Rename results/by_model/scfoundation_metrics.csv to benchmark results/by_model/scfoundation_metrics.csv
f3f07d9 verified | "Category ",Task,Prediction type,Cell population,Primary_site/cell type,Accuracy,Precision,Recall,F1 Score | |
| Tumor,Tumor cell identification,Binary,Primary tumor cells ,Overall,0.885,1,0.885,0.939 | |
| Tumor,Tumor cell identification,Binary,Primary tumor cells ,Lung,0.911,1,0.911,0.953 | |
| Tumor,Tumor cell identification,Binary,Primary tumor cells ,Pancreas,0.968,1,0.968,0.984 | |
| Tumor,Tumor cell identification,Binary,Primary tumor cells ,Colorectal,0.965,1,0.965,0.982 | |
| Tumor,Tumor cell identification,Binary,Primary tumor cells ,Cervical ,0.647,1,0.647,0.786 | |
| Tumor,Tumor cell identification,Binary,Primary tumor cells ,Kidney,0.554,1,0.554,0.713 | |
| Tumor,Tumor cell identification,Binary,Primary tumor cells ,Liver,0.956,1,0.956,0.978 | |
| Tumor,Tumor cell identification,Binary,Primary tumor cells ,Ovarian,0.949,1,0.949,0.974 | |
| Tumor,Tumor cell identification,Binary,Primary tumor cells ,Esophageal,0.904,1,0.904,0.949 | |
| Tumor,Tumor cell identification,Binary,Primary tumor cells ,Gastric,0.889,1,0.889,0.942 | |
| Tumor,Tumor cell identification,Binary,Primary tumor cells ,Breast,0.526,1,0.526,0.689 | |
| Tumor,Tumor cell identification,Binary,Primary tumor cells ,Head-neck,0.967,1,0.967,0.983 | |
| Tumor,Tumor cell identification,Binary,Primary tumor cells ,Glioma,0.301,1,0.301,0.463 | |
| Tumor,Tumor cell identification,Binary,Primary tumor cells ,Lymphoma,0.857,1,0.857,0.923 | |
| Tumor,Tumor cell identification,Binary,Primary tumor cells ,Melanoma,0.933,1,0.933,0.965 | |
| Tumor,Tumor cell identification,Binary,Primary tumor cells ,Thyroid,0.911,1,0.911,0.954 | |
| Tumor,Tumor cell identification,Binary,Primary tumor cells ,DSRCT,0.997,1,0.997,0.999 | |
| Tumor,Tumor cell identification,Binary,Primary tumor cells ,Myeloma,0.998,1,0.998,0.999 | |
| Tumor,Tumor cell identification,Binary,Primary tumor cells ,Osteosarcoma,0.789,1,0.789,0.882 | |
| Tumor,Tumor cell identification,Binary,Primary tumor cells ,Retinoblastoma,0.979,1,0.979,0.989 | |
| Tumor,Tumor cell identification,Binary,Primary tumor cells ,Prostate,1,1,1,1 | |
| Tumor,Tumor cell identification,Binary,Primary tumor cells ,Seminoma,0.951,1,0.951,0.975 | |
| Tumor,Tumor cell identification,Binary,Metastatic tumor cells ,Overall,0.95,1,0.95,0.974 | |
| Tumor,Tumor cell identification,Binary,Metastatic tumor cells ,Lung,0.869,1,0.869,0.93 | |
| Tumor,Tumor cell identification,Binary,Metastatic tumor cells ,Pancreas,0.982,1,0.982,0.991 | |
| Tumor,Tumor cell identification,Binary,Metastatic tumor cells ,Colorectal,0.867,1,0.867,0.929 | |
| Tumor,Tumor cell identification,Binary,Metastatic tumor cells ,Liver,0.992,1,0.992,0.996 | |
| Tumor,Tumor cell identification,Binary,Metastatic tumor cells ,Ovarian,0.961,1,0.961,0.98 | |
| Tumor,Tumor cell identification,Binary,Metastatic tumor cells ,Gastric,0.909,1,0.909,0.952 | |
