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17 evaluations · 102 results. Different protocols are not a single leaderboard.
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: EVO2 | Protocol: Genome-wide prophage detection (Genome-wide prophage detection) Dataset: LAMBDA genome-wide prophage test | 0.68 MCC unitless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceEVO2: 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, EVO2 row, MCC column |
| Configuration: geNomad | Protocol: Genome-wide prophage detection (Genome-wide prophage detection) Dataset: LAMBDA genome-wide prophage test | 0.794 MCC unitless · higher Uncertainty: Not reported 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: VirSorter2 | Protocol: Genome-wide prophage detection (Genome-wide prophage detection) Dataset: LAMBDA genome-wide prophage test | 0.046 FPR fraction · lower Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceVirSorter2: 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 VirSorter2, column FPR; XML row19 column5 |
| 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: megaDNA† | Protocol: Genome-wide prophage detection (Genome-wide prophage detection) Dataset: LAMBDA genome-wide prophage test | 0.595 F1 fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourcemegaDNA†: 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 megaDNA†, column F1; XML row12 column6 |
| Pipeline: ProkBERT-mini-c† | Protocol: Genome-wide prophage detection (Genome-wide prophage detection) Dataset: LAMBDA genome-wide prophage test | 0.603 Precision fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceProkBERT-mini-c†: 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-c†, column Precision; XML row16 column2 |
| Pipeline: DNABERT-2† | Protocol: Genome-wide prophage detection (Genome-wide prophage detection) Dataset: LAMBDA genome-wide prophage test | 0.991 Specificity fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceDNABERT-2†: 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 DNABERT-2†, column Specificity; XML row18 column4 |
| Pipeline: GENERanno† | Protocol: Genome-wide prophage detection (Genome-wide prophage detection) Dataset: LAMBDA genome-wide prophage test | 0.631 F1 fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceGENERanno†: 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 GENERanno†, column F1; XML row11 column6 |
| Pipeline: ProkBERT-mini-c† | Protocol: Genome-wide prophage detection (Genome-wide prophage detection) Dataset: LAMBDA genome-wide prophage test | 0.013 FPR fraction · lower Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceProkBERT-mini-c†: 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-c†, column FPR; XML row16 column5 |
| Configuration: PIDE‡ | Protocol: Genome-wide prophage detection (Genome-wide prophage detection) Dataset: LAMBDA genome-wide prophage test | 0.984 Specificity fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourcePIDE‡: 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 PIDE‡, column Specificity; XML row7 column4 |
| Pipeline: Caduceus† | Protocol: Genome-wide prophage detection (Genome-wide prophage detection) Dataset: LAMBDA genome-wide prophage test | 0.616 Precision fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceCaduceus†: 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 Caduceus†, column Precision; XML row15 column2 |
| Pipeline: DNABERT-2† | Protocol: Genome-wide prophage detection (Genome-wide prophage detection) Dataset: LAMBDA genome-wide prophage test | 0.009 FPR fraction · lower Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceDNABERT-2†: 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 DNABERT-2†, column FPR; XML row18 column5 |
| Pipeline: ProkBERT-mini-long† | Protocol: Genome-wide prophage detection (Genome-wide prophage detection) Dataset: LAMBDA genome-wide prophage test | 0.579 F1 fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceProkBERT-mini-long†: 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-long†, column F1; XML row13 column6 |
| Configuration: PIDE‡ | Protocol: Genome-wide prophage detection (Genome-wide prophage detection) Dataset: LAMBDA genome-wide prophage test | 0.715 MCC unitless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourcePIDE‡: 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 PIDE‡, column MCC; XML row7 column7 |
| Configuration: PhageBoost | Protocol: Genome-wide prophage detection (Genome-wide prophage detection) Dataset: LAMBDA genome-wide prophage test | 0.034 FPR fraction · lower Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourcePhageBoost: 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 PhageBoost, column FPR; XML row17 column5 |
| Configuration: VirSorter2 | Protocol: Genome-wide prophage detection (Genome-wide prophage detection) Dataset: LAMBDA genome-wide prophage test | 0.289 Precision fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceVirSorter2: 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 VirSorter2, column Precision; XML row19 column2 |
| Pipeline: megaDNA† | Protocol: Genome-wide prophage detection (Genome-wide prophage detection) Dataset: LAMBDA genome-wide prophage test | 0.671 Recall fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourcemegaDNA†: 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 megaDNA†, column Recall; XML row12 column3 |
| 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 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 |
| Pipeline: GENERanno† | Protocol: Genome-wide prophage detection (Genome-wide prophage detection) Dataset: LAMBDA genome-wide prophage test | 0.651 Precision fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceGENERanno†: 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 GENERanno†, column Precision; XML row11 column2 |
| Pipeline: megaDNA† | Protocol: Genome-wide prophage detection (Genome-wide prophage detection) Dataset: LAMBDA genome-wide prophage test | 0.012 FPR fraction · lower Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourcemegaDNA†: 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 megaDNA†, column FPR; XML row12 column5 |
| Pipeline: Caduceus† | Protocol: Genome-wide prophage detection (Genome-wide prophage detection) Dataset: LAMBDA genome-wide prophage test | 0.01 FPR fraction · lower Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceCaduceus†: 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 Caduceus†, column FPR; XML row15 column5 |
| Configuration: PHASTER | Protocol: Genome-wide prophage detection (Genome-wide prophage detection) Dataset: LAMBDA genome-wide prophage test | 0.011 FPR fraction · lower Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourcePHASTER: 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 PHASTER, column FPR; XML row4 column5 |
| Configuration: PhageBoost | Protocol: Genome-wide prophage detection (Genome-wide prophage detection) Dataset: LAMBDA genome-wide prophage test | 0.68 Recall fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourcePhageBoost: 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 PhageBoost, column Recall; XML row17 column3 |
| Pipeline: GENERanno† | Protocol: Genome-wide prophage detection (Genome-wide prophage detection) Dataset: LAMBDA genome-wide prophage test | 0.648 MCC unitless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceGENERanno†: 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 GENERanno†, column MCC; XML row11 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 |
Source checking is not independent reproduction. Release 2026-09-29-06401fd5b220.
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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 |
|---|---|---|
| attributes.split Not reported Context-only references | LAMBDA: A Prophage Detection Benchmark for Genomic Language Models No field-specific location recorded Version: PMC13041943.1 | missing or unspecified No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.version Not reported Context-only references | LAMBDA: A Prophage Detection Benchmark for Genomic Language Models No field-specific location recorded Version: PMC13041943.1 | missing or unspecified No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| description No value recorded Context-only references | LAMBDA: A Prophage Detection Benchmark for Genomic Language Models No field-specific location recorded Version: PMC13041943.1 | missing or unspecified No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| name LAMBDA genome-wide prophage test Context-only references | LAMBDA: A Prophage Detection Benchmark for Genomic Language Models No field-specific location recorded Version: PMC13041943.1 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
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Release 2026-09-29-06401fd5b220 · Record review: needs review
Stable ID: reported-dataset-1b4f6ea24c0587