scANVI (All genes)
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 (All genes) on Open Problems label projection CENGEN-BATCH-ACCURACY: Label projection on CeNGEN (split by batch), Accuracy Configuration: scANVI (All genes)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 | ||
| 0.6470940683043739 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(All genes), metric(accuracy) Source checking is not independent reproduction. |
| scANVI (All genes) on Open Problems label projection CENGEN-BATCH-F1: Label projection on CeNGEN (split by batch), F1 score Configuration: scANVI (All genes)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 | ||
| 0.6168788176313944 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(All genes), metric(f1) Source checking is not independent reproduction. |
| scANVI (All genes) on Open Problems label projection CENGEN-BATCH-F1-MACRO: Label projection on CeNGEN (split by batch), Macro F1 score Configuration: scANVI (All genes)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 | ||
| 0.19725738168553295 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(All genes), metric(f1_macro) Source checking is not independent reproduction. |
| scANVI (All genes) on Open Problems label projection CENGEN-RANDOM-ACCURACY: Label projection on CeNGEN (random split), Accuracy Configuration: scANVI (All genes)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 | ||
| 0.6659254867081728 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(All genes), metric(accuracy) Source checking is not independent reproduction. |
| scANVI (All genes) on Open Problems label projection CENGEN-RANDOM-F1: Label projection on CeNGEN (random split), F1 score Configuration: scANVI (All genes)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 | ||
| 0.5728069016471795 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(All genes), metric(f1) Source checking is not independent reproduction. |
| scANVI (All genes) on Open Problems label projection CENGEN-RANDOM-F1-MACRO: Label projection on CeNGEN (random split), Macro F1 score Configuration: scANVI (All genes)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 | ||
| 0.24022628852988878 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(All genes), metric(f1_macro) Source checking is not independent reproduction. |
| scANVI (All genes) on Open Problems label projection PANCREAS-BATCH-ACCURACY: Label projection on Pancreas (by batch), Accuracy Configuration: scANVI (All genes)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 | ||
| 0.9575331349743035 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(All genes), metric(accuracy) Source checking is not independent reproduction. |
| scANVI (All genes) on Open Problems label projection PANCREAS-BATCH-F1: Label projection on Pancreas (by batch), F1 score Configuration: scANVI (All genes)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 | ||
| 0.9561489780630695 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(All genes), metric(f1) Source checking is not independent reproduction. |
| scANVI (All genes) on Open Problems label projection PANCREAS-BATCH-F1-MACRO: Label projection on Pancreas (by batch), Macro F1 score Configuration: scANVI (All genes)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 | ||
| 0.6604518695765396 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(All genes), metric(f1_macro) Source checking is not independent reproduction. |
| scANVI (All genes) on Open Problems label projection PANCREAS-RANDOM-ACCURACY: Label projection on Pancreas (random split), Accuracy Configuration: scANVI (All genes)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 | ||
| 0.9747720364741641 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(All genes), metric(accuracy) Source checking is not independent reproduction. |
| scANVI (All genes) on Open Problems label projection PANCREAS-RANDOM-F1: Label projection on Pancreas (random split), F1 score Configuration: scANVI (All genes)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 | ||
| 0.9723111833999045 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(All genes), metric(f1) Source checking is not independent reproduction. |
| scANVI (All genes) on Open Problems label projection PANCREAS-RANDOM-F1-MACRO: Label projection on Pancreas (random split), Macro F1 score Configuration: scANVI (All genes)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 | ||
| 0.6753232347526958 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(All genes), metric(f1_macro) Source checking is not independent reproduction. |
| scANVI (All genes) on Open Problems label projection PANCREAS-RANDOM-LABEL-NOISE-ACCURACY: Label projection on Pancreas (random split with label noise), Accuracy Configuration: scANVI (All genes)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 | ||
| 0.9704160246533128 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(All genes), metric(accuracy) Source checking is not independent reproduction. |
| scANVI (All genes) on Open Problems label projection PANCREAS-RANDOM-LABEL-NOISE-F1: Label projection on Pancreas (random split with label noise), F1 score Configuration: scANVI (All genes)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 | ||
