Strengths and considerations
No source-reviewed explanatory claims are recorded here yet.
Protocol
E. coli sigma70 independent promoter test (E. coli sigma70 promoter prediction)
E. coli sigma70 independent promoter test · Table 3. Test-only evaluation on Cassiano and Silva-Rocha 2020 data; methods have different training histories. 865 high-evidence RegulonDB 10.5 promoters and 1,000 nucleotide-distribution-matched negative sequences. Promoter exact matches removed from model training.
Sources
ProkBERT family: genomic language models for microbiome applications · Table 3: Accuracy, E. coli sigma70 independent promoter testOverview
Key specifications have not been extracted for this record. See the linked evaluation and sources for the reported setup.
limited source coverage · Automated source review, 2026-09-17. All specifications and missing details
Results
Each comparison retains its reviewed evaluation scope, dataset and metric. Results are shown without a pooled ranking.
E. coli sigma70 independent promoter test · Table 3
Accuracy (unitless) · Higher values are better.
E. coli sigma70 independent promoter test (E. coli sigma70 promoter prediction) · E. coli sigma70 promoter dataset
Evidence origin: Author-reported evaluation, Result quoted from another source, Independent external evaluation.
ProkBERT family: genomic language models for microbiome applications · Table 3: Accuracy, E. coli sigma70 independent promoter test- Historical comparator implementations and training sets differ; source table alone does not prove matched training budget.
Comparison details and limitations
Test-only evaluation on Cassiano and Silva-Rocha 2020 data; methods have different training histories. 865 high-evidence RegulonDB 10.5 promoters and 1,000 nucleotide-distribution-matched negative sequences. Promoter exact matches removed from model training.
- No interval assigned unless printed in source cell.
Automated source review: 2026-09-17. 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 15 matching rows.
Tested configuration
00.250.50.751
Reported scoreMethods and evaluation design
Procedure, tasks and evaluated configurations
How it works
Evaluation in this paper
Test-only evaluation on Cassiano and Silva-Rocha 2020 data; methods have different training histories. 865 high-evidence RegulonDB 10.5 promoters and 1,000 nucleotide-distribution-matched negative sequences. Promoter exact matches removed from model training.
Sources
ProkBERT family: genomic language models for microbiome applications · Table 3: Accuracy, E. coli sigma70 independent promoter testEvaluation design
Benchmarks bring together tasks and protocols. A task describes the biological question; a protocol defines a particular test.
These source-backed links do not make different protocols or scores interchangeable.
Recorded evaluations
Each evaluation records what was tested and under which conditions.
- ProkBERT-mini: E. coli sigma70 promoter prediction
- Promotech: E. coli sigma70 promoter prediction
- CNNProm: E. coli sigma70 independent promoter test
- ProkBERT-mini-c: E. coli sigma70 independent promoter test
- Sigma70Pred: E. coli sigma70 independent promoter test
- 70ProPred: E. coli sigma70 independent promoter test
- ProkBERT-mini-long: E. coli sigma70 independent promoter test
- iPromoter-BnCNN: E. coli sigma70 independent promoter test
- BPROM: E. coli sigma70 independent promoter test
- iPro70-FMWin: E. coli sigma70 independent promoter test
- MULTiPly: E. coli sigma70 independent promoter test
- Multiply: E. coli sigma70 independent promoter test
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 2 active baseline roles have published Rewire measurements in this release. Measurements on a selected protocol do not establish coverage of an entire suite.
No execution recipe linked to this protocol. Recipe availability does not establish a completed evaluation.
No reviewed evaluations with results linked in this release.
Literature evidence is not a Rewire measurement. Executed but unpublished runs and private review status are not included.
Null control
Proposed control: requires review
Select a task-valid null control after reviewing inputs and metric
Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.
This is a suggested selection rule, not a validated method or a measured score.
Conventional reference
Proposed control: requires review
Select an upstream conventional reference after reviewing the full protocol
Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.
This is a suggested selection rule, not a validated method or a measured score.
Protocol coverage CSV · Model evaluation matrix · Source table · Release and checksums
Coverage is derived from release 2026-09-29-06401fd5b220. Source citations describe the original records; they do not validate an unreviewed baseline proposal. No results have been generated by this audit.
