Source

ProkBERT family: genomic language models for microbiome applications

PMC10810988.1

DOI: 10.3389/fmicb.2023.1331233 Original source

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Records in this release that cite this source. A record can cite several sources.

13 configurations
1 task
1 protocol
15 evaluations
60 results
5 evidence claims

Results

Values as the source printed them. Compare results only under compatible protocols, datasets and metrics.

Model or configuration	Metric	Value	Dataset	Evaluation
70ProPred	Accuracy	0.74 unitless	E. coli sigma70 promoter dataset	70ProPred: E. coli sigma70 independent promoter test
70ProPred	MCC	0.51 unitless	E. coli sigma70 promoter dataset	70ProPred: E. coli sigma70 independent promoter test
70ProPred	Recall	0.90 fraction	E. coli sigma70 promoter dataset	70ProPred: E. coli sigma70 independent promoter test
70ProPred	Specificity	0.60 fraction	E. coli sigma70 promoter dataset	70ProPred: E. coli sigma70 independent promoter test
BPROM	Accuracy	0.56 unitless	E. coli sigma70 promoter dataset	BPROM: E. coli sigma70 independent promoter test
BPROM	MCC	0.10 unitless	E. coli sigma70 promoter dataset	BPROM: E. coli sigma70 independent promoter test
BPROM	Recall	0.20 fraction	E. coli sigma70 promoter dataset	BPROM: E. coli sigma70 independent promoter test
BPROM	Specificity	0.87 fraction	E. coli sigma70 promoter dataset	BPROM: E. coli sigma70 independent promoter test
bTSSfinder	Accuracy	0.46 unitless	E. coli sigma70 promoter dataset	bTSSfinder: E. coli sigma70 independent promoter test
bTSSfinder	MCC	-0.07 unitless	E. coli sigma70 promoter dataset	bTSSfinder: E. coli sigma70 independent promoter test
bTSSfinder	Recall	0.48 fraction	E. coli sigma70 promoter dataset	bTSSfinder: E. coli sigma70 independent promoter test
bTSSfinder	Specificity	0.45 fraction	E. coli sigma70 promoter dataset	bTSSfinder: E. coli sigma70 independent promoter test
CNNProm	Accuracy	0.72 unitless	E. coli sigma70 promoter dataset	CNNProm: E. coli sigma70 independent promoter test
CNNProm	MCC	0.50 unitless	E. coli sigma70 promoter dataset	CNNProm: E. coli sigma70 independent promoter test
CNNProm	Recall	0.95 fraction	E. coli sigma70 promoter dataset	CNNProm: E. coli sigma70 independent promoter test
CNNProm	Specificity	0.51 fraction	E. coli sigma70 promoter dataset	CNNProm: E. coli sigma70 independent promoter test
IBPP	Accuracy	0.50 unitless	E. coli sigma70 promoter dataset	IBPP: E. coli sigma70 independent promoter test
IBPP	MCC	-0.03 unitless	E. coli sigma70 promoter dataset	IBPP: E. coli sigma70 independent promoter test
IBPP	Recall	0.26 fraction	E. coli sigma70 promoter dataset	IBPP: E. coli sigma70 independent promoter test
IBPP	Specificity	0.71 fraction	E. coli sigma70 promoter dataset	IBPP: E. coli sigma70 independent promoter test
iPro70-FMWin	Accuracy	0.76 unitless	E. coli sigma70 promoter dataset	iPro70-FMWin: E. coli sigma70 independent promoter test
iPro70-FMWin	MCC	0.53 unitless	E. coli sigma70 promoter dataset	iPro70-FMWin: E. coli sigma70 independent promoter test
iPro70-FMWin	Recall	0.84 fraction	E. coli sigma70 promoter dataset	iPro70-FMWin: E. coli sigma70 independent promoter test
iPro70-FMWin	Specificity	0.69 fraction	E. coli sigma70 promoter dataset	iPro70-FMWin: E. coli sigma70 independent promoter test
iPromoter-2L	Accuracy	0.64 unitless	E. coli sigma70 promoter dataset	iPromoter-2L: E. coli sigma70 independent promoter test
iPromoter-2L	MCC	0.37 unitless	E. coli sigma70 promoter dataset	iPromoter-2L: E. coli sigma70 independent promoter test
iPromoter-2L	Recall	0.94 fraction	E. coli sigma70 promoter dataset	iPromoter-2L: E. coli sigma70 independent promoter test
iPromoter-2L	Specificity	0.37 fraction	E. coli sigma70 promoter dataset	iPromoter-2L: E. coli sigma70 independent promoter test
iPromoter-BnCNN	Accuracy	0.55 unitless	E. coli sigma70 promoter dataset	iPromoter-BnCNN: E. coli sigma70 independent promoter test
iPromoter-BnCNN	MCC	0.27 unitless	E. coli sigma70 promoter dataset	iPromoter-BnCNN: E. coli sigma70 independent promoter test
iPromoter-BnCNN	Recall	0.99 fraction	E. coli sigma70 promoter dataset	iPromoter-BnCNN: E. coli sigma70 independent promoter test
iPromoter-BnCNN	Specificity	0.18 fraction	E. coli sigma70 promoter dataset	iPromoter-BnCNN: E. coli sigma70 independent promoter test
Multiply	Accuracy	0.50 unitless	E. coli sigma70 promoter dataset	Multiply: E. coli sigma70 independent promoter test
Multiply	MCC	0.05 unitless	E. coli sigma70 promoter dataset	Multiply: E. coli sigma70 independent promoter test
Multiply	Recall	0.81 fraction	E. coli sigma70 promoter dataset	Multiply: E. coli sigma70 independent promoter test
Multiply	Specificity	0.23 fraction	E. coli sigma70 promoter dataset	Multiply: E. coli sigma70 independent promoter test
MULTiPly	Accuracy	0.54 unitless	E. coli sigma70 promoter dataset	MULTiPly: E. coli sigma70 independent promoter test
MULTiPly	MCC	0.19 unitless	E. coli sigma70 promoter dataset	MULTiPly: E. coli sigma70 independent promoter test
MULTiPly	Recall	0.92 fraction	E. coli sigma70 promoter dataset	MULTiPly: E. coli sigma70 independent promoter test
MULTiPly	Specificity	0.22 fraction	E. coli sigma70 promoter dataset	MULTiPly: E. coli sigma70 independent promoter test
ProkBERT-mini-c	Accuracy	0.87 unitless	E. coli sigma70 promoter dataset	ProkBERT-mini-c: E. coli sigma70 independent promoter test
ProkBERT-mini-c	MCC	0.73 unitless	E. coli sigma70 promoter dataset	ProkBERT-mini-c: E. coli sigma70 independent promoter test
ProkBERT-mini-c	Recall	0.88 fraction	E. coli sigma70 promoter dataset	ProkBERT-mini-c: E. coli sigma70 independent promoter test
ProkBERT-mini-c	Specificity	0.85 fraction	E. coli sigma70 promoter dataset	ProkBERT-mini-c: E. coli sigma70 independent promoter test
ProkBERT-mini-long	Accuracy	0.87 unitless	E. coli sigma70 promoter dataset	ProkBERT-mini-long: E. coli sigma70 independent promoter test
ProkBERT-mini-long	MCC	0.74 unitless	E. coli sigma70 promoter dataset	ProkBERT-mini-long: E. coli sigma70 independent promoter test
ProkBERT-mini-long	Recall	0.89 fraction	E. coli sigma70 promoter dataset	ProkBERT-mini-long: E. coli sigma70 independent promoter test
ProkBERT-mini-long	Specificity	0.85 fraction	E. coli sigma70 promoter dataset	ProkBERT-mini-long: E. coli sigma70 independent promoter test
ProkBERT-mini	Accuracy	0.87 unitless	E. coli sigma70 promoter dataset	ProkBERT-mini: E. coli sigma70 promoter prediction
ProkBERT-mini	MCC	0.74 unitless	E. coli sigma70 promoter dataset	ProkBERT-mini: E. coli sigma70 promoter prediction