| Tumor,Tumor cell identification,Binary,Metastatic tumor cells ,Breast,0.976,1,0.976,0.988 | |
| Tumor,Tumor cell identification,Binary,Metastatic tumor cells ,Head-neck,0.982,1,0.982,0.991 | |
| Tumor,Tumor cell identification,Binary,Metastatic tumor cells ,Melanoma,0.973,1,0.973,0.986 | |
| Tumor,Tumor cell identification,Binary,Metastatic tumor cells ,Thyroid,0.992,1,0.992,0.996 | |
| Tumor,Tumor cell identification,Binary,Circulating Tumor Cells,Overall,0.149,1,0.149,0.259 | |
| Tumor,Tumor cell identification,Binary,Circulating Tumor Cells,Lung,0.1,1,0.1,0.182 | |
| Tumor,Tumor cell identification,Binary,Circulating Tumor Cells,Colorectal,0,0,0,0 | |
| Tumor,Tumor cell identification,Binary,Circulating Tumor Cells,Liver,0.973,1,0.973,0.986 | |
| Tumor,Tumor cell identification,Binary,Circulating Tumor Cells,Breast,0,0,0,0 | |
| Tumor,Tumor cell identification,Binary,Circulating Tumor Cells,Melanoma,0,0,0,0 | |
| Tumor,Tumor cell identification,Binary,Circulating Tumor Cells,Prostate,0.014,1,0.014,0.027 | |
| Tumor,Tumor cell identification,Binary,Normal cells,Overall,0.881,1,0.881,0.939 | |
| Tumor,Tumor cell identification,Binary,Normal cells,B cells,0.711,1,0.711,0.939 | |
| Tumor,Tumor cell identification,Binary,Normal cells,Myeloid,0.828,1,0.828,0.831 | |
| Tumor,Tumor cell identification,Binary,Normal cells,T/NK cells,0.712,1,0.712,0.907 | |
| Tumor,Tumor cell identification,Binary,Normal cells,Endothelial cells,0.878,1,0.878,0.831 | |
| Tumor,Tumor cell identification,Binary,Normal cells,Epithelial cells,0.403,1,0.403,0.933 | |
| Tumor,Tumor cell identification,Binary,Normal cells,Fibroblasts,0.848,1,0.848,0.573 | |
| Tumor,Tumor cell identification,Binary,Normal cells,Mesenchymal cells,0.981,1,0.981,0.921 | |
| Tumor,Tumor cell identification,Binary,Normal cells,Germ cells,1,1,1,0.99 | |
| Tumor,Tumor cell identification,Binary,Normal cells,Neural stem cells,1,1,1,1 | |
| Tumor,Tumor cell identification,Binary,Normal cells,Glioblasts,1,1,1,1 | |
| Tumor,Tumor cell identification,Binary,Normal cells,Neuronal IPCs,1,1,1,1 | |
| Tumor,Tumor cell identification,Binary,Normal cells,Neuron,0.999,1,0.999,1 | |
| Tumor,Tumor cell identification,Binary,Normal cells,Astrocytes,0.869,1,0.869,1 | |
| Tumor,Tumor cell identification,Binary,Normal cells,Oligodendrocytes,0.886,1,0.886,0.931 | |
| Tumor,Tumor cell identification,Binary,Normal cells,Microglias,1,1,1,0.94 | |
| Tumor,Tumor cell identification,Binary,Normal cells,OPCs,1,1,1,1 | |
| Tumor,Primary site tracing,Multi-class,Primary tumor cells ,Overall,0.658,0.661 (Macro),0.628 (Macro),0.593 (Macro) | |
| Tumor,Primary site tracing,Multi-class,Primary tumor cells ,Lung,0.025,0.056 (Macro),0.001 (Macro),0.003 (Macro) | |
| Tumor,Primary site tracing,Multi-class,Primary tumor cells ,Pancreas,0.612,0.071 (Macro),0.044 (Macro),0.054 (Macro) | |
| Tumor,Primary site tracing,Multi-class,Primary tumor cells ,Colorectal,0.784,0.077 (Macro),0.060 (Macro),0.068 (Macro) | |
