Datasets
Independent E. coli promoter datasets linked to the chenli-bioinfo/promoter repository.
Task
E. coli sigma70 promoter prediction
The E. coli promoter benchmark is an independent comparison within a broader promoter-prediction paper.
Sources
TSSNote-CyaPromBERT: Development of an integrated platform for highly accurate promoter prediction and visualization of Synechococcus sp. and Synechocystis sp. through a state-of-the-art natural language processing model BERT · Datasets; Evaluation criteria; Results: independent datasets from E. coli; cached text lines 12, 28–30, 42; comparative evaluation and ablation passagesOverview
Metrics
Precision, recall, F1, AUROC and average-precision-based AUPRC are described in the evaluation methods.
Allowed inputs
DNA promoter-window sequences.
Sources
TSSNote-CyaPromBERT: Development of an integrated platform for highly accurate promoter prediction and visualization of Synechococcus sp. and Synechocystis sp. through a state-of-the-art natural language processing model BERT · Datasets; Evaluation criteria; Results: independent datasets from E. coli; cached text lines 12, 28–30, 42; comparative evaluation and ablation passagesEvaluation 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
TSSNote-CyaPromBERT: Development of an integrated platform for highly accurate promoter prediction and visualization of Synechococcus sp. and Synechocystis sp. through a state-of-the-art natural language processing model BERT · Datasets; Evaluation criteria; Results: independent datasets from E. coli; cached text lines 12, 28–30, 42; comparative evaluation and ablation passageslimited source coverage · Automated source review, 2026-09-16. All specifications and missing details
Results
Results are available, but no reviewed comparison panel is linked in this release.
All evaluations
2 evaluations · 2 results. Different protocols are not a single leaderboard.
Filter evaluations
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: Eco70PromBERT | Task: E. coli sigma70 promoter prediction Dataset: Independent E. coli sigma70 test dataset | 0.91 Promoter-class F1 unitless · unknown Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceEco70PromBERT: E. coli sigma70 promoter prediction BERT-base with 1bp tokenizer; 110 promoters and 108 non-promoters. Aggregation: Not reported TSSNote-CyaPromBERT: Development of an integrated platform for highly accurate promoter prediction and visualization of Synechococcus sp. and Synechocystis sp. through a state-of-the-art natural language processing model BERT · TABLE 3, Eco70PromBERT (BERT-base + 1bp tokenizer) row, F1 score Promoter column |
| Configuration: iPro70-FMWin | Task: E. coli sigma70 promoter prediction Dataset: Independent E. coli sigma70 test dataset | 0.9 Promoter-class F1 unitless · unknown Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceiPro70-FMWin: E. coli sigma70 promoter prediction Compared on the same independent test dataset; 110 promoters and 108 non-promoters. Aggregation: Not reported TSSNote-CyaPromBERT: Development of an integrated platform for highly accurate promoter prediction and visualization of Synechococcus sp. and Synechocystis sp. through a state-of-the-art natural language processing model BERT · TABLE 3, iPro70-FMWin row, F1 score Promoter column |
Source checking is not independent reproduction. Release 2026-09-29-06401fd5b220.
Methods and evaluation design
Procedure, tasks and evaluated configurations
How it works
Evaluation methodology
Independent E. coli promoter datasets linked to the chenli-bioinfo/promoter repository. Precision, recall, F1, AUROC and average-precision-based AUPRC are described in the evaluation methods. iPro70-FMWin and iPromoter-2L2.0 evaluated on the independent E. coli sigma70 benchmark. The checked E. coli comparison identifies an independent dataset but does not specify sequence/homology overlap checks against comparator training 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
TSSNote-CyaPromBERT: Development of an integrated platform for highly accurate promoter prediction and visualization of Synechococcus sp. and Synechocystis sp. through a state-of-the-art natural language processing model BERT · Datasets; Evaluation criteria; Results: independent datasets from E. coli; cached text lines 12, 28–30, 42; comparative evaluation and ablation passagesRecorded evaluations
Each evaluation records what was tested and under which conditions.
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
- The paper also evaluates cyanobacterial data, but those species-transfer partitions do not specify the E. coli test. Table 3 reports the E. coli comparator setting separately.
