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benchmark results/results_neural_cell_identification.csv

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+Model,Cell population,Cell type,Accuracy,Precision,Recall,F1 Score
+Geneformer,Neural.cell,Overall,1.000 ,1.000 ,1.000 ,1.000 
+Geneformer,Neural.cell,Glutamatergic neurons,1.000 ,1.000 ,1.000 ,1.000 
+Geneformer,Neural.cell,Inhibitory interneurons,1.000 ,1.000 ,1.000 ,1.000 
+Geneformer,Neural.cell,Astrocytes,1.000 ,1.000 ,1.000 ,1.000 
+Geneformer,Neural.cell,Microglial cells,1.000 ,1.000 ,1.000 ,1.000 
+Geneformer,Neural.cell,Oligodendrocytes,1.000 ,1.000 ,1.000 ,1.000 
+Geneformer,Neural.cell,Oligodendrocyte precursor cells,1.000 ,1.000 ,1.000 ,1.000 
+Geneformer,Non.Neural.cell,Overall,0.811 ,1.000 ,0.811 ,0.895 
+Geneformer,Non.Neural.cell,B.cells,1.000 ,1.000 ,1.000 ,1.000 
+Geneformer,Non.Neural.cell,Endothelial.cells,1.000 ,1.000 ,1.000 ,1.000 
+Geneformer,Non.Neural.cell,Fibroblasts,1.000 ,1.000 ,1.000 ,1.000 
+Geneformer,Non.Neural.cell,Mesenchymal.cells,1.000 ,1.000 ,1.000 ,1.000 
+Geneformer,Non.Neural.cell,Myeloid,0.837 ,1.000 ,0.837 ,0.911 
+Geneformer,Non.Neural.cell,T/NK cells,0.026 ,1.000 ,0.026 ,0.051 
+Geneformer,Non.Neural.cell,Epithelial cells,1.000 ,1.000 ,1.000 ,1.000 
+Geneformer,Non.Neural.cell,Germ cells,1.000 ,1.000 ,1.000 ,1.000 
+scFoundation,Neural.cell,Overall,1.000 ,1.000 ,1.000 ,1.000 
+scFoundation,Neural.cell,Glutamatergic neurons,1.000 ,1.000 ,1.000 ,1.000 
+scFoundation,Neural.cell,Inhibitory interneurons,1.000 ,1.000 ,1.000 ,1.000 
+scFoundation,Neural.cell,Astrocytes,1.000 ,1.000 ,1.000 ,1.000 
+scFoundation,Neural.cell,Microglial cells,1.000 ,1.000 ,1.000 ,1.000 
+scFoundation,Neural.cell,Oligodendrocytes,1.000 ,1.000 ,1.000 ,1.000 
+scFoundation,Neural.cell,Oligodendrocyte precursor cells,1.000 ,1.000 ,1.000 ,1.000 
+scFoundation,Non.Neural.cell,Overall,0.998 ,1.000 ,0.998 ,0.999 
+scFoundation,Non.Neural.cell,B.cells,1.000 ,1.000 ,1.000 ,1.000 
+scFoundation,Non.Neural.cell,Endothelial.cells,0.992 ,1.000 ,0.992 ,0.996 
+scFoundation,Non.Neural.cell,Fibroblasts,0.998 ,1.000 ,0.998 ,0.999 
+scFoundation,Non.Neural.cell,Mesenchymal.cells,1.000 ,1.000 ,1.000 ,1.000 
+scFoundation,Non.Neural.cell,Myeloid,0.996 ,1.000 ,0.996 ,0.998 
+scFoundation,Non.Neural.cell,T/NK cells,1.000 ,1.000 ,1.000 ,1.000 
+scFoundation,Non.Neural.cell,Epithelial cells,1.000 ,1.000 ,1.000 ,1.000 
+scFoundation,Non.Neural.cell,Germ cells,1.000 ,1.000 ,1.000 ,1.000 
+scGPT,Neural.cell,Overall,1.000 ,1.000 ,1.000 ,1.000 
+scGPT,Neural.cell,Glutamatergic neurons,1.000 ,1.000 ,1.000 ,1.000 
+scGPT,Neural.cell,Inhibitory interneurons,1.000 ,1.000 ,1.000 ,1.000 
+scGPT,Neural.cell,Astrocytes,1.000 ,1.000 ,1.000 ,1.000 
+scGPT,Neural.cell,Microglial cells,0.999 ,1.000 ,0.999 ,0.999 
+scGPT,Neural.cell,Oligodendrocytes,1.000 ,1.000 ,1.000 ,1.000 
+scGPT,Neural.cell,Oligodendrocyte precursor cells,1.000 ,1.000 ,1.000 ,1.000 
+scGPT,Non.Neural.cell,Overall,0.989 ,1.000 ,0.989 ,0.995 
+scGPT,Non.Neural.cell,B.cells,1.000 ,1.000 ,1.000 ,1.000 
+scGPT,Non.Neural.cell,Endothelial.cells,0.965 ,1.000 ,0.965 ,0.982 
+scGPT,Non.Neural.cell,Fibroblasts,0.986 ,1.000 ,0.986 ,0.993 
+scGPT,Non.Neural.cell,Mesenchymal.cells,1.000 ,1.000 ,1.000 ,1.000 
+scGPT,Non.Neural.cell,Myeloid,0.984 ,1.000 ,0.984 ,0.992 
+scGPT,Non.Neural.cell,T/NK cells,1.000 ,1.000 ,1.000 ,1.000 
+scGPT,Non.Neural.cell,Epithelial cells,1.000 ,1.000 ,1.000 ,1.000 
+scGPT,Non.Neural.cell,Germ cells,1.000 ,1.000 ,1.000 ,1.000 
+UCE,Neural.cell,Overall,1.000 ,1.000 ,1.000 ,1.000 
+UCE,Neural.cell,Glutamatergic neurons,1.000 ,1.000 ,1.000 ,1.000 
+UCE,Neural.cell,Inhibitory interneurons,1.000 ,1.000 ,1.000 ,1.000 
+UCE,Neural.cell,Astrocytes,1.000 ,1.000 ,1.000 ,1.000 
+UCE,Neural.cell,Microglial cells,1.000 ,1.000 ,1.000 ,1.000 
+UCE,Neural.cell,Oligodendrocytes,1.000 ,1.000 ,1.000 ,1.000 
+UCE,Neural.cell,Oligodendrocyte precursor cells,1.000 ,1.000 ,1.000 ,1.000 
+UCE,Non.Neural.cell,Overall,0.984 ,1.000 ,0.984 ,0.992 
+UCE,Non.Neural.cell,B.cells,1.000 ,1.000 ,1.000 ,1.000 
+UCE,Non.Neural.cell,Endothelial.cells,0.940 ,1.000 ,0.940 ,0.969 
+UCE,Non.Neural.cell,Fibroblasts,0.982 ,1.000 ,0.982 ,0.991 
+UCE,Non.Neural.cell,Mesenchymal.cells,1.000 ,1.000 ,1.000 ,1.000 
+UCE,Non.Neural.cell,Myeloid,0.984 ,1.000 ,0.984 ,0.992 
+UCE,Non.Neural.cell,T/NK cells,1.000 ,1.000 ,1.000 ,1.000 
+UCE,Non.Neural.cell,Epithelial cells,1.000 ,1.000 ,1.000 ,1.000 
+UCE,Non.Neural.cell,Germ cells,1.000 ,1.000 ,1.000 ,1.000 
+scLong,Neural.cell,Overall,1.000 ,1.000 ,1.000 ,1.000 
+scLong,Neural.cell,Glutamatergic neurons,1.000 ,1.000 ,1.000 ,1.000 
+scLong,Neural.cell,Inhibitory interneurons,1.000 ,1.000 ,1.000 ,1.000 
+scLong,Neural.cell,Astrocytes,1.000 ,1.000 ,1.000 ,1.000 
+scLong,Neural.cell,Microglial cells,1.000 ,1.000 ,1.000 ,1.000 
+scLong,Neural.cell,Oligodendrocytes,1.000 ,1.000 ,1.000 ,1.000 
+scLong,Neural.cell,Oligodendrocyte precursor cells,1.000 ,1.000 ,1.000 ,1.000 
+scLong,Non.Neural.cell,Overall,0.993 ,1.000 ,0.993 ,0.997 
+scLong,Non.Neural.cell,B.cells,0.987 ,1.000 ,0.987 ,0.993 
+scLong,Non.Neural.cell,Endothelial.cells,0.993 ,1.000 ,0.993 ,0.996 
+scLong,Non.Neural.cell,Fibroblasts,0.993 ,1.000 ,0.993 ,0.996 
+scLong,Non.Neural.cell,Mesenchymal.cells,1.000 ,1.000 ,1.000 ,1.000 
+scLong,Non.Neural.cell,Myeloid,0.990 ,1.000 ,0.990 ,0.995 
+scLong,Non.Neural.cell,T/NK cells,0.998 ,1.000 ,0.998 ,0.999 
+scLong,Non.Neural.cell,Epithelial cells,1.000 ,1.000 ,1.000 ,1.000 
+scLong,Non.Neural.cell,Germ cells,1.000 ,1.000 ,1.000 ,1.000 

benchmark results/results_neural_cell_subtype_classification.csv

