scANVI (Seurat v3 2000 HVG)
scANVI or "single-cell ANnotation using Variational Inference" is a semi-supervised variant of the scVI(Lopez et al. 2018) algorithm. Like scVI, scANVI uses deep neural networks and stochastic optimization to model uncertainty caused by technical noise and bias in single - cell transcriptomics measurements. However, scANVI also leverages cell type labels in the generative modelling. In this approach, scANVI is used to predict the cell type labels of the unlabelled test data.
Overview
scANVI or "single-cell ANnotation using Variational Inference" is a semi-supervised variant of the scVI(Lopez et al. 2018) algorithm. Like scVI, scANVI uses deep neural networks and stochastic optimization to model uncertainty caused by technical noise and bias in single - cell transcriptomics measurements. However, scANVI also leverages cell type labels in the generative modelling. In this approach, scANVI is used to predict the cell type labels of the unlabelled test data.
Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.
Evaluations and results
Release 2026-09-17-134cd1815de8 · 24 evaluations · 24 metric rows. Different protocols are not a single leaderboard. Where several source tables report the same metric, the published comparisons above offer a pooled view that names what it does not hold constant.
| Metric and finding | Coverage and uncertainty | Evidence |
|---|---|---|
| scANVI (Seurat v3 2000 HVG) on Open Problems label projection CENGEN-BATCH-ACCURACY: Label projection on CeNGEN (split by batch), Accuracy Configuration: scANVI (Seurat v3 2000 HVG)Task: Open Problems label projection CENGEN-BATCH-ACCURACY: Label projection on CeNGEN (split by batch), AccuracyDataset subset: CeNGEN (split by batch) (Open Problems label projection split) 100k FACS-isolated C. elegans neurons from 17 experiments sequenced on 10x Genomics. Split into train/test by experimental batch. Dimensions: 100955 cells, 22469 genes. 169 cell types (avg. 597±800 cells per cell type). Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.26243259436788496 accuracy Unit: fraction · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedopenproblems-label primary benchmark evidence · results, dataset(cengen_batch), method(scanvi), paramset(Seurat v3 2000 HVG), metric(accuracy) Source checking is not independent reproduction. |
| scANVI (Seurat v3 2000 HVG) on Open Problems label projection CENGEN-BATCH-F1: Label projection on CeNGEN (split by batch), F1 score Configuration: scANVI (Seurat v3 2000 HVG)Task: Open Problems label projection CENGEN-BATCH-F1: Label projection on CeNGEN (split by batch), F1 scoreDataset subset: CeNGEN (split by batch) (Open Problems label projection split) 100k FACS-isolated C. elegans neurons from 17 experiments sequenced on 10x Genomics. Split into train/test by experimental batch. Dimensions: 100955 cells, 22469 genes. 169 cell types (avg. 597±800 cells per cell type). Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.22423389962996945 f1 Unit: fraction · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedopenproblems-label primary benchmark evidence · results, dataset(cengen_batch), method(scanvi), paramset(Seurat v3 2000 HVG), metric(f1) Source checking is not independent reproduction. |
| scANVI (Seurat v3 2000 HVG) on Open Problems label projection CENGEN-BATCH-F1-MACRO: Label projection on CeNGEN (split by batch), Macro F1 score Configuration: scANVI (Seurat v3 2000 HVG)Task: Open Problems label projection CENGEN-BATCH-F1-MACRO: Label projection on CeNGEN (split by batch), Macro F1 scoreDataset subset: CeNGEN (split by batch) (Open Problems label projection split) 100k FACS-isolated C. elegans neurons from 17 experiments sequenced on 10x Genomics. Split into train/test by experimental batch. Dimensions: 100955 cells, 22469 genes. 169 cell types (avg. 597±800 cells per cell type). Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.16123904954334095 f1-macro Unit: fraction · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedopenproblems-label primary benchmark evidence · results, dataset(cengen_batch), method(scanvi), paramset(Seurat v3 2000 HVG), metric(f1_macro) Source checking is not independent reproduction. |
