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 passages

2 evaluations · 2 metric rows

At a glance

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.

Data, procedure and scoring
Property	Description and evidence
Datasets	Independent E. coli promoter datasets linked to the chenli-bioinfo/promoter repository. 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
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 sources 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; Results: independent E. coli benchmarking; Table 3
Metrics	Precision, recall, F1, AUROC and average-precision-based AUPRC are described in the evaluation methods. 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
Baselines	iPro70-FMWin and iPromoter-2L2.0 evaluated on the independent E. coli sigma70 benchmark. 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
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 sources 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
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 sources 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
Entity type	Paper-specific computational evaluation 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 passages
Organisms	Escherichia coli for this sigma70 task; cyanobacterial tasks elsewhere in the paper are separate. 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
Assays	Curated sigma70 promoter/non-promoter labels. 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
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 passages
Adaptation	BERT-based supervised classification trained on the E. coli benchmark; evaluated against existing promoter web servers. 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

How it works

How it worksComputational evaluation flow

Conceptual summary of the cited evaluation; exact task configuration and source version remain part of the protocol.

Sources

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

Recorded evaluations

Each evaluation records what was tested and under which conditions.

Tested entities and results

Release 2026-09-17-d277315f7d76 · 2 evaluations · 2 metric rows. Different protocols are not a single leaderboard.

Evaluation setupMetricEvidence origin

Results grouped by the exact reported evaluation
Metric and finding	Coverage and uncertainty	Evidence
Eco70PromBERT: E. coli sigma70 promoter prediction Configuration: Eco70PromBERTTask: E. coli sigma70 promoter predictionDataset: Independent E. coli sigma70 test dataset BERT-base with 1bp tokenizer; 110 promoters and 108 non-promoters. Author-reported evaluation · Evaluation metadata: needs review
0.91 Promoter-class F1 Unit: unitless · Direction: unknown	Uncertainty: not reported in legacy extract Scored: Not reported · Eligible: Not reported	source checkedTSSNote-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 Source checking is not independent reproduction.
iPro70-FMWin: E. coli sigma70 promoter prediction Configuration: iPro70-FMWinTask: E. coli sigma70 promoter predictionDataset: Independent E. coli sigma70 test dataset Compared on the same independent test dataset; 110 promoters and 108 non-promoters. Independent external evaluation · Evaluation metadata: needs review
0.90 Promoter-class F1 Unit: unitless · Direction: unknown	Uncertainty: not reported in legacy extract Scored: Not reported · Eligible: Not reported	source checkedTSSNote-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.

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.

Paper or primary resource	Version	Reference
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	version of record	Read source

What is still missing

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

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-e5c34f686ac403

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

Claims, original sources and review scope · Release 2026-09-17-d277315f7d76
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 Original source ↗ 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 Retrieved: 2026-09-16T10:41:16.544033+00:00	source checked automated source review · 2026-09-16 Audit 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. Field: `attributes.profile.diagram.caption` Source artifact SHA-256: `74278ccd77b2bc00a3f4434546545e8bdec8b0652a0e5d1862ec0f91decccd8d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Diagram steps ["Input: DNA promoter-window sequences.","Evaluation: BERT-based supervised classification trained on the E. coli benchmark; evaluated against existing promoter web servers.","Readout: 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 Original source ↗ 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 Retrieved: 2026-09-16T10:41:16.544033+00:00	source checked automated source review · 2026-09-16 Audit 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. Field: `attributes.profile.diagram.steps` Source artifact SHA-256: `74278ccd77b2bc00a3f4434546545e8bdec8b0652a0e5d1862ec0f91decccd8d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
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 Original source ↗ 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 Retrieved: 2026-09-16T10:41:16.544033+00:00	source checked automated source review · 2026-09-16 Audit 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. Field: `attributes.profile.diagram.title` Source artifact SHA-256: `74278ccd77b2bc00a3f4434546545e8bdec8b0652a0e5d1862ec0f91decccd8d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
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 Original source ↗ 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 Retrieved: 2026-09-16T10:41:16.544033+00:00	source checked automated source review · 2026-09-16 Audit 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. Field: `attributes.profile.facts.0.value` Source artifact SHA-256: `74278ccd77b2bc00a3f4434546545e8bdec8b0652a0e5d1862ec0f91decccd8d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
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 Original source ↗ Datasets; Results: independent E. coli benchmarking; Table 3 Version: version of record Retrieved: 2026-09-16T10:41:16.544033+00:00	unreported automated source review · 2026-09-16 Audit 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. Field: `attributes.profile.facts.1.value` Source artifact SHA-256: `74278ccd77b2bc00a3f4434546545e8bdec8b0652a0e5d1862ec0f91decccd8d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
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 Original source ↗ 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 Retrieved: 2026-09-16T10:41:16.544033+00:00	source checked automated source review · 2026-09-16 Audit 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. Field: `attributes.profile.facts.10.value` Source artifact SHA-256: `74278ccd77b2bc00a3f4434546545e8bdec8b0652a0e5d1862ec0f91decccd8d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
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 Original source ↗ 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 Retrieved: 2026-09-16T10:41:16.544033+00:00	source checked automated source review · 2026-09-16 Audit 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. Field: `attributes.profile.facts.2.value` Source artifact SHA-256: `74278ccd77b2bc00a3f4434546545e8bdec8b0652a0e5d1862ec0f91decccd8d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
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 Original source ↗ 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 Retrieved: 2026-09-16T10:41:16.544033+00:00	source checked automated source review · 2026-09-16 Audit 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. Field: `attributes.profile.facts.3.value` Source artifact SHA-256: `74278ccd77b2bc00a3f4434546545e8bdec8b0652a0e5d1862ec0f91decccd8d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
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 Original source ↗ 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 Retrieved: 2026-09-16T10:41:16.544033+00:00	unreported automated source review · 2026-09-16 Audit 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. Field: `attributes.profile.facts.4.value` Source artifact SHA-256: `74278ccd77b2bc00a3f4434546545e8bdec8b0652a0e5d1862ec0f91decccd8d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
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 Original source ↗ 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 Retrieved: 2026-09-16T10:41:16.544033+00:00	unreported automated source review · 2026-09-16 Audit 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. Field: `attributes.profile.facts.5.value` Source artifact SHA-256: `74278ccd77b2bc00a3f4434546545e8bdec8b0652a0e5d1862ec0f91decccd8d` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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Sources and history

Release 2026-09-17-d277315f7d76 · Record review: needs review

2 source records and release history

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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.

Related records

dataset: Independent E. coli sigma70 test dataset
benchmark: Eco70PromBERT: E. coli sigma70 promoter prediction
benchmark: iPro70-FMWin: E. coli sigma70 promoter prediction

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