GENERanno†: 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.
Evaluation 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.
- Pipeline
- GENERanno†
- Protocol
- Genome-wide prophage detection (Genome-wide prophage detection)
- Dataset
- LAMBDA genome-wide prophage test
- origin
- Author-reported evaluation
- configuration
- Paper genome-scanning gLM pipeline, including filtered region postprocessing; exact encoder checkpoint not inferred from the label
- protocol id
- paper-protocol-41c6e227215346177d
- dataset version
- Not reported
- split
- 80 bacterial genomes,47 species,four phyla;386 annotated prophage locations.
- subset
- Genome-wide prophage detection
- population
- Not reported
- aggregation
- Region-level metrics macro-averaged across genomes.
- inputs
- Not reported
- adaptation
- Paper genome-scanning gLM pipeline, including filtered region postprocessing; exact encoder checkpoint not inferred from the label
- budget
- Not reported
- metric implementation
- Not reported
Metadata review: needs review. Unreported conditions prevent automatic comparisons.
Evaluation results
Release 2026-09-17-d277315f7d76 · 1 evaluation · 6 metric rows. Different protocols are not a single leaderboard.
| Metric and finding | Coverage and uncertainty | Evidence |
|---|---|---|
| GENERanno†: Genome-wide prophage detection Pipeline: GENERanno†Protocol: Genome-wide prophage detection (Genome-wide prophage detection)Dataset: LAMBDA genome-wide prophage test 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. Author-reported evaluation · Evaluation metadata: needs review | ||
| 0.631 F1 Unit: fraction · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedLAMBDA: A Prophage Detection Benchmark for Genomic Language Models · Table 5., row GENERanno†, column F1; XML row11 column6 Source checking is not independent reproduction. |
| 0.651 Precision Unit: fraction · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedLAMBDA: A Prophage Detection Benchmark for Genomic Language Models · Table 5., row GENERanno†, column Precision; XML row11 column2 Source checking is not independent reproduction. |
| 0.648 MCC Unit: unitless · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedLAMBDA: A Prophage Detection Benchmark for Genomic Language Models · Table 5., row GENERanno†, column MCC; XML row11 column7 Source checking is not independent reproduction. |
| 0.723 Recall Unit: fraction · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedLAMBDA: A Prophage Detection Benchmark for Genomic Language Models · Table 5., row GENERanno†, column Recall; XML row11 column3 Source checking is not independent reproduction. |
| 0.012 FPR Unit: fraction · Direction: lower | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedLAMBDA: A Prophage Detection Benchmark for Genomic Language Models · Table 5., row GENERanno†, column FPR; XML row11 column5 Source checking is not independent reproduction. |
| 0.988 Specificity Unit: fraction · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedLAMBDA: A Prophage Detection Benchmark for Genomic Language Models · Table 5., row GENERanno†, column Specificity; XML row11 column4 Source checking is not independent reproduction. |
Evidence table
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.
19 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| attributes.comparison.adaptation Paper genome-scanning gLM pipeline, including filtered region postprocessing; exact encoder checkpoint not inferred from the label Context-only references | LAMBDA: A Prophage Detection Benchmark for Genomic Language Models Table 5.: Precision, Genome-wide prophage detection Version: PMC13041943.1 | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| attributes.comparison.aggregation Region-level metrics macro-averaged across genomes. Context-only references | LAMBDA: A Prophage Detection Benchmark for Genomic Language Models Table 5.: Precision, Genome-wide prophage detection Version: PMC13041943.1 | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| attributes.comparison.budget No value recorded Context-only references | LAMBDA: A Prophage Detection Benchmark for Genomic Language Models Table 5.: Precision, Genome-wide prophage detection Version: PMC13041943.1 | missing or unspecified No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| attributes.comparison.dataset_version No value recorded Context-only references | LAMBDA: A Prophage Detection Benchmark for Genomic Language Models Table 5.: Precision, Genome-wide prophage detection Version: PMC13041943.1 | missing or unspecified No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| attributes.comparison.inputs No value recorded Context-only references | LAMBDA: A Prophage Detection Benchmark for Genomic Language Models Table 5.: Precision, Genome-wide prophage detection Version: PMC13041943.1 | missing or unspecified No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| attributes.comparison.metric_implementation No value recorded Context-only references | LAMBDA: A Prophage Detection Benchmark for Genomic Language Models Table 5.: Precision, Genome-wide prophage detection Version: PMC13041943.1 | missing or unspecified No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| attributes.comparison.population No value recorded Context-only references | LAMBDA: A Prophage Detection Benchmark for Genomic Language Models Table 5.: Precision, Genome-wide prophage detection Version: PMC13041943.1 | missing or unspecified No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| attributes.comparison.protocol_id paper-protocol-41c6e227215346177d Context-only references | LAMBDA: A Prophage Detection Benchmark for Genomic Language Models Table 5.: Precision, Genome-wide prophage detection Version: PMC13041943.1 | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| attributes.comparison.split 80 bacterial genomes,47 species,four phyla;386 annotated prophage locations. Context-only references | LAMBDA: A Prophage Detection Benchmark for Genomic Language Models Table 5.: Precision, Genome-wide prophage detection Version: PMC13041943.1 | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| attributes.comparison.subset Genome-wide prophage detection Context-only references | LAMBDA: A Prophage Detection Benchmark for Genomic Language Models Table 5.: Precision, Genome-wide prophage detection Version: PMC13041943.1 | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
Sources and history
Release 2026-09-17-d277315f7d76 · Record review: needs review
- LAMBDA: A Prophage Detection Benchmark for Genomic Language Models · Original source · PMC13041943.1
Technical metadata and extraction receipts
Stable ID: paper-evaluation-f70017f4c8535f2f73
- areas
- microbes-communities
- tasks
- Genome-wide prophage detection
- origin
- author_reported
- protocol
- 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.
- version
- Paper genome-scanning gLM pipeline, including filtered region postprocessing; exact encoder checkpoint not inferred from the label
- comparison
- protocol id: paper-protocol-41c6e227215346177d; dataset version: Not reported; split: 80 bacterial genomes,47 species,four phyla;386 annotated prophage locations.; subset: Genome-wide prophage detection; population: Not reported; aggregation: Region-level metrics macro-averaged across genomes.; inputs: Not reported; adaptation: Paper genome-scanning gLM pipeline, including filtered region postprocessing; exact encoder checkpoint not inferred from the label; budget: Not reported; metric implementation: Not reported
- source locator
- Table 5.: Precision, Genome-wide prophage detection
- missing metadata
- checkpoint revision: unextracted; budget: unreported; split manifest: unextracted
Related records
- model: GENERanno†
- benchmark: Genome-wide prophage detection (Genome-wide prophage detection)
- dataset: LAMBDA genome-wide prophage test
- evaluation: GENERanno†: F1 on Genome-wide prophage detection
- evaluation: GENERanno†: Precision on Genome-wide prophage detection
- evaluation: GENERanno†: MCC on Genome-wide prophage detection
- evaluation: GENERanno†: Recall on Genome-wide prophage detection
- evaluation: GENERanno†: FPR on Genome-wide prophage detection
- evaluation: GENERanno†: Specificity on Genome-wide prophage detection