Strengths and considerations
No source-reviewed explanatory claims are recorded here yet.
Pipeline
ProkBERT-mini†
ProkBERT-mini† as evaluated in the cited study. Paper genome-scanning gLM pipeline, including filtered region postprocessing; exact encoder checkpoint not inferred from the label
Sources
LAMBDA: A Prophage Detection Benchmark for Genomic Language Models · Table 5., row ProkBERT-mini†, column Precision; XML row9 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 · 6 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 |
|---|---|---|---|
| Pipeline: ProkBERT-mini† | Protocol: Genome-wide prophage detection (Genome-wide prophage detection) Dataset: LAMBDA genome-wide prophage test | 0.658 MCC unitless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceProkBERT-mini†: Genome-wide prophage detection Scan complete genomes with overlapping windows and postprocess predictions into prophage regions. Genome-wide metrics are computed at region level and macro-averaged across genomes. Filtered gLM pipelines include normalization, smoothing, clustering and size filtering; these are not standalone encoder scores. 80 bacterial genomes,47 species,four phyla;386 annotated prophage locations. Aggregation: Not reported LAMBDA: A Prophage Detection Benchmark for Genomic Language Models · Table 5., row ProkBERT-mini†, column MCC; XML row9 column7 |
| Pipeline: ProkBERT-mini† | Protocol: Genome-wide prophage detection (Genome-wide prophage detection) Dataset: LAMBDA genome-wide prophage test | 0.651 Recall fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceProkBERT-mini†: Genome-wide prophage detection Scan complete genomes with overlapping windows and postprocess predictions into prophage regions. Genome-wide metrics are computed at region level and macro-averaged across genomes. Filtered gLM pipelines include normalization, smoothing, clustering and size filtering; these are not standalone encoder scores. 80 bacterial genomes,47 species,four phyla;386 annotated prophage locations. Aggregation: Not reported LAMBDA: A Prophage Detection Benchmark for Genomic Language Models · Table 5., row ProkBERT-mini†, column Recall; XML row9 column3 |
| Pipeline: ProkBERT-mini† | Protocol: Genome-wide prophage detection (Genome-wide prophage detection) Dataset: LAMBDA genome-wide prophage test | 0.006 FPR fraction · lower Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceProkBERT-mini†: Genome-wide prophage detection Scan complete genomes with overlapping windows and postprocess predictions into prophage regions. Genome-wide metrics are computed at region level and macro-averaged across genomes. Filtered gLM pipelines include normalization, smoothing, clustering and size filtering; these are not standalone encoder scores. 80 bacterial genomes,47 species,four phyla;386 annotated prophage locations. Aggregation: Not reported LAMBDA: A Prophage Detection Benchmark for Genomic Language Models · Table 5., row ProkBERT-mini†, column FPR; XML row9 column5 |
| Pipeline: ProkBERT-mini† | Protocol: Genome-wide prophage detection (Genome-wide prophage detection) Dataset: LAMBDA genome-wide prophage test | 0.743 Precision fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceProkBERT-mini†: Genome-wide prophage detection Scan complete genomes with overlapping windows and postprocess predictions into prophage regions. Genome-wide metrics are computed at region level and macro-averaged across genomes. Filtered gLM pipelines include normalization, smoothing, clustering and size filtering; these are not standalone encoder scores. 80 bacterial genomes,47 species,four phyla;386 annotated prophage locations. Aggregation: Not reported LAMBDA: A Prophage Detection Benchmark for Genomic Language Models · Table 5., row ProkBERT-mini†, column Precision; XML row9 column2 |
| Pipeline: ProkBERT-mini† | Protocol: Genome-wide prophage detection (Genome-wide prophage detection) Dataset: LAMBDA genome-wide prophage test | 0.64 F1 fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceProkBERT-mini†: Genome-wide prophage detection Scan complete genomes with overlapping windows and postprocess predictions into prophage regions. Genome-wide metrics are computed at region level and macro-averaged across genomes. Filtered gLM pipelines include normalization, smoothing, clustering and size filtering; these are not standalone encoder scores. 80 bacterial genomes,47 species,four phyla;386 annotated prophage locations. Aggregation: Not reported LAMBDA: A Prophage Detection Benchmark for Genomic Language Models · Table 5., row ProkBERT-mini†, column F1; XML row9 column6 |
| Pipeline: ProkBERT-mini† | Protocol: Genome-wide prophage detection (Genome-wide prophage detection) Dataset: LAMBDA genome-wide prophage test | 0.994 Specificity fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceProkBERT-mini†: Genome-wide prophage detection Scan complete genomes with overlapping windows and postprocess predictions into prophage regions. Genome-wide metrics are computed at region level and macro-averaged across genomes. Filtered gLM pipelines include normalization, smoothing, clustering and size filtering; these are not standalone encoder scores. 80 bacterial genomes,47 species,four phyla;386 annotated prophage locations. Aggregation: Not reported LAMBDA: A Prophage Detection Benchmark for Genomic Language Models · Table 5., row ProkBERT-mini†, column Specificity; XML row9 column4 |
Source checking is not independent reproduction. Release 2026-09-29-06401fd5b220.