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+Model,Cell population,Cell type,Accuracy,Macro_Precision,Macro_Recall,Macro_F1
+Geneformer,Neural.cell,Overall,0.237 ,0.320 ,0.237 ,0.190 
+Geneformer,Neural.cell,Glutamatergic neurons,0.017 ,0.333 ,0.017 ,0.034 
+Geneformer,Neural.cell,Inhibitory interneurons,0.009 ,0.333 ,0.009 ,0.018 
+Geneformer,Neural.cell,Astrocytes,0.017 ,0.333 ,0.017 ,0.033 
+Geneformer,Neural.cell,Microglial cells,0.069 ,0.500 ,0.069 ,0.129 
+Geneformer,Neural.cell,Oligodendrocytes,0.312 ,0.500 ,0.312 ,0.476 
+Geneformer,Neural.cell,Oligodendrocyte precursor cells,1.000 ,1.000 ,1.000 ,1.000 
+scFoundation,Neural.cell,Overall,0.999 ,0.999 ,0.999 ,0.999 
+scFoundation,Neural.cell,Glutamatergic neurons,0.998 ,0.333 ,0.998 ,0.999 
+scFoundation,Neural.cell,Inhibitory interneurons,1.000 ,1.000 ,1.000 ,1.000 
+scFoundation,Neural.cell,Astrocytes,0.998 ,0.333 ,0.998 ,0.999 
+scFoundation,Neural.cell,Microglial cells,1.000 ,1.000 ,1.000 ,1.000 
+scFoundation,Neural.cell,Oligodendrocytes,1.000 ,1.000 ,1.000 ,1.000 
+scFoundation,Neural.cell,Oligodendrocyte precursor cells,0.999 ,0.500 ,0.999 ,0.999 
+scGPT,Neural.cell,Overall,0.997 ,0.997 ,0.997 ,0.997 
+scGPT,Neural.cell,Glutamatergic neurons,0.994 ,0.250 ,0.994 ,0.997 
+scGPT,Neural.cell,Inhibitory interneurons,0.993 ,0.333 ,0.993 ,0.996 
+scGPT,Neural.cell,Astrocytes,0.999 ,0.500 ,0.999 ,0.999 
+scGPT,Neural.cell,Microglial cells,0.999 ,0.500 ,0.999 ,0.999 
+scGPT,Neural.cell,Oligodendrocytes,0.999 ,0.500 ,0.999 ,0.999 
+scGPT,Neural.cell,Oligodendrocyte precursor cells,0.997 ,0.500 ,0.997 ,0.998 
+UCE,Neural.cell,Overall,0.998 ,0.998 ,0.998 ,0.998 
+UCE,Neural.cell,Glutamatergic neurons,0.998 ,0.500 ,0.998 ,0.999 
+UCE,Neural.cell,Inhibitory interneurons,0.996 ,0.333 ,0.996 ,0.998 
+UCE,Neural.cell,Astrocytes,0.998 ,0.333 ,0.998 ,0.999 
+UCE,Neural.cell,Microglial cells,1.000 ,1.000 ,1.000 ,1.000 
+UCE,Neural.cell,Oligodendrocytes,0.998 ,0.500 ,0.998 ,0.999 
+UCE,Neural.cell,Oligodendrocyte precursor cells,0.999 ,0.500 ,0.999 ,0.999 
+scLong,Neural.cell,Overall,0.580 ,0.582 ,0.580 ,0.561 
+scLong,Neural.cell,Glutamatergic neurons,0.485 ,0.167 ,0.485 ,0.654 
+scLong,Neural.cell,Inhibitory interneurons,0.303 ,0.167 ,0.303 ,0.465 
+scLong,Neural.cell,Astrocytes,0.329 ,0.167 ,0.329 ,0.495 
+scLong,Neural.cell,Microglial cells,0.833 ,0.167 ,0.833 ,0.909 
+scLong,Neural.cell,Oligodendrocytes,0.812 ,0.167 ,0.812 ,0.896 
+scLong,Neural.cell,Oligodendrocyte precursor cells,0.716 ,0.167 ,0.716 ,0.834 

benchmark results/results_stem_cell_identification.csv

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+Model,Cell population,Cell type,Accuracy,Precision,Recall,F1 Score
+Geneformer,Stem.cell,Overall,1,1,1,1
+Geneformer,Stem.cell,Hematopoietic Stem Cells,1,1,1,1
+Geneformer,Stem.cell,Neural Stem Cells,1,1,1,1
+Geneformer,Stem.cell,Mesenchymal Stem Cells,1,1,1,1
+Geneformer,Stem.cell,Embryonic Stem Cells,1,1,1,1
+Geneformer,Non.Stem.cell,Overall,0.522,1,0.522,0.686
+Geneformer,Non.Stem.cell,Astrocytes,1,1,1,1
+Geneformer,Non.Stem.cell,B.cells,1,1,1,1
+Geneformer,Non.Stem.cell,Endothelial cells,1,1,1,1
+Geneformer,Non.Stem.cell,Epithelial cells,1,1,1,1
+Geneformer,Non.Stem.cell,Fibroblasts,1,1,1,1
+Geneformer,Non.Stem.cell,Germ cells,1,1,1,1
+Geneformer,Non.Stem.cell,Glioblasts,0.997,1,0.997,0.998
+Geneformer,Non.Stem.cell,Microglias,0.306,1,0.306,0.469
+Geneformer,Non.Stem.cell,Myeloid cells,0,0,0,0
+Geneformer,Non.Stem.cell,Neuron,0,0,0,0
+Geneformer,Non.Stem.cell,Neuronal.IPCs ,0,0,0,0
+Geneformer,Non.Stem.cell,Oligodendrocytes,0,0,0,0
+Geneformer,Non.Stem.cell,OPCs,0,0,0,0
+Geneformer,Non.Stem.cell,T/NK cells,0,0,0,0
+scFoundation,Stem.cell,Overall,0.979,1,0.979,0.989
+scFoundation,Stem.cell,Hematopoietic Stem Cells,0.998,1,0.998,0.999
+scFoundation,Stem.cell,Neural Stem Cells,0.947,1,0.947,0.973
+scFoundation,Stem.cell,Mesenchymal Stem Cells,0.971,1,0.971,0.985
+scFoundation,Stem.cell,Embryonic Stem Cells,1,1,1,1
+scFoundation,Non.Stem.cell,Overall,0.961,1,0.961,0.98
+scFoundation,Non.Stem.cell,Astrocytes,1,1,1,1
+scFoundation,Non.Stem.cell,B.cells,0.987,1,0.987,0.993
+scFoundation,Non.Stem.cell,Endothelial cells,0.998,1,0.998,0.999
+scFoundation,Non.Stem.cell,Epithelial cells,1,1,1,1
+scFoundation,Non.Stem.cell,Fibroblasts,0.906,1,0.906,0.951
+scFoundation,Non.Stem.cell,Germ cells,1,1,1,1
+scFoundation,Non.Stem.cell,Glioblasts,0.732,1,0.732,0.845
+scFoundation,Non.Stem.cell,Microglias,1,1,1,1
+scFoundation,Non.Stem.cell,Myeloid cells,0.981,1,0.981,0.99
+scFoundation,Non.Stem.cell,Neuron,1,1,1,1
+scFoundation,Non.Stem.cell,Neuronal.IPCs ,0.857,1,0.857,0.923
+scFoundation,Non.Stem.cell,Oligodendrocytes,1,1,1,1
+scFoundation,Non.Stem.cell,OPCs,1,1,1,1
+scFoundation,Non.Stem.cell,T/NK cells,0.996,1,0.996,0.998
+scGPT,Stem.cell,Overall,0.964,1,0.964,0.982
+scGPT,Stem.cell,Hematopoietic Stem Cells,0.936,1,0.936,0.967
+scGPT,Stem.cell,Neural Stem Cells,0.94,1,0.94,0.969
+scGPT,Stem.cell,Mesenchymal Stem Cells,0.982,1,0.982,0.991
+scGPT,Stem.cell,Embryonic Stem Cells,0.997,1,0.997,0.998
+scGPT,Non.Stem.cell,Overall,0.957,1,0.957,0.978
+scGPT,Non.Stem.cell,Astrocytes,1,1,1,1
+scGPT,Non.Stem.cell,B.cells,0.998,1,0.998,0.999
+scGPT,Non.Stem.cell,Endothelial cells,1,1,1,1
+scGPT,Non.Stem.cell,Epithelial cells,1,1,1,1
+scGPT,Non.Stem.cell,Fibroblasts,0.931,1,0.931,0.964
+scGPT,Non.Stem.cell,Germ cells,1,1,1,1
+scGPT,Non.Stem.cell,Glioblasts,0.675,1,0.675,0.806
+scGPT,Non.Stem.cell,Microglias,1,1,1,1
+scGPT,Non.Stem.cell,Myeloid cells,0.992,1,0.992,0.996
+scGPT,Non.Stem.cell,Neuron,1,1,1,1
+scGPT,Non.Stem.cell,Neuronal.IPCs ,0.807,1,0.807,0.893
+scGPT,Non.Stem.cell,Oligodendrocytes,0.998,1,0.998,0.999
+scGPT,Non.Stem.cell,OPCs,1,1,1,1
+scGPT,Non.Stem.cell,T/NK cells,0.996,1,0.996,0.998
