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.
ProkBERT family: genomic language models for microbiome applications · Table 3: Accuracy, E. coli sigma70 independent promoter testAt a glance
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.
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.
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
Published comparisons
Explore the results reported under one evaluation protocol. Each figure keeps its source, dataset and metric together; it is not a ranking across studies.
E. coli sigma70 independent promoter test · Table 3
Accuracy (unitless) · Higher values are better for this metric.
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.
- ProkBERT-mini · Configuration · Author-reported evaluation0.87
- ProkBERT-mini-c · Configuration · Author-reported evaluation0.87
- ProkBERT-mini-long · Configuration · Author-reported evaluation0.87
- CNNProm · Configuration · Result quoted from another source0.72
- iPro70-FMWin · Configuration · Result quoted from another source0.76
- 70ProPred · Configuration · Result quoted from another source0.74
- iPromoter-2L · Configuration · Result quoted from another source0.64
- Multiply · Configuration · Result quoted from another source0.50
- bTSSfinder · Configuration · Result quoted from another source0.46
- BPROM · Configuration · Result quoted from another source0.56
- IBPP · Configuration · Result quoted from another source0.50
- Promotech · Configuration · Independent external evaluation0.71
- Sigma70Pred · Configuration · Independent external evaluation0.66
- iPromoter-BnCNN · Configuration · Independent external evaluation0.55
- MULTiPly · Configuration · Independent external evaluation0.54
Source order is preserved. Plotted marks show point estimates; uncertainty, where reported, is retained in the printed values and table. Differences do not establish statistical significance.
ProkBERT family: genomic language models for microbiome applications · Table 3: Accuracy, E. coli sigma70 independent promoter testValues, uncertainty and evidence
| Tested entity | Printed value | Uncertainty | Evidence |
|---|---|---|---|
| ProkBERT-mini · Configuration | 0.87 unitless | Not reported | Author-reported evaluation · source checkedProkBERT family: genomic language models for microbiome applications; ProkBERT family: genomic language models for microbiome applications · Table 3, ProkBERT-mini row, Accuracy column |
| ProkBERT-mini-c · Configuration | 0.87 unitless | Not reported | Author-reported evaluation · source checkedProkBERT family: genomic language models for microbiome applications · Table 3, row ProkBERT-mini-c, column Accuracy; XML row3 column2 |
| ProkBERT-mini-long · Configuration | 0.87 unitless | Not reported | Author-reported evaluation · source checkedProkBERT family: genomic language models for microbiome applications · Table 3, row ProkBERT-mini-long, column Accuracy; XML row4 column2 |
| CNNProm · Configuration | 0.72 unitless | Not reported | Result quoted from another source · source checkedProkBERT family: genomic language models for microbiome applications · Table 3, row CNNProm, column Accuracy; XML row5 column2 |
| iPro70-FMWin · Configuration | 0.76 unitless | Not reported | Result quoted from another source · source checkedProkBERT family: genomic language models for microbiome applications · Table 3, row iPro70-FMWin, column Accuracy; XML row6 column2 |
| 70ProPred · Configuration | 0.74 unitless | Not reported | Result quoted from another source · source checkedProkBERT family: genomic language models for microbiome applications · Table 3, row 70ProPred, column Accuracy; XML row7 column2 |
| iPromoter-2L · Configuration | 0.64 unitless | Not reported | Result quoted from another source · source checkedProkBERT family: genomic language models for microbiome applications · Table 3, row iPromoter-2L, column Accuracy; XML row8 column2 |
| Multiply · Configuration | 0.50 unitless | Not reported | Result quoted from another source · source checkedProkBERT family: genomic language models for microbiome applications · Table 3, row Multiply, column Accuracy; XML row9 column2 |
| bTSSfinder · Configuration | 0.46 unitless | Not reported | Result quoted from another source · source checkedProkBERT family: genomic language models for microbiome applications · Table 3, row bTSSfinder, column Accuracy; XML row10 column2 |
| BPROM · Configuration | 0.56 unitless | Not reported | Result quoted from another source · source checkedProkBERT family: genomic language models for microbiome applications · Table 3, row BPROM, column Accuracy; XML row11 column2 |
