Source

LAMBDA: A Prophage Detection Benchmark for Genomic Language Models

PMC13041943.1

DOI: 10.64898/2026.03.26.714501 Original source

What this source contributed

Records in this release that cite this source. A record can cite several sources.

7 configurations
8 pipelines
1 task
1 protocol
17 evaluations
102 results
8 evidence claims

Results

Values as the source printed them. Compare results only under compatible protocols, datasets and metrics.

Model or configuration	Metric	Value	Dataset	Evaluation
Caduceus†	F1	0.567 fraction	LAMBDA genome-wide prophage test	Caduceus†: Genome-wide prophage detection
Caduceus†	False positive rate	0.010 fraction	LAMBDA genome-wide prophage test	Caduceus†: Genome-wide prophage detection
Caduceus†	MCC	0.583 unitless	LAMBDA genome-wide prophage test	Caduceus†: Genome-wide prophage detection
Caduceus†	Precision	0.616 fraction	LAMBDA genome-wide prophage test	Caduceus†: Genome-wide prophage detection
Caduceus†	Recall	0.625 fraction	LAMBDA genome-wide prophage test	Caduceus†: Genome-wide prophage detection
Caduceus†	Specificity	0.990 fraction	LAMBDA genome-wide prophage test	Caduceus†: Genome-wide prophage detection
DNABERT-2†	F1	0.413 fraction	LAMBDA genome-wide prophage test	DNABERT-2†: Genome-wide prophage detection
DNABERT-2†	False positive rate	0.009 fraction	LAMBDA genome-wide prophage test	DNABERT-2†: Genome-wide prophage detection
DNABERT-2†	MCC	0.425 unitless	LAMBDA genome-wide prophage test	DNABERT-2†: Genome-wide prophage detection
DNABERT-2†	Precision	0.492 fraction	LAMBDA genome-wide prophage test	DNABERT-2†: Genome-wide prophage detection
DNABERT-2†	Recall	0.436 fraction	LAMBDA genome-wide prophage test	DNABERT-2†: Genome-wide prophage detection
DNABERT-2†	Specificity	0.991 fraction	LAMBDA genome-wide prophage test	DNABERT-2†: Genome-wide prophage detection
EVO2	F1	0.665 fraction	LAMBDA genome-wide prophage test	EVO2: Genome-wide prophage detection
EVO2	False positive rate	0.012 fraction	LAMBDA genome-wide prophage test	EVO2: Genome-wide prophage detection
EVO2	MCC	0.680 unitless	LAMBDA genome-wide prophage test	EVO2: Genome-wide prophage detection
EVO2	Precision	0.694 fraction	LAMBDA genome-wide prophage test	EVO2: Genome-wide prophage detection
EVO2	Recall	0.742 fraction	LAMBDA genome-wide prophage test	EVO2: Genome-wide prophage detection
EVO2	Specificity	0.988 fraction	LAMBDA genome-wide prophage test	EVO2: Genome-wide prophage detection
GENERanno†	F1	0.631 fraction	LAMBDA genome-wide prophage test	GENERanno†: Genome-wide prophage detection
GENERanno†	False positive rate	0.012 fraction	LAMBDA genome-wide prophage test	GENERanno†: Genome-wide prophage detection
GENERanno†	MCC	0.648 unitless	LAMBDA genome-wide prophage test	GENERanno†: Genome-wide prophage detection
GENERanno†	Precision	0.651 fraction	LAMBDA genome-wide prophage test	GENERanno†: Genome-wide prophage detection
GENERanno†	Recall	0.723 fraction	LAMBDA genome-wide prophage test	GENERanno†: Genome-wide prophage detection
GENERanno†	Specificity	0.988 fraction	LAMBDA genome-wide prophage test	GENERanno†: Genome-wide prophage detection
geNomad	F1	0.786 fraction	LAMBDA genome-wide prophage test	geNomad: Genome-wide prophage detection
geNomad	False positive rate	0.009 fraction	LAMBDA genome-wide prophage test	geNomad: Genome-wide prophage detection
geNomad	MCC	0.794 unitless	LAMBDA genome-wide prophage test	geNomad: Genome-wide prophage detection
geNomad	Precision	0.761 fraction	LAMBDA genome-wide prophage test	geNomad: Genome-wide prophage detection
geNomad	Recall	0.873 fraction	LAMBDA genome-wide prophage test	geNomad: Genome-wide prophage detection
geNomad	Specificity	0.991 fraction	LAMBDA genome-wide prophage test	geNomad: Genome-wide prophage detection
megaDNA†	F1	0.595 fraction	LAMBDA genome-wide prophage test	megaDNA†: Genome-wide prophage detection
megaDNA†	False positive rate	0.012 fraction	LAMBDA genome-wide prophage test	megaDNA†: Genome-wide prophage detection
megaDNA†	MCC	0.609 unitless	LAMBDA genome-wide prophage test	megaDNA†: Genome-wide prophage detection
megaDNA†	Precision	0.627 fraction	LAMBDA genome-wide prophage test	megaDNA†: Genome-wide prophage detection
megaDNA†	Recall	0.671 fraction	LAMBDA genome-wide prophage test	megaDNA†: Genome-wide prophage detection
megaDNA†	Specificity	0.988 fraction	LAMBDA genome-wide prophage test	megaDNA†: Genome-wide prophage detection
NTv2†	F1	0.644 fraction	LAMBDA genome-wide prophage test	NTv2†: Genome-wide prophage detection
NTv2†	False positive rate	0.005 fraction	LAMBDA genome-wide prophage test	NTv2†: Genome-wide prophage detection
NTv2†	MCC	0.658 unitless	LAMBDA genome-wide prophage test	NTv2†: Genome-wide prophage detection
NTv2†	Precision	0.756 fraction	LAMBDA genome-wide prophage test	NTv2†: Genome-wide prophage detection
NTv2†	Recall	0.627 fraction	LAMBDA genome-wide prophage test	NTv2†: Genome-wide prophage detection
NTv2†	Specificity	0.995 fraction	LAMBDA genome-wide prophage test	NTv2†: Genome-wide prophage detection
PhageBoost	F1	0.494 fraction	LAMBDA genome-wide prophage test	PhageBoost: Genome-wide prophage detection
PhageBoost	False positive rate	0.034 fraction	LAMBDA genome-wide prophage test	PhageBoost: Genome-wide prophage detection
PhageBoost	MCC	0.513 unitless	LAMBDA genome-wide prophage test	PhageBoost: Genome-wide prophage detection
PhageBoost	Precision	0.468 fraction	LAMBDA genome-wide prophage test	PhageBoost: Genome-wide prophage detection
PhageBoost	Recall	0.680 fraction	LAMBDA genome-wide prophage test	PhageBoost: Genome-wide prophage detection
PhageBoost	Specificity	0.966 fraction	LAMBDA genome-wide prophage test	PhageBoost: Genome-wide prophage detection
PHASTER	F1	0.780 fraction	LAMBDA genome-wide prophage test	PHASTER: Genome-wide prophage detection
PHASTER	False positive rate	0.011 fraction	LAMBDA genome-wide prophage test	PHASTER: Genome-wide prophage detection