Claims

Statements this source supports, each with where in the source it was checked.

E. coli sigma70 independent promoter test (E. coli sigma70 promoter prediction): links:evaluates_task:reported-task-3891811dcce8b3: Evaluates task E. coli sigma70 promoter prediction (Table 3: Accuracy, E. coli sigma70 independent promoter test)
ProkBERT-mini · Accuracy · E. coli sigma70 promoter dataset: attributes.metric_direction: Metric direction higher (Table 3, row ProkBERT-mini, column Accuracy; XML row2 column2)
ProkBERT-mini-c: family ProkBERT: Family ProkBERT (Table 3, row ProkBERT-mini-c, column Accuracy; XML row3 column2; ProkBERT official README variant list and primary paper Table 1)
ProkBERT-mini-long: family ProkBERT: Family ProkBERT (Table 3, row ProkBERT-mini-long, column Accuracy; XML row4 column2; ProkBERT official README variant list and primary paper Table 1)
Promotech · Accuracy · E. coli sigma70 promoter dataset: attributes.metric_direction: Metric direction higher (Table 3, row Promotech, column Accuracy; XML row13 column2)

Models, benchmarks and other records

Configurations (13)

Tasks (1)

E. coli sigma70 promoter prediction

Protocols (1)

E. coli sigma70 independent promoter test (E. coli sigma70 promoter prediction)

Evaluations (15)

Evidence

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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.