| IBPP · Configuration | 0.50 unitless | Not reported | Result quoted from another source · source checkedProkBERT family: genomic language models for microbiome applications · Table 3, row IBPP, column Accuracy; XML row12 column2 |
| Promotech · Configuration | 0.71 unitless | Not reported | Independent external evaluation · source checkedProkBERT family: genomic language models for microbiome applications; ProkBERT family: genomic language models for microbiome applications · Table 3, Promotech row, Accuracy column |
| Sigma70Pred · Configuration | 0.66 unitless | Not reported | Independent external evaluation · source checkedProkBERT family: genomic language models for microbiome applications · Table 3, row Sigma70Pred, column Accuracy; XML row14 column2 |
| iPromoter-BnCNN · Configuration | 0.55 unitless | Not reported | Independent external evaluation · source checkedProkBERT family: genomic language models for microbiome applications · Table 3, row iPromoter-BnCNN, column Accuracy; XML row15 column2 |
| MULTiPly · Configuration | 0.54 unitless | Not reported | Independent external evaluation · source checkedProkBERT family: genomic language models for microbiome applications · Table 3, row MULTiPly, column Accuracy; XML row16 column2 |
Scope and limitations
- Historical comparator implementations and training sets differ; source table alone does not prove matched training budget.
- No interval assigned unless printed in source cell.
Source transcription and grouping reviewed by automated source review on 2026-09-17. These experiments were not independently reproduced by rewire.
Tested entities and results
Release 2026-09-17-d277315f7d76 · 15 evaluations · 60 metric rows. Different protocols are not a single leaderboard.
| Metric and finding | Coverage and uncertainty | Evidence |
|---|---|---|
| ProkBERT-mini: E. coli sigma70 promoter prediction Configuration: ProkBERT-miniProtocol: E. coli sigma70 independent promoter test (E. coli sigma70 promoter prediction)Dataset: E. coli sigma70 promoter dataset 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. Author-reported evaluation · Evaluation metadata: needs review | ||
| 0.87 Accuracy Unit: unitless · Direction: higher | Uncertainty: not reported in legacy extract Scored: Not reported · Eligible: Not reported | source checkedProkBERT family: genomic language models for microbiome applications; ProkBERT family: genomic language models for microbiome applications · Table 3, ProkBERT-mini row, Accuracy column Source checking is not independent reproduction. |
| 0.90 Sensitivity Unit: fraction · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedProkBERT family: genomic language models for microbiome applications · Table 3, row ProkBERT-mini, column Sensitivity; XML row2 column4 Source checking is not independent reproduction. |
| 0.85 Specificity Unit: fraction · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedProkBERT family: genomic language models for microbiome applications · Table 3, row ProkBERT-mini, column Specificity; XML row2 column5 Source checking is not independent reproduction. |
| Promotech: E. coli sigma70 promoter prediction Configuration: PromotechProtocol: E. coli sigma70 independent promoter test (E. coli sigma70 promoter prediction)Dataset: E. coli sigma70 promoter dataset 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. Independent external evaluation · Evaluation metadata: needs review | ||
| 0.71 Accuracy Unit: unitless · Direction: higher | Uncertainty: not reported in legacy extract Scored: Not reported · Eligible: Not reported | source checkedProkBERT family: genomic language models for microbiome applications; ProkBERT family: genomic language models for microbiome applications · Table 3, Promotech row, Accuracy column Source checking is not independent reproduction. |
| 0.49 Sensitivity Unit: fraction · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedProkBERT family: genomic language models for microbiome applications · Table 3, row Promotech, column Sensitivity; XML row13 column4 Source checking is not independent reproduction. |
| Sigma70Pred: E. coli sigma70 independent promoter test Configuration: Sigma70PredProtocol: E. coli sigma70 independent promoter test (E. coli sigma70 promoter prediction)Dataset: E. coli sigma70 promoter dataset 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. Independent external evaluation · Evaluation metadata: needs review | ||
| 0.66 Accuracy Unit: unitless · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedProkBERT family: genomic language models for microbiome applications · Table 3, row Sigma70Pred, column Accuracy; XML row14 column2 Source checking is not independent reproduction. |