Run instructions
No runnable recipe has been reviewed for this protocol. Dataset access, model requirements, licences and compute requirements must be checked against its sources before execution.
Strengths, limitations and unresolved questions
Strengths and limitations
Limitations and conditions
No source-reviewed explanatory claims are recorded here yet.
Profile review details
Primary-source transcription and separate automated review. No human sign-off or experimental reproduction.
Stable record: paper-protocol-94fa3494d41bcd98d2Specifications
Inputs, training, access and other details
Explanatory profile: limited source coverage · Automated source review, 2026-09-17. Review applies to the cited claims; unresolved fields are listed below. Numerical results retain their own review status.
| Property | Description and evidence |
|---|---|
| Datasets | Not extracted or verified for this record. |
| Organisms | Not extracted or verified for this record. |
| Assays | Not extracted or verified for this record. |
| Splits | Not extracted or verified for this record. |
| Allowed inputs | Not extracted or verified for this record. |
| Adaptation | Not extracted or verified for this record. |
| Metrics | Not extracted or verified for this record. |
| Baselines | Not extracted or verified for this record. |
Evidence
Source checking verifies the cited claim or transcription. It does not establish independent reproduction.
Papers and result coverage
Last literature check: 2026-09-17. Primary-source discovery and table/protocol screening; source checked is not independently reproduced. Raw acquisitions not automatically numerical publication approval.
| Paper or primary resource | Version | Reference |
|---|---|---|
| ProkBERT family: genomic language models for microbiome applications | PMC10810988.1 | Read source DOI: 10.3389/fmicb.2023.1331233 |
Historical gaps recorded on 2026-09-17
The catalogue now holds 60 result rows for this benchmark. A note below about pending extraction describes the state on 2026-09-17 and may since have been answered by a later batch. The result rows and their sources are the current record.
- Independent batch review before import; preserve existing observation identities.
Search and extraction details
complete comparison tables extracted pending publication review
Searches
- ProkBERT family: genomic language models for microbiome applications primary paper benchmark results
Evidence locations
- Table 3: Accuracy, E. coli sigma70 independent promoter test
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.
3 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Evaluation in this paper Test-only evaluation on Cassiano and Silva-Rocha 2020 data; methods have different training histories. 865 high-evidence RegulonDB 10.5 promoters and 1,000 nucleotide-distribution-matched negative sequences. Promoter exact matches removed from model training. Individual claims | ProkBERT family: genomic language models for microbiome applications Table 3: Accuracy, E. coli sigma70 independent promoter test Version: PMC10810988.1 | source checked automated source review · 2026-09-17 Audit detailsPrimary-source transcription and separate automated review. No human sign-off or experimental reproduction. Field: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| Introduction E. coli sigma70 independent promoter test · Table 3. Test-only evaluation on Cassiano and Silva-Rocha 2020 data; methods have different training histories. 865 high-evidence RegulonDB 10.5 promoters and 1,000 nucleotide-distribution-matched negative sequences. Promoter exact matches removed from model training. Individual claims | ProkBERT family: genomic language models for microbiome applications Table 3: Accuracy, E. coli sigma70 independent promoter test Version: PMC10810988.1 | source checked automated source review · 2026-09-17 Audit detailsPrimary-source transcription and separate automated review. No human sign-off or experimental reproduction. Field: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| Relationship: evaluates task reported-task-3891811dcce8b3 Individual claims | ProkBERT family: genomic language models for microbiome applications Table 3: Accuracy, E. coli sigma70 independent promoter test Version: PMC10810988.1 | source checked automated source review · 2026-09-17 Audit detailsField: Claim: paper-claim-410c7dd40fbe291a7c 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: needs review
1 source records and release history
- ProkBERT family: genomic language models for microbiome applications · Original source · PMC10810988.1
Technical metadata and extraction receipts
Stable ID: paper-protocol-94fa3494d41bcd98d2
- areas
- microbes-communities
- tasks
- E. coli sigma70 promoter prediction
- entity level
- protocol
- protocol
- Test-only evaluation on Cassiano and Silva-Rocha 2020 data; methods have different training histories. 865 high-evidence RegulonDB 10.5 promoters and 1,000 nucleotide-distribution-matched negative sequences. Promoter exact matches removed from model training.