+UCE,Stem.cell,Overall,0.979,1,0.979,0.989
+UCE,Stem.cell,Hematopoietic Stem Cells,0.999,1,0.999,0.999
+UCE,Stem.cell,Neural Stem Cells,0.934,1,0.934,0.966
+UCE,Stem.cell,Mesenchymal Stem Cells,0.984,1,0.984,0.992
+UCE,Stem.cell,Embryonic Stem Cells,1,1,1,1
+UCE,Non.Stem.cell,Overall,0.963,1,0.963,0.981
+UCE,Non.Stem.cell,Astrocytes,1,1,1,1
+UCE,Non.Stem.cell,B.cells,0.999,1,0.999,0.999
+UCE,Non.Stem.cell,Endothelial cells,0.999,1,0.999,0.999
+UCE,Non.Stem.cell,Epithelial cells,1,1,1,1
+UCE,Non.Stem.cell,Fibroblasts,0.943,1,0.943,0.971
+UCE,Non.Stem.cell,Germ cells,1,1,1,1
+UCE,Non.Stem.cell,Glioblasts,0.743,1,0.743,0.853
+UCE,Non.Stem.cell,Microglias,1,1,1,1
+UCE,Non.Stem.cell,Myeloid cells,0.989,1,0.989,0.994
+UCE,Non.Stem.cell,Neuron,1,1,1,1
+UCE,Non.Stem.cell,Neuronal.IPCs ,0.816,1,0.816,0.899
+UCE,Non.Stem.cell,Oligodendrocytes,1,1,1,1
+UCE,Non.Stem.cell,OPCs,1,1,1,1
+UCE,Non.Stem.cell,T/NK cells,0.999,1,0.999,0.999
+scLong,Stem.cell,Overall,0.904,1,0.904,0.95
+scLong,Stem.cell,Hematopoietic Stem Cells,0.989,1,0.989,0.994
+scLong,Stem.cell,Neural Stem Cells,0.8,1,0.8,0.889
+scLong,Stem.cell,Mesenchymal Stem Cells,0.83,1,0.83,0.907
+scLong,Stem.cell,Embryonic Stem Cells,0.997,1,0.997,0.998
+scLong,Non.Stem.cell,Overall,0.704,1,0.704,0.827
+scLong,Non.Stem.cell,Astrocytes,0.994,1,0.994,0.997
+scLong,Non.Stem.cell,B.cells,0.74,1,0.74,0.851
+scLong,Non.Stem.cell,Endothelial cells,0.627,1,0.627,0.771
+scLong,Non.Stem.cell,Epithelial cells,0.5,1,0.5,0.667
+scLong,Non.Stem.cell,Fibroblasts,0.281,1,0.281,0.439
+scLong,Non.Stem.cell,Germ cells,0.929,1,0.929,0.963
+scLong,Non.Stem.cell,Glioblasts,0.425,1,0.425,0.596
+scLong,Non.Stem.cell,Microglias,0.993,1,0.993,0.996
+scLong,Non.Stem.cell,Myeloid cells,0.613,1,0.613,0.76
+scLong,Non.Stem.cell,Neuron,1,1,1,1
+scLong,Non.Stem.cell,Neuronal.IPCs ,0.263,1,0.263,0.416
+scLong,Non.Stem.cell,Oligodendrocytes,0.995,1,0.995,0.997
+scLong,Non.Stem.cell,OPCs,0.997,1,0.997,0.998
+scLong,Non.Stem.cell,T/NK cells,0.505,1,0.505,0.671

benchmark results/results_stem_cell_subtype_classification.csv

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+Model,Cell population,Cell type,Accuracy,Macro_Precision,Macro_Recall,Macro_F1
+Geneformer,Stem.cell,Overall,0.335,0.169,0.333,0.505
+Geneformer,Stem.cell,Hematopoietic Stem Cells,0,0,0,NA
+Geneformer,Stem.cell,Neural Stem Cells,0,0,0,NA
+Geneformer,Stem.cell,Mesenchymal Stem Cells,1,1,1,1
+scFoundation,Stem.cell,Overall,1,1,1,1
+scFoundation,Stem.cell,Hematopoietic Stem Cells,1,1,1,1
+scFoundation,Stem.cell,Neural Stem Cells,1,1,1,1
+scFoundation,Stem.cell,Mesenchymal Stem Cells,1,1,1,1
+scGPT,Stem.cell,Overall,1,1,1,1
+scGPT,Stem.cell,Hematopoietic Stem Cells,1,1,1,1
+scGPT,Stem.cell,Neural Stem Cells,1,1,1,1
+scGPT,Stem.cell,Mesenchymal Stem Cells,1,1,1,1
+UCE,Stem.cell,Overall,1,1,1,1
+UCE,Stem.cell,Hematopoietic Stem Cells,1,1,1,1
+UCE,Stem.cell,Neural Stem Cells,1,1,1,1
+UCE,Stem.cell,Mesenchymal Stem Cells,1,1,1,1
+scLong,Stem.cell,Overall,0.995,0.333,0.995,0.997
+scLong,Stem.cell,Hematopoietic Stem Cells,0.985,0.5,0.985,0.992
+scLong,Stem.cell,Neural Stem Cells,0.985,0.333,0.985,0.992
+scLong,Stem.cell,Mesenchymal Stem Cells,0.988,0.988,0.988,0.988

benchmark results/results_tumor_cell_identification.csv

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+Model,Cell population,Primary_site/cell type,Accuracy,Precision,Recall,F1 Score
+Geneformer,Primary tumor cells ,Overall,0.008 ,1,0.008 ,0.017 
+Geneformer,Primary tumor cells ,Lung,0.000 ,0,0.000 ,0.000 
+Geneformer,Primary tumor cells ,Pancreas,0.000 ,0,0.000 ,0.000 
+Geneformer,Primary tumor cells ,Colorectal,0.004 ,1,0.004 ,0.008 
+Geneformer,Primary tumor cells ,Cervical ,0.004 ,1,0.004 ,0.008 
+Geneformer,Primary tumor cells ,Kidney,0.008 ,1,0.008 ,0.016 
+Geneformer,Primary tumor cells ,Liver,0.005 ,1,0.005 ,0.010 
+Geneformer,Primary tumor cells ,Ovarian,0.006 ,1,0.006 ,0.012 
+Geneformer,Primary tumor cells ,Esophageal,0.001 ,1,0.001 ,0.002 
+Geneformer,Primary tumor cells ,Gastric,0.005 ,1,0.005 ,0.010 
+Geneformer,Primary tumor cells ,Breast,0.129 ,1,0.129 ,0.229 
+Geneformer,Primary tumor cells ,Head-neck,0.000 ,0,0.000 ,0.000 
+Geneformer,Primary tumor cells ,Glioma,0.000 ,0,0.000 ,0.000 
+Geneformer,Primary tumor cells ,Lymphoma,0.000 ,0,0.000 ,0.000 
+Geneformer,Primary tumor cells ,Melanoma,0.001 ,1,0.001 ,0.002 
+Geneformer,Primary tumor cells ,Thyroid,0.000 ,0,0.000 ,0.000 
+Geneformer,Primary tumor cells ,DSRCT,0.000 ,0,0.000 ,0.000 
+Geneformer,Primary tumor cells ,Myeloma,0.000 ,0,0.000 ,0.000 
+Geneformer,Primary tumor cells ,Osteosarcoma,0.001 ,1,0.001 ,0.002 
+Geneformer,Primary tumor cells ,Retinoblastoma,0.004 ,1,0.004 ,0.008 
+Geneformer,Primary tumor cells ,Prostate,0.002 ,1,0.002 ,0.004 
+Geneformer,Primary tumor cells ,Seminoma,0.002 ,1,0.002 ,0.003 
+Geneformer,Metastatic tumor cells ,Overall,0.002 ,1,0.002 ,0.005 
+Geneformer,Metastatic tumor cells ,Lung,0.000 ,0,0.000 ,0.000 
+Geneformer,Metastatic tumor cells ,Pancreas,0.000 ,0,0.000 ,0.000 
+Geneformer,Metastatic tumor cells ,Colorectal,0.004 ,1,0.004 ,0.008 
+Geneformer,Metastatic tumor cells ,Liver,0.003 ,1,0.003 ,0.006 
+Geneformer,Metastatic tumor cells ,Ovarian,0.005 ,1,0.005 ,0.010 
+Geneformer,Metastatic tumor cells ,Gastric,0.004 ,1,0.004 ,0.008 
+Geneformer,Metastatic tumor cells ,Breast,0.007 ,1,0.007 ,0.014 
+Geneformer,Metastatic tumor cells ,Head-neck,0.000 ,0,0.000 ,0.000 
+Geneformer,Metastatic tumor cells ,Melanoma,0.000 ,0,0.000 ,0.000 
+Geneformer,Metastatic tumor cells ,Thyroid,0.000 ,0,0.000 ,0.000 
+Geneformer,Circulating Tumor Cells,Overall,0.036 ,1,0.036 ,0.069 
+Geneformer,Circulating Tumor Cells,Lung,0.000 ,0,0.000 ,0.000 
