F1 of ProkBERT-mini-c† on LAMBDA genome-wide prophage test
0.551 F1
Methods
- Tested pipeline
- ProkBERT-mini-c†
- Protocol
- Genome-wide prophage detection (Genome-wide prophage detection)
- Dataset
- LAMBDA genome-wide prophage test
- Procedure
- 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.
- Evaluation
- ProkBERT-mini-c†: Genome-wide prophage detection
- Coverage
- Not reported scored / Not reported eligible
- Uncertainty
- Not reported by the source
- Evidence
- Author-reported evaluation · source checkedLAMBDA: A Prophage Detection Benchmark for Genomic Language Models · Table 5., row ProkBERT-mini-c†, column F1; XML row16 column6
A source-checked result verifies the numerical transcription, not every model or protocol detail. Evaluation metadata: needs review. Source checked does not mean independently reproduced.
Reproduction
- Split
- 80 bacterial genomes,47 species,four phyla;386 annotated prophage locations.
- Adaptation
- Paper genome-scanning gLM pipeline, including filtered region postprocessing; exact encoder checkpoint not inferred from the label
- Scoring implementation
- Not reported
No execution recipe has been verified for this exact configuration and evaluation. A benchmark's general instructions may use different inputs, splits or model settings.
Reproducing this published result requires matching its model configuration, data, split and scorer. Source checking or a successful smoke test does not establish score reproduction.
Evidence
Source checking verifies the cited claim or transcription. It does not establish independent reproduction.
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.
1 evidence row matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Reported result 0.551 Individual claims | LAMBDA: A Prophage Detection Benchmark for Genomic Language Models Table 5., row ProkBERT-mini-c†, column F1; XML row16 column6 Version: PMC13041943.1 | source checked ["transcription","automated-source-review"] · 2026-09-17 author reported Audit detailsSource checked does not mean experimentally reproduced. Field: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
Sources and history
Release 2026-11-02-a7f03c9e55a5 · Record review: source checked
1 source record and release history
- LAMBDA: A Prophage Detection Benchmark for Genomic Language Models · Original source · PMC13041943.1
Technical metadata and extraction receipts
Stable ID: paper-result-5db8cdaca7588fa5ca
- areas
- microbes-communities
- tasks
- Genome-wide prophage detection
- printed value
- 0.551
- numeric value
- 0.551
- metric
- f1-score
- metric direction
- higher
- unit
- fraction
- source locator
- Table 5., row ProkBERT-mini-c†, column F1; XML row16 column6
- source occurrences
- source id: part2-lambda-prophage-2026; locator: Table 5., row ProkBERT-mini-c†, column F1; XML row16 column6
- review
- method: transcription; automated-source-review; date: 2026-09-17; note: Source checked does not mean experimentally reproduced.; method note: primary table; source review separate from transcription
- missing metadata
- checkpoint revision: reason: unextracted; eligible count: reason: unextracted; reported population: reason: unextracted; scored count: reason: unreported; uncertainty: reason: unreported
Related records
- evaluation: ProkBERT-mini-c†: Genome-wide prophage detection