scArches+scANVI (Seurat v3 2000 HVG)
scArches+scANVI or "Single-cell architecture surgery" is a deep learning method for mapping new datasets onto a pre-existing reference model, using transfer learning and parameter optimization. It first uses scANVI to build a reference model from the training data, and then apply scArches to map the test data onto the reference model and make predictions.
Overview
scArches+scANVI or "Single-cell architecture surgery" is a deep learning method for mapping new datasets onto a pre-existing reference model, using transfer learning and parameter optimization. It first uses scANVI to build a reference model from the training data, and then apply scArches to map the test data onto the reference model and make predictions.
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 |
|---|---|---|
| scArches+scANVI (Seurat v3 2000 HVG) on Open Problems label projection CENGEN-BATCH-ACCURACY: Label projection on CeNGEN (split by batch), Accuracy Configuration: scArches+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 | ||
| 0.08028759736369083 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(scarches_scanvi), paramset(Seurat v3 2000 HVG), metric(accuracy) Source checking is not independent reproduction. |
| scArches+scANVI (Seurat v3 2000 HVG) on Open Problems label projection CENGEN-BATCH-F1: Label projection on CeNGEN (split by batch), F1 score Configuration: scArches+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 | ||
| 0.03725296782270025 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(scarches_scanvi), paramset(Seurat v3 2000 HVG), metric(f1) Source checking is not independent reproduction. |
| scArches+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: scArches+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 | ||
| 0.036846248365176415 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(scarches_scanvi), paramset(Seurat v3 2000 HVG), metric(f1_macro) Source checking is not independent reproduction. |
| scArches+scANVI (Seurat v3 2000 HVG) on Open Problems label projection CENGEN-RANDOM-ACCURACY: Label projection on CeNGEN (random split), Accuracy Configuration: scArches+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 | ||
| 0.34884870046447275 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(scarches_scanvi), paramset(Seurat v3 2000 HVG), metric(accuracy) Source checking is not independent reproduction. |
| scArches+scANVI (Seurat v3 2000 HVG) on Open Problems label projection CENGEN-RANDOM-F1: Label projection on CeNGEN (random split), F1 score Configuration: scArches+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 | ||
| 0.21567196436308758 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(scarches_scanvi), paramset(Seurat v3 2000 HVG), metric(f1) Source checking is not independent reproduction. |
| scArches+scANVI (Seurat v3 2000 HVG) on Open Problems label projection CENGEN-RANDOM-F1-MACRO: Label projection on CeNGEN (random split), Macro F1 score Configuration: scArches+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 | ||
| 0.04927592126738169 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(scarches_scanvi), paramset(Seurat v3 2000 HVG), metric(f1_macro) Source checking is not independent reproduction. |
| scArches+scANVI (Seurat v3 2000 HVG) on Open Problems label projection PANCREAS-BATCH-ACCURACY: Label projection on Pancreas (by batch), Accuracy Configuration: scArches+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 | ||
| 0.9540167703543414 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(scarches_scanvi), paramset(Seurat v3 2000 HVG), metric(accuracy) Source checking is not independent reproduction. |
| scArches+scANVI (Seurat v3 2000 HVG) on Open Problems label projection PANCREAS-BATCH-F1: Label projection on Pancreas (by batch), F1 score Configuration: scArches+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 | ||
| 0.9517252686049228 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(scarches_scanvi), paramset(Seurat v3 2000 HVG), metric(f1) Source checking is not independent reproduction. |
| scArches+scANVI (Seurat v3 2000 HVG) on Open Problems label projection PANCREAS-BATCH-F1-MACRO: Label projection on Pancreas (by batch), Macro F1 score Configuration: scArches+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 | ||
| 0.5816215781285415 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(scarches_scanvi), paramset(Seurat v3 2000 HVG), metric(f1_macro) Source checking is not independent reproduction. |
| scArches+scANVI (Seurat v3 2000 HVG) on Open Problems label projection PANCREAS-RANDOM-ACCURACY: Label projection on Pancreas (random split), Accuracy Configuration: scArches+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 | ||
| 0.956838905775076 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(scarches_scanvi), paramset(Seurat v3 2000 HVG), metric(accuracy) Source checking is not independent reproduction. |
| scArches+scANVI (Seurat v3 2000 HVG) on Open Problems label projection PANCREAS-RANDOM-F1: Label projection on Pancreas (random split), F1 score Configuration: scArches+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 | ||
| 0.9478276041369139 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(scarches_scanvi), paramset(Seurat v3 2000 HVG), metric(f1) Source checking is not independent reproduction. |
| scArches+scANVI (Seurat v3 2000 HVG) on Open Problems label projection PANCREAS-RANDOM-F1-MACRO: Label projection on Pancreas (random split), Macro F1 score Configuration: scArches+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 | ||
| 0.529456773064677 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(scarches_scanvi), paramset(Seurat v3 2000 HVG), metric(f1_macro) Source checking is not independent reproduction. |
| scArches+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: scArches+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 | ||
| 0.9476117103235747 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(scarches_scanvi), paramset(Seurat v3 2000 HVG), metric(accuracy) Source checking is not independent reproduction. |
| scArches+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: scArches+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 | ||
| 0.9372298848234738 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(scarches_scanvi), paramset(Seurat v3 2000 HVG), metric(f1) Source checking is not independent reproduction. |
| scArches+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: scArches+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 | ||