| ProkBERT-mini-long: E. coli sigma70 independent promoter test Configuration: ProkBERT-mini-longProtocol: E. coli sigma70 independent promoter test (E. coli sigma70 promoter prediction)Dataset: E. coli sigma70 promoter dataset 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. Author-reported evaluation · Evaluation metadata: needs review | ||
| 0.89 Sensitivity Unit: fraction · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedProkBERT family: genomic language models for microbiome applications · Table 3, row ProkBERT-mini-long, column Sensitivity; XML row4 column4 Source checking is not independent reproduction. |
| 0.87 Accuracy Unit: unitless · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedProkBERT family: genomic language models for microbiome applications · Table 3, row ProkBERT-mini-long, column Accuracy; XML row4 column2 Source checking is not independent reproduction. |
| CNNProm: E. coli sigma70 independent promoter test Configuration: CNNPromProtocol: E. coli sigma70 independent promoter test (E. coli sigma70 promoter prediction)Dataset: E. coli sigma70 promoter dataset 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. Result quoted from another source · Evaluation metadata: needs review | ||
| 0.51 Specificity Unit: fraction · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedProkBERT family: genomic language models for microbiome applications · Table 3, row CNNProm, column Specificity; XML row5 column5 Source checking is not independent reproduction. |
| iPromoter-2L: E. coli sigma70 independent promoter test Configuration: iPromoter-2LProtocol: E. coli sigma70 independent promoter test (E. coli sigma70 promoter prediction)Dataset: E. coli sigma70 promoter dataset 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. Result quoted from another source · Evaluation metadata: needs review | ||
| 0.64 Accuracy Unit: unitless · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedProkBERT family: genomic language models for microbiome applications · Table 3, row iPromoter-2L, column Accuracy; XML row8 column2 Source checking is not independent reproduction. |
| 0.37 MCC Unit: dimensionless · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedProkBERT family: genomic language models for microbiome applications · Table 3, row iPromoter-2L, column MCC; XML row8 column3 Source checking is not independent reproduction. |
| 0.37 Specificity Unit: fraction · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedProkBERT family: genomic language models for microbiome applications · Table 3, row iPromoter-2L, column Specificity; XML row8 column5 Source checking is not independent reproduction. |
| 70ProPred: E. coli sigma70 independent promoter test Configuration: 70ProPredProtocol: E. coli sigma70 independent promoter test (E. coli sigma70 promoter prediction)Dataset: E. coli sigma70 promoter dataset 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. Result quoted from another source · Evaluation metadata: needs review | ||
| 0.74 Accuracy Unit: unitless · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedProkBERT family: genomic language models for microbiome applications · Table 3, row 70ProPred, column Accuracy; XML row7 column2 Source checking is not independent reproduction. |
| 0.51 MCC Unit: dimensionless · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedProkBERT family: genomic language models for microbiome applications · Table 3, row 70ProPred, column MCC; XML row7 column3 Source checking is not independent reproduction. |
| bTSSfinder: E. coli sigma70 independent promoter test Configuration: bTSSfinderProtocol: E. coli sigma70 independent promoter test (E. coli sigma70 promoter prediction)Dataset: E. coli sigma70 promoter dataset 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. Result quoted from another source · Evaluation metadata: needs review | ||
| 0.46 Accuracy Unit: unitless · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedProkBERT family: genomic language models for microbiome applications · Table 3, row bTSSfinder, column Accuracy; XML row10 column2 Source checking is not independent reproduction. |
| BPROM: E. coli sigma70 independent promoter test Configuration: BPROMProtocol: E. coli sigma70 independent promoter test (E. coli sigma70 promoter prediction)Dataset: E. coli sigma70 promoter dataset 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. Result quoted from another source · Evaluation metadata: needs review | ||
| 0.10 MCC Unit: dimensionless · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedProkBERT family: genomic language models for microbiome applications · Table 3, row BPROM, column MCC; XML row11 column3 Source checking is not independent reproduction. |