16 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-11-02-a7f03c9e55a5
Property and statement	Original source and location	Review and provenance
Artifact SHA-256 8610e2a54aa877c8dc565a9cdb6e82099f284c5e0907a52cab18d994ea732436 Source metadata	ProkBERT family: genomic language models for microbiome applications Original source ↗ No field-specific location recorded Version: PMC10810988.1 Retrieved: 2026-09-17T07:56:14.890826+00:00	catalogued No individual claim review recorded Audit details Field: `attributes.artifact_sha256` Source artifact SHA-256: `8610e2a54aa877c8dc565a9cdb6e82099f284c5e0907a52cab18d994ea732436` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
Artifact url https://www.ebi.ac.uk/europepmc/webservices/rest/PMC10810988/fullTextXML Source metadata	ProkBERT family: genomic language models for microbiome applications Original source ↗ No field-specific location recorded Version: PMC10810988.1 Retrieved: 2026-09-17T07:56:14.890826+00:00	catalogued No individual claim review recorded Audit details Field: `attributes.artifact_url` Source artifact SHA-256: `8610e2a54aa877c8dc565a9cdb6e82099f284c5e0907a52cab18d994ea732436` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
Doi 10.3389/fmicb.2023.1331233 Source metadata	ProkBERT family: genomic language models for microbiome applications Original source ↗ No field-specific location recorded Version: PMC10810988.1 Retrieved: 2026-09-17T07:56:14.890826+00:00	catalogued No individual claim review recorded Audit details Field: `attributes.doi` Source artifact SHA-256: `8610e2a54aa877c8dc565a9cdb6e82099f284c5e0907a52cab18d994ea732436` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
Hash scope Exact retrieved primary paper artifact bytes. Source metadata	ProkBERT family: genomic language models for microbiome applications Original source ↗ No field-specific location recorded Version: PMC10810988.1 Retrieved: 2026-09-17T07:56:14.890826+00:00	catalogued No individual claim review recorded Audit details Field: `attributes.hash_scope` Source artifact SHA-256: `8610e2a54aa877c8dc565a9cdb6e82099f284c5e0907a52cab18d994ea732436` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
Retrieved at 2026-09-17T07:56:14.890826+00:00 Source metadata	ProkBERT family: genomic language models for microbiome applications Original source ↗ No field-specific location recorded Version: PMC10810988.1 Retrieved: 2026-09-17T07:56:14.890826+00:00	catalogued No individual claim review recorded Audit details Field: `attributes.retrieved_at` Source artifact SHA-256: `8610e2a54aa877c8dc565a9cdb6e82099f284c5e0907a52cab18d994ea732436` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
Review method 1 values automated-source-review Source metadata	ProkBERT family: genomic language models for microbiome applications Original source ↗ No field-specific location recorded Version: PMC10810988.1 Retrieved: 2026-09-17T07:56:14.890826+00:00	catalogued No individual claim review recorded Audit details Field: `attributes.review.method` Source artifact SHA-256: `8610e2a54aa877c8dc565a9cdb6e82099f284c5e0907a52cab18d994ea732436` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
Review: scope Source identification and table transcription; no independent experimental reproduction. Source metadata	ProkBERT family: genomic language models for microbiome applications Original source ↗ No field-specific location recorded Version: PMC10810988.1 Retrieved: 2026-09-17T07:56:14.890826+00:00	catalogued No individual claim review recorded Audit details Field: `attributes.review.scope` Source artifact SHA-256: `8610e2a54aa877c8dc565a9cdb6e82099f284c5e0907a52cab18d994ea732436` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
Url https://www.ebi.ac.uk/europepmc/webservices/rest/PMC10810988/fullTextXML Source metadata	ProkBERT family: genomic language models for microbiome applications Original source ↗ No field-specific location recorded Version: PMC10810988.1 Retrieved: 2026-09-17T07:56:14.890826+00:00	catalogued No individual claim review recorded Audit details Field: `attributes.url` Source artifact SHA-256: `8610e2a54aa877c8dc565a9cdb6e82099f284c5e0907a52cab18d994ea732436` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
Version PMC10810988.1 Source metadata	ProkBERT family: genomic language models for microbiome applications Original source ↗ No field-specific location recorded Version: PMC10810988.1 Retrieved: 2026-09-17T07:56:14.890826+00:00	catalogued No individual claim review recorded Audit details Field: `attributes.version` Source artifact SHA-256: `8610e2a54aa877c8dc565a9cdb6e82099f284c5e0907a52cab18d994ea732436` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
Description Primary reference; inspect retrieval status and review scope. Source metadata	ProkBERT family: genomic language models for microbiome applications Original source ↗ No field-specific location recorded Version: PMC10810988.1 Retrieved: 2026-09-17T07:56:14.890826+00:00	catalogued No individual claim review recorded Audit details Field: `description` Source artifact SHA-256: `8610e2a54aa877c8dc565a9cdb6e82099f284c5e0907a52cab18d994ea732436` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact

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Release 2026-11-02-a7f03c9e55a5 · Record review: source checked

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Technical metadata and extraction receipts

Stable ID: part2-prokbert-2024

url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC10810988/fullTextXML
doi: 10.3389/fmicb.2023.1331233
version: PMC10810988.1
retrieved at: 2026-09-17T07:56:14.890826+00:00
artifact sha256: 8610e2a54aa877c8dc565a9cdb6e82099f284c5e0907a52cab18d994ea732436
artifact url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC10810988/fullTextXML
hash scope: Exact retrieved primary paper artifact bytes.
review: scope: Source identification and table transcription; no independent experimental reproduction.; method: automated-source-review

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