| scANVI (Seurat v3 2000 HVG) on Open Problems label projection CENGEN-RANDOM-ACCURACY: Label projection on CeNGEN (random split), Accuracy Configuration: scANVI (Seurat v3 2000 HVG)Task: Open Problems label projection CENGEN-RANDOM-ACCURACY: Label projection on CeNGEN (random split), AccuracyDataset subset: CeNGEN (random split) (Open Problems label projection split) 100k FACS-isolated C. elegans neurons from 17 experiments sequenced on 10x Genomics. Split into train/test randomly. Dimensions: 100955 cells, 22469 genes. 169 cell types avg. 597±800 cells per cell type). Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.6517936554995553 accuracy Unit: fraction · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedopenproblems-label primary benchmark evidence · results, dataset(cengen_random), method(scanvi), paramset(Seurat v3 2000 HVG), metric(accuracy) Source checking is not independent reproduction. |
| scANVI (Seurat v3 2000 HVG) on Open Problems label projection CENGEN-RANDOM-F1: Label projection on CeNGEN (random split), F1 score Configuration: scANVI (Seurat v3 2000 HVG)Task: Open Problems label projection CENGEN-RANDOM-F1: Label projection on CeNGEN (random split), F1 scoreDataset subset: CeNGEN (random split) (Open Problems label projection split) 100k FACS-isolated C. elegans neurons from 17 experiments sequenced on 10x Genomics. Split into train/test randomly. Dimensions: 100955 cells, 22469 genes. 169 cell types avg. 597±800 cells per cell type). Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.5691463256932892 f1 Unit: fraction · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedopenproblems-label primary benchmark evidence · results, dataset(cengen_random), method(scanvi), paramset(Seurat v3 2000 HVG), metric(f1) Source checking is not independent reproduction. |
| scANVI (Seurat v3 2000 HVG) on Open Problems label projection CENGEN-RANDOM-F1-MACRO: Label projection on CeNGEN (random split), Macro F1 score Configuration: scANVI (Seurat v3 2000 HVG)Task: Open Problems label projection CENGEN-RANDOM-F1-MACRO: Label projection on CeNGEN (random split), Macro F1 scoreDataset subset: CeNGEN (random split) (Open Problems label projection split) 100k FACS-isolated C. elegans neurons from 17 experiments sequenced on 10x Genomics. Split into train/test randomly. Dimensions: 100955 cells, 22469 genes. 169 cell types avg. 597±800 cells per cell type). Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.23546364663002034 f1-macro Unit: fraction · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedopenproblems-label primary benchmark evidence · results, dataset(cengen_random), method(scanvi), paramset(Seurat v3 2000 HVG), metric(f1_macro) Source checking is not independent reproduction. |
| scANVI (Seurat v3 2000 HVG) on Open Problems label projection PANCREAS-BATCH-ACCURACY: Label projection on Pancreas (by batch), Accuracy Configuration: scANVI (Seurat v3 2000 HVG)Task: Open Problems label projection PANCREAS-BATCH-ACCURACY: Label projection on Pancreas (by batch), AccuracyDataset subset: Pancreas (by batch) (Open Problems label projection split) Human pancreatic islet scRNA-seq data from 6 datasets across technologies (CEL-seq, CEL-seq2, Smart-seq2, inDrop, Fluidigm C1, and SMARTER-seq). Split into train/test by experimental batch. Dimensions: 16382 cells, 18771 genes. 14 cell types (avg. 1170±1703 cells per cell type). Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.9596970516635109 accuracy Unit: fraction · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedopenproblems-label primary benchmark evidence · results, dataset(pancreas_batch), method(scanvi), paramset(Seurat v3 2000 HVG), metric(accuracy) Source checking is not independent reproduction. |
