BEND VARIANT-EXPRESSION: Noncoding variant effects on expression
Noncoding variant effects on expression. Scored with AUROC on DeepSEA expression variants. A downstream head trained on frozen embeddings, except for the expert methods and the fully supervised baselines, which are trained end to end. Metric and splits are from Table 1.
Overview
Noncoding variant effects on expression. Scored with AUROC on DeepSEA expression variants. A downstream head trained on frozen embeddings, except for the expert methods and the fully supervised baselines, which are trained end to end. Metric and splits are from Table 1.
Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.
Results
Each comparison retains its reviewed evaluation scope, dataset and metric. Results are shown without a pooled ranking.
BEND VARIANT-EXPRESSION: Noncoding variant effects on expression
auroc (fraction) · Higher values are better.
BEND VARIANT-EXPRESSION: Noncoding variant effects on expression · DeepSEA expression variants (BEND split)
Evidence origin: Author-reported evaluation.
BEND: Benchmarking DNA Language Models on Biologically Meaningful Tasks · Table 1, row(Noncoding variant effects on expression)- The expert entries are specialist published models, each compared on one task only.
- The metric differs by task, taken from Table 1, so these figures cannot be averaged into one score.
Comparison details and limitations
Every method BEND reports on Noncoding variant effects on expression, scored with AUROC on DeepSEA expression variants.
- Author-reported numbers, source checked but not independently reproduced.
Automated source review: 2026-09-18. Numerical source review does not establish independent reproduction.
Dots show point estimates. Whiskers show only explicitly defined uncertainty (standard deviation, standard error or a labelled interval); their definitions remain in Table. Unresolved uncertainty is not plotted. Differences do not establish statistical significance.
Showing 12 of 14 matching rows.
Methods and evaluation design
Procedure, tasks and evaluated configurations
Evaluation design
Benchmarks bring together tasks and protocols. A task describes the biological question; a protocol defines a particular test.
Benchmarks
These source-backed links do not make different protocols or scores interchangeable.
Recorded evaluations
Each evaluation records what was tested and under which conditions.
- AWD-LSTM on BEND VARIANT-EXPRESSION: Noncoding variant effects on expression
- DEEPSEA on BEND VARIANT-EXPRESSION: Noncoding variant effects on expression
- DNABERT-2 on BEND VARIANT-EXPRESSION: Noncoding variant effects on expression
- DNABERT on BEND VARIANT-EXPRESSION: Noncoding variant effects on expression
- GENA-LM BERT on BEND VARIANT-EXPRESSION: Noncoding variant effects on expression
- GENA-LM BigBird on BEND VARIANT-EXPRESSION: Noncoding variant effects on expression
- GROVER on BEND VARIANT-EXPRESSION: Noncoding variant effects on expression
- HyenaDNA large on BEND VARIANT-EXPRESSION: Noncoding variant effects on expression
- HyenaDNA tiny on BEND VARIANT-EXPRESSION: Noncoding variant effects on expression
- NT-1000G on BEND VARIANT-EXPRESSION: Noncoding variant effects on expression
- NT-H on BEND VARIANT-EXPRESSION: Noncoding variant effects on expression
- NT-MS on BEND VARIANT-EXPRESSION: Noncoding variant effects on expression
Run instructions
No runnable recipe has been reviewed for this task. Dataset access, model requirements, licences and compute requirements must be checked against its sources before execution.
A task describes a biological question. Choose a linked protocol to obtain concrete split and scoring instructions.