| 0.527328944140918 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(scarches_scanvi), paramset(Seurat v3 2000 HVG), metric(f1_macro) Source checking is not independent reproduction. |
| scArches+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: scArches+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 | ||
| 0.7223671013039117 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(scarches_scanvi), paramset(Seurat v3 2000 HVG), metric(accuracy) Source checking is not independent reproduction. |
| scArches+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: scArches+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 | ||
| 0.6280996816595446 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(scarches_scanvi), paramset(Seurat v3 2000 HVG), metric(f1) Source checking is not independent reproduction. |
| scArches+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: scArches+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 | ||
| 0.23443165472180164 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(scarches_scanvi), paramset(Seurat v3 2000 HVG), metric(f1_macro) Source checking is not independent reproduction. |
| scArches+scANVI (Seurat v3 2000 HVG) on Open Problems label projection ZEBRAFISH-LABS-ACCURACY: Label projection on Zebrafish (by laboratory), Accuracy Configuration: scArches+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 | ||
| 0.13280134942260283 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(scarches_scanvi), paramset(Seurat v3 2000 HVG), metric(accuracy) Source checking is not independent reproduction. |
| scArches+scANVI (Seurat v3 2000 HVG) on Open Problems label projection ZEBRAFISH-LABS-F1: Label projection on Zebrafish (by laboratory), F1 score Configuration: scArches+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 | ||
| 0.1309776775288379 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(scarches_scanvi), paramset(Seurat v3 2000 HVG), metric(f1) Source checking is not independent reproduction. |
| scArches+scANVI (Seurat v3 2000 HVG) on Open Problems label projection ZEBRAFISH-LABS-F1-MACRO: Label projection on Zebrafish (by laboratory), Macro F1 score Configuration: scArches+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 | ||
| 0.21771900557535676 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(scarches_scanvi), paramset(Seurat v3 2000 HVG), metric(f1_macro) Source checking is not independent reproduction. |
| scArches+scANVI (Seurat v3 2000 HVG) on Open Problems label projection ZEBRAFISH-RANDOM-ACCURACY: Label projection on Zebrafish (random split), Accuracy Configuration: scArches+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 | ||
| 0.637277648878577 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(scarches_scanvi), paramset(Seurat v3 2000 HVG), metric(accuracy) Source checking is not independent reproduction. |
| scArches+scANVI (Seurat v3 2000 HVG) on Open Problems label projection ZEBRAFISH-RANDOM-F1: Label projection on Zebrafish (random split), F1 score Configuration: scArches+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 | ||
| 0.5346413116985615 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(scarches_scanvi), paramset(Seurat v3 2000 HVG), metric(f1) Source checking is not independent reproduction. |
| scArches+scANVI (Seurat v3 2000 HVG) on Open Problems label projection ZEBRAFISH-RANDOM-F1-MACRO: Label projection on Zebrafish (random split), Macro F1 score Configuration: scArches+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 | ||
| 0.2832056442403825 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(scarches_scanvi), paramset(Seurat v3 2000 HVG), metric(f1_macro) Source checking is not independent reproduction. |
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Release 2026-09-17-134cd1815de8 · Record review: source checked
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Stable ID: open-problems-method-scarches-plus-scanvi-seurat-v3-2000-hvg
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- model: scArches+scANVI (Seurat v3 2000 HVG) on Open Problems label projection CENGEN-RANDOM-F1: Label projection on CeNGEN (random split), F1 score
- model: scArches+scANVI (Seurat v3 2000 HVG) on Open Problems label projection CENGEN-RANDOM-F1-MACRO: Label projection on CeNGEN (random split), Macro F1 score
- model: scArches+scANVI (Seurat v3 2000 HVG) on Open Problems label projection PANCREAS-BATCH-ACCURACY: Label projection on Pancreas (by batch), Accuracy
- model: scArches+scANVI (Seurat v3 2000 HVG) on Open Problems label projection PANCREAS-BATCH-F1: Label projection on Pancreas (by batch), F1 score
- model: scArches+scANVI (Seurat v3 2000 HVG) on Open Problems label projection PANCREAS-BATCH-F1-MACRO: Label projection on Pancreas (by batch), Macro F1 score
- model: scArches+scANVI (Seurat v3 2000 HVG) on Open Problems label projection PANCREAS-RANDOM-ACCURACY: Label projection on Pancreas (random split), Accuracy
- model: scArches+scANVI (Seurat v3 2000 HVG) on Open Problems label projection PANCREAS-RANDOM-F1: Label projection on Pancreas (random split), F1 score
- model: scArches+scANVI (Seurat v3 2000 HVG) on Open Problems label projection PANCREAS-RANDOM-F1-MACRO: Label projection on Pancreas (random split), Macro F1 score
- model: scArches+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: scArches+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: scArches+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: scArches+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: scArches+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: scArches+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: scArches+scANVI (Seurat v3 2000 HVG) on Open Problems label projection ZEBRAFISH-LABS-ACCURACY: Label projection on Zebrafish (by laboratory), Accuracy
- model: scArches+scANVI (Seurat v3 2000 HVG) on Open Problems label projection ZEBRAFISH-LABS-F1: Label projection on Zebrafish (by laboratory), F1 score
- model: scArches+scANVI (Seurat v3 2000 HVG) on Open Problems label projection ZEBRAFISH-LABS-F1-MACRO: Label projection on Zebrafish (by laboratory), Macro F1 score
- model: scArches+scANVI (Seurat v3 2000 HVG) on Open Problems label projection ZEBRAFISH-RANDOM-ACCURACY: Label projection on Zebrafish (random split), Accuracy
- model: scArches+scANVI (Seurat v3 2000 HVG) on Open Problems label projection ZEBRAFISH-RANDOM-F1: Label projection on Zebrafish (random split), F1 score
- model: scArches+scANVI (Seurat v3 2000 HVG) on Open Problems label projection ZEBRAFISH-RANDOM-F1-MACRO: Label projection on Zebrafish (random split), Macro F1 score