| scANVI (Seurat v3 2000 HVG) on Open Problems label projection PANCREAS-BATCH-F1: Label projection on Pancreas (by batch), F1 score Configuration: scANVI (Seurat v3 2000 HVG)Task: Open Problems label projection PANCREAS-BATCH-F1: Label projection on Pancreas (by batch), F1 scoreDataset subset: Pancreas (by batch) (Open Problems label projection split) Human pancreatic islet scRNA-seq data from 6 datasets across technologies (CEL-seq, CEL-seq2, Smart-seq2, inDrop, Fluidigm C1, and SMARTER-seq). Split into train/test by experimental batch. Dimensions: 16382 cells, 18771 genes. 14 cell types (avg. 1170±1703 cells per cell type). Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.9583537069413711 f1 Unit: fraction · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedopenproblems-label primary benchmark evidence · results, dataset(pancreas_batch), method(scanvi), paramset(Seurat v3 2000 HVG), metric(f1) Source checking is not independent reproduction. |
| scANVI (Seurat v3 2000 HVG) on Open Problems label projection PANCREAS-BATCH-F1-MACRO: Label projection on Pancreas (by batch), Macro F1 score Configuration: scANVI (Seurat v3 2000 HVG)Task: Open Problems label projection PANCREAS-BATCH-F1-MACRO: Label projection on Pancreas (by batch), Macro F1 scoreDataset subset: Pancreas (by batch) (Open Problems label projection split) Human pancreatic islet scRNA-seq data from 6 datasets across technologies (CEL-seq, CEL-seq2, Smart-seq2, inDrop, Fluidigm C1, and SMARTER-seq). Split into train/test by experimental batch. Dimensions: 16382 cells, 18771 genes. 14 cell types (avg. 1170±1703 cells per cell type). Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.6689106599819379 f1-macro Unit: fraction · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedopenproblems-label primary benchmark evidence · results, dataset(pancreas_batch), method(scanvi), paramset(Seurat v3 2000 HVG), metric(f1_macro) Source checking is not independent reproduction. |
| scANVI (Seurat v3 2000 HVG) on Open Problems label projection PANCREAS-RANDOM-ACCURACY: Label projection on Pancreas (random split), Accuracy Configuration: scANVI (Seurat v3 2000 HVG)Task: Open Problems label projection PANCREAS-RANDOM-ACCURACY: Label projection on Pancreas (random split), AccuracyDataset subset: Pancreas (random split) (Open Problems label projection split) Human pancreatic islet scRNA-seq data from 6 datasets across technologies (CEL-seq, CEL-seq2, Smart-seq2, inDrop, Fluidigm C1, and SMARTER-seq). Split into train/test randomly. Dimensions: 16382 cells, 18771 genes. 14 cell types (avg. 1170±1703 cells per cell type). Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.978419452887538 accuracy Unit: fraction · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedopenproblems-label primary benchmark evidence · results, dataset(pancreas_random), method(scanvi), paramset(Seurat v3 2000 HVG), metric(accuracy) Source checking is not independent reproduction. |
| scANVI (Seurat v3 2000 HVG) on Open Problems label projection PANCREAS-RANDOM-F1: Label projection on Pancreas (random split), F1 score Configuration: scANVI (Seurat v3 2000 HVG)Task: Open Problems label projection PANCREAS-RANDOM-F1: Label projection on Pancreas (random split), F1 scoreDataset subset: Pancreas (random split) (Open Problems label projection split) Human pancreatic islet scRNA-seq data from 6 datasets across technologies (CEL-seq, CEL-seq2, Smart-seq2, inDrop, Fluidigm C1, and SMARTER-seq). Split into train/test randomly. Dimensions: 16382 cells, 18771 genes. 14 cell types (avg. 1170±1703 cells per cell type). Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.975807690913863 f1 Unit: fraction · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedopenproblems-label primary benchmark evidence · results, dataset(pancreas_random), method(scanvi), paramset(Seurat v3 2000 HVG), metric(f1) Source checking is not independent reproduction. |