+Geneformer,Circulating Tumor Cells,Colorectal,0.412 ,1,0.412 ,0.583 
+Geneformer,Circulating Tumor Cells,Liver,0.000 ,0,0.000 ,0.000 
+Geneformer,Circulating Tumor Cells,Breast,0.000 ,0,0.000 ,0.000 
+Geneformer,Circulating Tumor Cells,Melanoma,0.037 ,1,0.037 ,0.071 
+Geneformer,Circulating Tumor Cells,Prostate,0.208 ,1,0.208 ,0.344 
+Geneformer,Normal cells,Overall,0.009 ,1,0.009 ,0.018 
+Geneformer,Normal cells,B cells,0.000 ,0,0.000 ,0.000 
+Geneformer,Normal cells,Myeloid,0.000 ,0,0.000 ,0.000 
+Geneformer,Normal cells,T/NK cells,0.000 ,0,0.000 ,0.000 
+Geneformer,Normal cells,Endothelial cells,0.000 ,0,0.000 ,0.000 
+Geneformer,Normal cells,Epithelial cells,0.001 ,1,0.001 ,0.001 
+Geneformer,Normal cells,Fibroblasts,0.000 ,0,0.000 ,0.000 
+Geneformer,Normal cells,Mesenchymal cells,0.000 ,0,0.000 ,0.000 
+Geneformer,Normal cells,Germ cells,0.000 ,0,0.000 ,0.000 
+Geneformer,Normal cells,Neural stem cells,0.000 ,0,0.000 ,0.000 
+Geneformer,Normal cells,Glioblasts,0.000 ,0,0.000 ,0.000 
+Geneformer,Normal cells,Neuronal IPCs,0.000 ,0,0.000 ,0.000 
+Geneformer,Normal cells,Neuron,0.000 ,0,0.000 ,0.000 
+Geneformer,Normal cells,Astrocytes,0.134 ,1,0.134 ,0.236 
+Geneformer,Normal cells,Oligodendrocytes,0.000 ,0,0.000 ,0.000 
+Geneformer,Normal cells,Microglias,0.000 ,0,0.000 ,0.000 
+Geneformer,Normal cells,OPCs,0.000 ,0,0.000 ,0.000 
+scFoundation,Primary tumor cells ,Overall,0.885 ,1,0.885 ,0.939 
+scFoundation,Primary tumor cells ,Lung,0.911 ,1,0.911 ,0.953 
+scFoundation,Primary tumor cells ,Pancreas,0.968 ,1,0.968 ,0.984 
+scFoundation,Primary tumor cells ,Colorectal,0.965 ,1,0.965 ,0.982 
+scFoundation,Primary tumor cells ,Cervical ,0.647 ,1,0.647 ,0.786 
+scFoundation,Primary tumor cells ,Kidney,0.554 ,1,0.554 ,0.713 
+scFoundation,Primary tumor cells ,Liver,0.956 ,1,0.956 ,0.978 
+scFoundation,Primary tumor cells ,Ovarian,0.949 ,1,0.949 ,0.974 
+scFoundation,Primary tumor cells ,Esophageal,0.904 ,1,0.904 ,0.949 
+scFoundation,Primary tumor cells ,Gastric,0.889 ,1,0.889 ,0.942 
+scFoundation,Primary tumor cells ,Breast,0.526 ,1,0.526 ,0.689 
+scFoundation,Primary tumor cells ,Head-neck,0.967 ,1,0.967 ,0.983 
+scFoundation,Primary tumor cells ,Glioma,0.301 ,1,0.301 ,0.463 
+scFoundation,Primary tumor cells ,Lymphoma,0.857 ,1,0.857 ,0.923 
+scFoundation,Primary tumor cells ,Melanoma,0.933 ,1,0.933 ,0.965 
+scFoundation,Primary tumor cells ,Thyroid,0.911 ,1,0.911 ,0.954 
+scFoundation,Primary tumor cells ,DSRCT,0.997 ,1,0.997 ,0.999 
+scFoundation,Primary tumor cells ,Myeloma,0.998 ,1,0.998 ,0.999 
+scFoundation,Primary tumor cells ,Osteosarcoma,0.789 ,1,0.789 ,0.882 
+scFoundation,Primary tumor cells ,Retinoblastoma,0.979 ,1,0.979 ,0.989 
+scFoundation,Primary tumor cells ,Prostate,1.000 ,1,1.000 ,1.000 
+scFoundation,Primary tumor cells ,Seminoma,0.951 ,1,0.951 ,0.975 
+scFoundation,Metastatic tumor cells ,Overall,0.950 ,1,0.950 ,0.974 
+scFoundation,Metastatic tumor cells ,Lung,0.869 ,1,0.869 ,0.930 
+scFoundation,Metastatic tumor cells ,Pancreas,0.982 ,1,0.982 ,0.991 
+scFoundation,Metastatic tumor cells ,Colorectal,0.867 ,1,0.867 ,0.929 
+scFoundation,Metastatic tumor cells ,Liver,0.992 ,1,0.992 ,0.996 
+scFoundation,Metastatic tumor cells ,Ovarian,0.961 ,1,0.961 ,0.980 
+scFoundation,Metastatic tumor cells ,Gastric,0.909 ,1,0.909 ,0.952 
+scFoundation,Metastatic tumor cells ,Breast,0.976 ,1,0.976 ,0.988 
+scFoundation,Metastatic tumor cells ,Head-neck,0.982 ,1,0.982 ,0.991 
+scFoundation,Metastatic tumor cells ,Melanoma,0.973 ,1,0.973 ,0.986 
+scFoundation,Metastatic tumor cells ,Thyroid,0.992 ,1,0.992 ,0.996 
+scFoundation,Circulating Tumor Cells,Overall,0.149 ,1,0.149 ,0.259 
+scFoundation,Circulating Tumor Cells,Lung,0.100 ,1,0.100 ,0.182 
+scFoundation,Circulating Tumor Cells,Colorectal,0.000 ,0,0.000 ,0.000 
+scFoundation,Circulating Tumor Cells,Liver,0.973 ,1,0.973 ,0.986 
+scFoundation,Circulating Tumor Cells,Breast,0.000 ,0,0.000 ,0.000 
+scFoundation,Circulating Tumor Cells,Melanoma,0.000 ,0,0.000 ,0.000 
+scFoundation,Circulating Tumor Cells,Prostate,0.014 ,1,0.014 ,0.027 
+scFoundation,Normal cells,Overall,0.881 ,1,0.881 ,0.939 
+scFoundation,Normal cells,B cells,0.711 ,1,0.711 ,0.939
+scFoundation,Normal cells,Myeloid,0.828 ,1,0.828 ,0.831
+scFoundation,Normal cells,T/NK cells,0.712 ,1,0.712 ,0.907 
+scFoundation,Normal cells,Endothelial cells,0.878 ,1,0.878 ,0.831 
+scFoundation,Normal cells,Epithelial cells,0.403 ,1,0.403 ,0.933 
+scFoundation,Normal cells,Fibroblasts,0.848 ,1,0.848 ,0.573 
+scFoundation,Normal cells,Mesenchymal cells,0.981 ,1,0.981 ,0.921 
+scFoundation,Normal cells,Germ cells,1.000 ,1,1.000 ,0.990 
+scFoundation,Normal cells,Neural stem cells,1.000 ,1,1.000 ,1.000 
+scFoundation,Normal cells,Glioblasts,1.000 ,1,1.000 ,1.000 
+scFoundation,Normal cells,Neuronal IPCs,1.000 ,1,1.000 ,1.000 
+scFoundation,Normal cells,Neuron,0.999 ,1,0.999 ,1.000 
+scFoundation,Normal cells,Astrocytes,0.869 ,1,0.869 ,1.000 
+scFoundation,Normal cells,Oligodendrocytes,0.886 ,1,0.886 ,0.931 
+scFoundation,Normal cells,Microglias,1.000 ,1,1.000 ,0.940 
+scFoundation,Normal cells,OPCs,1.000 ,1,1.000 ,1.000 
+scGPT,Primary tumor cells ,Overall,0.932 ,1,0.932 ,0.965 
+scGPT,Primary tumor cells ,Lung,0.985 ,1,0.985 ,0.992 
+scGPT,Primary tumor cells ,Pancreas,0.996 ,1,0.996 ,0.998 
+scGPT,Primary tumor cells ,Colorectal,0.999 ,1,0.999 ,0.999 
+scGPT,Primary tumor cells ,Cervical ,0.995 ,1,0.995 ,0.997 
+scGPT,Primary tumor cells ,Kidney,0.858 ,1,0.858 ,0.923 
+scGPT,Primary tumor cells ,Liver,0.933 ,1,0.933 ,0.965 
+scGPT,Primary tumor cells ,Ovarian,0.994 ,1,0.994 ,0.997 
+scGPT,Primary tumor cells ,Esophageal,0.988 ,1,0.988 ,0.994 
