Datasets
PPD-derived promoter data and a separately identified E. coli sigma70 test collection.
Task
E. coli sigma70 promoter prediction
The E. coli promoter task is an independent test setting within ProkBERT’s broader prokaryotic evaluation.
Sources
ProkBERT family: genomic language models for microbiome applications · Methods §2.3.1; Results: promoter comparison; cached text lines 66–67, 138–141Overview
Metrics
Sensitivity, specificity and accuracy are discussed together to expose false-positive tradeoffs.
Allowed inputs
DNA promoter-window sequence.
Sources
ProkBERT family: genomic language models for microbiome applications · Methods §2.3.1; Results: promoter comparison; cached text lines 66–67, 138–141Evaluation procedure diagram
How it worksComputational evaluation flow
Conceptual summary of the cited evaluation; exact task configuration and source version remain part of the protocol.
Sources
ProkBERT family: genomic language models for microbiome applications · Methods §2.3.1; Results: promoter comparison; cached text lines 66–67, 138–141limited source coverage · Automated source review, 2026-09-16. 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 methodology
PPD-derived promoter data and a separately identified E. coli sigma70 test collection. Independent E. coli testing is described; exact training exclusions remain unextracted. Sensitivity, specificity and accuracy are discussed together to expose false-positive tradeoffs. CNNProm, Sigma70Pred, iPromoter-BnCNN, iPromoter-2L and Promotech. The source warns that some comparator training data may overlap or be closely related to the E. coli evaluation data. The cited text-accessible evaluation sections give no confidence-interval, resampling or repeat-run error-bar specification. Image-only tables and uninspected supplements are outside this absence claim.
Sources
ProkBERT family: genomic language models for microbiome applications · Methods §2.3.1; Results: promoter comparison; cached text lines 66–67, 138–141Evaluation 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.
Run this benchmark
Choose a concrete protocol before running an evaluation. Its inputs, split and scoring rules determine which results can be compared.
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
Strengths and limitations
Strengths and considerations
No source-reviewed explanatory claims are recorded here yet.
Limitations and conditions
- Comparator source versions remain unextracted.
Sources
ProkBERT family: genomic language models for microbiome applications · Methods §2.3.1; Results: promoter comparison; cached text lines 66–67, 138–141
Profile review details
Task-specific computational methodology and field context checked in the cited primary-source artifact. Source-backed fields, inapplicable evaluator dimensions and unresolved details are distinguished. Numerical results were not reproduced.
Stable record: reported-task-3891811dcce8b3Specifications
Inputs, training, access and other details
Explanatory profile: limited source coverage · Automated source review, 2026-09-16. Review applies to the cited claims; unresolved fields are listed below. Numerical results retain their own review status.
| Property | Description and evidence |
|---|---|
| Datasets | PPD-derived promoter data and a separately identified E. coli sigma70 test collection.SourcesProkBERT family: genomic language models for microbiome applications · Methods §2.3.1; Results: promoter comparison; cached text lines 66–67, 138–141 |
| Splits | Independent E. coli testing is described; exact training exclusions remain unextracted.SourcesProkBERT family: genomic language models for microbiome applications · Methods §2.3.1; Results: promoter comparison; cached text lines 66–67, 138–141 |
| Metrics | Sensitivity, specificity and accuracy are discussed together to expose false-positive tradeoffs.SourcesProkBERT family: genomic language models for microbiome applications · Methods §2.3.1; Results: promoter comparison; cached text lines 66–67, 138–141 |
| Baselines | CNNProm, Sigma70Pred, iPromoter-BnCNN, iPromoter-2L and Promotech.SourcesProkBERT family: genomic language models for microbiome applications · Methods §2.3.1; Results: promoter comparison; cached text lines 66–67, 138–141 |
| Leakage controls | The source warns that some comparator training data may overlap or be closely related to the E. coli evaluation data.SourcesProkBERT family: genomic language models for microbiome applications · Methods §2.3.1; Results: promoter comparison; cached text lines 66–67, 138–141 |
| Uncertainty | The cited text-accessible evaluation sections give no confidence-interval, resampling or repeat-run error-bar specification. Image-only tables and uninspected supplements are outside this absence claim. · Not reported in inspected sourcesSourcesProkBERT family: genomic language models for microbiome applications · Methods §2.3.1; Results: promoter comparison; cached text lines 66–67, 138–141 |
