Plant Genomic Benchmark (PGB)
Plant genomic evaluations introduced with AgroNT. This release contains the complete promoter and terminator comparison tables from Figure 3e and 3f; other tasks remain unextracted.
Overview
Plant genomic evaluations introduced with AgroNT. This release contains the complete promoter and terminator comparison tables from Figure 3e and 3f; other tasks remain unextracted.
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.
PGB promoter strength maize protoplasts: A. thaliana: promoter strength prediction
r2 (coefficient of determination) · Higher values are better.
Every method PGB promoter strength reports on promoter strength prediction, scored with R² on promoter strength test sequences: maize protoplasts: A. thaliana.
PGB promoter strength maize protoplasts: A. thaliana: promoter strength prediction · promoter strength test sequences: maize protoplasts: A. thaliana (PGB promoter strength split)
Evidence origin: Author-reported evaluation. Numerical source review does not establish independent reproduction.
AgroNT Figure 3e source table · Fig3_panele.txt, column R2, maize protoplasts: A. thaliana; Methods Sec21Author-reported R² values, source checked but not independently reproduced. No uncertainty is supplied in these tables.
All comparison limitations (3)
- Author-reported R² values, source checked but not independently reproduced. No uncertainty is supplied in these tables.
- Compare only within the same task, assay system and sequence class. No aggregate across these conditions is reported here.
- Exact fitted checkpoint hashes, seeds and scoring denominators have not been established for these source rows.
Automated source review: 2026-09-23.
No unavailable values; missing scores remain labelled and are never plotted as zero.
Showing 2 of 2 matching rows.
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.
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.
Protocols
- PGB promoter strength maize protoplasts: A. thaliana: promoter strength prediction
- PGB promoter strength maize protoplasts: S. bicolor: promoter strength prediction
- PGB promoter strength maize protoplasts: Z. mays: promoter strength prediction
- PGB promoter strength tobacco leaves: A. thaliana: promoter strength prediction
- PGB promoter strength tobacco leaves: S. bicolor: promoter strength prediction
- PGB promoter strength tobacco leaves: Z. mays: promoter strength prediction
- PGB terminator strength maize protoplasts: A. thaliana: terminator strength prediction
- PGB terminator strength maize protoplasts: randomized GC sequences: terminator strength prediction
- PGB terminator strength maize protoplasts: Z. mays: terminator strength prediction
- PGB terminator strength tobacco leaves: A. thaliana: terminator strength prediction
- PGB terminator strength tobacco leaves: randomized GC sequences: terminator strength prediction
- PGB terminator strength tobacco leaves: Z. mays: terminator strength prediction
These source-backed links do not make different protocols or scores interchangeable.
Baseline coverage
Reference methods help show what a model adds beyond simple controls. We track a null control and a conventional method for each protocol.
0 of 24 active baseline roles have published Rewire measurements in this release. Measurements on a selected protocol do not establish coverage of an entire suite.
Baseline status by linked protocol
- PGB promoter strength maize protoplasts: A. thaliana: promoter strength prediction · 0/2 roles measured
- PGB promoter strength maize protoplasts: S. bicolor: promoter strength prediction · 0/2 roles measured
- PGB promoter strength maize protoplasts: Z. mays: promoter strength prediction · 0/2 roles measured
- PGB promoter strength tobacco leaves: A. thaliana: promoter strength prediction · 0/2 roles measured
- PGB promoter strength tobacco leaves: S. bicolor: promoter strength prediction · 0/2 roles measured
- PGB promoter strength tobacco leaves: Z. mays: promoter strength prediction · 0/2 roles measured
- PGB terminator strength maize protoplasts: A. thaliana: terminator strength prediction · 0/2 roles measured
- PGB terminator strength maize protoplasts: randomized GC sequences: terminator strength prediction · 0/2 roles measured
- PGB terminator strength maize protoplasts: Z. mays: terminator strength prediction · 0/2 roles measured
- PGB terminator strength tobacco leaves: A. thaliana: terminator strength prediction · 0/2 roles measured
- PGB terminator strength tobacco leaves: randomized GC sequences: terminator strength prediction · 0/2 roles measured
- PGB terminator strength tobacco leaves: Z. mays: terminator strength prediction · 0/2 roles measured
Protocol coverage CSV · Model evaluation matrix · Source table · Release and checksums
Coverage is derived from release 2026-09-23-2b89723c6dd9. Source citations describe the original records; they do not validate an unreviewed baseline proposal. No results have been generated by this audit.