Claims

Statements this source supports, each with where in the source it was checked.

DNABERT-2†: uses model DNABERT-2: Uses model DNABERT-2 (LAMBDA Table 1 DNABERT-2 and Table 5 DNABERT-2 dagger; genome scanning and filtering methods | Existing reviewed locator: Table 5., row DNABERT-2†, column Precision; XML row18 column2)
EVO2 · MCC · LAMBDA genome-wide prophage test: attributes.metric_direction: Metric direction higher (Table 5., row EVO2†, column MCC; XML row8 column7)
geNomad · MCC · LAMBDA genome-wide prophage test: attributes.metric_direction: Metric direction higher (Table 5., row geNomad, column MCC; XML row3 column7)
Genome-wide prophage detection (Genome-wide prophage detection): links:evaluates_task:reported-task-dd001540e0f4ec: Evaluates task Genome-wide prophage detection (Table 5.: Precision, Genome-wide prophage detection)
NTv2†: uses model Nucleotide Transformer: Uses model Nucleotide Transformer (LAMBDA Table 1 Nucleotide Transformer v2 500M and Table 5 NTv2 dagger | Existing reviewed locator: Table 5., row NTv2†, column Precision; XML row10 column2)
ProkBERT-mini-c†: uses model ProkBERT: Uses model ProkBERT (Table 5., row ProkBERT-mini-c†, column Precision; XML row16 column2; ProkBERT official README variant list and primary paper Table 1)
ProkBERT-mini-long†: uses model ProkBERT: Uses model ProkBERT (Table 5., row ProkBERT-mini-long†, column Precision; XML row13 column2; ProkBERT official README variant list and primary paper Table 1)
ProkBERT-mini†: uses model ProkBERT: Uses model ProkBERT (Table 5., row ProkBERT-mini†, column Precision; XML row9 column2; ProkBERT official README variant list and primary paper Table 1)

Models, benchmarks and other records

Configurations (7)

Pipelines (8)

Tasks (1)

Genome-wide prophage detection

Protocols (1)

Genome-wide prophage detection (Genome-wide prophage detection)

Evaluations (17)

Evidence

Source checking verifies the cited claim or transcription. It does not establish independent reproduction.

Evidence table

Inspect claims, sources and review details

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.