+scGPT,Primary tumor cells ,Gastric,0.962 ,1,0.962 ,0.981 
+scGPT,Primary tumor cells ,Breast,0.987 ,1,0.987 ,0.993 
+scGPT,Primary tumor cells ,Head-neck,0.999 ,1,0.999 ,0.999 
+scGPT,Primary tumor cells ,Glioma,0.362 ,1,0.362 ,0.532 
+scGPT,Primary tumor cells ,Lymphoma,0.586 ,1,0.586 ,0.739 
+scGPT,Primary tumor cells ,Melanoma,0.941 ,1,0.941 ,0.970 
+scGPT,Primary tumor cells ,Thyroid,0.934 ,1,0.934 ,0.966 
+scGPT,Primary tumor cells ,DSRCT,1.000 ,1,1.000 ,1.000 
+scGPT,Primary tumor cells ,Myeloma,1.000 ,1,1.000 ,1.000 
+scGPT,Primary tumor cells ,Osteosarcoma,0.956 ,1,0.956 ,0.978 
+scGPT,Primary tumor cells ,Retinoblastoma,0.993 ,1,0.993 ,0.996 
+scGPT,Primary tumor cells ,Prostate,0.999 ,1,0.999 ,0.999 
+scGPT,Primary tumor cells ,Seminoma,0.950 ,1,0.950 ,0.974 
+scGPT,Metastatic tumor cells ,Overall,0.965 ,1,0.965 ,0.982 
+scGPT,Metastatic tumor cells ,Lung,0.980 ,1,0.980 ,0.990 
+scGPT,Metastatic tumor cells ,Pancreas,0.997 ,1,0.997 ,0.998 
+scGPT,Metastatic tumor cells ,Colorectal,0.924 ,1,0.924 ,0.960 
+scGPT,Metastatic tumor cells ,Liver,0.949 ,1,0.949 ,0.974 
+scGPT,Metastatic tumor cells ,Ovarian,0.972 ,1,0.972 ,0.986 
+scGPT,Metastatic tumor cells ,Gastric,0.929 ,1,0.929 ,0.963 
+scGPT,Metastatic tumor cells ,Breast,0.973 ,1,0.973 ,0.986 
+scGPT,Metastatic tumor cells ,Head-neck,0.947 ,1,0.947 ,0.973 
+scGPT,Metastatic tumor cells ,Melanoma,0.983 ,1,0.983 ,0.991 
+scGPT,Metastatic tumor cells ,Thyroid,0.978 ,1,0.978 ,0.989 
+scGPT,Circulating Tumor Cells,Overall,0.405 ,1,0.405 ,0.577 
+scGPT,Circulating Tumor Cells,Lung,0.800 ,1,0.800 ,0.889 
+scGPT,Circulating Tumor Cells,Colorectal,0.059 ,1,0.059 ,0.111 
+scGPT,Circulating Tumor Cells,Liver,0.088 ,1,0.088 ,0.163 
+scGPT,Circulating Tumor Cells,Breast,0.422 ,1,0.422 ,0.594 
+scGPT,Circulating Tumor Cells,Melanoma,0.330 ,1,0.330 ,0.497 
+scGPT,Circulating Tumor Cells,Prostate,0.909 ,1,0.909 ,0.952 
+scGPT,Normal cells,Overall,0.921 ,1,0.921 ,0.959 
+scGPT,Normal cells,B cells,0.841 ,1,0.841 ,0.913 
+scGPT,Normal cells,Myeloid,0.814 ,1,0.814 ,0.898 
+scGPT,Normal cells,T/NK cells,0.661 ,1,0.661 ,0.796 
+scGPT,Normal cells,Endothelial cells,0.865 ,1,0.865 ,0.928 
+scGPT,Normal cells,Epithelial cells,0.953 ,1,0.953 ,0.976 
+scGPT,Normal cells,Fibroblasts,0.886 ,1,0.886 ,0.939 
+scGPT,Normal cells,Mesenchymal cells,1.000 ,1,1.000 ,1.000 
+scGPT,Normal cells,Germ cells,1.000 ,1,1.000 ,1.000 
+scGPT,Normal cells,Neural stem cells,1.000 ,1,1.000 ,1.000 
+scGPT,Normal cells,Glioblasts,0.999 ,1,0.999 ,1.000 
+scGPT,Normal cells,Neuronal IPCs,0.998 ,1,0.998 ,0.999 
+scGPT,Normal cells,Neuron,1.000 ,1,1.000 ,1.000 
+scGPT,Normal cells,Astrocytes,0.879 ,1,0.879 ,0.936 
+scGPT,Normal cells,Oligodendrocytes,0.907 ,1,0.907 ,0.951 
+scGPT,Normal cells,Microglias,1.000 ,1,1.000 ,1.000 
+scGPT,Normal cells,OPCs,1.000 ,1,1.000 ,1.000 
+UCE,Primary tumor cells ,Overall,0.923 ,1,0.923 ,0.960 
+UCE,Primary tumor cells ,Lung,0.961 ,1,0.961 ,0.980 
+UCE,Primary tumor cells ,Pancreas,0.998 ,1,0.998 ,0.999 
+UCE,Primary tumor cells ,Colorectal,0.983 ,1,0.983 ,0.991 
+UCE,Primary tumor cells ,Cervical ,0.987 ,1,0.987 ,0.993 
+UCE,Primary tumor cells ,Kidney,0.928 ,1,0.928 ,0.963 
+UCE,Primary tumor cells ,Liver,0.936 ,1,0.936 ,0.967 
+UCE,Primary tumor cells ,Ovarian,0.995 ,1,0.995 ,0.997 
+UCE,Primary tumor cells ,Esophageal,0.903 ,1,0.903 ,0.949 
+UCE,Primary tumor cells ,Gastric,0.976 ,1,0.976 ,0.988 
+UCE,Primary tumor cells ,Breast,0.979 ,1,0.979 ,0.989 
+UCE,Primary tumor cells ,Head-neck,0.790 ,1,0.790 ,0.883 
+UCE,Primary tumor cells ,Glioma,0.347 ,1,0.347 ,0.515 
+UCE,Primary tumor cells ,Lymphoma,0.801 ,1,0.801 ,0.890 
+UCE,Primary tumor cells ,Melanoma,0.993 ,1,0.993 ,0.996 
+UCE,Primary tumor cells ,Thyroid,0.808 ,1,0.808 ,0.894 
+UCE,Primary tumor cells ,DSRCT,0.999 ,1,0.999 ,0.999 
+UCE,Primary tumor cells ,Myeloma,0.973 ,1,0.973 ,0.986 
+UCE,Primary tumor cells ,Osteosarcoma,0.992 ,1,0.992 ,0.996 
+UCE,Primary tumor cells ,Retinoblastoma,1.000 ,1,1.000 ,1.000 
+UCE,Primary tumor cells ,Prostate,1.000 ,1,1.000 ,1.000 
+UCE,Primary tumor cells ,Seminoma,0.825 ,1,0.825 ,0.904 
+UCE,Metastatic tumor cells ,Overall,0.948 ,1,0.948 ,0.973 
+UCE,Metastatic tumor cells ,Lung,0.984 ,1,0.984 ,0.992 
+UCE,Metastatic tumor cells ,Pancreas,0.997 ,1,0.997 ,0.998 
+UCE,Metastatic tumor cells ,Colorectal,0.925 ,1,0.925 ,0.961 
+UCE,Metastatic tumor cells ,Liver,0.994 ,1,0.994 ,0.997 
+UCE,Metastatic tumor cells ,Ovarian,0.960 ,1,0.960 ,0.980 
+UCE,Metastatic tumor cells ,Gastric,0.869 ,1,0.869 ,0.930 
+UCE,Metastatic tumor cells ,Breast,0.948 ,1,0.948 ,0.973 
+UCE,Metastatic tumor cells ,Head-neck,0.960 ,1,0.960 ,0.980 
+UCE,Metastatic tumor cells ,Melanoma,0.884 ,1,0.884 ,0.938 
+UCE,Metastatic tumor cells ,Thyroid,0.964 ,1,0.964 ,0.982 
+UCE,Circulating Tumor Cells,Overall,0.425 ,1,0.425 ,0.597 
+UCE,Circulating Tumor Cells,Lung,0.900 ,1,0.900 ,0.947 
+UCE,Circulating Tumor Cells,Colorectal,0.059 ,1,0.059 ,0.111 
+UCE,Circulating Tumor Cells,Liver,0.053 ,1,0.053 ,0.101 
+UCE,Circulating Tumor Cells,Breast,0.460 ,1,0.460 ,0.630 
+UCE,Circulating Tumor Cells,Melanoma,0.330 ,1,0.330 ,0.497 
+UCE,Circulating Tumor Cells,Prostate,0.935 ,1,0.935 ,0.966 
+UCE,Normal cells,Overall,0.930 ,1,0.930 ,0.964 
+UCE,Normal cells,B cells,0.878 ,1,0.878 ,0.935 
+UCE,Normal cells,Myeloid,0.861 ,1,0.861 ,0.925 
+UCE,Normal cells,T/NK cells,0.637 ,1,0.637 ,0.778 
+UCE,Normal cells,Endothelial cells,0.903 ,1,0.903 ,0.949 
+UCE,Normal cells,Epithelial cells,0.983 ,1,0.983 ,0.992 
+UCE,Normal cells,Fibroblasts,0.893 ,1,0.893 ,0.943 
+UCE,Normal cells,Mesenchymal cells,1.000 ,1,1.000 ,1.000 
+UCE,Normal cells,Germ cells,1.000 ,1,1.000 ,1.000 
