plot=plot_name, |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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66 save=True, |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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67 plot_kwargs={ |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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68 'micro': False, |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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69 'macro': False, |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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70 'per_class': False, |
4
4aa511539199
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit cf47efb521b91a9cb44ae5c5ade860627f9b9030
goeckslab
parents:
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71 'binary': True}) |
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915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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72 plot_paths[plot_name] = plot_path |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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73 continue |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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74 |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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75 plot_path = exp.plot_model(self.model, |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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76 plot=plot_name, save=True) |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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77 plot_paths[plot_name] = plot_path |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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78 except Exception as e: |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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79 LOG.error(f"Error generating plot {plot_name}: {e}") |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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80 continue |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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81 generate_html_report(plot_paths, metrics) |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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82 |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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83 else: |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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84 exp = ClassificationExperiment() |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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85 exp.setup(data, target=None, test_data=data, index=False) |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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86 predictions = exp.predict_model(self.model, data=data) |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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87 |
915447b14520
planemo upload for repository https://github.com/goeckslab/Galaxy-Pycaret commit d79b0f722b7d09505a526d1a4332f87e548a3df1
goeckslab
parents:
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88 return predictions, metrics, plot_paths |
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89 |
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90 |
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91 class RegressionEvaluator(PyCaretModelEvaluator): |
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92 def evaluate(self, data_path): |
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93 metrics = None |
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94 plot_paths = {} |
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95 data = pd.read_csv(data_path, engine='python', sep=None) |
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96 if self.target: |
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97 names = data.columns.to_list() |
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98 target_index = int(self.target) - 1 |
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99 target_name = names[target_index] |
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100 exp = RegressionExperiment() |
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101 exp.setup(data, target=target_name, test_data=data, index=False) |
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102 predictions = exp.predict_model(self.model) |
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103 metrics = exp.pull() |
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104 plots = ['residuals', 'error', 'cooks', |
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105 'learning', 'vc', 'manifold', |
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106 'rfe', 'feature', 'feature_all'] |
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107 for plot_name in plots: |
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108 try: |
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109 plot_path = exp.plot_model(self.model, |
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110 plot=plot_name, save=True) |
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111 plot_paths[plot_name] = plot_path |
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112 except Exception as e: |
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113 LOG.error(f"Error generating plot {plot_name}: {e}") |
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114 continue |
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115 generate_html_report(plot_paths, metrics) |
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116 else: |
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117 exp = RegressionExperiment() |
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118 exp.setup(data, target=None, test_data=data, index=False) |
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119 predictions = exp.predict_model(self.model, data=data) |
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120 |
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121 return predictions, metrics, plot_paths |
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122 |
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123 |
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124 def generate_html_report(plots, metrics): |
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125 """Generate an HTML evaluation report.""" |
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126 plots_html = "" |
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127 for plot_name, plot_path in plots.items(): |
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128 encoded_image = encode_image_to_base64(plot_path) |
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129 plots_html += f""" |
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130 <div class="plot"> |
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131 <h3>{plot_name.capitalize()}</h3> |
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132 <img src="data:image/png;base64,{encoded_image}" alt="{plot_name}"> |
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133 </div> |
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134 <hr> |
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135 """ |
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136 |
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137 metrics_html = metrics.to_html(index=False, classes="table") |
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138 |
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139 html_content = f""" |
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140 {get_html_template()} |
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141 <h1>Model Evaluation Report</h1> |
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142 <div class="tabs"> |
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143 <div class="tab" onclick="openTab(event, 'metrics')">Metrics</div> |
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144 <div class="tab" onclick="openTab(event, 'plots')">Plots</div> |
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145 </div> |
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146 <div id="metrics" class="tab-content"> |
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147 <h2>Metrics</h2> |
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148 <table> |
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149 {metrics_html} |
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150 </table> |
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151 </div> |
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152 <div id="plots" class="tab-content"> |
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153 <h2>Plots</h2> |
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154 {plots_html} |
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155 </div> |
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156 {get_html_closing()} |
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157 """ |
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158 |
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159 # Save HTML report |
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160 with open("evaluation_report.html", "w") as html_file: |
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161 html_file.write(html_content) |
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162 |
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163 |
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164 if __name__ == "__main__": |
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165 parser = argparse.ArgumentParser( |
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166 description="Evaluate a PyCaret model stored in HDF5 format.") |
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167 parser.add_argument("--model_path", |
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168 type=str, |
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169 help="Path to the HDF5 model file.") |
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170 parser.add_argument("--data_path", |
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171 type=str, |
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172 help="Path to the evaluation data CSV file.") |
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173 parser.add_argument("--task", |
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174 type=str, |
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175 choices=["classification", "regression"], |
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176 help="Specify the task: classification or regression.") |
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177 parser.add_argument("--target", |
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178 default=None, |
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179 help="Column number of the target") |
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180 args = parser.parse_args() |
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181 |
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182 if args.task == "classification": |
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183 evaluator = ClassificationEvaluator( |
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184 args.model_path, args.task, args.target) |
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185 elif args.task == "regression": |
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186 evaluator = RegressionEvaluator( |
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187 args.model_path, args.task, args.target) |
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188 else: |
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189 raise ValueError( |
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190 "Unsupported task type. Use 'classification' or 'regression'.") |
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191 |
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192 predictions, metrics, plots = evaluator.evaluate(args.data_path) |
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193 |
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194 predictions.to_csv("predictions.csv", index=False) |