Run this benchmark
Choose a concrete protocol before running an evaluation. Its inputs, split and scoring rules determine which results can be compared.
- PGB promoter strength maize protoplasts: A. thaliana: promoter strength prediction
- PGB promoter strength maize protoplasts: S. bicolor: promoter strength prediction
- PGB promoter strength maize protoplasts: Z. mays: promoter strength prediction
- PGB promoter strength tobacco leaves: A. thaliana: promoter strength prediction
- PGB promoter strength tobacco leaves: S. bicolor: promoter strength prediction
- PGB promoter strength tobacco leaves: Z. mays: promoter strength prediction
- PGB terminator strength maize protoplasts: A. thaliana: terminator strength prediction
- PGB terminator strength maize protoplasts: randomized GC sequences: terminator strength prediction
- PGB terminator strength maize protoplasts: Z. mays: terminator strength prediction
- PGB terminator strength tobacco leaves: A. thaliana: terminator strength prediction
- PGB terminator strength tobacco leaves: randomized GC sequences: terminator strength prediction
- PGB terminator strength tobacco leaves: Z. mays: terminator strength prediction
Run this benchmark
The paper describes IA3 fine-tuning on 170 bp sequences using the original studies' train/test datasets. Rewire has no maintained runner for this benchmark. Exact fitted checkpoints, split manifests and execution settings have not been verified; these reported scores are not a reproduction recipe.
A maintained rewire runner has not been verified for this benchmark. Check data access, weights, licences, dependencies and hardware in the linked official documentation; requirements have not been fully extracted.
AgroNT: published methods and Figure 3 · Methods: Fine-tuning strategy (Sec16), Promoter and terminator strength prediction (Sec21); Figure 3 captionStrengths, 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.
0 evidence rows matching the loaded filters
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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
- AgroNT: published methods and Figure 3 · Original source · Version of record, 2024-07-09; retrieved XML snapshot
Technical metadata and extraction receipts
Stable ID: agront-2024-plant-genomic-benchmark
- areas
- genomics
- entity level
- suite
- source locator
- Methods: Fine-tuning strategy (Sec16), Promoter and terminator strength prediction (Sec21); Figure 3 caption
- run documentation
- record id: agront-2024-plant-genomic-benchmark; status: source_reviewed_not_executed; source ids: agront-2024-paper-methods; source locator: Methods: Fine-tuning strategy (Sec16), Promoter and terminator strength prediction (Sec21); Figure 3 caption; summary: The paper describes IA3 fine-tuning on 170 bp sequences using the original studies' train/test datasets. Rewire has no maintained runner for this benchmark. Exact fitted checkpoints, split manifests and execution settings have not been verified; these reported scores are not a reproduction recipe.
- missing metadata
- runner: unavailable; split manifest: unextracted
Related records
- part of: PGB promoter strength maize protoplasts: A. thaliana: promoter strength prediction
- part of: PGB promoter strength maize protoplasts: S. bicolor: promoter strength prediction
- part of: PGB promoter strength maize protoplasts: Z. mays: promoter strength prediction
- part of: PGB promoter strength tobacco leaves: A. thaliana: promoter strength prediction
- part of: PGB promoter strength tobacco leaves: S. bicolor: promoter strength prediction
- part of: PGB promoter strength tobacco leaves: Z. mays: promoter strength prediction
- part of: PGB terminator strength maize protoplasts: A. thaliana: terminator strength prediction
- part of: PGB terminator strength maize protoplasts: randomized GC sequences: terminator strength prediction
- part of: PGB terminator strength maize protoplasts: Z. mays: terminator strength prediction
- part of: PGB terminator strength tobacco leaves: A. thaliana: terminator strength prediction
- part of: PGB terminator strength tobacco leaves: randomized GC sequences: terminator strength prediction
- part of: PGB terminator strength tobacco leaves: Z. mays: terminator strength prediction