+UCE,Normal cells,Neural stem cells,1.000 ,1,1.000 ,1.000 
+UCE,Normal cells,Glioblasts,1.000 ,1,1.000 ,1.000 
+UCE,Normal cells,Neuronal IPCs,1.000 ,1,1.000 ,1.000 
+UCE,Normal cells,Neuron,1.000 ,1,1.000 ,1.000 
+UCE,Normal cells,Astrocytes,0.880 ,1,0.880 ,0.936 
+UCE,Normal cells,Oligodendrocytes,0.908 ,1,0.908 ,0.952 
+UCE,Normal cells,Microglias,1.000 ,1,1.000 ,1.000 
+UCE,Normal cells,OPCs,1.000 ,1,1.000 ,1.000 
+scLong,Primary tumor cells ,Overall,0.838 ,1,0.838 ,0.912 
+scLong,Primary tumor cells ,Lung,0.986 ,1,0.986 ,0.993 
+scLong,Primary tumor cells ,Pancreas,0.973 ,1,0.973 ,0.986 
+scLong,Primary tumor cells ,Colorectal,0.938 ,1,0.938 ,0.968 
+scLong,Primary tumor cells ,Cervical ,0.630 ,1,0.630 ,0.773 
+scLong,Primary tumor cells ,Kidney,0.894 ,1,0.894 ,0.944 
+scLong,Primary tumor cells ,Liver,0.746 ,1,0.746 ,0.855 
+scLong,Primary tumor cells ,Ovarian,0.944 ,1,0.944 ,0.971 
+scLong,Primary tumor cells ,Esophageal,0.893 ,1,0.893 ,0.943 
+scLong,Primary tumor cells ,Gastric,0.866 ,1,0.866 ,0.928 
+scLong,Primary tumor cells ,Breast,0.287 ,1,0.287 ,0.446 
+scLong,Primary tumor cells ,Head-neck,0.867 ,1,0.867 ,0.929 
+scLong,Primary tumor cells ,Glioma,0.322 ,1,0.322 ,0.488 
+scLong,Primary tumor cells ,Lymphoma,0.827 ,1,0.827 ,0.905 
+scLong,Primary tumor cells ,Melanoma,0.997 ,1,0.997 ,0.998 
+scLong,Primary tumor cells ,Thyroid,0.880 ,1,0.880 ,0.936 
+scLong,Primary tumor cells ,DSRCT,0.949 ,1,0.949 ,0.974 
+scLong,Primary tumor cells ,Myeloma,0.743 ,1,0.743 ,0.853 
+scLong,Primary tumor cells ,Osteosarcoma,0.957 ,1,0.957 ,0.978 
+scLong,Primary tumor cells ,Retinoblastoma,0.996 ,1,0.996 ,0.998 
+scLong,Primary tumor cells ,Prostate,0.816 ,1,0.816 ,0.899 
+scLong,Primary tumor cells ,Seminoma,0.983 ,1,0.983 ,0.991 
+scLong,Metastatic tumor cells ,Overall,0.910 ,1,0.910 ,0.953 
+scLong,Metastatic tumor cells ,Lung,0.961 ,1,0.961 ,0.980 
+scLong,Metastatic tumor cells ,Pancreas,0.852 ,1,0.852 ,0.920 
+scLong,Metastatic tumor cells ,Colorectal,0.903 ,1,0.903 ,0.949 
+scLong,Metastatic tumor cells ,Liver,0.924 ,1,0.924 ,0.960 
+scLong,Metastatic tumor cells ,Ovarian,0.850 ,1,0.850 ,0.919 
+scLong,Metastatic tumor cells ,Gastric,0.923 ,1,0.923 ,0.960 
+scLong,Metastatic tumor cells ,Breast,0.954 ,1,0.954 ,0.977 
+scLong,Metastatic tumor cells ,Head-neck,0.722 ,1,0.722 ,0.839 
+scLong,Metastatic tumor cells ,Melanoma,0.914 ,1,0.914 ,0.955 
+scLong,Metastatic tumor cells ,Thyroid,0.953 ,1,0.953 ,0.976 
+scLong,Circulating Tumor Cells,Overall,0.715 ,1,0.715 ,0.834 
+scLong,Circulating Tumor Cells,Lung,0.900 ,1,0.900 ,0.947 
+scLong,Circulating Tumor Cells,Colorectal,0.941 ,1,0.941 ,0.970 
+scLong,Circulating Tumor Cells,Liver,0.000 ,NA,0.000 ,NA
+scLong,Circulating Tumor Cells,Breast,0.840 ,1,0.840 ,0.913 
+scLong,Circulating Tumor Cells,Melanoma,0.743 ,1,0.743 ,0.853 
+scLong,Circulating Tumor Cells,Prostate,0.961 ,1,0.961 ,0.980 
+scLong,Normal cells,Overall,0.726 ,1,0.726 ,0.842 
+scLong,Normal cells,B cells,0.421 ,1,0.421 ,0.593 
+scLong,Normal cells,Myeloid,0.447 ,1,0.447 ,0.618 
+scLong,Normal cells,T/NK cells,0.427 ,1,0.427 ,0.598 
+scLong,Normal cells,Endothelial cells,0.532 ,1,0.532 ,0.695 
+scLong,Normal cells,Epithelial cells,0.742 ,1,0.742 ,0.852 
+scLong,Normal cells,Fibroblasts,0.501 ,1,0.501 ,0.668 
+scLong,Normal cells,Mesenchymal cells,0.619 ,1,0.619 ,0.765 
+scLong,Normal cells,Germ cells,0.817 ,1,0.817 ,0.899 
+scLong,Normal cells,Neural stem cells,0.973 ,1,0.973 ,0.986 
+scLong,Normal cells,Glioblasts,0.984 ,1,0.984 ,0.992 
+scLong,Normal cells,Neuronal IPCs,0.971 ,1,0.971 ,0.985 
+scLong,Normal cells,Neuron,0.992 ,1,0.992 ,0.996 
+scLong,Normal cells,Astrocytes,0.713 ,1,0.713 ,0.832 
+scLong,Normal cells,Oligodendrocytes,0.663 ,1,0.663 ,0.798 
+scLong,Normal cells,Microglias,0.972 ,1,0.972 ,0.986 
+scLong,Normal cells,OPCs,0.996 ,1,0.996 ,0.998 

benchmark results/results_tumor_primary_site_tracing.csv

@@ -0,0 +1,196 @@
+Model,Cell population,Primary_site/cell type,Accuracy,Macro_Precision,Macro_Recall,Macro_F1
+Geneformer,Primary tumor cells ,Overall,0.123 ,0.104 ,0.117 ,0.130 
+Geneformer,Primary tumor cells ,Lung,0.081 ,0.071 ,0.081 ,0.150 
+Geneformer,Primary tumor cells ,Pancreas,0.000 ,0.000 ,0.000 ,NA
+Geneformer,Primary tumor cells ,Colorectal,0.007 ,0.050 ,0.007 ,0.014 
+Geneformer,Primary tumor cells ,Cervical ,0.006 ,0.053 ,0.006 ,0.012 
+Geneformer,Primary tumor cells ,Kidney,0.006 ,0.071 ,0.006 ,0.012 
+Geneformer,Primary tumor cells ,Liver,0.006 ,0.067 ,0.006 ,0.012 
+Geneformer,Primary tumor cells ,Ovarian,0.089 ,0.077 ,0.089 ,0.163 
+Geneformer,Primary tumor cells ,Esophageal,0.366 ,0.111 ,0.366 ,0.536 
+Geneformer,Primary tumor cells ,Gastric,0.712 ,0.167 ,0.712 ,0.832 
+Geneformer,Primary tumor cells ,Breast,0.987 ,0.500 ,0.987 ,0.993 
+Geneformer,Primary tumor cells ,Head-neck,0.000 ,0.000 ,0.000 ,NA
+Geneformer,Primary tumor cells ,Glioma,0.000 ,0.000 ,0.000 ,NA
+Geneformer,Primary tumor cells ,Lymphoma,0.002 ,0.063 ,0.002 ,0.004 
+Geneformer,Primary tumor cells ,Melanoma,0.005 ,0.053 ,0.005 ,0.010 
+Geneformer,Primary tumor cells ,Thyroid,0.002 ,0.053 ,0.002 ,0.004 
+Geneformer,Primary tumor cells ,DSRCT,0.002 ,0.053 ,0.002 ,0.004 
+Geneformer,Primary tumor cells ,Myeloma,0.000 ,0.000 ,0.000 ,NA
+Geneformer,Primary tumor cells ,Osteosarcoma,0.004 ,0.050 ,0.004 ,0.008 
+Geneformer,Primary tumor cells ,Retinoblastoma,0.013 ,0.050 ,0.013 ,0.026 
+Geneformer,Primary tumor cells ,Prostate,0.005 ,0.050 ,0.005 ,0.010 
+Geneformer,Metastatic tumor cells ,Overall,0.097 ,0.079 ,0.094 ,0.122 
+Geneformer,Metastatic tumor cells ,Lung,0.118 ,0.091 ,0.118 ,0.211 
+Geneformer,Metastatic tumor cells ,Pancreas,0.000 ,0.000 ,0.000 ,NA
