Example: Metabolomics Classification 20260106_025027Completed

Algorithm: Random Forest | Created: January 06, 2026 at 02:50

Performance Metrics
F1

0.8898

± 0.0737
Auc

0.922

± 0.0797
Recall

0.89

± 0.0735
Accuracy

0.89

± 0.0735
Precision

0.8923

± 0.074

Detailed Metrics (Across All Folds)
MetricMeanStd DevMinMax
F10.88980.07370.74940.9499
Auc0.92200.07970.77501.0000
Recall0.89000.07350.75000.9500
Accuracy0.89000.07350.75000.9500
Precision0.89230.07400.75250.9545
Feature Selection Frequency
Feature selection frequency
Top Features (Avg. Importance)
RankFeatureMeanStd Dev
1asparagine0.1820.0315
2isoleucine0.15230.0147
3aspartate0.12470.018
4succinate0.11960.0218
5valine0.10720.0301
6malate0.08960.0192
7pyruvate0.07670.0191
8urea0.06250.0028
9glutamine0.05930.0111
10glutamate0.05660.0
Classification Analysis
Confusion Matrix
Aggregate confusion matrix
ROC Curve
Average roc
Configuration
Hyperparameters
Max depth10
N estimators50
Random state42
Data Configuration
Feature Selectionkbest_f
Validationstratified_kfold
Target Columntarget
Generated Reports
Pipeline Data & Stages

Pipeline execution flow and intermediate datasets.