| scANVI (Seurat v3 2000 HVG) on Open Problems label projection PANCREAS-RANDOM-F1-MACRO: Label projection on Pancreas (random split), Macro F1 score Configuration: scANVI (Seurat v3 2000 HVG)Task: Open Problems label projection PANCREAS-RANDOM-F1-MACRO: Label projection on Pancreas (random split), Macro F1 scoreDataset subset: Pancreas (random split) (Open Problems label projection split) Human pancreatic islet scRNA-seq data from 6 datasets across technologies (CEL-seq, CEL-seq2, Smart-seq2, inDrop, Fluidigm C1, and SMARTER-seq). Split into train/test randomly. Dimensions: 16382 cells, 18771 genes. 14 cell types (avg. 1170±1703 cells per cell type). Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.6870492664816059 f1-macro Unit: fraction · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedopenproblems-label primary benchmark evidence · results, dataset(pancreas_random), method(scanvi), paramset(Seurat v3 2000 HVG), metric(f1_macro) Source checking is not independent reproduction. |
| scANVI (Seurat v3 2000 HVG) on Open Problems label projection PANCREAS-RANDOM-LABEL-NOISE-ACCURACY: Label projection on Pancreas (random split with label noise), Accuracy Configuration: scANVI (Seurat v3 2000 HVG)Task: Open Problems label projection PANCREAS-RANDOM-LABEL-NOISE-ACCURACY: Label projection on Pancreas (random split with label noise), AccuracyDataset subset: Pancreas (random split with label noise) (Open Problems label projection split) Human pancreatic islet scRNA-seq data from 6 datasets across technologies (CEL-seq, CEL-seq2, Smart-seq2, inDrop, Fluidigm C1, and SMARTER-seq). Split into train/test randomly with 20% label noise. Dimensions: 16382 cells, 18771 genes. 14 cell types (avg. 1170±1703 cells per cell type). Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.9673343605546996 accuracy Unit: fraction · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedopenproblems-label primary benchmark evidence · results, dataset(pancreas_random_label_noise), method(scanvi), paramset(Seurat v3 2000 HVG), metric(accuracy) Source checking is not independent reproduction. |
| scANVI (Seurat v3 2000 HVG) on Open Problems label projection PANCREAS-RANDOM-LABEL-NOISE-F1: Label projection on Pancreas (random split with label noise), F1 score Configuration: scANVI (Seurat v3 2000 HVG)Task: Open Problems label projection PANCREAS-RANDOM-LABEL-NOISE-F1: Label projection on Pancreas (random split with label noise), F1 scoreDataset subset: Pancreas (random split with label noise) (Open Problems label projection split) Human pancreatic islet scRNA-seq data from 6 datasets across technologies (CEL-seq, CEL-seq2, Smart-seq2, inDrop, Fluidigm C1, and SMARTER-seq). Split into train/test randomly with 20% label noise. Dimensions: 16382 cells, 18771 genes. 14 cell types (avg. 1170±1703 cells per cell type). Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.963942105070359 f1 Unit: fraction · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedopenproblems-label primary benchmark evidence · results, dataset(pancreas_random_label_noise), method(scanvi), paramset(Seurat v3 2000 HVG), metric(f1) Source checking is not independent reproduction. |
| scANVI (Seurat v3 2000 HVG) on Open Problems label projection PANCREAS-RANDOM-LABEL-NOISE-F1-MACRO: Label projection on Pancreas (random split with label noise), Macro F1 score Configuration: scANVI (Seurat v3 2000 HVG)Task: Open Problems label projection PANCREAS-RANDOM-LABEL-NOISE-F1-MACRO: Label projection on Pancreas (random split with label noise), Macro F1 scoreDataset subset: Pancreas (random split with label noise) (Open Problems label projection split) Human pancreatic islet scRNA-seq data from 6 datasets across technologies (CEL-seq, CEL-seq2, Smart-seq2, inDrop, Fluidigm C1, and SMARTER-seq). Split into train/test randomly with 20% label noise. Dimensions: 16382 cells, 18771 genes. 14 cell types (avg. 1170±1703 cells per cell type). Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.6849998633357023 f1-macro Unit: fraction · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedopenproblems-label primary benchmark evidence · results, dataset(pancreas_random_label_noise), method(scanvi), paramset(Seurat v3 2000 HVG), metric(f1_macro) Source checking is not independent reproduction. |