+Geneformer,Metastatic tumor cells ,Colorectal,0.023 ,0.077 ,0.023 ,0.045 
+Geneformer,Metastatic tumor cells ,Liver,0.000 ,0.000 ,0.000 ,NA
+Geneformer,Metastatic tumor cells ,Ovarian,0.007 ,0.125 ,0.007 ,0.014 
+Geneformer,Metastatic tumor cells ,Gastric,0.386 ,0.143 ,0.386 ,0.557 
+Geneformer,Metastatic tumor cells ,Breast,0.378 ,0.333 ,0.378 ,0.549 
+Geneformer,Metastatic tumor cells ,Head-neck,0.018 ,0.143 ,0.018 ,0.036 
+Geneformer,Metastatic tumor cells ,Melanoma,0.000 ,0.000 ,0.000 ,NA
+Geneformer,Metastatic tumor cells ,Thyroid,0.005 ,0.056 ,0.005 ,0.010 
+Geneformer,Circulating Tumor Cells,Overall,0.000 ,0.000 ,0.000 ,NA
+Geneformer,Circulating Tumor Cells,Lung,0.000 ,0.000 ,0.000 ,NA
+Geneformer,Circulating Tumor Cells,Colorectal,0.000 ,0.000 ,0.000 ,NA
+Geneformer,Circulating Tumor Cells,Liver,0.000 ,0.000 ,0.000 ,NA
+Geneformer,Circulating Tumor Cells,Breast,0.000 ,0.000 ,0.000 ,NA
+Geneformer,Circulating Tumor Cells,Melanoma,0.000 ,0.000 ,0.000 ,NA
+Geneformer,Circulating Tumor Cells,Prostate,0.000 ,0.000 ,0.000 ,NA
+scFoundation,Primary tumor cells ,Overall,0.658 ,0.661 ,0.628 ,0.593 
+scFoundation,Primary tumor cells ,Lung,0.025 ,0.056 ,0.001 ,0.003 
+scFoundation,Primary tumor cells ,Pancreas,0.612 ,0.071 ,0.044 ,0.054 
+scFoundation,Primary tumor cells ,Colorectal,0.784 ,0.077 ,0.060 ,0.068 
+scFoundation,Primary tumor cells ,Cervical ,0.199 ,0.071 ,0.014 ,0.024 
+scFoundation,Primary tumor cells ,Kidney,0.748 ,0.063 ,0.047 ,0.054 
+scFoundation,Primary tumor cells ,Liver,0.380 ,0.100 ,0.038 ,0.055 
+scFoundation,Primary tumor cells ,Ovarian,0.815 ,0.063 ,0.051 ,0.056 
+scFoundation,Primary tumor cells ,Esophageal,0.415 ,0.077 ,0.032 ,0.045 
+scFoundation,Primary tumor cells ,Gastric,0.360 ,0.071 ,0.026 ,0.038 
+scFoundation,Primary tumor cells ,Breast,0.674 ,0.056 ,0.037 ,0.045 
+scFoundation,Primary tumor cells ,Head-neck,0.192 ,0.091 ,0.017 ,0.029 
+scFoundation,Primary tumor cells ,Glioma,0.984 ,0.200 ,0.197 ,0.198 
+scFoundation,Primary tumor cells ,Lymphoma,0.611 ,0.077 ,0.047 ,0.058 
+scFoundation,Primary tumor cells ,Melanoma,0.753 ,0.063 ,0.047 ,0.054 
+scFoundation,Primary tumor cells ,Thyroid,0.703 ,0.071 ,0.050 ,0.059 
+scFoundation,Primary tumor cells ,DSRCT,0.952 ,0.091 ,0.087 ,0.089 
+scFoundation,Primary tumor cells ,Myeloma,0.466 ,0.083 ,0.039 ,0.053 
+scFoundation,Primary tumor cells ,Osteosarcoma,0.996 ,0.125 ,0.125 ,0.125 
+scFoundation,Primary tumor cells ,Retinoblastoma,0.886 ,0.100 ,0.089 ,0.094 
+scFoundation,Primary tumor cells ,Prostate,0.999 ,0.500 ,0.500 ,0.500 
+scFoundation,Metastatic tumor cells ,Overall,0.733 ,0.265 ,0.286 ,0.254 
+scFoundation,Metastatic tumor cells ,Lung,0.032 ,0.071 ,0.002 ,0.004 
+scFoundation,Metastatic tumor cells ,Pancreas,0.666 ,0.063 ,0.042 ,0.050 
+scFoundation,Metastatic tumor cells ,Colorectal,0.660 ,0.050 ,0.033 ,0.040 
+scFoundation,Metastatic tumor cells ,Liver,0.990 ,0.200 ,0.198 ,0.199 
+scFoundation,Metastatic tumor cells ,Ovarian,0.687 ,0.059 ,0.040 ,0.048 
+scFoundation,Metastatic tumor cells ,Gastric,0.230 ,0.056 ,0.013 ,0.021 
+scFoundation,Metastatic tumor cells ,Breast,0.800 ,0.050 ,0.040 ,0.044 
+scFoundation,Metastatic tumor cells ,Head-neck,0.026 ,0.100 ,0.003 ,0.005 
+scFoundation,Metastatic tumor cells ,Melanoma,0.831 ,0.056 ,0.046 ,0.050 
+scFoundation,Metastatic tumor cells ,Thyroid,0.797 ,0.067 ,0.053 ,0.059 
+scFoundation,Circulating Tumor Cells,Overall,0.114 ,0.035 ,0.050 ,0.021 
+scFoundation,Circulating Tumor Cells,Lung,0.000 ,0.000 ,0.000 ,0.000 
+scFoundation,Circulating Tumor Cells,Colorectal,0.000 ,0.000 ,0.000 ,0.000 
+scFoundation,Circulating Tumor Cells,Liver,0.752 ,0.250 ,0.188 ,0.215 
+scFoundation,Circulating Tumor Cells,Breast,0.002 ,0.100 ,0.000 ,0.001 
+scFoundation,Circulating Tumor Cells,Melanoma,0.000 ,0.000 ,0.000 ,0.000 
+scFoundation,Circulating Tumor Cells,Prostate,0.000 ,0.000 ,0.000 ,0.000 
+scGPT,Primary tumor cells ,Overall,0.660 ,0.665 ,0.698 ,0.644 
+scGPT,Primary tumor cells ,Lung,0.031 ,0.059 ,0.031 ,0.060 
+scGPT,Primary tumor cells ,Pancreas,0.814 ,0.100 ,0.814 ,0.898 
+scGPT,Primary tumor cells ,Colorectal,0.838 ,0.125 ,0.838 ,0.912 
+scGPT,Primary tumor cells ,Cervical ,0.470 ,0.100 ,0.470 ,0.639 
+scGPT,Primary tumor cells ,Kidney,0.602 ,0.067 ,0.602 ,0.752 
+scGPT,Primary tumor cells ,Liver,0.274 ,0.067 ,0.274 ,0.430 
+scGPT,Primary tumor cells ,Ovarian,0.929 ,0.067 ,0.929 ,0.963 
+scGPT,Primary tumor cells ,Esophageal,0.208 ,0.083 ,0.208 ,0.344 
+scGPT,Primary tumor cells ,Gastric,0.520 ,0.067 ,0.520 ,0.684 
+scGPT,Primary tumor cells ,Breast,0.727 ,0.071 ,0.727 ,0.842 
+scGPT,Primary tumor cells ,Head-neck,0.858 ,0.250 ,0.858 ,0.924 
+scGPT,Primary tumor cells ,Glioma,0.977 ,0.167 ,0.977 ,0.989 
+scGPT,Primary tumor cells ,Lymphoma,0.781 ,0.083 ,0.781 ,0.877 
+scGPT,Primary tumor cells ,Melanoma,0.922 ,0.077 ,0.922 ,0.959 
+scGPT,Primary tumor cells ,Thyroid,0.519 ,0.067 ,0.519 ,0.683 
+scGPT,Primary tumor cells ,DSRCT,0.993 ,0.250 ,0.993 ,0.996 
+scGPT,Primary tumor cells ,Myeloma,0.981 ,0.200 ,0.981 ,0.990 
+scGPT,Primary tumor cells ,Osteosarcoma,0.831 ,0.125 ,0.831 ,0.908 
+scGPT,Primary tumor cells ,Retinoblastoma,0.977 ,0.167 ,0.977 ,0.988 
+scGPT,Primary tumor cells ,Prostate,0.995 ,0.200 ,0.995 ,0.997 
+scGPT,Metastatic tumor cells ,Overall,0.642 ,0.335 ,0.698 ,0.562 
+scGPT,Metastatic tumor cells ,Lung,0.057 ,0.063 ,0.057 ,0.108 
+scGPT,Metastatic tumor cells ,Pancreas,0.969 ,0.100 ,0.969 ,0.984 
+scGPT,Metastatic tumor cells ,Colorectal,0.713 ,0.091 ,0.713 ,0.832 
+scGPT,Metastatic tumor cells ,Liver,0.984 ,0.333 ,0.984 ,0.992 
+scGPT,Metastatic tumor cells ,Ovarian,0.897 ,0.167 ,0.897 ,0.946 
+scGPT,Metastatic tumor cells ,Gastric,0.325 ,0.056 ,0.325 ,0.491 