CLI Command (Copy-Paste Ready)
OMP_NUM_THREADS=1 OPENBLAS_NUM_THREADS=1 MKL_NUM_THREADS=1 VECLIB_MAXIMUM_THREADS=1 NUMEXPR_NUM_THREADS=1 /opt/ml-env/bin/python /app/scripts/ml_pipeline.py --config /app/public/ml_results/79/job_config.json
Standard Output (stdout)
{"job_id": 79, "algorithm": "random_forest", "n_folds": 5, "holdout_used": false, "per_fold_results": [{"fold": 1, "metrics": {"accuracy": 0.95, "precision": 0.9545454545454545, "recall": 0.95, "f1": 0.949874686716792, "auc": 0.96}, "selected_features": ["pyruvate", "succinate", "malate", "valine", "isoleucine", "aspartate", "asparagine", "threonine", "phenylalanine", "uracil"], "feature_importance": {"pyruvate": 0.045989566280054024, "succinate": 0.1319809872887862, "malate": 0.08274912024060814, "valine": 0.09742267319916634, "isoleucine": 0.17234238851775416, "aspartate": 0.1492152938040533, "asparagine": 0.19495076007646278, "threonine": 0.04479561594688145, "phenylalanine": 0.041290369192781146, "uracil": 0.03926322545345247}, "y_true": [0, 0, 0, 1, 1, 1, 1, 0, 1, 0, 1, 0, 1, 1, 1, 0, 0, 0, 1, 0], "y_pred": [0, 0, 0, 1, 1, 1, 1, 0, 1, 0, 1, 0, 1, 1, 0, 0, 0, 0, 1, 0], "y_proba": [[1.0, 0.0], [0.56, 0.44], [0.88, 0.12], [0.2, 0.8], [0.22, 0.78], [0.18, 0.82], [0.04, 0.96], [0.82, 0.18], [0.04, 0.96], [0.9, 0.1], [0.34, 0.66], [0.54, 0.46], [0.18, 0.82], [0.46, 0.54], [0.8, 0.2], [0.56, 0.44], [0.82, 0.18], [0.74, 0.26], [0.24, 0.76], [0.88, 0.12]]}, {"fold": 2, "metrics": {"accuracy": 0.95, "precision": 0.9545454545454545, "recall": 0.95, "f1": 0.949874686716792, "auc": 1.0}, "selected_features": ["pyruvate", "succinate", "malate", "valine", "isoleucine", "glutamine", "aspartate", "asparagine", "urea", "uracil"], "feature_importance": {"pyruvate": 0.07525315972224556, "succinate": 0.09129149870154286, "malate": 0.11199261162855342, "valine": 0.058125982298849146, "isoleucine": 0.16551685273131791, "glutamine": 0.06706090962296464, "aspartate": 0.1325963112602954, "asparagine": 0.18672820061820353, "urea": 0.059701987151288084, "uracil": 0.051732486264739516}, "y_true": [1, 1, 0, 0, 1, 1, 0, 0, 0, 1, 0, 0, 1, 1, 0, 0, 1, 0, 1, 1], "y_pred": [1, 1, 0, 0, 1, 1, 0, 0, 1, 1, 0, 0, 1, 1, 0, 0, 1, 0, 1, 1], "y_proba": [[0.38, 0.62], [0.3, 0.7], [0.94, 0.06], [0.92, 0.08], [0.32, 0.68], [0.26, 0.74], [0.98, 0.02], [0.74, 0.26], [0.48, 0.52], [0.24, 0.76], [0.96, 0.04], [0.62, 0.38], [0.16, 0.84], [0.22, 0.78], [0.58, 0.42], [0.98, 0.02], [0.12, 0.88], [0.54, 0.46], [0.26, 0.74], [0.16, 0.84]]}, {"fold": 3, "metrics": {"accuracy": 0.75, "precision": 0.7525252525252526, "recall": 0.75, "f1": 0.7493734335839599, "auc": 0.775}, "selected_features": ["glucose", "pyruvate", "succinate", "malate", "valine", "isoleucine", "glutamine", "aspartate", "asparagine", "uracil"], "feature_importance": {"glucose": 0.04942380840814473, "pyruvate": 0.09309949319191319, "succinate": 0.15133353809137837, "malate": 0.0605694674451807, "valine": 0.13737465284691044, "isoleucine": 0.13505392389080143, "glutamine": 0.06732297011703627, "aspartate": 0.09383507950357146, "asparagine": 0.1624213244805886, "uracil": 0.049565742024474994}, "y_true": [0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 0, 1, 1, 0, 1], "y_pred": [1, 0, 1, 1, 0, 0, 0, 0, 1, 0, 1, 1, 1, 1, 1, 0, 0, 1, 1, 0], "y_proba": [[0.44, 0.56], [0.58, 0.42], [0.24, 0.76], [0.48, 0.52], [0.54, 0.46], [0.78, 0.22], [0.68, 0.32], [0.82, 0.18], [0.26, 0.74], [0.96, 0.04], [0.3, 0.7], [0.3, 0.7], [0.38, 0.62], [0.28, 0.72], [0.38, 0.62], [0.68, 0.32], [0.64, 0.36], [0.16, 0.84], [0.28, 0.72], [0.66, 0.34]]}, {"fold": 4, "metrics": {"accuracy": 0.9, "precision": 0.9, "recall": 0.9, "f1": 0.9, "auc": 0.905}, "selected_features": ["succinate", "malate", "valine", "isoleucine", "glutamate", "aspartate", "asparagine", "taurine", "urea", "uracil"], "feature_importance": {"succinate": 0.12367363044792724, "malate": 0.10966633981165862, "valine": 0.14011894757527144, "isoleucine": 0.1501961398673615, "glutamate": 0.05658344889263087, "aspartate": 0.12306034127201829, "asparagine": 0.13619357343659189, "taurine": 0.04923109232350893, "urea": 0.06534048885109058, "uracil": 0.04593599752194046}, "y_true": [1, 1, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 1, 1, 0, 1, 1, 0, 1, 1], "y_pred": [1, 1, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 1, 1, 0, 1, 1, 0, 1, 0], "y_proba": [[0.38, 0.62], [0.24, 0.76], [0.64, 0.36], [0.9, 0.1], [0.54, 0.46], [0.22, 0.78], [0.52, 0.48], [0.16, 0.84], [0.88, 0.12], [0.58, 0.42], [0.38, 0.62], [0.64, 0.36], [0.06, 0.94], [0.46, 0.54], [0.8, 0.2], [0.4, 0.6], [0.3, 0.7], [0.68, 0.32], [0.18, 0.82], [0.78, 0.22]]}, {"fold": 5, "metrics": {"accuracy": 0.9, "precision": 0.9, "recall": 0.9, "f1": 0.9, "auc": 0.9699999999999999}, "selected_features": ["pyruvate", "succinate", "malate", "valine", "isoleucine", "glutamine", "aspartate", "asparagine", "tryptophan", "uracil"], "feature_importance": {"pyruvate": 0.09246614374371728, "succinate": 