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Table 1 Classification results for 40 cancer subtypes

From: A pan-cancer somatic mutation embedding using autoencoders

Primary siteProject nameTest samplesAUC latentAUC De.AUC Nd.
Head and neckORCA-IN360.750.500.55
BrainLGG-US560.810.620.80
BloodCLLE-ES1020.830.840.76
Head and neckTHCA-SA280.820.660.81
LiverLINC-JP790.540.500.50
LungLUSC-KR340.770.570.50
SkinGACA-CN240.790.500.50
StomachLICA-FR490.670.500.51
BloodESCA-CN650.770.50.61
LungEOPC-DE400.810.740.55
ColorectalCOCA-CN630.600.500.51
SkinSKCM-US670.840.500.50
LiverLICA-CN790.610.500.50
BloodALL-US150.830.910.94
SkinSKCA-BR200.840.500.50
BrainGBM-US550.870.500.66
Nervous systemNBL-US180.960.950.96
BloodLAML-KR410.970.730.64
ProstatePRAD-UK280.650.50.50
ProstatePRAD-US510.830.580.74
BloodMALY-DE490.820.500.50
KidneyKIRC-US820.900.500.58
BrainPBCA-DE900.790.770.59
KidneyRECA-EU490.840.50.5
BloodAML-US180.940.960.96
BreastBRCA-UK280.590.500.50
KidneyKIRP-US330.900.500.57
ProstatePRAD-CA580.880.710.50
StomachSTAD-US580.840.500.50
StomachGACA-JP1150.800.500.50
LiverLIRI-JP320.880.500.75
BreastBRCA-US1890.750.600.50
LungLUSC-US390.910.500.50
EsophagousESAD-UK610.900.500.50
ColorectalCOAD-US510.830.500.50
BreastBRCA-FR150.820.500.56
PancreasPACA-AU730.720.600.50
PancreasPACA-CA540.870.500.89
Head & NeckTHCA-US760.850.850.50
BreastBRCA-EU1140.790.560.50
  1. The number of the test samples for the corresponding class is detailed. Area under the Roc curve is detailed for classifiers on Latent Space, Deleterious and Non-Deleterious input data. Tumor subtypes where the classification performance is improved in the latent space are highlighted in bold