+scGPT,Metastatic tumor cells ,Breast,0.875 ,0.250 ,0.875 ,0.933 
+scGPT,Metastatic tumor cells ,Head-neck,0.418 ,0.083 ,0.418 ,0.590 
+scGPT,Metastatic tumor cells ,Melanoma,0.939 ,0.143 ,0.939 ,0.969 
+scGPT,Metastatic tumor cells ,Thyroid,0.798 ,0.077 ,0.798 ,0.888 
+scGPT,Circulating Tumor Cells,Overall,0.275 ,0.214 ,0.284 ,0.497 
+scGPT,Circulating Tumor Cells,Lung,0.000 ,0.000 ,0.000 ,NA
+scGPT,Circulating Tumor Cells,Colorectal,0.000 ,0.000 ,0.000 ,NA
+scGPT,Circulating Tumor Cells,Liver,0.575 ,0.200 ,0.575 ,0.730 
+scGPT,Circulating Tumor Cells,Breast,0.137 ,0.077 ,0.137 ,0.241 
+scGPT,Circulating Tumor Cells,Melanoma,0.211 ,0.111 ,0.211 ,0.348 
+scGPT,Circulating Tumor Cells,Prostate,0.779 ,0.167 ,0.779 ,0.876 
+UCE,Primary tumor cells ,Overall,0.769 ,0.751 ,0.781 ,0.739 
+UCE,Primary tumor cells ,Lung,0.107 ,0.059 ,0.107 ,0.193 
+UCE,Primary tumor cells ,Pancreas,0.882 ,0.143 ,0.882 ,0.937 
+UCE,Primary tumor cells ,Colorectal,0.939 ,0.200 ,0.939 ,0.969 
+UCE,Primary tumor cells ,Cervical ,0.819 ,0.083 ,0.819 ,0.900 
+UCE,Primary tumor cells ,Kidney,0.945 ,0.250 ,0.945 ,0.972 
+UCE,Primary tumor cells ,Liver,0.346 ,0.083 ,0.346 ,0.514 
+UCE,Primary tumor cells ,Ovarian,0.981 ,0.111 ,0.981 ,0.990 
+UCE,Primary tumor cells ,Esophageal,0.462 ,0.091 ,0.462 ,0.632 
+UCE,Primary tumor cells ,Gastric,0.488 ,0.067 ,0.488 ,0.656 
+UCE,Primary tumor cells ,Breast,0.845 ,0.100 ,0.845 ,0.916 
+UCE,Primary tumor cells ,Head-neck,0.357 ,0.250 ,0.357 ,0.526 
+UCE,Primary tumor cells ,Glioma,0.999 ,0.500 ,0.999 ,0.999 
+UCE,Primary tumor cells ,Lymphoma,0.922 ,0.167 ,0.922 ,0.959 
+UCE,Primary tumor cells ,Melanoma,0.987 ,0.200 ,0.987 ,0.993 
+UCE,Primary tumor cells ,Thyroid,0.813 ,0.071 ,0.813 ,0.897 
+UCE,Primary tumor cells ,DSRCT,0.993 ,0.200 ,0.993 ,0.996 
+UCE,Primary tumor cells ,Myeloma,0.947 ,0.091 ,0.947 ,0.973 
+UCE,Primary tumor cells ,Osteosarcoma,0.981 ,0.167 ,0.981 ,0.990 
+UCE,Primary tumor cells ,Retinoblastoma,0.999 ,0.500 ,0.999 ,0.999 
+UCE,Primary tumor cells ,Prostate,1.000 ,1.000 ,1.000 ,1.000 
+UCE,Metastatic tumor cells ,Overall,0.658 ,0.318 ,0.707 ,0.593 
+UCE,Metastatic tumor cells ,Lung,0.042 ,0.067 ,0.042 ,0.081 
+UCE,Metastatic tumor cells ,Pancreas,0.983 ,0.200 ,0.983 ,0.991 
+UCE,Metastatic tumor cells ,Colorectal,0.655 ,0.125 ,0.655 ,0.792 
+UCE,Metastatic tumor cells ,Liver,0.992 ,0.250 ,0.992 ,0.996 
+UCE,Metastatic tumor cells ,Ovarian,0.952 ,0.333 ,0.952 ,0.975 
+UCE,Metastatic tumor cells ,Gastric,0.307 ,0.063 ,0.307 ,0.470 
+UCE,Metastatic tumor cells ,Breast,0.850 ,0.167 ,0.850 ,0.919 
+UCE,Metastatic tumor cells ,Head-neck,0.436 ,0.111 ,0.436 ,0.608 
+UCE,Metastatic tumor cells ,Melanoma,0.969 ,0.250 ,0.969 ,0.984 
+UCE,Metastatic tumor cells ,Thyroid,0.887 ,0.100 ,0.887 ,0.940 
+UCE,Circulating Tumor Cells,Overall,0.157 ,0.194 ,0.160 ,0.342 
+UCE,Circulating Tumor Cells,Lung,0.000 ,0.000 ,0.000 ,NA
+UCE,Circulating Tumor Cells,Colorectal,0.000 ,0.000 ,0.000 ,NA
+UCE,Circulating Tumor Cells,Liver,0.425 ,0.167 ,0.425 ,0.596 
+UCE,Circulating Tumor Cells,Breast,0.064 ,0.071 ,0.064 ,0.120 
+UCE,Circulating Tumor Cells,Melanoma,0.211 ,0.125 ,0.211 ,0.348 
+UCE,Circulating Tumor Cells,Prostate,0.260 ,0.091 ,0.260 ,0.412 
+scLong,Primary tumor cells ,Overall,0.051 ,0.051 ,0.050 ,0.096 
+scLong,Primary tumor cells ,Lung,0.000 ,0.000 ,0.000 ,NA
+scLong,Primary tumor cells ,Pancreas,0.000 ,0.000 ,0.000 ,NA
+scLong,Primary tumor cells ,Colorectal,0.000 ,0.000 ,0.000 ,NA
+scLong,Primary tumor cells ,Cervical ,0.000 ,0.000 ,0.000 ,NA
+scLong,Primary tumor cells ,Kidney,0.000 ,0.000 ,0.000 ,NA
+scLong,Primary tumor cells ,Liver,0.000 ,0.000 ,0.000 ,NA
+scLong,Primary tumor cells ,Ovarian,0.000 ,0.000 ,0.000 ,NA
+scLong,Primary tumor cells ,Esophageal,0.000 ,0.000 ,0.000 ,NA
+scLong,Primary tumor cells ,Gastric,0.000 ,0.000 ,0.000 ,NA
+scLong,Primary tumor cells ,Breast,0.000 ,0.000 ,0.000 ,NA
+scLong,Primary tumor cells ,Head-neck,0.000 ,0.000 ,0.000 ,NA
+scLong,Primary tumor cells ,Glioma,0.000 ,0.000 ,0.000 ,NA
+scLong,Primary tumor cells ,Lymphoma,0.000 ,0.000 ,0.000 ,NA
+scLong,Primary tumor cells ,Melanoma,0.000 ,0.000 ,0.000 ,NA
+scLong,Primary tumor cells ,Thyroid,0.000 ,0.000 ,0.000 ,NA
+scLong,Primary tumor cells ,DSRCT,0.000 ,0.000 ,0.000 ,NA
+scLong,Primary tumor cells ,Myeloma,0.000 ,0.000 ,0.000 ,NA
+scLong,Primary tumor cells ,Osteosarcoma,0.000 ,0.000 ,0.000 ,NA
+scLong,Primary tumor cells ,Retinoblastoma,1.000 ,1.000 ,1.000 ,1.000 
+scLong,Primary tumor cells ,Prostate,0.000 ,0.000 ,0.000 ,NA
+scLong,Metastatic tumor cells ,Overall,0.000 ,0.000 ,0.000 ,NA
+scLong,Metastatic tumor cells ,Lung,0.000 ,0.000 ,0.000 ,NA
+scLong,Metastatic tumor cells ,Pancreas,0.000 ,0.000 ,0.000 ,NA
+scLong,Metastatic tumor cells ,Colorectal,0.000 ,0.000 ,0.000 ,NA
+scLong,Metastatic tumor cells ,Liver,0.000 ,0.000 ,0.000 ,NA
+scLong,Metastatic tumor cells ,Ovarian,0.000 ,0.000 ,0.000 ,NA
+scLong,Metastatic tumor cells ,Gastric,0.000 ,0.000 ,0.000 ,NA
+scLong,Metastatic tumor cells ,Breast,0.000 ,0.000 ,0.000 ,NA
+scLong,Metastatic tumor cells ,Head-neck,0.000 ,0.000 ,0.000 ,NA
+scLong,Metastatic tumor cells ,Melanoma,0.000 ,0.000 ,0.000 ,NA
+scLong,Metastatic tumor cells ,Thyroid,0.000 ,0.000 ,0.000 ,NA
+scLong,Circulating Tumor Cells,Overall,0.000 ,0.000 ,0.000 ,NA
+scLong,Circulating Tumor Cells,Lung,0.000 ,0.000 ,0.000 ,NA
+scLong,Circulating Tumor Cells,Colorectal,0.000 ,0.000 ,0.000 ,NA
+scLong,Circulating Tumor Cells,Liver,0.000 ,0.000 ,0.000 ,NA
+scLong,Circulating Tumor Cells,Breast,0.000 ,0.000 ,0.000 ,NA
+scLong,Circulating Tumor Cells,Melanoma,0.000 ,0.000 ,0.000 ,NA
+scLong,Circulating Tumor Cells,Prostate,0.000 ,0.000 ,0.000 ,NA