16 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-11-02-a7f03c9e55a5
Property and statement	Original source and location	Review and provenance
Artifact SHA-256 22c2e218e87dce757907f6086a0e2ad37c13f785b34fff5bea7cfa1a6c276b16 Source metadata	LAMBDA: A Prophage Detection Benchmark for Genomic Language Models Original source ↗ No field-specific location recorded Version: PMC13041943.1 Retrieved: 2026-09-17T07:56:21.006973+00:00	catalogued No individual claim review recorded Audit details Field: `attributes.artifact_sha256` Source artifact SHA-256: `22c2e218e87dce757907f6086a0e2ad37c13f785b34fff5bea7cfa1a6c276b16` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
Artifact url https://www.ebi.ac.uk/europepmc/webservices/rest/PMC13041943/fullTextXML Source metadata	LAMBDA: A Prophage Detection Benchmark for Genomic Language Models Original source ↗ No field-specific location recorded Version: PMC13041943.1 Retrieved: 2026-09-17T07:56:21.006973+00:00	catalogued No individual claim review recorded Audit details Field: `attributes.artifact_url` Source artifact SHA-256: `22c2e218e87dce757907f6086a0e2ad37c13f785b34fff5bea7cfa1a6c276b16` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
Doi 10.64898/2026.03.26.714501 Source metadata	LAMBDA: A Prophage Detection Benchmark for Genomic Language Models Original source ↗ No field-specific location recorded Version: PMC13041943.1 Retrieved: 2026-09-17T07:56:21.006973+00:00	catalogued No individual claim review recorded Audit details Field: `attributes.doi` Source artifact SHA-256: `22c2e218e87dce757907f6086a0e2ad37c13f785b34fff5bea7cfa1a6c276b16` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
Hash scope Exact retrieved primary paper artifact bytes. Source metadata	LAMBDA: A Prophage Detection Benchmark for Genomic Language Models Original source ↗ No field-specific location recorded Version: PMC13041943.1 Retrieved: 2026-09-17T07:56:21.006973+00:00	catalogued No individual claim review recorded Audit details Field: `attributes.hash_scope` Source artifact SHA-256: `22c2e218e87dce757907f6086a0e2ad37c13f785b34fff5bea7cfa1a6c276b16` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
Retrieved at 2026-09-17T07:56:21.006973+00:00 Source metadata	LAMBDA: A Prophage Detection Benchmark for Genomic Language Models Original source ↗ No field-specific location recorded Version: PMC13041943.1 Retrieved: 2026-09-17T07:56:21.006973+00:00	catalogued No individual claim review recorded Audit details Field: `attributes.retrieved_at` Source artifact SHA-256: `22c2e218e87dce757907f6086a0e2ad37c13f785b34fff5bea7cfa1a6c276b16` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
Review method 1 values automated-source-review Source metadata	LAMBDA: A Prophage Detection Benchmark for Genomic Language Models Original source ↗ No field-specific location recorded Version: PMC13041943.1 Retrieved: 2026-09-17T07:56:21.006973+00:00	catalogued No individual claim review recorded Audit details Field: `attributes.review.method` Source artifact SHA-256: `22c2e218e87dce757907f6086a0e2ad37c13f785b34fff5bea7cfa1a6c276b16` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
Review: scope Source identification and table transcription; no independent experimental reproduction. Source metadata	LAMBDA: A Prophage Detection Benchmark for Genomic Language Models Original source ↗ No field-specific location recorded Version: PMC13041943.1 Retrieved: 2026-09-17T07:56:21.006973+00:00	catalogued No individual claim review recorded Audit details Field: `attributes.review.scope` Source artifact SHA-256: `22c2e218e87dce757907f6086a0e2ad37c13f785b34fff5bea7cfa1a6c276b16` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
Url https://www.ebi.ac.uk/europepmc/webservices/rest/PMC13041943/fullTextXML Source metadata	LAMBDA: A Prophage Detection Benchmark for Genomic Language Models Original source ↗ No field-specific location recorded Version: PMC13041943.1 Retrieved: 2026-09-17T07:56:21.006973+00:00	catalogued No individual claim review recorded Audit details Field: `attributes.url` Source artifact SHA-256: `22c2e218e87dce757907f6086a0e2ad37c13f785b34fff5bea7cfa1a6c276b16` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
Version PMC13041943.1 Source metadata	LAMBDA: A Prophage Detection Benchmark for Genomic Language Models Original source ↗ No field-specific location recorded Version: PMC13041943.1 Retrieved: 2026-09-17T07:56:21.006973+00:00	catalogued No individual claim review recorded Audit details Field: `attributes.version` Source artifact SHA-256: `22c2e218e87dce757907f6086a0e2ad37c13f785b34fff5bea7cfa1a6c276b16` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
Description Primary reference; inspect retrieval status and review scope. Source metadata	LAMBDA: A Prophage Detection Benchmark for Genomic Language Models Original source ↗ No field-specific location recorded Version: PMC13041943.1 Retrieved: 2026-09-17T07:56:21.006973+00:00	catalogued No individual claim review recorded Audit details Field: `description` Source artifact SHA-256: `22c2e218e87dce757907f6086a0e2ad37c13f785b34fff5bea7cfa1a6c276b16` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact

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Release 2026-11-02-a7f03c9e55a5 · Record review: source checked

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Technical metadata and extraction receipts

Stable ID: part2-lambda-prophage-2026

url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC13041943/fullTextXML
doi: 10.64898/2026.03.26.714501
version: PMC13041943.1
retrieved at: 2026-09-17T07:56:21.006973+00:00
artifact sha256: 22c2e218e87dce757907f6086a0e2ad37c13f785b34fff5bea7cfa1a6c276b16
artifact url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC13041943/fullTextXML
hash scope: Exact retrieved primary paper artifact bytes.
review: scope: Source identification and table transcription; no independent experimental reproduction.; method: automated-source-review

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