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PhiSpy

PhiSpy as evaluated in the cited study. Paper-specific evaluated pipeline; exact checkpoint not inferred from label

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LAMBDA: A Prophage Detection Benchmark for Genomic Language Models · Table 5., row PhiSpy, column Precision; XML row14 column2

1 evaluation · 6 results

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limited source coverage · Automated source review, 2026-09-17. All specifications and missing details

Evaluations and results

1 evaluation · 6 results. Different protocols are not a single leaderboard.

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Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: PhiSpy	Protocol: Genome-wide prophage detection (Genome-wide prophage detection) Dataset: LAMBDA genome-wide prophage test	0.585 MCC unitless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source PhiSpy: 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 PhiSpy, column MCC; XML row14 column7
Configuration: PhiSpy	Protocol: Genome-wide prophage detection (Genome-wide prophage detection) Dataset: LAMBDA genome-wide prophage test	0.668 Recall fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source PhiSpy: 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 PhiSpy, column Recall; XML row14 column3
Configuration: PhiSpy	Protocol: Genome-wide prophage detection (Genome-wide prophage detection) Dataset: LAMBDA genome-wide prophage test	0.604 Precision fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source PhiSpy: 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 PhiSpy, column Precision; XML row14 column2
Configuration: PhiSpy	Protocol: Genome-wide prophage detection (Genome-wide prophage detection) Dataset: LAMBDA genome-wide prophage test	0.567 F1 fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source PhiSpy: 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 PhiSpy, column F1; XML row14 column6
Configuration: PhiSpy	Protocol: Genome-wide prophage detection (Genome-wide prophage detection) Dataset: LAMBDA genome-wide prophage test	0.018 FPR fraction · lower Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source PhiSpy: 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 PhiSpy, column FPR; XML row14 column5
Configuration: PhiSpy	Protocol: Genome-wide prophage detection (Genome-wide prophage detection) Dataset: LAMBDA genome-wide prophage test	0.982 Specificity fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source PhiSpy: 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 PhiSpy, column Specificity; XML row14 column4

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Paper-specific evaluated pipeline; exact checkpoint not inferred from label

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LAMBDA: A Prophage Detection Benchmark for Genomic Language Models · Table 5., row PhiSpy, column Precision; XML row14 column2

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Stable record: paper-model-dfb2a7c242675592a4

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Claims, original sources and review scope · Release 2026-09-29-06401fd5b220
Property and statement	Original source and location	Review and provenance
Evaluation in this paper Paper-specific evaluated pipeline; exact checkpoint not inferred from label Individual claims	LAMBDA: A Prophage Detection Benchmark for Genomic Language Models Original source ↗ Table 5., row PhiSpy, column Precision; XML row14 column2 Version: PMC13041943.1 Retrieved: 2026-09-17T07:56:21.006973+00:00	source checked automated source review · 2026-09-17 Audit details Primary-source transcription and separate automated review. No human sign-off or experimental reproduction. Field: `attributes.profile.sections.0.body` Source artifact SHA-256: `22c2e218e87dce757907f6086a0e2ad37c13f785b34fff5bea7cfa1a6c276b16` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
Introduction PhiSpy as evaluated in the cited study. Paper-specific evaluated pipeline; exact checkpoint not inferred from label Individual claims	LAMBDA: A Prophage Detection Benchmark for Genomic Language Models Original source ↗ Table 5., row PhiSpy, column Precision; XML row14 column2 Version: PMC13041943.1 Retrieved: 2026-09-17T07:56:21.006973+00:00	source checked automated source review · 2026-09-17 Audit details Primary-source transcription and separate automated review. No human sign-off or experimental reproduction. Field: `attributes.profile.summary` Source artifact SHA-256: `22c2e218e87dce757907f6086a0e2ad37c13f785b34fff5bea7cfa1a6c276b16` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact

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Release 2026-09-29-06401fd5b220 · Record review: needs review

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LAMBDA: A Prophage Detection Benchmark for Genomic Language Models · Original source · PMC13041943.1

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Stable ID: paper-model-dfb2a7c242675592a4

areas: microbes-communities
tasks: Genome-wide prophage detection
entity level: method
configuration type: reported_configuration
version: Paper-specific evaluated pipeline; exact checkpoint not inferred from label
legacy kinds: model
entity classification: review date: 2026-09-17; rationale: This source-scoped entry preserves the method/configuration actually named in an evaluation. It is neither a global family identity nor proof of an immutable checkpoint; the linked evaluation retains adaptation, fitting and scoring details.; source ids: part2-lambda-prophage-2026; source locator: Table 5., row PhiSpy, column Precision; XML row14 column2; ambiguities: Configuration means the source-labelled evaluated identity. It does not establish missing checkpoint hashes, default settings or equivalence to same-named records in other papers.

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model: PhiSpy: Genome-wide prophage detection

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