Enformer CAGE gene-expression comparison evaluation of Enformer on Mean across-experiment Pearson correlation of human test-gene CAGE expression, scored with Mean across-experiment Pearson correlation across genes.
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1 evaluation · 1 result. Different protocols are not a single leaderboard.
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| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: Enformer | Protocol: Enformer CAGE gene-expression comparison Across genes CAGE Pearson: Mean across-experiment Pearson correlation of human test-gene CAGE expression Dataset subset: Enformer/Basenji2 human held-out test genes and CAGE experiments (Enformer CAGE gene-expression comparison split) | 0.85 mean_across_experiment_gene_pearson dimensionless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceHuman held-out test-set protein-coding genes; CAGE read counts summed over all unique TSS locations, using TSS-overlapping 128-bp bin plus two neighboring bins, log(1+x)-transformed and standardized across genes separately per experiment. Pearson correlation across genes per CAGE experiment, then mean across experiments. Same Basenji2 dataset and genomic intervals; human split 34,021 training/2,213 validation/1,937 test sequences. Cross-species homologous 1 Mb regions partitioned by connected components. Test-time mean of 8 random ≤3 bp shift/reverse-complement augmentations. Enformer input 196,608 bp, Basenji2 131,072 bp; receptive fields differ. Validation used for tuning; main comparison on test set. Aggregation: Not reported Enformer primary article: exact Figure 1b across-genes comparison reported in text · Results / Enformer improves gene expression prediction, Par7; Fig1b left caption; Methods Par32–36; exact narrative comparison, Enformer value 0.85 |
Source checking is not independent reproduction. Release 2026-09-29-06401fd5b220.
Human held-out test-set protein-coding genes; CAGE read counts summed over all unique TSS locations, using TSS-overlapping 128-bp bin plus two neighboring bins, log(1+x)-transformed and standardized across genes separately per experiment. Pearson correlation across genes per CAGE experiment, then mean across experiments. Same Basenji2 dataset and genomic intervals; human split 34,021 training/2,213 validation/1,937 test sequences. Cross-species homologous 1 Mb regions partitioned by connected components. Test-time mean of 8 random ≤3 bp shift/reverse-complement augmentations. Enformer input 196,608 bp, Basenji2 131,072 bp; receptive fields differ. Validation used for tuning; main comparison on test set.
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15 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| attributes.adaptation Joint human/mouse supervised training followed by 30,000 human fine-tuning steps (Par34). Context-only references | Enformer primary article: exact Figure 1b across-genes comparison reported in text Results / Enformer improves gene expression prediction, Par7; Fig1b left caption; Methods Par32–36; exact narrative comparison, Enformer value 0.85 Version: PMC8490152; SHA-256 pinned XML snapshot | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.comparison.metric_implementation Mean across-experiment Pearson correlation across genes Context-only references | Enformer primary article: exact Figure 1b across-genes comparison reported in text Results / Enformer improves gene expression prediction, Par7; Fig1b left caption; Methods Par32–36; exact narrative comparison, Enformer value 0.85 Version: PMC8490152; SHA-256 pinned XML snapshot | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.comparison.protocol_id enformer-cage-2021-task-across-genes-cage-pearson Context-only references | Enformer primary article: exact Figure 1b across-genes comparison reported in text Results / Enformer improves gene expression prediction, Par7; Fig1b left caption; Methods Par32–36; exact narrative comparison, Enformer value 0.85 Version: PMC8490152; SHA-256 pinned XML snapshot | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.evidence_overlap Both values belong to the same primary-paper Figure 1b-left experiment set and are rounded narrative summaries, not new independent model runs. Context-only references | Enformer primary article: exact Figure 1b across-genes comparison reported in text Results / Enformer improves gene expression prediction, Par7; Fig1b left caption; Methods Par32–36; exact narrative comparison, Enformer value 0.85 Version: PMC8490152; SHA-256 pinned XML snapshot | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.origin author_reported Context-only references | Enformer primary article: exact Figure 1b across-genes comparison reported in text Results / Enformer improves gene expression prediction, Par7; Fig1b left caption; Methods Par32–36; exact narrative comparison, Enformer value 0.85 Version: PMC8490152; SHA-256 pinned XML snapshot | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.protocol Human held-out test-set protein-coding genes; CAGE read counts summed over all unique TSS locations, using TSS-overlapping 128-bp bin plus two neighboring bins, log(1+x)-transformed and standardized across genes separately per experiment. Pearson correlation across genes per CAGE experiment, then mean across experiments. Same Basenji2 dataset and genomic intervals; human split 34,021 training/2,213 validation/1,937 test sequences. Cross-species homologous 1 Mb regions partitioned by connected components. Test-time mean of 8 random ≤3 bp shift/reverse-complement augmentations. Enformer input 196,608 bp, Basenji2 131,072 bp; receptive fields differ. Validation used for tuning; main comparison on test set. Context-only references | Enformer primary article: exact Figure 1b across-genes comparison reported in text Results / Enformer improves gene expression prediction, Par7; Fig1b left caption; Methods Par32–36; exact narrative comparison, Enformer value 0.85 Version: PMC8490152; SHA-256 pinned XML snapshot | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.published_score_reproduction false Context-only references | Enformer primary article: exact Figure 1b across-genes comparison reported in text Results / Enformer improves gene expression prediction, Par7; Fig1b left caption; Methods Par32–36; exact narrative comparison, Enformer value 0.85 Version: PMC8490152; SHA-256 pinned XML snapshot | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.same_paper_experiment_set enformer-2021-fig1b-left Context-only references | Enformer primary article: exact Figure 1b across-genes comparison reported in text Results / Enformer improves gene expression prediction, Par7; Fig1b left caption; Methods Par32–36; exact narrative comparison, Enformer value 0.85 Version: PMC8490152; SHA-256 pinned XML snapshot | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.source_locator Results / Enformer improves gene expression prediction, Par7; Fig1b left caption; Methods Par32–36; exact narrative comparison, Enformer value 0.85 Context-only references | Enformer primary article: exact Figure 1b across-genes comparison reported in text Results / Enformer improves gene expression prediction, Par7; Fig1b left caption; Methods Par32–36; exact narrative comparison, Enformer value 0.85 Version: PMC8490152; SHA-256 pinned XML snapshot | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.suite_complete false Context-only references | Enformer primary article: exact Figure 1b across-genes comparison reported in text Results / Enformer improves gene expression prediction, Par7; Fig1b left caption; Methods Par32–36; exact narrative comparison, Enformer value 0.85 Version: PMC8490152; SHA-256 pinned XML snapshot | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
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Release 2026-09-29-06401fd5b220 · Record review: source checked
Stable ID: enformer-cage-2021-evaluation-enformer-across-genes-cage-pearson