| iPromoter-BnCNN: E. coli sigma70 independent promoter test Configuration: iPromoter-BnCNNProtocol: E. coli sigma70 independent promoter test (E. coli sigma70 promoter prediction)Dataset: E. coli sigma70 promoter dataset 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. Independent external evaluation · Evaluation metadata: needs review | ||
| 0.18 Specificity Unit: fraction · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedProkBERT family: genomic language models for microbiome applications · Table 3, row iPromoter-BnCNN, column Specificity; XML row15 column5 Source checking is not independent reproduction. |
| IBPP: E. coli sigma70 independent promoter test Configuration: IBPPProtocol: E. coli sigma70 independent promoter test (E. coli sigma70 promoter prediction)Dataset: E. coli sigma70 promoter dataset 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. Result quoted from another source · Evaluation metadata: needs review | ||
| -0.03 MCC Unit: dimensionless · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedProkBERT family: genomic language models for microbiome applications · Table 3, row IBPP, column MCC; XML row12 column3 Source checking is not independent reproduction. |
| ProkBERT-mini-c: E. coli sigma70 independent promoter test Configuration: ProkBERT-mini-cProtocol: E. coli sigma70 independent promoter test (E. coli sigma70 promoter prediction)Dataset: E. coli sigma70 promoter dataset 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. Author-reported evaluation · Evaluation metadata: needs review | ||
| 0.88 Sensitivity Unit: fraction · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedProkBERT family: genomic language models for microbiome applications · Table 3, row ProkBERT-mini-c, column Sensitivity; XML row3 column4 Source checking is not independent reproduction. |
| 0.85 Specificity Unit: fraction · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedProkBERT family: genomic language models for microbiome applications · Table 3, row ProkBERT-mini-c, column Specificity; XML row3 column5 Source checking is not independent reproduction. |
| iPro70-FMWin: E. coli sigma70 independent promoter test Configuration: iPro70-FMWinProtocol: E. coli sigma70 independent promoter test (E. coli sigma70 promoter prediction)Dataset: E. coli sigma70 promoter dataset 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. Result quoted from another source · Evaluation metadata: needs review | ||
| 0.76 Accuracy Unit: unitless · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedProkBERT family: genomic language models for microbiome applications · Table 3, row iPro70-FMWin, column Accuracy; XML row6 column2 Source checking is not independent reproduction. |
| 0.53 MCC Unit: dimensionless · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedProkBERT family: genomic language models for microbiome applications · Table 3, row iPro70-FMWin, column MCC; XML row6 column3 Source checking is not independent reproduction. |
| MULTiPly: E. coli sigma70 independent promoter test Configuration: MULTiPlyProtocol: E. coli sigma70 independent promoter test (E. coli sigma70 promoter prediction)Dataset: E. coli sigma70 promoter dataset 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. Independent external evaluation · Evaluation metadata: needs review | ||
| 0.92 Sensitivity Unit: fraction · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedProkBERT family: genomic language models for microbiome applications · Table 3, row MULTiPly, column Sensitivity; XML row16 column4 Source checking is not independent reproduction. |
| Multiply: E. coli sigma70 independent promoter test Configuration: MultiplyProtocol: E. coli sigma70 independent promoter test (E. coli sigma70 promoter prediction)Dataset: E. coli sigma70 promoter dataset 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. Result quoted from another source · Evaluation metadata: needs review | ||
| 0.05 MCC Unit: dimensionless · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedProkBERT family: genomic language models for microbiome applications · Table 3, row Multiply, column MCC; XML row9 column3 Source checking is not independent reproduction. |
| 0.81 Sensitivity Unit: fraction · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedProkBERT family: genomic language models for microbiome applications · Table 3, row Multiply, column Sensitivity; XML row9 column4 Source checking is not 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 |
What is still missing
- 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
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-94fa3494d41bcd98d2Evidence table
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
Release 2026-09-17-d277315f7d76 · Record review: needs review
- 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