scArches+scANVI (All genes)
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 (All genes) on Open Problems label projection CENGEN-BATCH-ACCURACY: Label projection on CeNGEN (split by batch), Accuracy Configuration: scArches+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 | ||
| 0.24565608148591972 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(All genes), metric(accuracy) Source checking is not independent reproduction. |
| scArches+scANVI (All genes) on Open Problems label projection CENGEN-BATCH-F1: Label projection on CeNGEN (split by batch), F1 score Configuration: scArches+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 | ||
| 0.19501179569318067 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(All genes), metric(f1) Source checking is not independent reproduction. |
| scArches+scANVI (All genes) on Open Problems label projection CENGEN-BATCH-F1-MACRO: Label projection on CeNGEN (split by batch), Macro F1 score Configuration: scArches+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 | ||
| 0.09068453934420202 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(All genes), metric(f1_macro) Source checking is not independent reproduction. |
| scArches+scANVI (All genes) on Open Problems label projection CENGEN-RANDOM-ACCURACY: Label projection on CeNGEN (random split), Accuracy Configuration: scArches+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 | ||
| 0.4243996442336199 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(All genes), metric(accuracy) Source checking is not independent reproduction. |
| scArches+scANVI (All genes) on Open Problems label projection CENGEN-RANDOM-F1: Label projection on CeNGEN (random split), F1 score Configuration: scArches+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 | ||
| 0.28984918948885136 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(All genes), metric(f1) Source checking is not independent reproduction. |
| scArches+scANVI (All genes) on Open Problems label projection CENGEN-RANDOM-F1-MACRO: Label projection on CeNGEN (random split), Macro F1 score Configuration: scArches+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 | ||
| 0.07585896370042627 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(All genes), metric(f1_macro) Source checking is not independent reproduction. |
| scArches+scANVI (All genes) on Open Problems label projection PANCREAS-BATCH-ACCURACY: Label projection on Pancreas (by batch), Accuracy Configuration: scArches+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 | ||
| 0.9507708953205302 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(All genes), metric(accuracy) Source checking is not independent reproduction. |
| scArches+scANVI (All genes) on Open Problems label projection PANCREAS-BATCH-F1: Label projection on Pancreas (by batch), F1 score Configuration: scArches+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 | ||
| 0.9494991049364069 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(All genes), metric(f1) Source checking is not independent reproduction. |
| scArches+scANVI (All genes) on Open Problems label projection PANCREAS-BATCH-F1-MACRO: Label projection on Pancreas (by batch), Macro F1 score Configuration: scArches+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 | ||
| 0.6454766237283966 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(All genes), metric(f1_macro) Source checking is not independent reproduction. |
| scArches+scANVI (All genes) on Open Problems label projection PANCREAS-RANDOM-ACCURACY: Label projection on Pancreas (random split), Accuracy Configuration: scArches+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 | ||
| 0.9556231003039514 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(All genes), metric(accuracy) Source checking is not independent reproduction. |
| scArches+scANVI (All genes) on Open Problems label projection PANCREAS-RANDOM-F1: Label projection on Pancreas (random split), F1 score Configuration: scArches+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 | ||
| 0.9460786047979668 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(All genes), metric(f1) Source checking is not independent reproduction. |
| scArches+scANVI (All genes) on Open Problems label projection PANCREAS-RANDOM-F1-MACRO: Label projection on Pancreas (random split), Macro F1 score Configuration: scArches+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 | ||
| 0.5347595613474366 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(All genes), metric(f1_macro) Source checking is not independent reproduction. |
| scArches+scANVI (All genes) on Open Problems label projection PANCREAS-RANDOM-LABEL-NOISE-ACCURACY: Label projection on Pancreas (random split with label noise), Accuracy Configuration: scArches+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 | ||
| 0.9463790446841295 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(All genes), metric(accuracy) Source checking is not independent reproduction. |
| scArches+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: scArches+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 | ||
| 0.9363141652450575 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(All genes), metric(f1) Source checking is not independent reproduction. |
| scArches+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: scArches+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 | ||
| 0.5241903797681743 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(All genes), metric(f1_macro) Source checking is not independent reproduction. |
| scArches+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: scArches+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 | ||
| 0.7837512537612839 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(All genes), metric(accuracy) Source checking is not independent reproduction. |
| scArches+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: scArches+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 | ||
| 0.7239101602555007 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(All genes), metric(f1) Source checking is not independent reproduction. |
| scArches+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: scArches+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 | ||
| 0.2807778194761088 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(All genes), metric(f1_macro) Source checking is not independent reproduction. |
| scArches+scANVI (All genes) on Open Problems label projection ZEBRAFISH-LABS-ACCURACY: Label projection on Zebrafish (by laboratory), Accuracy Configuration: scArches+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 | ||
| 0.22602828597379007 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(All genes), metric(accuracy) Source checking is not independent reproduction. |
| scArches+scANVI (All genes) on Open Problems label projection ZEBRAFISH-LABS-F1: Label projection on Zebrafish (by laboratory), F1 score Configuration: scArches+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 | ||
| 0.25597266236180566 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(All genes), metric(f1) Source checking is not independent reproduction. |
| scArches+scANVI (All genes) on Open Problems label projection ZEBRAFISH-LABS-F1-MACRO: Label projection on Zebrafish (by laboratory), Macro F1 score Configuration: scArches+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 | ||
| 0.23106180199762813 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(All genes), metric(f1_macro) Source checking is not independent reproduction. |
| scArches+scANVI (All genes) on Open Problems label projection ZEBRAFISH-RANDOM-ACCURACY: Label projection on Zebrafish (random split), Accuracy Configuration: scArches+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 | ||
| 0.6477184841453983 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(All genes), metric(accuracy) Source checking is not independent reproduction. |
| scArches+scANVI (All genes) on Open Problems label projection ZEBRAFISH-RANDOM-F1: Label projection on Zebrafish (random split), F1 score Configuration: scArches+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 | ||
| 0.5550225618420579 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(All genes), metric(f1) Source checking is not independent reproduction. |
| scArches+scANVI (All genes) on Open Problems label projection ZEBRAFISH-RANDOM-F1-MACRO: Label projection on Zebrafish (random split), Macro F1 score Configuration: scArches+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 | ||
| 0.3165801404765449 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(All genes), metric(f1_macro) Source checking is not independent reproduction. |
Evidence table
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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-all-genes
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Related records
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- model: scArches+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
- model: scArches+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: scArches+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
- model: scArches+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
- model: scArches+scANVI (All genes) on Open Problems label projection ZEBRAFISH-LABS-ACCURACY: Label projection on Zebrafish (by laboratory), Accuracy
- model: scArches+scANVI (All genes) on Open Problems label projection ZEBRAFISH-LABS-F1: Label projection on Zebrafish (by laboratory), F1 score
- model: scArches+scANVI (All genes) on Open Problems label projection ZEBRAFISH-LABS-F1-MACRO: Label projection on Zebrafish (by laboratory), Macro F1 score
- model: scArches+scANVI (All genes) on Open Problems label projection ZEBRAFISH-RANDOM-ACCURACY: Label projection on Zebrafish (random split), Accuracy
- model: scArches+scANVI (All genes) on Open Problems label projection ZEBRAFISH-RANDOM-F1: Label projection on Zebrafish (random split), F1 score
- model: scArches+scANVI (All genes) on Open Problems label projection ZEBRAFISH-RANDOM-F1-MACRO: Label projection on Zebrafish (random split), Macro F1 score