Strengths and considerations
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Configuration
ProkBERT-mini-c
ProkBERT-mini-c as evaluated in the cited study. Paper-specific evaluated pipeline; exact checkpoint not inferred from label
Sources
ProkBERT family: genomic language models for microbiome applications · Table 3, row ProkBERT-mini-c, column Accuracy; XML row3 column2Overview
Key specifications have not been extracted for this record. See the linked evaluation and sources for the reported setup.
limited source coverage · Automated source review, 2026-09-17. All specifications and missing details
Evaluations and results
1 evaluation · 4 results. Different protocols are not a single leaderboard.
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Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: ProkBERT-mini-c | Protocol: E. coli sigma70 independent promoter test (E. coli sigma70 promoter prediction) Dataset: E. coli sigma70 promoter dataset | 0.88 Sensitivity fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceProkBERT-mini-c: E. coli sigma70 independent promoter test 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. Aggregation: Not reported ProkBERT family: genomic language models for microbiome applications · Table 3, row ProkBERT-mini-c, column Sensitivity; XML row3 column4 |
| Configuration: ProkBERT-mini-c | Protocol: E. coli sigma70 independent promoter test (E. coli sigma70 promoter prediction) Dataset: E. coli sigma70 promoter dataset | 0.85 Specificity fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceProkBERT-mini-c: E. coli sigma70 independent promoter test 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. Aggregation: Not reported ProkBERT family: genomic language models for microbiome applications · Table 3, row ProkBERT-mini-c, column Specificity; XML row3 column5 |
| Configuration: ProkBERT-mini-c | Protocol: E. coli sigma70 independent promoter test (E. coli sigma70 promoter prediction) Dataset: E. coli sigma70 promoter dataset | 0.73 MCC dimensionless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceProkBERT-mini-c: E. coli sigma70 independent promoter test 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. Aggregation: Not reported ProkBERT family: genomic language models for microbiome applications · Table 3, row ProkBERT-mini-c, column MCC; XML row3 column3 |
| Configuration: ProkBERT-mini-c | Protocol: E. coli sigma70 independent promoter test (E. coli sigma70 promoter prediction) Dataset: E. coli sigma70 promoter dataset | 0.87 Accuracy unitless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceProkBERT-mini-c: E. coli sigma70 independent promoter test 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. Aggregation: Not reported ProkBERT family: genomic language models for microbiome applications · Table 3, row ProkBERT-mini-c, column Accuracy; XML row3 column2 |
Source checking is not independent reproduction. Release 2026-09-29-06401fd5b220.
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How it works, versions and access
Related profile: ProkBERT. This page retains the exact record and its evaluation context.
How it works
Evaluation in this paper
Paper-specific evaluated pipeline; exact checkpoint not inferred from label
Sources
ProkBERT family: genomic language models for microbiome applications · Table 3, row ProkBERT-mini-c, column Accuracy; XML row3 column2Strengths, limitations and unresolved questions
Strengths and limitations
Limitations and conditions
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Profile review details
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Stable record: paper-model-779b487305cf463659Specifications
Inputs, training, access and other details
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.
| Property | Description and evidence |
|---|---|
| Model type | Not extracted or verified for this record. |
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| Outputs | Not extracted or verified for this record. |
| Parameters | Not extracted or verified for this record. |
| Known versions | Not extracted or verified for this record. |
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Evidence
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Evidence table
Inspect claims, sources and review details
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One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.
4 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Evaluation in this paper Paper-specific evaluated pipeline; exact checkpoint not inferred from label Individual claims | ProkBERT family: genomic language models for microbiome applications Table 3, row ProkBERT-mini-c, column Accuracy; XML row3 column2 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 ProkBERT-mini-c as evaluated in the cited study. Paper-specific evaluated pipeline; exact checkpoint not inferred from label Individual claims | ProkBERT family: genomic language models for microbiome applications Table 3, row ProkBERT-mini-c, column Accuracy; XML row3 column2 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: family catalog-model-prokbert Individual claims | nbrg-ppcu/prokbert: README.md Table 3, row ProkBERT-mini-c, column Accuracy; XML row3 column2; ProkBERT official README variant list and primary paper Table 1 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 8670ae92b816cff158a0b85647a8dea122e251eb | source checked automated source review · 2026-09-23 Audit detailsSource review establishes this relationship only. Exact evaluated configurations and original numerical review status remain unchanged. Catalog model explicitly describes the microbial encoder family including mini, mini-c and mini-long. Preserve paper-specific variant and pipeline identity. Field: Claim: model-evaluation-identity-3772d753b84d3704803c Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| Relationship: family catalog-model-prokbert Individual claims | ProkBERT family: genomic language models for microbiome applications Table 3, row ProkBERT-mini-c, column Accuracy; XML row3 column2; ProkBERT official README variant list and primary paper Table 1 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: PMC10810988.1 | source checked automated source review · 2026-09-23 Audit detailsSource review establishes this relationship only. Exact evaluated configurations and original numerical review status remain unchanged. Catalog model explicitly describes the microbial encoder family including mini, mini-c and mini-long. Preserve paper-specific variant and pipeline identity. Field: Claim: model-evaluation-identity-3772d753b84d3704803c Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
Sources and history
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Release 2026-09-29-06401fd5b220 · Record review: needs review
1 source records and release history
- ProkBERT family: genomic language models for microbiome applications · Original source · PMC10810988.1
Technical metadata and extraction receipts
Stable ID: paper-model-779b487305cf463659
- areas
- microbes-communities
- tasks
- E. coli sigma70 promoter prediction
- entity level
- method
- configuration type
- reported_configuration
- version
- Paper-specific evaluated pipeline; exact checkpoint not inferred from label
- legacy kinds
- model
- entity classification
- review date: 2026-09-17; rationale: This source-scoped entry preserves the method/configuration actually named in an evaluation. It is neither a global family identity nor proof of an immutable checkpoint; the linked evaluation retains adaptation, fitting and scoring details.; source ids: part2-prokbert-2024; source locator: Table 3, row ProkBERT-mini-c, column Accuracy; XML row3 column2; ambiguities: Configuration means the source-labelled evaluated identity. It does not establish missing checkpoint hashes, default settings or equivalence to same-named records in other papers.