| scANVI (Seurat v3 2000 HVG) on Open Problems label projection TABULA-MURIS-SENIS-LUNG-RANDOM-ACCURACY: Label projection on Tabula Muris Senis Lung (random split), Accuracy Configuration: scANVI (Seurat v3 2000 HVG)Task: Open Problems label projection TABULA-MURIS-SENIS-LUNG-RANDOM-ACCURACY: Label projection on Tabula Muris Senis Lung (random split), AccuracyDataset subset: Tabula Muris Senis Lung (random split) (Open Problems label projection split) All lung cells from Tabula Muris Senis, a 500k cell-atlas from 18 organs and tissues across the mouse lifespan. Split into train/test randomly. Dimensions: 24540 cells, 17985 genes. 39 cell types (avg. 629±999 cells per cell type). Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.8409227683049147 accuracy Unit: fraction · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedopenproblems-label primary benchmark evidence · results, dataset(tabula_muris_senis_lung_random), method(scanvi), paramset(Seurat v3 2000 HVG), metric(accuracy) Source checking is not independent reproduction. |
| scANVI (Seurat v3 2000 HVG) on Open Problems label projection TABULA-MURIS-SENIS-LUNG-RANDOM-F1: Label projection on Tabula Muris Senis Lung (random split), F1 score Configuration: scANVI (Seurat v3 2000 HVG)Task: Open Problems label projection TABULA-MURIS-SENIS-LUNG-RANDOM-F1: Label projection on Tabula Muris Senis Lung (random split), F1 scoreDataset subset: Tabula Muris Senis Lung (random split) (Open Problems label projection split) All lung cells from Tabula Muris Senis, a 500k cell-atlas from 18 organs and tissues across the mouse lifespan. Split into train/test randomly. Dimensions: 24540 cells, 17985 genes. 39 cell types (avg. 629±999 cells per cell type). Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.8013792223646742 f1 Unit: fraction · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedopenproblems-label primary benchmark evidence · results, dataset(tabula_muris_senis_lung_random), method(scanvi), paramset(Seurat v3 2000 HVG), metric(f1) Source checking is not independent reproduction. |
| scANVI (Seurat v3 2000 HVG) on Open Problems label projection TABULA-MURIS-SENIS-LUNG-RANDOM-F1-MACRO: Label projection on Tabula Muris Senis Lung (random split), Macro F1 score Configuration: scANVI (Seurat v3 2000 HVG)Task: Open Problems label projection TABULA-MURIS-SENIS-LUNG-RANDOM-F1-MACRO: Label projection on Tabula Muris Senis Lung (random split), Macro F1 scoreDataset subset: Tabula Muris Senis Lung (random split) (Open Problems label projection split) All lung cells from Tabula Muris Senis, a 500k cell-atlas from 18 organs and tissues across the mouse lifespan. Split into train/test randomly. Dimensions: 24540 cells, 17985 genes. 39 cell types (avg. 629±999 cells per cell type). Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.39398162218102567 f1-macro Unit: fraction · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedopenproblems-label primary benchmark evidence · results, dataset(tabula_muris_senis_lung_random), method(scanvi), paramset(Seurat v3 2000 HVG), metric(f1_macro) Source checking is not independent reproduction. |
| scANVI (Seurat v3 2000 HVG) on Open Problems label projection ZEBRAFISH-LABS-ACCURACY: Label projection on Zebrafish (by laboratory), Accuracy Configuration: scANVI (Seurat v3 2000 HVG)Task: Open Problems label projection ZEBRAFISH-LABS-ACCURACY: Label projection on Zebrafish (by laboratory), AccuracyDataset subset: Zebrafish (by laboratory) (Open Problems label projection split) 90k cells from zebrafish embryos throughout the first day of development, with and without a knockout of chordin, an important developmental gene. Split into train/test by laboratory. Dimensions: 26022 cells, 25258 genes. 24 cell types (avg. 1084±1156 cells per cell type). Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.21006876865187493 accuracy Unit: fraction · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedopenproblems-label primary benchmark evidence · results, dataset(zebrafish_labs), method(scanvi), paramset(Seurat v3 2000 HVG), metric(accuracy) Source checking is not independent reproduction. |