Sources
TSSNote-CyaPromBERT: Development of an integrated platform for highly accurate promoter prediction and visualization of Synechococcus sp. and Synechocystis sp. through a state-of-the-art natural language processing model BERT · Datasets; Evaluation criteria; Results: independent datasets from E. coli; cached text lines 12, 28–30, 42; comparative evaluation and ablation passages
Profile review details
Relevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged.
Stable record: reported-task-e5c34f686ac403Specifications
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 | Independent E. coli promoter datasets linked to the chenli-bioinfo/promoter repository.SourcesTSSNote-CyaPromBERT: Development of an integrated platform for highly accurate promoter prediction and visualization of Synechococcus sp. and Synechocystis sp. through a state-of-the-art natural language processing model BERT · Datasets; Evaluation criteria; Results: independent datasets from E. coli; cached text lines 12, 28–30, 42; comparative evaluation and ablation passages |
| Splits | The E. coli comparison uses the independent σ70-promoter dataset from the linked Zhang/chenli-bioinfo study and reports class support in Table 3. The E. coli subsection does not specify the exact training/test file allocation; cyanobacterial cross-species partitions elsewhere are not its split definition. · Not reported in inspected sourcesSourcesTSSNote-CyaPromBERT: Development of an integrated platform for highly accurate promoter prediction and visualization of Synechococcus sp. and Synechocystis sp. through a state-of-the-art natural language processing model BERT · Datasets; Results: independent E. coli benchmarking; Table 3 |
| Metrics | Precision, recall, F1, AUROC and average-precision-based AUPRC are described in the evaluation methods.SourcesTSSNote-CyaPromBERT: Development of an integrated platform for highly accurate promoter prediction and visualization of Synechococcus sp. and Synechocystis sp. through a state-of-the-art natural language processing model BERT · Datasets; Evaluation criteria; Results: independent datasets from E. coli; cached text lines 12, 28–30, 42; comparative evaluation and ablation passages |
| Baselines | iPro70-FMWin and iPromoter-2L2.0 evaluated on the independent E. coli sigma70 benchmark.SourcesTSSNote-CyaPromBERT: Development of an integrated platform for highly accurate promoter prediction and visualization of Synechococcus sp. and Synechocystis sp. through a state-of-the-art natural language processing model BERT · Datasets; Evaluation criteria; Results: independent datasets from E. coli; cached text lines 12, 28–30, 42; comparative evaluation and ablation passages |
| Leakage controls | The checked E. coli comparison identifies an independent dataset but does not specify sequence/homology overlap checks against comparator training data. · Not reported in inspected sourcesSourcesTSSNote-CyaPromBERT: Development of an integrated platform for highly accurate promoter prediction and visualization of Synechococcus sp. and Synechocystis sp. through a state-of-the-art natural language processing model BERT · Datasets; Evaluation criteria; Results: independent datasets from E. coli; cached text lines 12, 28–30, 42; comparative evaluation and ablation passages |
| 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 sourcesSourcesTSSNote-CyaPromBERT: Development of an integrated platform for highly accurate promoter prediction and visualization of Synechococcus sp. and Synechocystis sp. through a state-of-the-art natural language processing model BERT · Datasets; Evaluation criteria; Results: independent datasets from E. coli; cached text lines 12, 28–30, 42; comparative evaluation and ablation passages |
| Entity type | Paper-specific computational evaluation protocol.SourcesTSSNote-CyaPromBERT: Development of an integrated platform for highly accurate promoter prediction and visualization of Synechococcus sp. and Synechocystis sp. through a state-of-the-art natural language processing model BERT · Datasets; Evaluation criteria; Results: independent datasets from E. coli; cached text lines 12, 28–30, 42; comparative evaluation and ablation passages |
| Organisms | Escherichia coli for this sigma70 task; cyanobacterial tasks elsewhere in the paper are separate.SourcesTSSNote-CyaPromBERT: Development of an integrated platform for highly accurate promoter prediction and visualization of Synechococcus sp. and Synechocystis sp. through a state-of-the-art natural language processing model BERT · Datasets; Evaluation criteria; Results: independent datasets from E. coli; cached text lines 12, 28–30, 42; comparative evaluation and ablation passages |
| Assays | Curated sigma70 promoter/non-promoter labels.SourcesTSSNote-CyaPromBERT: Development of an integrated platform for highly accurate promoter prediction and visualization of Synechococcus sp. and Synechocystis sp. through a state-of-the-art natural language processing model BERT · Datasets; Evaluation criteria; Results: independent datasets from E. coli; cached text lines 12, 28–30, 42; comparative evaluation and ablation passages |