- comparison panels
- id: part2-prokbert-2024-T3-28db1fe651; title: E. coli sigma70 independent promoter test · Table 3; protocol id: paper-protocol-94fa3494d41bcd98d2; dataset id: reported-dataset-48def1da574597; metric: Accuracy; unit: unitless; direction: higher; result ids: lit-033; paper-result-feb6117d798c298b3a; paper-result-4c8aea33e9c70cd11f; paper-result-6f98ff1a4772f9ccb3; paper-result-410891a647e6249a90; paper-result-13fec9cc9a02b9ade1; paper-result-0c5fed0bf3be3b8d58; paper-result-bc336af932cc34bfff; paper-result-1e1456e63f197bf736; paper-result-9b1c2838a500cd6be1; paper-result-68a650408dc07175aa; lit-034; paper-result-01c368320e32c0ab0e; paper-result-9656f7e500dc93dcbb; paper-result-8f3993306e0616cbfc; source ids: part2-prokbert-2024; source locator: Table 3: Accuracy, E. coli sigma70 independent promoter test; context: Test-only evaluation on Cassiano and Silva-Rocha 2020 data; methods have different training histories. 865 high-evidence RegulonDB 10.5 promoters and 1,000 nucleotide-distribution-matched negative sequences. Promoter exact matches removed from model training.; caveats: Historical comparator implementations and training sets differ; source table alone does not prove matched training budget.; No interval assigned unless printed in source cell.; review: method: automated_source_review; date: 2026-09-17; id: part2-prokbert-2024-T3-8c8321b937; title: E. coli sigma70 independent promoter test · Table 3; protocol id: paper-protocol-94fa3494d41bcd98d2; dataset id: reported-dataset-48def1da574597; metric: MCC; unit: dimensionless; direction: higher; result ids: paper-result-feb8e65e7cf4e58b24; paper-result-60e6848b40696ac12e; paper-result-dc6aa1769ce2cd3f4e; paper-result-7a77ab58dafad4a2aa; paper-result-4735c3c4f977af0fce; paper-result-37c1083392f34f9406; paper-result-2c8339165057825390; paper-result-4a2c32c0125b04d6d4; paper-result-e75353105223f1e447; paper-result-208a44d26d306cd65a; paper-result-2a20fdc870d161095a; paper-result-5b13f4aa84f244913e; paper-result-a48e2ed7a547d27527; paper-result-4d73754c1cb397329c; paper-result-e8fc9cd21d61cf7e9d; source ids: part2-prokbert-2024; source locator: Table 3: MCC, E. coli sigma70 independent promoter test; context: Test-only evaluation on Cassiano and Silva-Rocha 2020 data; methods have different training histories. 865 high-evidence RegulonDB 10.5 promoters and 1,000 nucleotide-distribution-matched negative sequences. Promoter exact matches removed from model training.; caveats: Historical comparator implementations and training sets differ; source table alone does not prove matched training budget.; No interval assigned unless printed in source cell.; review: method: automated_source_review; date: 2026-09-17; id: part2-prokbert-2024-T3-9956d5103b; title: E. coli sigma70 independent promoter test · Table 3; protocol id: paper-protocol-94fa3494d41bcd98d2; dataset id: reported-dataset-48def1da574597; metric: Sensitivity; unit: fraction; direction: higher; result ids: paper-result-26d268756b8a662fd8; paper-result-3d5f92c4cb77e67f50; paper-result-03b41950c492f3431d; paper-result-e555e071d181460c12; paper-result-6e84f7880c063cbdd7; paper-result-e29c79b8c8cd56be14; paper-result-b3b697a5be7a34fe24; paper-result-4ab4d0f27fcfd2347b; paper-result-ba12a8ea88fda90346; paper-result-7a7d041d187d9e7189; paper-result-d562aac34ec0538c9b; paper-result-074f43f6d5f3283258; paper-result-77a6d05afe1045f61a; paper-result-a560ff80bc0c25f435; paper-result-42d188ba97fceb115b; source ids: part2-prokbert-2024; source locator: Table 3: Sensitivity, E. coli sigma70 independent promoter test; context: Test-only evaluation on Cassiano and Silva-Rocha 2020 data; methods have different training histories. 