Enformer CAGE gene-expression comparison Across genes CAGE Pearson: Mean across-experiment Pearson correlation of human test-gene CAGE expression
Mean across-experiment Pearson correlation of human test-gene CAGE expression. Scored with Mean across-experiment Pearson correlation across genes on Enformer/Basenji2 human held-out test genes and CAGE experiments. 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.
Overview
Mean across-experiment Pearson correlation of human test-gene CAGE expression. Scored with Mean across-experiment Pearson correlation across genes on Enformer/Basenji2 human held-out test genes and CAGE experiments. 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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Results
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Enformer CAGE gene-expression comparison Across genes CAGE Pearson: Mean across-experiment Pearson correlation of human test-gene CAGE expression
mean_across_experiment_gene_pearson (dimensionless) · Higher values are better.
Every method Enformer CAGE gene-expression comparison reports on Mean across-experiment Pearson correlation of human test-gene CAGE expression, scored with Mean across-experiment Pearson correlation across genes on Enformer/Basenji2 human held-out test genes and CAGE experiments.
Enformer CAGE gene-expression comparison Across genes CAGE Pearson: Mean across-experiment Pearson correlation of human test-gene CAGE expression · Enformer/Basenji2 human held-out test genes and CAGE experiments (Enformer CAGE gene-expression comparison split)
Evidence origin: Author-reported evaluation. Numerical source review does not establish independent reproduction.
Enformer primary article: exact Figure 1b across-genes comparison reported in text · Results / Enformer improves gene expression prediction, Par7; Fig1b left caption; Methods Par32–36Only the complete two-model Figure 1b-left across-genes comparison is extracted; no claim to cover the full paper.
All comparison limitations (5)
- Only the complete two-model Figure 1b-left across-genes comparison is extracted; no claim to cover the full paper.
- Mean Pearson values 0.81/0.85 are printed in Par7; separate ExPecto Spearman values 0.812/0.850 later in that paragraph are a different comparison.
- Figure 1b caption states bootstrap SD 0.004 for across-genes estimates; retained as shared source context, not converted into confidence intervals or assumed per-model training-run variability.
- Basenji2 is the pretrained main-comparison configuration, distinct from original Basenji1 and from retrained ablation models.
- Experimental replicate accuracy 0.94 is contextual, not a third model score. Input lengths, architectures and training procedures differ.
Automated source review: 2026-09-23.
No unavailable values; missing scores remain labelled and are never plotted as zero.
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- Basenji2 on Enformer CAGE gene-expression comparison Across genes CAGE Pearson: Mean across-experiment Pearson correlation of human test-gene CAGE expression
- Enformer on Enformer CAGE gene-expression comparison Across genes CAGE Pearson: Mean across-experiment Pearson correlation of human test-gene CAGE expression
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Evidence table
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1 evidence row matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Relationship: part of enformer-cage-gene-expression-2021 Individual claims | 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 Version: PMC8490152; SHA-256 pinned XML snapshot | source checked automated source review · 2026-09-23 Audit detailsPrimary-source transcription with no human sign-off and no independent reproduction. Field: Claim: enformer-cage-2021-association-across-genes-cage-pearson Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
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Release 2026-09-23-2b89723c6dd9 · Record review: source checked
1 source records and release history
- Enformer primary article: exact Figure 1b across-genes comparison reported in text · Original source · PMC8490152; SHA-256 pinned XML snapshot
Technical metadata and extraction receipts
Stable ID: enformer-cage-2021-task-across-genes-cage-pearson
- areas
- genomics
- tasks
- Mean across-experiment Pearson correlation of human test-gene CAGE expression
- metric
- Mean across-experiment Pearson correlation across genes
- metric direction
- higher
- dataset
- Enformer/Basenji2 human held-out test genes and CAGE experiments
- 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.
- source locator
- Results / Enformer improves gene expression prediction, Par7; Fig1b left caption; Methods Par32–36
- comparison panels
- id: enformer-cage-2021-panel-across-genes-cage-pearson; title: Enformer CAGE gene-expression comparison Across genes CAGE Pearson: Mean across-experiment Pearson correlation of human test-gene CAGE expression; protocol id: enformer-cage-2021-task-across-genes-cage-pearson; dataset id: enformer-cage-2021-dataset-enformer-basenji2-human-held-out-test-genes-and-cage-experiments; metric: mean_across_experiment_gene_pearson; unit: dimensionless; direction: higher; result ids: enformer-cage-2021-result-basenji2-across-genes-cage-pearson-mean-across-experiment-gene-pearson; enformer-cage-2021-result-enformer-across-genes-cage-pearson-mean-across-experiment-gene-pearson; source ids: coverage-enformer-2021-primary; source locator: Results / Enformer improves gene expression prediction, Par7; Fig1b left caption; Methods Par32–36; context: Every method Enformer CAGE gene-expression comparison reports on Mean across-experiment Pearson correlation of human test-gene CAGE expression, scored with Mean across-experiment Pearson correlation across genes on Enformer/Basenji2 human held-out test genes and CAGE experiments.; caveats: Only the complete two-model Figure 1b-left across-genes comparison is extracted; no claim to cover the full paper.; Mean Pearson values 0.81/0.85 are printed in Par7; separate ExPecto Spearman values 0.812/0.850 later in that paragraph are a different comparison.; Figure 1b caption states bootstrap SD 0.004 for across-genes estimates; retained as shared source context, not converted into confidence intervals or assumed per-model training-run variability.; Basenji2 is the pretrained main-comparison configuration, distinct from original Basenji1 and from retrained ablation models.; Experimental replicate accuracy 0.94 is contextual, not a third model score. Input lengths, architectures and training procedures differ.; review: method: automated_source_review; date: 2026-09-23
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Related records
- part of: Enformer CAGE gene-expression comparison
- subject: Enformer CAGE gene-expression comparison Across genes CAGE Pearson: part of enformer-cage-gene-expression-2021
- benchmark: Basenji2 on Enformer CAGE gene-expression comparison Across genes CAGE Pearson: Mean across-experiment Pearson correlation of human test-gene CAGE expression
- benchmark: Enformer on Enformer CAGE gene-expression comparison Across genes CAGE Pearson: Mean across-experiment Pearson correlation of human test-gene CAGE expression