| Allowed inputs | DNA promoter-window sequences.SourcesTSSNote-CyaPromBERT: Development of an integrated platform for highly accurate promoter prediction and visualization of Synechococcus sp. and Synechocystis sp. through a state-of-the-art natural language processing model BERT · Datasets; Evaluation criteria; Results: independent datasets from E. coli; cached text lines 12, 28–30, 42; comparative evaluation and ablation passages |
| Adaptation | BERT-based supervised classification trained on the E. coli benchmark; evaluated against existing promoter web servers.SourcesTSSNote-CyaPromBERT: Development of an integrated platform for highly accurate promoter prediction and visualization of Synechococcus sp. and Synechocystis sp. through a state-of-the-art natural language processing model BERT · Datasets; Evaluation criteria; Results: independent datasets from E. coli; cached text lines 12, 28–30, 42; comparative evaluation and ablation passages |
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. Dated primary-source discovery and protocol/table screening. Source checking does not mean experimental reproduction. Only separately extracted and independently reviewed numeric batches are publishable.
Historical gaps recorded on 2026-09-17
The catalogue now holds 2 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.
- complete numerical transcription and independent cell review: Full primary artifact and table inventory preserved; no new numeric row is published from this audit alone.
- exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size.
Search and extraction details
primary comparison tables located
Searches
- TSSNote-CyaPromBERT: Development of an integrated platform for highly accurate promoter prediction and visualization of Synechococcus sp. and Synechocystis sp. through a state-of-the-art natural language processing model BERT 10.3389/fgene.2022.1067562
Evidence locations
- TABLE 3; XML table T3
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 | TSSNote-CyaPromBERT: Development of an integrated platform for highly accurate promoter prediction and visualization of Synechococcus sp. and Synechocystis sp. through a state-of-the-art natural language processing model BERT Datasets; Evaluation criteria; Results: independent datasets from E. coli; cached text lines 12, 28–30, 42; comparative evaluation and ablation passages Version: version of record | source checked automated source review · 2026-09-16 Audit detailsRelevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Diagram steps
| TSSNote-CyaPromBERT: Development of an integrated platform for highly accurate promoter prediction and visualization of Synechococcus sp. and Synechocystis sp. through a state-of-the-art natural language processing model BERT Datasets; Evaluation criteria; Results: independent datasets from E. coli; cached text lines 12, 28–30, 42; comparative evaluation and ablation passages Version: version of record | source checked automated source review · 2026-09-16 Audit detailsRelevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Diagram title Computational evaluation flow Individual claims | TSSNote-CyaPromBERT: Development of an integrated platform for highly accurate promoter prediction and visualization of Synechococcus sp. and Synechocystis sp. through a state-of-the-art natural language processing model BERT Datasets; Evaluation criteria; Results: independent datasets from E. coli; cached text lines 12, 28–30, 42; comparative evaluation and ablation passages Version: version of record | source checked automated source review · 2026-09-16 Audit detailsRelevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Datasets Independent E. coli promoter datasets linked to the chenli-bioinfo/promoter repository. Individual claims | TSSNote-CyaPromBERT: Development of an integrated platform for highly accurate promoter prediction and visualization of Synechococcus sp. and Synechocystis sp. through a state-of-the-art natural language processing model BERT Datasets; Evaluation criteria; Results: independent datasets from E. coli; cached text lines 12, 28–30, 42; comparative evaluation and ablation passages Version: version of record | source checked automated source review · 2026-09-16 Audit detailsRelevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Splits The E. coli comparison uses the independent σ70-promoter dataset from the linked Zhang/chenli-bioinfo study and reports class support in Table 3. The E. coli subsection does not specify the exact training/test file allocation; cyanobacterial cross-species partitions elsewhere are not its split definition. Individual claims | TSSNote-CyaPromBERT: Development of an integrated platform for highly accurate promoter prediction and visualization of Synechococcus sp. and Synechocystis sp. through a state-of-the-art natural language processing model BERT Datasets; Results: independent E. coli benchmarking; Table 3 Version: version of record | unreported automated source review · 2026-09-16 Audit detailsRelevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Adaptation BERT-based supervised classification trained on the E. coli benchmark; evaluated against existing