865 high-evidence RegulonDB 10.5 promoters and 1,000 nucleotide-distribution-matched negative sequences. Promoter exact matches removed from model training.; caveats: Historical comparator implementations and training sets differ; source table alone does not prove matched training budget.; No interval assigned unless printed in source cell.; review: method: automated_source_review; date: 2026-09-17; id: part2-prokbert-2024-T3-0f5f4b674d; title: E. coli sigma70 independent promoter test · Table 3; protocol id: paper-protocol-94fa3494d41bcd98d2; dataset id: reported-dataset-48def1da574597; metric: Specificity; unit: fraction; direction: higher; result ids: paper-result-2ad5c1987a41ae98d8; paper-result-43e98ef9fed2b6cabd; paper-result-c505c37d3a9bd19568; paper-result-0ba7173d41197d3830; paper-result-d6f5d354ed1d3656ba; paper-result-dc1256b9ef86c3feef; paper-result-442110ff6e4a09bb12; paper-result-e3fe9457bfda3bc5e9; paper-result-eb1bf95d87961d46a3; paper-result-6f3b1fc0ec99ea98ae; paper-result-65020951c24bd83246; paper-result-c9b2fec5bfd04f7818; paper-result-5927468ae054290ab3; paper-result-26e19e7a3c593c8e0d; paper-result-d7f6e83cdf5b05dd97; source ids: part2-prokbert-2024; source locator: Table 3: Specificity, E. coli sigma70 independent promoter test; context: Test-only evaluation on Cassiano and Silva-Rocha 2020 data; methods have different training histories. 865 high-evidence RegulonDB 10.5 promoters and 1,000 nucleotide-distribution-matched negative sequences. Promoter exact matches removed from model training.; caveats: Historical comparator implementations and training sets differ; source table alone does not prove matched training budget.; No interval assigned unless printed in source cell.; review: method: automated_source_review; date: 2026-09-17
- benchmark research
- review date: 2026-09-17; status: complete_comparison_tables_extracted_pending_publication_review; primary sources: part2-prokbert-2024; inspected locators: Table 3: Accuracy, E. coli sigma70 independent promoter test; searched queries: ProkBERT family: genomic language models for microbiome applications primary paper benchmark results; gaps: Independent batch review before import; preserve existing observation identities.; claim scope: Primary-source discovery and table/protocol screening; source checked is not independently reproduced. Raw acquisitions not automatically numerical publication approval.
- legacy kinds
- benchmark
- entity classification
- review date: 2026-09-17; rationale: The source-backed record identifies a specified evaluated procedure and its dataset/split/scoring context. Classify it as a protocol while preserving version and comparison restrictions.; source ids: part2-prokbert-2024; source locator: Table 3: Accuracy, E. coli sigma70 independent promoter test; ambiguities: None recorded
Related records
- evaluates task: E. coli sigma70 promoter prediction
- benchmark: ProkBERT-mini: E. coli sigma70 promoter prediction
- benchmark: Promotech: E. coli sigma70 promoter prediction
- subject: E. coli sigma70 independent promoter test (E. coli sigma70 promoter prediction): links:evaluates_task:reported-task-3891811dcce8b3
- benchmark: CNNProm: E. coli sigma70 independent promoter test
- benchmark: ProkBERT-mini-c: E. coli sigma70 independent promoter test
- benchmark: Sigma70Pred: E. coli sigma70 independent promoter test
- benchmark: 70ProPred: E. coli sigma70 independent promoter test
- benchmark: ProkBERT-mini-long: E. coli sigma70 independent promoter test
- benchmark: iPromoter-BnCNN: E. coli sigma70 independent promoter test
- benchmark: BPROM: E. coli sigma70 independent promoter test
- benchmark: iPro70-FMWin: E. coli sigma70 independent promoter test
- benchmark: MULTiPly: E. coli sigma70 independent promoter test
- benchmark: Multiply: E. coli sigma70 independent promoter test
- benchmark: IBPP: E. coli sigma70 independent promoter test
- benchmark: iPromoter-2L: E. coli sigma70 independent promoter test
- benchmark: bTSSfinder: E. coli sigma70 independent promoter test