| Tumor,Primary site tracing,Multi-class,Primary tumor cells ,Cervical ,0.199,0.071 (Macro),0.014 (Macro),0.024 (Macro) | |
| Tumor,Primary site tracing,Multi-class,Primary tumor cells ,Kidney,0.748,0.063 (Macro),0.047 (Macro),0.054 (Macro) | |
| Tumor,Primary site tracing,Multi-class,Primary tumor cells ,Liver,0.38,0.100 (Macro),0.038 (Macro),0.055 (Macro) | |
| Tumor,Primary site tracing,Multi-class,Primary tumor cells ,Ovarian,0.815,0.063 (Macro),0.051 (Macro),0.056 (Macro) | |
| Tumor,Primary site tracing,Multi-class,Primary tumor cells ,Esophageal,0.415,0.077 (Macro),0.032 (Macro),0.045 (Macro) | |
| Tumor,Primary site tracing,Multi-class,Primary tumor cells ,Gastric,0.36,0.071 (Macro),0.026 (Macro),0.038 (Macro) | |
| Tumor,Primary site tracing,Multi-class,Primary tumor cells ,Breast,0.674,0.056 (Macro),0.037 (Macro),0.045 (Macro) | |
| Tumor,Primary site tracing,Multi-class,Primary tumor cells ,Head-neck,0.192,0.091 (Macro),0.017 (Macro),0.029 (Macro) | |
| Tumor,Primary site tracing,Multi-class,Primary tumor cells ,Glioma,0.984,0.200 (Macro),0.197 (Macro),0.198 (Macro) | |
| Tumor,Primary site tracing,Multi-class,Primary tumor cells ,Lymphoma,0.611,0.077 (Macro),0.047 (Macro),0.058 (Macro) | |
| Tumor,Primary site tracing,Multi-class,Primary tumor cells ,Melanoma,0.753,0.063 (Macro),0.047 (Macro),0.054 (Macro) | |
| Tumor,Primary site tracing,Multi-class,Primary tumor cells ,Thyroid,0.703,0.071 (Macro),0.050 (Macro),0.059 (Macro) | |
| Tumor,Primary site tracing,Multi-class,Primary tumor cells ,DSRCT,0.952,0.091 (Macro),0.087 (Macro),0.089 (Macro) | |
| Tumor,Primary site tracing,Multi-class,Primary tumor cells ,Myeloma,0.466,0.083 (Macro),0.039 (Macro),0.053 (Macro) | |
| Tumor,Primary site tracing,Multi-class,Primary tumor cells ,Osteosarcoma,0.996,0.125 (Macro),0.125 (Macro),0.125 (Macro) | |
| Tumor,Primary site tracing,Multi-class,Primary tumor cells ,Retinoblastoma,0.886,0.100 (Macro),0.089 (Macro),0.094 (Macro) | |
| Tumor,Primary site tracing,Multi-class,Primary tumor cells ,Prostate,0.999,0.500 (Macro),0.500 (Macro),0.500 (Macro) | |
| Tumor,Primary site tracing,Multi-class,Metastatic tumor cells ,Overall,0.733,0.265 (Macro),0.286 (Macro),0.254 (Macro) | |
| Tumor,Primary site tracing,Multi-class,Metastatic tumor cells ,Lung,0.032,0.071 (Macro),0.002 (Macro),0.004 (Macro) | |
| Tumor,Primary site tracing,Multi-class,Metastatic tumor cells ,Pancreas,0.666,0.063 (Macro),0.042 (Macro),0.050 (Macro) | |
| Tumor,Primary site tracing,Multi-class,Metastatic tumor cells ,Colorectal,0.66,0.050 (Macro),0.033 (Macro),0.040 (Macro) | |
| Tumor,Primary site tracing,Multi-class,Metastatic tumor cells ,Liver,0.99,0.200 (Macro),0.198 (Macro),0.199 (Macro) | |
| Tumor,Primary site tracing,Multi-class,Metastatic tumor cells ,Ovarian,0.687,0.059 (Macro),0.040 (Macro),0.048 (Macro) | |
| Tumor,Primary site tracing,Multi-class,Metastatic tumor cells ,Gastric,0.23,0.056 (Macro),0.013 (Macro),0.021 (Macro) | |