| scANVI (Seurat v3 2000 HVG) on Open Problems label projection ZEBRAFISH-LABS-F1: Label projection on Zebrafish (by laboratory), F1 score Configuration: scANVI (Seurat v3 2000 HVG)Task: Open Problems label projection ZEBRAFISH-LABS-F1: Label projection on Zebrafish (by laboratory), F1 scoreDataset subset: Zebrafish (by laboratory) (Open Problems label projection split) 90k cells from zebrafish embryos throughout the first day of development, with and without a knockout of chordin, an important developmental gene. Split into train/test by laboratory. Dimensions: 26022 cells, 25258 genes. 24 cell types (avg. 1084±1156 cells per cell type). Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.22606919943933246 f1 Unit: fraction · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedopenproblems-label primary benchmark evidence · results, dataset(zebrafish_labs), method(scanvi), paramset(Seurat v3 2000 HVG), metric(f1) Source checking is not independent reproduction. |
| scANVI (Seurat v3 2000 HVG) on Open Problems label projection ZEBRAFISH-LABS-F1-MACRO: Label projection on Zebrafish (by laboratory), Macro F1 score Configuration: scANVI (Seurat v3 2000 HVG)Task: Open Problems label projection ZEBRAFISH-LABS-F1-MACRO: Label projection on Zebrafish (by laboratory), Macro F1 scoreDataset subset: Zebrafish (by laboratory) (Open Problems label projection split) 90k cells from zebrafish embryos throughout the first day of development, with and without a knockout of chordin, an important developmental gene. Split into train/test by laboratory. Dimensions: 26022 cells, 25258 genes. 24 cell types (avg. 1084±1156 cells per cell type). Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.2371223938182558 f1-macro Unit: fraction · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedopenproblems-label primary benchmark evidence · results, dataset(zebrafish_labs), method(scanvi), paramset(Seurat v3 2000 HVG), metric(f1_macro) Source checking is not independent reproduction. |
| scANVI (Seurat v3 2000 HVG) on Open Problems label projection ZEBRAFISH-RANDOM-ACCURACY: Label projection on Zebrafish (random split), Accuracy Configuration: scANVI (Seurat v3 2000 HVG)Task: Open Problems label projection ZEBRAFISH-RANDOM-ACCURACY: Label projection on Zebrafish (random split), AccuracyDataset subset: Zebrafish (random split) (Open Problems label projection split) 90k cells from zebrafish embryos throughout the first day of development, with and without a knockout of chordin, an important developmental gene. Split into train/test randomly. Dimensions: 26022 cells, 25258 genes. 24 cell types (avg. 1084±1156 cells per cell type). Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.7790023201856149 accuracy Unit: fraction · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedopenproblems-label primary benchmark evidence · results, dataset(zebrafish_random), method(scanvi), paramset(Seurat v3 2000 HVG), metric(accuracy) Source checking is not independent reproduction. |
| scANVI (Seurat v3 2000 HVG) on Open Problems label projection ZEBRAFISH-RANDOM-F1: Label projection on Zebrafish (random split), F1 score Configuration: scANVI (Seurat v3 2000 HVG)Task: Open Problems label projection ZEBRAFISH-RANDOM-F1: Label projection on Zebrafish (random split), F1 scoreDataset subset: Zebrafish (random split) (Open Problems label projection split) 90k cells from zebrafish embryos throughout the first day of development, with and without a knockout of chordin, an important developmental gene. Split into train/test randomly. Dimensions: 26022 cells, 25258 genes. 24 cell types (avg. 1084±1156 cells per cell type). Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.7278565236325139 f1 Unit: fraction · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedopenproblems-label primary benchmark evidence · results, dataset(zebrafish_random), method(scanvi), paramset(Seurat v3 2000 HVG), metric(f1) Source checking is not independent reproduction. |