0.09971215755786313, "malate": 0.08314586515960576, "valine": 0.10295597262383768, "isoleucine": 0.1382179786283865, "glutamine": 0.04354208245088025, "aspartate": 0.12470173458723299, "asparagine": 0.22981491904918896, "tryptophan": 0.04956287554505147, "uracil": 0.03588027065423605}, "y_true": [0, 1, 0, 0, 1, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 1, 1, 0, 1, 1], "y_pred": [1, 1, 0, 0, 1, 0, 1, 0, 1, 0, 0, 0, 0, 0, 1, 1, 1, 0, 1, 1], "y_proba": [[0.42, 0.58], [0.26, 0.74], [0.7, 0.3], [0.7, 0.3], [0.38, 0.62], [0.62, 0.38], [0.44, 0.56], [0.72, 0.28], [0.26, 0.74], [0.64, 0.36], [0.78, 0.22], [0.5, 0.5], [0.68, 0.32], [0.82, 0.18], [0.46, 0.54], [0.06, 0.94], [0.32, 0.68], [0.68, 0.32], [0.2, 0.8], [0.2, 0.8]]}], "aggregated_metrics": {"accuracy": {"mean": 0.89, "std": 0.07348469228349533, "min": 0.75, "max": 0.95}, "precision": {"mean": 0.8923232323232323, "std": 0.07403316899345276, "min": 0.7525252525252526, "max": 0.9545454545454545}, "recall": {"mean": 0.89, "std": 0.07348469228349533, "min": 0.75, "max": 0.95}, "f1": {"mean": 0.8898245614035087, "std": 0.07368260786281551, "min": 0.7493734335839599, "max": 0.949874686716792}, "auc": {"mean": 0.9219999999999999, "std": 0.07966178506661771, "min": 0.775, "max": 1.0}}, "aggregated_feature_importance": {"pyruvate": {"mean": 0.0767020907344825, "std": 0.019122883765733446}, "succinate": {"mean": 0.11959836241749955, "std": 0.021788980060700205}, "malate": {"mean": 0.08962468085712133, "std": 0.019159573239989975}, "valine": {"mean": 0.10719964570880702, "std": 0.030053398757345903}, "isoleucine": {"mean": 0.15226545672712427, "std": 0.014673331332468436}, "aspartate": {"mean": 0.12468175208543428, "std": 0.01799267349723484}, "asparagine": {"mean": 0.18202175553220717, "std": 0.03148934878466675}, "threonine": {"mean": 0.04479561594688145, "std": 0.0}, "phenylalanine": {"mean": 0.041290369192781146, "std": 0.0}, "uracil": {"mean": 0.0444755443837687, "std": 0.0060291498566707215}, "glutamine": {"mean": 0.05930865406362706, "std": 0.011149163025104715}, "urea": {"mean": 0.06252123800118933, "std": 0.0028192508499012454}, "glucose": {"mean": 0.04942380840814473, "std": 0.0}, "glutamate": {"mean": 0.05658344889263087, "std": 0.0}, "taurine": {"mean": 0.04923109232350893, "std": 0.0}, "tryptophan": {"mean": 0.04956287554505147, "std": 0.0}}, "feature_selection_stats": [{"feature": "succinate", "count": 5, "frequency": 1.0}, {"feature": "asparagine", "count": 5, "frequency": 1.0}, {"feature": "malate", "count": 5, "frequency": 1.0}, {"feature": "uracil", "count": 5, "frequency": 1.0}, {"feature": "aspartate", "count": 5, "frequency": 1.0}, {"feature": "isoleucine", "count": 5, "frequency": 1.0}, {"feature": "valine", "count": 5, "frequency": 1.0}, {"feature": "pyruvate", "count": 4, "frequency": 0.8}, {"feature": "glutamine", "count": 3, "frequency": 0.6}, {"feature": "urea", "count": 2, "frequency": 0.4}, {"feature": "glucose", "count": 1, "frequency": 0.2}, {"feature": "phenylalanine", "count": 1, "frequency": 0.2}, {"feature": "glutamate", "count": 1, "frequency": 0.2}, {"feature": "taurine", "count": 1, "frequency": 0.2}, {"feature": "tryptophan", "count": 1, "frequency": 0.2}, {"feature": "threonine", "count": 1, "frequency": 0.2}], "feature_importance": {"pyruvate": {"mean": 0.0767020907344825, "std": 0.019122883765733446}, "succinate": {"mean": 0.11959836241749955, "std": 0.021788980060700205}, "malate": {"mean": 0.08962468085712133, "std": 0.019159573239989975}, "valine": {"mean": 0.10719964570880702, "std": 0.030053398757345903}, "isoleucine": {"mean": 0.15226545672712427, "std": 0.014673331332468436}, "aspartate": {"mean": 0.12468175208543428, "std": 0.01799267349723484}, "asparagine": {"mean": 0.18202175553220717, "std": 0.03148934878466675}, "threonine": {"mean": 0.04479561594688145, "std": 0.0}, "phenylalanine": {"mean": 0.041290369192781146, "std": 0.0}, "uracil": {"mean": 0.0444755443837687, "std": 0.0060291498566707215}, "glutamine": {"mean": 0.05930865406362706, "std": 0.011149163025104715}, "urea": {"mean": 0.06252123800118933, "std": 0.0028192508499012454}, "glucose": {"mean": 0.04942380840814473, "std": 0.0}, "glutamate": {"mean": 0.05658344889263087, "std": 0.0}, "taurine": {"mean": 0.04923109232350893, "std": 0.0}, "tryptophan": {"mean": 0.04956287554505147, "std": 0.0}}, "charts": {"feature_importance": "feature_selection_frequency.png", "roc_curve": "average_roc.png", "confusion_matrix": "aggregate_confusion_matrix.png"}, "reports": ["report_79.md"]}
Standard Error (stderr)
Starting pipeline execution for Job: 79
Loaded data: (100, 50) features, (100,) targets.
Running nested cross-validation...
Generating visualizations...
Generating reports...
Warning: weasyprint not installed. PDF report skipped.
Warning: python-docx not installed. DOCX report skipped.
Warning: excel writer dependency missing. Excel report skipped.
Analysis complete. Results saved to /app/public/ml_results/79