| 0.9672436357663169 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(All genes), metric(f1) Source checking is not independent reproduction. |
| scANVI (All genes) 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 (All genes)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 | ||
| 0.6735752035664337 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(All genes), metric(f1_macro) Source checking is not independent reproduction. |
| scANVI (All genes) on Open Problems label projection TABULA-MURIS-SENIS-LUNG-RANDOM-ACCURACY: Label projection on Tabula Muris Senis Lung (random split), Accuracy Configuration: scANVI (All genes)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 | ||
| 0.8641925777331996 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(All genes), metric(accuracy) Source checking is not independent reproduction. |
| scANVI (All genes) on Open Problems label projection TABULA-MURIS-SENIS-LUNG-RANDOM-F1: Label projection on Tabula Muris Senis Lung (random split), F1 score Configuration: scANVI (All genes)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 | ||
| 0.8323005307396097 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(All genes), metric(f1) Source checking is not independent reproduction. |
| scANVI (All genes) 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 (All genes)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 | ||
| 0.43557549460855116 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(All genes), metric(f1_macro) Source checking is not independent reproduction. |
| scANVI (All genes) on Open Problems label projection ZEBRAFISH-LABS-ACCURACY: Label projection on Zebrafish (by laboratory), Accuracy Configuration: scANVI (All genes)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 | ||
| 0.21999480991306605 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(All genes), metric(accuracy) Source checking is not independent reproduction. |
| scANVI (All genes) on Open Problems label projection ZEBRAFISH-LABS-F1: Label projection on Zebrafish (by laboratory), F1 score Configuration: scANVI (All genes)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 | ||
| 0.2442120891364309 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(All genes), metric(f1) Source checking is not independent reproduction. |
| scANVI (All genes) on Open Problems label projection ZEBRAFISH-LABS-F1-MACRO: Label projection on Zebrafish (by laboratory), Macro F1 score Configuration: scANVI (All genes)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 | ||
| 0.263874405982815 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(All genes), metric(f1_macro) Source checking is not independent reproduction. |
| scANVI (All genes) on Open Problems label projection ZEBRAFISH-RANDOM-ACCURACY: Label projection on Zebrafish (random split), Accuracy Configuration: scANVI (All genes)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 | ||
| 0.7521268368136118 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(All genes), metric(accuracy) Source checking is not independent reproduction. |
| scANVI (All genes) on Open Problems label projection ZEBRAFISH-RANDOM-F1: Label projection on Zebrafish (random split), F1 score Configuration: scANVI (All genes)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 | ||
| 0.6923656409218792 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(All genes), metric(f1) Source checking is not independent reproduction. |
| scANVI (All genes) on Open Problems label projection ZEBRAFISH-RANDOM-F1-MACRO: Label projection on Zebrafish (random split), Macro F1 score Configuration: scANVI (All genes)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 | ||
| 0.40005402866576983 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(All genes), metric(f1_macro) Source checking is not independent reproduction. |
Evidence table
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Sources and history
Release 2026-09-17-134cd1815de8 · Record review: source checked
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Related records
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- model: scANVI (All genes) on Open Problems label projection TABULA-MURIS-SENIS-LUNG-RANDOM-ACCURACY: Label projection on Tabula Muris Senis Lung (random split), Accuracy
- model: scANVI (All genes) on Open Problems label projection TABULA-MURIS-SENIS-LUNG-RANDOM-F1: Label projection on Tabula Muris Senis Lung (random split), F1 score
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- model: scANVI (All genes) on Open Problems label projection ZEBRAFISH-LABS-F1-MACRO: Label projection on Zebrafish (by laboratory), Macro F1 score
- model: scANVI (All genes) on Open Problems label projection ZEBRAFISH-RANDOM-ACCURACY: Label projection on Zebrafish (random split), Accuracy
- model: scANVI (All genes) on Open Problems label projection ZEBRAFISH-RANDOM-F1: Label projection on Zebrafish (random split), F1 score
- model: scANVI (All genes) on Open Problems label projection ZEBRAFISH-RANDOM-F1-MACRO: Label projection on Zebrafish (random split), Macro F1 score