| Tumor,Primary site tracing,Multi-class,Metastatic tumor cells ,Breast,0.8,0.050 (Macro),0.040 (Macro),0.044 (Macro) | |
| Tumor,Primary site tracing,Multi-class,Metastatic tumor cells ,Head-neck,0.026,0.100 (Macro),0.003 (Macro),0.005 (Macro) | |
| Tumor,Primary site tracing,Multi-class,Metastatic tumor cells ,Melanoma,0.831,0.056 (Macro),0.046 (Macro),0.050 (Macro) | |
| Tumor,Primary site tracing,Multi-class,Metastatic tumor cells ,Thyroid,0.797,0.067 (Macro),0.053 (Macro),0.059 (Macro) | |
| Tumor,Primary site tracing,Multi-class,Circulating Tumor Cells,Overall,0.114,0.035 (Macro),0.050 (Macro),0.021 (Macro) | |
| Tumor,Primary site tracing,Multi-class,Circulating Tumor Cells,Lung,0,0.000 (Macro),0.000 (Macro),0.000 (Macro) | |
| Tumor,Primary site tracing,Multi-class,Circulating Tumor Cells,Colorectal,0,0.000 (Macro),0.000 (Macro),0.000 (Macro) | |
| Tumor,Primary site tracing,Multi-class,Circulating Tumor Cells,Liver,0.752,0.250 (Macro),0.188 (Macro),0.215 (Macro) | |
| Tumor,Primary site tracing,Multi-class,Circulating Tumor Cells,Breast,0.002,0.100 (Macro),0.000 (Macro),0.001 (Macro) | |
| Tumor,Primary site tracing,Multi-class,Circulating Tumor Cells,Melanoma,0,0.000 (Macro),0.000 (Macro),0.000 (Macro) | |
| Tumor,Primary site tracing,Multi-class,Circulating Tumor Cells,Prostate,0,0.000 (Macro),0.000 (Macro),0.000 (Macro) | |
| Stem,Stem cell identification,Binary,Stem.cell,Overall,0.979,1,0.979,0.989 | |
| Stem,Stem cell identification,Binary,Stem.cell,Hematopoietic Stem Cells,0.998,1,0.998,0.999 | |
| Stem,Stem cell identification,Binary,Stem.cell,Neural Stem Cells,0.947,1,0.947,0.973 | |
| Stem,Stem cell identification,Binary,Stem.cell,Mesenchymal Stem Cells,0.971,1,0.971,0.985 | |
| Stem,Stem cell identification,Binary,Stem.cell,Embryonic Stem Cells,1,1,1,1 | |
| Stem,Stem cell identification,Binary,Non.Stem.cell,Overall,0.961,1,0.961,0.98 | |
| Stem,Stem cell identification,Binary,Non.Stem.cell,Astrocytes,1,1,1,1 | |
| Stem,Stem cell identification,Binary,Non.Stem.cell,B.cells,0.987,1,0.987,0.993 | |
| Stem,Stem cell identification,Binary,Non.Stem.cell,Endothelial cells,0.998,1,0.998,0.999 | |
| Stem,Stem cell identification,Binary,Non.Stem.cell,Epithelial cells,1,1,1,1 | |
| Stem,Stem cell identification,Binary,Non.Stem.cell,Fibroblasts,0.906,1,0.906,0.951 | |
| Stem,Stem cell identification,Binary,Non.Stem.cell,Germ cells,1,1,1,1 | |
| Stem,Stem cell identification,Binary,Non.Stem.cell,Glioblasts,0.732,1,0.732,0.845 | |
| Stem,Stem cell identification,Binary,Non.Stem.cell,Microglias,1,1,1,1 | |
| Stem,Stem cell identification,Binary,Non.Stem.cell,Myeloid cells,0.981,1,0.981,0.99 | |
| Stem,Stem cell identification,Binary,Non.Stem.cell,Neuron,1,1,1,1 | |
| Stem,Stem cell identification,Binary,Non.Stem.cell,Neuronal.IPCs ,0.857,1,0.857,0.923 | |
| Stem,Stem cell identification,Binary,Non.Stem.cell,Oligodendrocytes,1,1,1,1 | |
| Stem,Stem cell identification,Binary,Non.Stem.cell,OPCs,1,1,1,1 | |
