1 evaluation · 6 results. Different protocols are not a single leaderboard.
Protocol: Genome-wide prophage detection (Genome-wide prophage detection) · Dataset: LAMBDA genome-wide prophage test
Sorted by F1 (higher is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: geNomad | Protocol: Genome-wide prophage detection (Genome-wide prophage detection) Dataset: LAMBDA genome-wide prophage test | 0.794 MCC unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourcegeNomad: 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; LAMBDA: A Prophage Detection Benchmark for Genomic Language Models · Table 5, geNomad row, MCC column |
| Configuration: geNomad | Protocol: Genome-wide prophage detection (Genome-wide prophage detection) Dataset: LAMBDA genome-wide prophage test | 0.786 F1 fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourcegeNomad: 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 geNomad, column F1; XML row3 column6 |
| Configuration: geNomad | Protocol: Genome-wide prophage detection (Genome-wide prophage detection) Dataset: LAMBDA genome-wide prophage test | 0.009 False positive rate fraction · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourcegeNomad: 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 geNomad, column FPR; XML row3 column5 |
| Configuration: geNomad | Protocol: Genome-wide prophage detection (Genome-wide prophage detection) Dataset: LAMBDA genome-wide prophage test | 0.873 Recall fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourcegeNomad: 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 geNomad, column Recall; XML row3 column3 |
| Configuration: geNomad | Protocol: Genome-wide prophage detection (Genome-wide prophage detection) Dataset: LAMBDA genome-wide prophage test | 0.991 Specificity fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourcegeNomad: 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 geNomad, column Specificity; XML row3 column4 |
| Configuration: geNomad | Protocol: Genome-wide prophage detection (Genome-wide prophage detection) Dataset: LAMBDA genome-wide prophage test | 0.761 Precision fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourcegeNomad: 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 geNomad, column Precision; XML row3 column2 |
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Release 2026-11-02-a7f03c9e55a5 · Evidence verified: Not verified
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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.
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38 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Comparison: adaptation Paper-specific evaluated pipeline; exact checkpoint not inferred from label Context-only references | LAMBDA: A Prophage Detection Benchmark for Genomic Language Models Table 5.: MCC, Genome-wide prophage detection Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: PMC13041943.1 | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Comparison: adaptation Paper-specific evaluated pipeline; exact checkpoint not inferred from label Context-only references | LAMBDA: A Prophage Detection Benchmark for Genomic Language Models Table 5.: MCC, Genome-wide prophage detection Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: PMC13041943.1 | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| Comparison: aggregation Region-level metrics macro-averaged across genomes. Context-only references | LAMBDA: A Prophage Detection Benchmark for Genomic Language Models Table 5.: MCC, Genome-wide prophage detection Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: PMC13041943.1 | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Comparison: aggregation Region-level metrics macro-averaged across genomes. Context-only references | LAMBDA: A Prophage Detection Benchmark for Genomic Language Models Table 5.: MCC, Genome-wide prophage detection Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: PMC13041943.1 | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| Comparison: budget Not reported Context-only references | LAMBDA: A Prophage Detection Benchmark for Genomic Language Models Table 5.: MCC, Genome-wide prophage detection Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: PMC13041943.1 | missing or unspecified No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Comparison: budget Not reported Context-only references | LAMBDA: A Prophage Detection Benchmark for Genomic Language Models Table 5.: MCC, Genome-wide prophage detection Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: PMC13041943.1 | missing or unspecified No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| Comparison: dataset version Not reported Context-only references | LAMBDA: A Prophage Detection Benchmark for Genomic Language Models Table 5.: MCC, Genome-wide prophage detection Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: PMC13041943.1 | missing or unspecified No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Comparison: dataset version Not reported Context-only references | LAMBDA: A Prophage Detection Benchmark for Genomic Language Models Table 5.: MCC, Genome-wide prophage detection Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: PMC13041943.1 | missing or unspecified No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| Comparison: inputs Not reported Context-only references | LAMBDA: A Prophage Detection Benchmark for Genomic Language Models Table 5.: MCC, Genome-wide prophage detection Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: PMC13041943.1 | missing or unspecified No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Comparison: inputs Not reported Context-only references | LAMBDA: A Prophage Detection Benchmark for Genomic Language Models Table 5.: MCC, Genome-wide prophage detection Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: PMC13041943.1 | missing or unspecified No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
Release 2026-11-02-a7f03c9e55a5 · Record review: needs review
Stable ID: evaluation-lit-038