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.
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.
| Tested configuration | F1 | False positive rate | MCC | Precision | Recall | Specificity |
|---|---|---|---|---|---|---|
| ProkBERT-mini-c†Evaluation | 0.551 | 0.013 | 0.572 | 0.603 | 0.632 | 0.987 |
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| 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 by the source 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: ProkBERT-mini-c† | Protocol: Genome-wide prophage detection (Genome-wide prophage detection) Dataset: LAMBDA genome-wide prophage test | 0.013 False positive rate fraction · lower Uncertainty: Not reported by the source 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 |
| Pipeline: ProkBERT-mini-c† | Protocol: Genome-wide prophage detection (Genome-wide prophage detection) Dataset: LAMBDA genome-wide prophage test | 0.551 F1 fraction · higher Uncertainty: Not reported by the source 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 F1; XML row16 column6 |
| Pipeline: ProkBERT-mini-c† | Protocol: Genome-wide prophage detection (Genome-wide prophage detection) Dataset: LAMBDA genome-wide prophage test | 0.572 MCC unitless · higher Uncertainty: Not reported by the source 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 MCC; XML row16 column7 |
| Pipeline: ProkBERT-mini-c† | Protocol: Genome-wide prophage detection (Genome-wide prophage detection) Dataset: LAMBDA genome-wide prophage test | 0.632 Recall fraction · higher Uncertainty: Not reported by the source 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 Recall; XML row16 column3 |
| Pipeline: ProkBERT-mini-c† | Protocol: Genome-wide prophage detection (Genome-wide prophage detection) Dataset: LAMBDA genome-wide prophage test | 0.987 Specificity fraction · higher Uncertainty: Not reported by the source 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 Specificity; XML row16 column4 |
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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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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 |
|---|---|---|
| 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. |
| 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. |
| Comparison: budget Not reported 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. |
| Comparison: dataset version Not reported 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. |
| Comparison: inputs Not reported 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. |
| Comparison: metric implementation Not reported 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. |
| Comparison: population Not reported 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. |
| 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. |
| 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. |
| 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. |
Release 2026-11-02-a7f03c9e55a5 · Record review: needs review
Stable ID: paper-evaluation-7f472b86089986cbd0