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Metagenomics
EMG produced TPA metagenomics assembly of the PRJNA275349 data set (Human Microbiome Environment Metagenome).
Assembled Human Microbiome Project sequences from samples collected across several body sites in healthy adults. The benchmark uses MGnify InterPro functional-abundance profiles to predict each sample's recorded isolation source.
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At this operating point
Model comparison
p=10,000, n=100 · Higher Macro-F1 is better
No scores at this operating point. Select another feature or sample budget.
Random Forest is marked with a diamond. Models are ordered by the selected metric.
Across sample budgets
Learning curves
All metric values at this operating point
| Model | Macro-F1 | MCC | Balanced accuracy | ROC-AUC |
|---|---|---|---|---|
| AutoGluon | 1 | 1 | 1 | 1 |
| Causilo | 1 | 1 | 1 | 1 |
| GeneICL | 1 | 1 | 1 | 1 |
| Kumo Tabular (M) | 1 | 1 | 1 | 1 |
| LimiX2 | 1 | 1 | 1 | 1 |
| Logistic Regression | 1 | 1 | 1 | 1 |
| MLP | 1 | 1 | 1 | 1 |
| MLP (tuned) | 1 | 1 | 1 | 1 |
| RealMLP | 1 | 1 | 1 | 1 |
| RealTabPFN v2 | 1 | 1 | 1 | 1 |
| RealTabPFN 2.5 | 1 | 1 | 1 | 1 |
| TabDPT | 1 | 1 | 1 | 1 |
| TabFM | 1 | 1 | 1 | 1 |
| TabPFN 3.5 | 1 | 1 | 1 | 1 |
| Logistic Regression (tuned) | 0.9957 | 0.9916 | 0.9944 | 1 |
| MITRA | 0.9957 | 0.9916 | 0.9944 | 1 |
| TabPFN Wide 5k (ne3) | 0.9957 | 0.9916 | 0.9944 | 1 |
| TabM | 0.9917 | 0.9838 | 0.9894 | 1 |
| Extra Trees (tuned) | 0.9917 | 0.9838 | 0.9894 | 1 |
| Random Forest | 0.9913 | 0.9832 | 0.9889 | 1 |
| Extra Trees | 0.9913 | 0.9832 | 0.9889 | 1 |
| Random Forest (tuned) | 0.9873 | 0.9755 | 0.9839 | 1 |
| XGBoost | 0.9775 | 0.9582 | 0.9719 | 0.9719 |
| XGBoost (tuned) | 0.9737 | 0.9499 | 0.9666 | 0.9783 |