| Stem,Stem cell identification,Binary,Non.Stem.cell,T/NK cells,0.996,1,0.996,0.998 | |
| Stem,Stem cell subtype classification,Multi-class,Stem.cell,Overall,1,1.000 (Macro),1.000 (Macro),1.000 (Macro) | |
| Stem,Stem cell subtype classification,Multi-class,Stem.cell,Hematopoietic Stem Cells,1,1.000 (Macro),1.000 (Macro),1.000 (Macro) | |
| Stem,Stem cell subtype classification,Multi-class,Stem.cell,Neural Stem Cells,1,1.000 (Macro),1.000 (Macro),1.000 (Macro) | |
| Stem,Stem cell subtype classification,Multi-class,Stem.cell,Mesenchymal Stem Cells,1,1.000 (Macro),1.000 (Macro),1.000 (Macro) | |
| Neural,Neural cell identification,Binary,Neural.cell,Overall,1,1,1,1 | |
| Neural,Neural cell identification,Binary,Neural.cell,Glutamatergic neurons,1,1,1,1 | |
| Neural,Neural cell identification,Binary,Neural.cell,Inhibitory interneurons,1,1,1,1 | |
| Neural,Neural cell identification,Binary,Neural.cell,Astrocytes,1,1,1,1 | |
| Neural,Neural cell identification,Binary,Neural.cell,Microglial cells,1,1,1,1 | |
| Neural,Neural cell identification,Binary,Neural.cell,Oligodendrocytes,1,1,1,1 | |
| Neural,Neural cell identification,Binary,Neural.cell,Oligodendrocyte precursor cells,1,1,1,1 | |
| Neural,Neural cell identification,Binary,Non.Neural.cell,Overall,0.998,1,0.998,0.999 | |
| Neural,Neural cell identification,Binary,Non.Neural.cell,B.cells,1,1,1,1 | |
| Neural,Neural cell identification,Binary,Non.Neural.cell,Endothelial.cells,0.992,1,0.992,0.996 | |
| Neural,Neural cell identification,Binary,Non.Neural.cell,Fibroblasts,0.998,1,0.998,0.999 | |
| Neural,Neural cell identification,Binary,Non.Neural.cell,Mesenchymal.cells,1,1,1,1 | |
| Neural,Neural cell identification,Binary,Non.Neural.cell,Myeloid,0.996,1,0.996,0.998 | |
| Neural,Neural cell identification,Binary,Non.Neural.cell,T/NK cells,1,1,1,1 | |
| Neural,Neural cell identification,Binary,Non.Neural.cell,Epithelial cells,1,1,1,1 | |
| Neural,Neural cell identification,Binary,Non.Neural.cell,Germ cells,1,1,1,1 | |
| Neural,Neural cell subtype classification,Multi-class,Neural.cell,Overall,0.999,0.999 (Macro),0.999 (Macro),0.999 (Macro) | |
| Neural,Neural cell subtype classification,Multi-class,Neural.cell,Glutamatergic neurons,0.998,0.333 (Macro),0.998 (Macro),0.999 (Macro) | |
| Neural,Neural cell subtype classification,Multi-class,Neural.cell,Inhibitory interneurons,1,1.000 (Macro),1.000 (Macro),1.000 (Macro) | |
| Neural,Neural cell subtype classification,Multi-class,Neural.cell,Astrocytes,0.998,0.333 (Macro),0.998 (Macro),0.999 (Macro) | |
| Neural,Neural cell subtype classification,Multi-class,Neural.cell,Microglial cells,1,1.000 (Macro),1.000 (Macro),1.000 (Macro) | |
| Neural,Neural cell subtype classification,Multi-class,Neural.cell,Oligodendrocytes,1,1.000 (Macro),1.000 (Macro),1.000 (Macro) | |
| Neural,Neural cell subtype classification,Multi-class,Neural.cell,Oligodendrocyte precursor cells,0.999,0.500 (Macro),0.999 (Macro),0.999 (Macro) | |