Table 6.

The evaluation metrics of cancer classification using only the top 20 genes obtained by XOmiVAE (columns 1 and 3) or 20 random genes chosen from the overall gene set of 58 043 features (columns 2 and 4). The metrics for each individual tumour type of interest are shown in columns 1 and 2, and the metrics for all of the other tumour types (except the target one) are shown in columns 3 and 4. The results were averaged among all 33 target tumour types and 10 random seeds

Average metric across all 33 tumour types
	Target tumour trained by top 20 XOmiVAE genes	Target tumour trained by 20 random genes	All other tumours trained by top 20 XOmiVAE genes of the target tumour	All other tumours trained by 20 random genes of the target tumour
F1	0.90 ± 0.11	0.46 ± 0.21	0.66 ± 0.11	0.48 ± 0.01
PPV	0.91 ± 0.11	0.48 ± 0.20	0.69 ± 0.08	0.50 ± 0.01
TPR	0.91 ± 0.10	0.66 ± 0.11	0.48 ± 0.01	0.48 ± 0.01
AUC	0.94 ± 0.07	0.67 ± 0.11	0.83 ± 0.06	0.68 ± 0.00