Enformer
Main Enformer configuration with 1,536 channels, trained jointly on human/mouse and fine-tuned on human data (Par34).
Overview
Main Enformer configuration with 1,536 channels, trained jointly on human/mouse and fine-tuned on human data (Par34).
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Evaluations and results
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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 |
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Sources and history
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Release 2026-09-23-2b89723c6dd9 · Record review: source checked
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- 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-method-enformer
- areas
- genomics
- source locator
- Results / Enformer improves gene expression prediction, Par7; Fig1b left caption; Methods Par32–36
- missing metadata
- checkpoint revision: unreported; parameters: unextracted