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How it works, versions and access
Underlying model: ProkBERT. Results on this page belong to this pipeline and its evaluated settings.
How it works
Evaluation in this paper
Paper genome-scanning gLM pipeline, including filtered region postprocessing; exact encoder checkpoint not inferred from the label
Sources
LAMBDA: A Prophage Detection Benchmark for Genomic Language Models · Table 5., row ProkBERT-mini†, column Precision; XML row9 column2Strengths, limitations and unresolved questions
Strengths and limitations
Limitations and conditions
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Profile review details
Primary-source transcription and separate automated review. No human sign-off or experimental reproduction.
Stable record: paper-model-ebe8e20b92526285d9Specifications
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 |
|---|---|
| Components | Not extracted or verified for this record. |
| Inputs | Not extracted or verified for this record. |
| Outputs | Not extracted or verified for this record. |
| Adaptation | Not extracted or verified for this record. |
| Implementation | Not extracted or verified for this record. |
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.
4 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Evaluation in this paper Paper genome-scanning gLM pipeline, including filtered region postprocessing; exact encoder checkpoint not inferred from the label Individual claims | LAMBDA: A Prophage Detection Benchmark for Genomic Language Models Table 5., row ProkBERT-mini†, column Precision; XML row9 column2 Version: PMC13041943.1 | 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† as evaluated in the cited study. Paper genome-scanning gLM pipeline, including filtered region postprocessing; exact encoder checkpoint not inferred from the label Individual claims | LAMBDA: A Prophage Detection Benchmark for Genomic Language Models Table 5., row ProkBERT-mini†, column Precision; XML row9 column2 Version: PMC13041943.1 | 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: uses model catalog-model-prokbert Individual claims | nbrg-ppcu/prokbert: README.md Table 5., row ProkBERT-mini†, column Precision; XML row9 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-cce8a783db164d697b11 Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| Relationship: uses model catalog-model-prokbert Individual claims | LAMBDA: A Prophage Detection Benchmark for Genomic Language Models Table 5., row ProkBERT-mini†, column Precision; XML row9 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: PMC13041943.1 | 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-cce8a783db164d697b11 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
- LAMBDA: A Prophage Detection Benchmark for Genomic Language Models · Original source · PMC13041943.1
Technical metadata and extraction receipts
Stable ID: paper-model-ebe8e20b92526285d9
- areas
- microbes-communities
- tasks
- Genome-wide prophage detection
- entity level
- method
- configuration type
- reported_configuration
- version
- Paper genome-scanning gLM pipeline, including filtered region postprocessing; exact encoder checkpoint not inferred from the label
- legacy kinds
- model
- entity classification
- review date: 2026-09-17; rationale: Genome scanning with overlapping windows is followed by per-genome score normalization, smoothing, clustering/merging and size/score filtering to identify prophage regions. The reported row evaluates that complete workflow, not the unprocessed encoder. Preserve the exact source-scoped composition and its results; no additional checkpoint or family equivalence is inferred.; source ids: part2-lambda-prophage-2026; source locator: Table 5., row ProkBERT-mini†, column Precision; XML row9 column2 | Table 5 dagger-labelled genome-scanning rows; genome-wide detection Methods; Figure 2 caption; raw versus filtered region evaluation; ambiguities: This is the paper-specific pipeline identity. Missing component versions or checkpoint hashes remain unknown; a shared upstream name does not establish equivalent pipelines.
Related records
- uses model: ProkBERT
- subject: ProkBERT-mini†: uses model ProkBERT
- model: ProkBERT-mini†: Genome-wide prophage detection