| Entity type | Paper-specific computational evaluation protocol.SourcesProkBERT family: genomic language models for microbiome applications · Methods §2.3.1; Results: promoter comparison; cached text lines 66–67, 138–141 |
| Organisms | Escherichia coli for the sigma70 test.SourcesProkBERT family: genomic language models for microbiome applications · Methods §2.3.1; Results: promoter comparison; cached text lines 66–67, 138–141 |
| Assays | PPD and independent sigma70 promoter annotations.SourcesProkBERT family: genomic language models for microbiome applications · Methods §2.3.1; Results: promoter comparison; cached text lines 66–67, 138–141 |
| Allowed inputs | DNA promoter-window sequence.SourcesProkBERT family: genomic language models for microbiome applications · Methods §2.3.1; Results: promoter comparison; cached text lines 66–67, 138–141 |
| Adaptation | Supervised promoter prediction compared with established task-specific methods.SourcesProkBERT family: genomic language models for microbiome applications · Methods §2.3.1; Results: promoter comparison; cached text lines 66–67, 138–141 |
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
- Table3; independent E.coli sigma70 set in Section2.3
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.
17 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Diagram caption Conceptual summary of the cited evaluation; exact task configuration and source version remain part of the protocol. Individual claims | ProkBERT family: genomic language models for microbiome applications Methods §2.3.1; Results: promoter comparison; cached text lines 66–67, 138–141 Version: PMC10810988.1 | source checked automated source review · 2026-09-16 Audit detailsTask-specific computational methodology and field context checked in the cited primary-source artifact. Source-backed fields, inapplicable evaluator dimensions and unresolved details are distinguished. Numerical results were not reproduced. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Diagram steps
| ProkBERT family: genomic language models for microbiome applications Methods §2.3.1; Results: promoter comparison; cached text lines 66–67, 138–141 Version: PMC10810988.1 | source checked automated source review · 2026-09-16 Audit detailsTask-specific computational methodology and field context checked in the cited primary-source artifact. Source-backed fields, inapplicable evaluator dimensions and unresolved details are distinguished. Numerical results were not reproduced. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Diagram title Computational evaluation flow Individual claims | ProkBERT family: genomic language models for microbiome applications Methods §2.3.1; Results: promoter comparison; cached text lines 66–67, 138–141 Version: PMC10810988.1 | source checked automated source review · 2026-09-16 Audit detailsTask-specific computational methodology and field context checked in the cited primary-source artifact. Source-backed fields, inapplicable evaluator dimensions and unresolved details are distinguished. Numerical results were not reproduced. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Datasets PPD-derived promoter data and a separately identified E. coli sigma70 test collection. Individual claims | ProkBERT family: genomic language models for microbiome applications Methods §2.3.1; Results: promoter comparison; cached text lines 66–67, 138–141 Version: PMC10810988.1 | source checked automated source review · 2026-09-16 Audit detailsTask-specific computational methodology and field context checked in the cited primary-source artifact. Source-backed fields, inapplicable evaluator dimensions and unresolved details are distinguished. Numerical results were not reproduced. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Splits Independent E. coli testing is described; exact training exclusions remain unextracted. Individual claims | ProkBERT family: genomic language models for microbiome applications Methods §2.3.1; Results: promoter comparison; cached text lines 66–67, 138–141 Version: PMC10810988.1 | source checked automated source review · 2026-09-16 Audit detailsTask-specific computational methodology and field context checked in the cited primary-source artifact. Source-backed fields, inapplicable evaluator dimensions and unresolved details are distinguished. Numerical results were not reproduced. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Adaptation Supervised promoter prediction compared with established task-specific methods. Individual claims | ProkBERT family: genomic language models for microbiome applications Methods §2.3.1; Results: promoter comparison; cached text lines 66–67, 138–141 Version: PMC10810988.1 | source checked automated source review · 2026-09-16 Audit detailsTask-specific computational methodology and field context checked in the cited primary-source artifact. Source-backed fields, inapplicable evaluator dimensions and unresolved details are distinguished. Numerical results were not reproduced. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Metrics Sensitivity, specificity and accuracy are discussed together to expose false-positive tradeoffs. Individual claims | ProkBERT family: genomic language models for microbiome applications Methods §2.3.1; Results: promoter comparison; cached text lines 66–67, 138–141 Version: PMC10810988.1 | source checked automated source review · 2026-09-16 Audit detailsTask-specific computational methodology and field context checked in the cited primary-source artifact. Source-backed fields, inapplicable evaluator dimensions and unresolved details are distinguished. Numerical results were not reproduced. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Baselines CNNProm, Sigma70Pred, iPromoter-BnCNN, iPromoter-2L and Promotech. Individual claims | ProkBERT family: genomic language models for microbiome applications Methods §2.3.1; Results: promoter comparison; cached text lines 66–67, 138–141 Version: PMC10810988.1 | source checked automated source review · 2026-09-16 Audit detailsTask-specific computational methodology and field context checked in the cited primary-source artifact. Source-backed fields, inapplicable evaluator dimensions and unresolved details are distinguished. Numerical results were not reproduced. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Leakage controls The source warns that some comparator training data may overlap or be closely related to the E. coli evaluation data. Individual claims | ProkBERT family: genomic language models for microbiome applications Methods §2.3.1; Results: promoter comparison; cached text lines 66–67, 138–141 Version: PMC10810988.1 | source checked automated source review · 2026-09-16 Audit detailsTask-specific computational methodology and field context checked in the cited primary-source artifact. Source-backed fields, inapplicable evaluator dimensions and unresolved details are distinguished. Numerical results were not reproduced. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Uncertainty The cited text-accessible evaluation sections give no confidence-interval, resampling or repeat-run error-bar specification. Image-only tables and uninspected supplements are outside this absence claim. Individual claims | ProkBERT family: genomic language models for microbiome applications Methods §2.3.1; Results: promoter comparison; cached text lines 66–67, 138–141 Version: PMC10810988.1 | unreported automated source review · 2026-09-16 Audit detailsTask-specific computational methodology and field context checked in the cited primary-source artifact. Source-backed fields, inapplicable evaluator dimensions and unresolved details are distinguished. Numerical results were not reproduced. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Sources and history
View linked audit checks and correction history
Release 2026-09-29-06401fd5b220 · Record review: needs review
2 source records and release history
- ProkBERT family: genomic language models for microbiome applications · Original source · PMC10810988.1
- ProkBERT family: genomic language models for microbiome applications · Original source · PMC10810988.1
Technical metadata and extraction receipts
Stable ID: reported-task-3891811dcce8b3
- areas
- microbes-communities
- tasks
- E. coli sigma70 promoter prediction
- entity level
- task
- version
- Not reported
- task
- E. coli sigma70 promoter prediction
- scope note
- Paper-specific evaluation task; protocol completeness requires further extraction.
- 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: Table3; independent E.coli sigma70 set in Section2.3; 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.
- historical missing metadata
- protocol version: not_reported_in_legacy_extract; split: not_reported_in_legacy_extract
- metadata review scope
- historical_missing_metadata preserves the original discovery state. Current descriptive evidence and missingness are recorded in profile.facts; numerical-result review is separate.
- legacy kinds
- benchmark
- entity classification
- review date: 2026-09-17; rationale: This source-scoped record identifies the biological prediction task and holds its paper context. Preserve the existing task identity; exact split, model adaptation and scoring remain in linked evaluations or separate protocol records.; source ids: prokbert-2024; source locator: Methods §2.3.1; Results: promoter comparison; cached text lines 66–67, 138–141; ambiguities: A paper- or suite-specific task may constrain some inputs or metrics; that alone does not make it interchangeable with a complete versioned protocol. No protocol equivalence is inferred.; Some legacy profile Entity type facts use the generic phrase computational evaluation protocol. That boilerplate is not sufficient to establish a single fixed protocol identity or to merge this task with another protocol record.