promoter web servers. Individual claims | TSSNote-CyaPromBERT: Development of an integrated platform for highly accurate promoter prediction and visualization of Synechococcus sp. and Synechocystis sp. through a state-of-the-art natural language processing model BERT Datasets; Evaluation criteria; Results: independent datasets from E. coli; cached text lines 12, 28–30, 42; comparative evaluation and ablation passages Version: version of record | source checked automated source review · 2026-09-16 Audit detailsRelevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Metrics Precision, recall, F1, AUROC and average-precision-based AUPRC are described in the evaluation methods. Individual claims | TSSNote-CyaPromBERT: Development of an integrated platform for highly accurate promoter prediction and visualization of Synechococcus sp. and Synechocystis sp. through a state-of-the-art natural language processing model BERT Datasets; Evaluation criteria; Results: independent datasets from E. coli; cached text lines 12, 28–30, 42; comparative evaluation and ablation passages Version: version of record | source checked automated source review · 2026-09-16 Audit detailsRelevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Baselines iPro70-FMWin and iPromoter-2L2.0 evaluated on the independent E. coli sigma70 benchmark. Individual claims | TSSNote-CyaPromBERT: Development of an integrated platform for highly accurate promoter prediction and visualization of Synechococcus sp. and Synechocystis sp. through a state-of-the-art natural language processing model BERT Datasets; Evaluation criteria; Results: independent datasets from E. coli; cached text lines 12, 28–30, 42; comparative evaluation and ablation passages Version: version of record | source checked automated source review · 2026-09-16 Audit detailsRelevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Leakage controls The checked E. coli comparison identifies an independent dataset but does not specify sequence/homology overlap checks against comparator training data. Individual claims | TSSNote-CyaPromBERT: Development of an integrated platform for highly accurate promoter prediction and visualization of Synechococcus sp. and Synechocystis sp. through a state-of-the-art natural language processing model BERT Datasets; Evaluation criteria; Results: independent datasets from E. coli; cached text lines 12, 28–30, 42; comparative evaluation and ablation passages Version: version of record | unreported automated source review · 2026-09-16 Audit detailsRelevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. 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 | TSSNote-CyaPromBERT: Development of an integrated platform for highly accurate promoter prediction and visualization of Synechococcus sp. and Synechocystis sp. through a state-of-the-art natural language processing model BERT Datasets; Evaluation criteria; Results: independent datasets from E. coli; cached text lines 12, 28–30, 42; comparative evaluation and ablation passages Version: version of record | unreported automated source review · 2026-09-16 Audit detailsRelevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. 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
- TSSNote-CyaPromBERT: Development of an integrated platform for highly accurate promoter prediction and visualization of Synechococcus sp. and Synechocystis sp. through a state-of-the-art natural language processing model BERT · Original source · version of record
- TSSNote-CyaPromBERT: Development of an integrated platform for highly accurate promoter prediction and visualization of Synechococcus sp. and Synechocystis sp. through a state-of-the-art natural language processing model BERT · Original source · version of record
Technical metadata and extraction receipts
Stable ID: reported-task-e5c34f686ac403
- 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.
- benchmark research
- review date: 2026-09-17; status: primary_comparison_tables_located; primary sources: evidence-expansion-cyaprombert-2022-74278ccd; inspected locators: TABLE 3; XML table T3; searched queries: TSSNote-CyaPromBERT: Development of an integrated platform for highly accurate promoter prediction and visualization of Synechococcus sp. and Synechocystis sp. through a state-of-the-art natural language processing model BERT 10.3389/fgene.2022.1067562; gaps: complete numerical transcription and independent cell review: Full primary artifact and table inventory preserved; no new numeric row is published from this audit alone.; exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size.; claim scope: Dated primary-source discovery and protocol/table screening. Source checking does not mean experimental reproduction. Only separately extracted and independently reviewed numeric batches are publishable.
- historical missing metadata
- protocol version: 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: cyaprombert-2022; source locator: Datasets; Evaluation criteria; Results: independent datasets from E. coli; cached text lines 12, 28–30, 42; comparative evaluation and ablation passages; 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.