Strengths, limitations and unresolved questions
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 |
|---|---|---|
| Relationship: part of discovery-benchmark-bend Individual claims | BEND: Benchmarking DNA Language Models on Biologically Meaningful Tasks Table 1, row(Noncoding variant effects on expression) Version: Primary full-text snapshot retrieved 2026-09-17; exact bytes pinned by SHA-256 | source checked automated source review · 2026-09-18 Audit detailsPrimary-source transcription with no human sign-off and no independent reproduction. Field: Claim: bend-association-variant-expression Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
Sources and history
View linked audit checks and correction history
Release 2026-09-29-06401fd5b220 · Record review: source checked
1 source records and release history
- BEND: Benchmarking DNA Language Models on Biologically Meaningful Tasks · Original source · Primary full-text snapshot retrieved 2026-09-17; exact bytes pinned by SHA-256
Technical metadata and extraction receipts
Stable ID: bend-task-variant-expression
- areas
- dna-genomes
- tasks
- Noncoding variant effects on expression
- metric
- AUROC
- metric direction
- higher
- dataset
- DeepSEA expression variants
- protocol
- A downstream head trained on frozen embeddings, except for the expert methods and the fully supervised baselines, which are trained end to end. Metric and splits are from Table 1.
- source locator
- Table 1, row(Noncoding variant effects on expression)
- comparison panels
- id: bend-panel-variant-expression; title: BEND VARIANT-EXPRESSION: Noncoding variant effects on expression; protocol id: bend-task-variant-expression; dataset id: bend-dataset-deepsea-expression-variants; metric: auroc; unit: fraction; direction: higher; result ids: bend-result-deepsea-variant-expression-auroc; bend-result-resnet-lm-variant-expression-auroc; bend-result-awd-lstm-variant-expression-auroc; bend-result-nt-h-variant-expression-auroc; bend-result-nt-ms-variant-expression-auroc; bend-result-nt-1000g-variant-expression-auroc; bend-result-nt-v2-variant-expression-auroc; bend-result-dnabert-variant-expression-auroc; bend-result-dnabert-2-variant-expression-auroc; bend-result-gena-lm-bert-variant-expression-auroc; bend-result-gena-lm-bigbird-variant-expression-auroc; bend-result-hyenadna-large-variant-expression-auroc; bend-result-hyenadna-tiny-variant-expression-auroc; bend-result-grover-variant-expression-auroc; source ids: evidence-expansion-bend-final-f709b6be; source locator: Table 1, row(Noncoding variant effects on expression); context: Every method BEND reports on Noncoding variant effects on expression, scored with AUROC on DeepSEA expression variants.; caveats: Author-reported numbers, source checked but not independently reproduced.; The expert entries are specialist published models, each compared on one task only.; The metric differs by task, taken from Table 1, so these figures cannot be averaged into one score.; review: method: automated_source_review; date: 2026-09-18
Related records
- part of: BEND
- subject: BEND VARIANT-EXPRESSION: part of discovery-benchmark-bend
- benchmark: AWD-LSTM on BEND VARIANT-EXPRESSION: Noncoding variant effects on expression
- benchmark: DEEPSEA on BEND VARIANT-EXPRESSION: Noncoding variant effects on expression
- benchmark: DNABERT-2 on BEND VARIANT-EXPRESSION: Noncoding variant effects on expression
- benchmark: DNABERT on BEND VARIANT-EXPRESSION: Noncoding variant effects on expression
- benchmark: GENA-LM BERT on BEND VARIANT-EXPRESSION: Noncoding variant effects on expression
- benchmark: GENA-LM BigBird on BEND VARIANT-EXPRESSION: Noncoding variant effects on expression
- benchmark: GROVER on BEND VARIANT-EXPRESSION: Noncoding variant effects on expression
- benchmark: HyenaDNA large on BEND VARIANT-EXPRESSION: Noncoding variant effects on expression
- benchmark: HyenaDNA tiny on BEND VARIANT-EXPRESSION: Noncoding variant effects on expression
- benchmark: NT-1000G on BEND VARIANT-EXPRESSION: Noncoding variant effects on expression
- benchmark: NT-H on BEND VARIANT-EXPRESSION: Noncoding variant effects on expression
- benchmark: NT-MS on BEND VARIANT-EXPRESSION: Noncoding variant effects on expression
- benchmark: NT-V2 on BEND VARIANT-EXPRESSION: Noncoding variant effects on expression
- benchmark: ResNet-LM on BEND VARIANT-EXPRESSION: Noncoding variant effects on expression