DNA methylation

Smoking Status DNA Methylation (GSE50660)

Peripheral blood DNA methylation profiles measured with Illumina HumanMethylation450 arrays in a study of cigarette smoking. The task is to classify each participant as a never, former, or current smoker using methylation levels at CpG sites.

ClassificationLicence: NCBI GEO public data; study-specific terms require verification before re-hostingGEO-GSE50660-Methylation-SmokingTarget: smoking (0, 1 and 2, which represent never, former and current smokers)geo_matrix ↗

At this operating point

Model comparison

p=10,000, n=100 · Higher Macro-F1 is better

Random Forest is marked with a diamond. Models are ordered by the selected metric.

Across sample budgets

Learning curves

Models

All metric values at this operating point

Model	Macro-F1	MCC	Balanced accuracy	ROC-AUC
Kumo Tabular (M)	0.4266	0.294	0.4352	0.7249
MLP	0.4016	0.2213	0.4122	0.6623
GeneICL	0.3975	0.2114	0.4017	0.6773
Logistic Regression	0.3963	0.2139	0.4063	0.6874
MLP (tuned)	0.3938	0.225	0.4122	0.6603
RealMLP	0.3936	0.2244	0.4061	0.676
Logistic Regression (tuned)	0.3908	0.2081	0.3984	0.6675
XGBoost (tuned)	0.3894	0.1978	0.3999	0.6401
RealTabPFN 2.5	0.3844	0.2013	0.3975	0.6766
TabM	0.3836	0.1938	0.4004	0.6753
XGBoost	0.3819	0.172	0.3927	0.6204
Extra Trees (tuned)	0.3817	0.1946	0.3961	0.6751
TabPFN 3.5	0.3807	0.2027	0.3962	0.6929
Random Forest	0.3688	0.1981	0.3896	0.6792
RealTabPFN v2	0.3687	0.2114	0.3951	0.6908
Random Forest (tuned)	0.3645	0.1724	0.3845	0.6625
Causilo	0.3416	0.1265	0.3763	0.69
Extra Trees	0.331	0.1141	0.3623	0.6426
TabDPT	0.3248	0.1446	0.3664	0.6723
AutoGluon	0.318	0.1107	0.3596	0.6686
TabPFN Wide 5k (ne3)	0.3161	0.1292	0.3619	0.6811
TabFM	0.3096	0.16	0.3659	0.7158
MITRA	0.3056	0.1273	0.3602	0.5696
LimiX2	0.164	0.001766	0.2911	0.467