| scANVI (Seurat v3 2000 HVG) on Open Problems label projection ZEBRAFISH-RANDOM-F1-MACRO: Label projection on Zebrafish (random split), Macro F1 score Configuration: scANVI (Seurat v3 2000 HVG)Task: Open Problems label projection ZEBRAFISH-RANDOM-F1-MACRO: Label projection on Zebrafish (random split), Macro F1 scoreDataset subset: Zebrafish (random split) (Open Problems label projection split) 90k cells from zebrafish embryos throughout the first day of development, with and without a knockout of chordin, an important developmental gene. Split into train/test randomly. Dimensions: 26022 cells, 25258 genes. 24 cell types (avg. 1084±1156 cells per cell type). Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.43734666546002615 f1-macro Unit: fraction · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedopenproblems-label primary benchmark evidence · results, dataset(zebrafish_random), method(scanvi), paramset(Seurat v3 2000 HVG), metric(f1_macro) Source checking is not independent reproduction. |
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- model: scANVI (Seurat v3 2000 HVG) on Open Problems label projection PANCREAS-RANDOM-ACCURACY: Label projection on Pancreas (random split), Accuracy
- model: scANVI (Seurat v3 2000 HVG) on Open Problems label projection PANCREAS-RANDOM-F1: Label projection on Pancreas (random split), F1 score
- model: scANVI (Seurat v3 2000 HVG) on Open Problems label projection PANCREAS-RANDOM-F1-MACRO: Label projection on Pancreas (random split), Macro F1 score
- model: scANVI (Seurat v3 2000 HVG) on Open Problems label projection PANCREAS-RANDOM-LABEL-NOISE-ACCURACY: Label projection on Pancreas (random split with label noise), Accuracy
- model: scANVI (Seurat v3 2000 HVG) on Open Problems label projection PANCREAS-RANDOM-LABEL-NOISE-F1: Label projection on Pancreas (random split with label noise), F1 score
- model: scANVI (Seurat v3 2000 HVG) on Open Problems label projection PANCREAS-RANDOM-LABEL-NOISE-F1-MACRO: Label projection on Pancreas (random split with label noise), Macro F1 score
- model: scANVI (Seurat v3 2000 HVG) on Open Problems label projection TABULA-MURIS-SENIS-LUNG-RANDOM-ACCURACY: Label projection on Tabula Muris Senis Lung (random split), Accuracy
- model: scANVI (Seurat v3 2000 HVG) on Open Problems label projection TABULA-MURIS-SENIS-LUNG-RANDOM-F1: Label projection on Tabula Muris Senis Lung (random split), F1 score
- model: scANVI (Seurat v3 2000 HVG) on Open Problems label projection TABULA-MURIS-SENIS-LUNG-RANDOM-F1-MACRO: Label projection on Tabula Muris Senis Lung (random split), Macro F1 score
- model: scANVI (Seurat v3 2000 HVG) on Open Problems label projection ZEBRAFISH-LABS-ACCURACY: Label projection on Zebrafish (by laboratory), Accuracy
- model: scANVI (Seurat v3 2000 HVG) on Open Problems label projection ZEBRAFISH-LABS-F1: Label projection on Zebrafish (by laboratory), F1 score
- model: scANVI (Seurat v3 2000 HVG) on Open Problems label projection ZEBRAFISH-LABS-F1-MACRO: Label projection on Zebrafish (by laboratory), Macro F1 score
- model: scANVI (Seurat v3 2000 HVG) on Open Problems label projection ZEBRAFISH-RANDOM-ACCURACY: Label projection on Zebrafish (random split), Accuracy
- model: scANVI (Seurat v3 2000 HVG) on Open Problems label projection ZEBRAFISH-RANDOM-F1: Label projection on Zebrafish (random split), F1 score
- model: scANVI (Seurat v3 2000 HVG) on Open Problems label projection ZEBRAFISH-RANDOM-F1-MACRO: Label projection on Zebrafish (random split), Macro F1 score