0.85 mean_across_experiment_gene_pearson
Enformer · Enformer CAGE gene-expression comparison Across genes CAGE Pearson · Mean across-experiment Pearson correlation across genes
- Tested 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)
- 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.
- Evaluation
- Enformer on Enformer CAGE gene-expression comparison Across genes CAGE Pearson: Mean across-experiment Pearson correlation of human test-gene CAGE expression
- Coverage
- scored: unreported; eligible: unreported
- Uncertainty
- Not reported
- Evidence
- Author-reported evaluation · source checkedEnformer 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
A source-checked result verifies the numerical transcription, not every model or protocol detail. Evaluation metadata: source checked. Source checked does not mean independently reproduced.
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.
1 evidence row matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Reported result 0.85 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; exact narrative comparison, Enformer value 0.85 Version: PMC8490152; SHA-256 pinned XML snapshot | source checked Extracted the complete exact two-model comparison from primary article Par7, resolved metric and evaluation scope against Fig1b caption and Methods Par32–36. No plot digitization, recomputation or model execution. · 2026-09-23 author reported Audit detailsSource checked, not reproduced. Metrics differ by task, so no composite score across tasks is computed or implied. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record Extraction artifact SHA-256: |
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-result-enformer-across-genes-cage-pearson-mean-across-experiment-gene-pearson
- areas
- genomics
- tasks
- Mean across-experiment Pearson correlation of human test-gene CAGE expression
- metric
- mean_across_experiment_gene_pearson
- metric direction
- higher
- unit
- dimensionless
- printed value
- 0.85
- numeric value
- 0.85
- uncertainty
- Not reported
- source locator
- Results / Enformer improves gene expression prediction, Par7; Fig1b left caption; Methods Par32–36; exact narrative comparison, Enformer value 0.85
- missing metadata
- denominator: unextracted; seeds: unreported
- review
- method: Extracted the complete exact two-model comparison from primary article Par7, resolved metric and evaluation scope against Fig1b caption and Methods Par32–36. No plot digitization, recomputation or model execution.; reviewer: automated-source-review; date: 2026-09-23; artifact sha256: 354632b465ccce978c56e049a314134cb74ad78a5301c8c8bf3127aa06d6c3b0; retrieval url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC8490152/fullTextXML; notes: Source checked, not reproduced. Metrics differ by task, so no composite score across tasks is computed or implied.
- same paper experiment set
- enformer-2021-fig1b-left
- source statistic
- mean correlation across CAGE experiments, rounded to two decimals in primary text
- source uncertainty note
- Figure 1b caption reports bootstrapped SD 0.004 for Across genes estimates; this shared statement is not encoded as a model-specific interval.
- 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.