Basenji2 on Enformer CAGE gene-expression comparison Across genes CAGE Pearson: Mean across-experiment Pearson correlation of human test-gene CAGE expression
Enformer CAGE gene-expression comparison evaluation of Basenji2 on Mean across-experiment Pearson correlation of human test-gene CAGE expression, scored with Mean across-experiment Pearson correlation across genes.
Evaluation results
1 evaluation · 1 metric rows. Different protocols are not a single leaderboard.
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| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: Basenji2 | 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) | 0.81 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, Basenji2 value 0.81 |
Source checking is not independent reproduction. Release 2026-09-23-2b89723c6dd9.
Evaluation procedure
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.
- Configuration
- Basenji2
- 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)
- origin
- Author-reported evaluation
- configuration
- Not reported
- protocol id
- enformer-cage-2021-task-across-genes-cage-pearson
- metric implementation
- Mean across-experiment Pearson correlation across genes
Metadata review: source checked. Unreported conditions prevent automatic comparisons.
Reproduction
- Split
- Not reported
- Adaptation
- Not reported
- Scoring implementation
- Mean across-experiment Pearson correlation across genes
No execution recipe has been verified for this exact configuration and evaluation. A benchmark's general instructions may use different inputs, splits or model settings.
Reproducing this published result requires matching its model configuration, data, split and scorer. Source checking or a successful smoke test does not establish score reproduction.
Evidence
Source checking verifies the cited claim or transcription. It does not establish independent reproduction.
Evidence table
Inspect claims, sources and review details
Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.
One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.
15 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| attributes.adaptation Pretrained Basenji2 used directly for main paper comparisons (Par35). 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, Basenji2 value 0.81 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, Basenji2 value 0.81 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, Basenji2 value 0.81 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, Basenji2 value 0.81 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, Basenji2 value 0.81 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, Basenji2 value 0.81 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, Basenji2 value 0.81 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, Basenji2 value 0.81 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, Basenji2 value 0.81 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, Basenji2 value 0.81 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, Basenji2 value 0.81 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 |
Sources and history
View linked audit checks and correction history
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-evaluation-basenji2-across-genes-cage-pearson
- areas
- genomics
- tasks
- Mean across-experiment Pearson correlation of human test-gene CAGE expression
- origin
- author_reported
- 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.
- comparison
- protocol id: enformer-cage-2021-task-across-genes-cage-pearson; metric implementation: Mean across-experiment Pearson correlation across genes
- missing metadata
- checkpoint revision: unreported; seeds: unreported; budget: unreported; split manifest: unextracted
- source locator
- Results / Enformer improves gene expression prediction, Par7; Fig1b left caption; Methods Par32–36; exact narrative comparison, Basenji2 value 0.81
- same paper experiment set
- enformer-2021-fig1b-left
- adaptation
- Pretrained Basenji2 used directly for main paper comparisons (Par35).
- 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.
- published score reproduction
- false
- suite complete
- false
Related records
- benchmark: Enformer CAGE gene-expression comparison Across genes CAGE Pearson: Mean across-experiment Pearson correlation of human test-gene CAGE expression
- model: Basenji2
- dataset: Enformer/Basenji2 human held-out test genes and CAGE experiments (Enformer CAGE gene-expression comparison split)
- evaluation: Basenji2 · Enformer CAGE gene-expression comparison Across genes CAGE Pearson · Mean across-experiment Pearson correlation across genes