0.794 MCC
geNomad · MCC · LAMBDA genome-wide prophage test
- Tested configuration
- geNomad
- Protocol
- Genome-wide prophage detection (Genome-wide prophage detection)
- Dataset
- LAMBDA genome-wide prophage test
- Procedure
- 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.
- Evaluation
- geNomad: Genome-wide prophage detection
- Coverage
- scored: unreported; eligible: unreported
- Uncertainty
- Not reported
- Evidence
- Independent external evaluation · source checkedLAMBDA: A Prophage Detection Benchmark for Genomic Language Models; LAMBDA: A Prophage Detection Benchmark for Genomic Language Models · Table 5, geNomad row, MCC column
A source-checked result verifies the numerical transcription, not every model or protocol detail. Evaluation metadata: needs review. Source checked does not mean independently reproduced.
Reproduction
- Split
- 80 bacterial genomes,47 species,four phyla;386 annotated prophage locations.
- Adaptation
- Paper-specific evaluated pipeline; exact checkpoint not inferred from label
- Scoring implementation
- Not reported
No execution recipe has been verified for this exact configuration and evaluation. A benchmark's general instructions may use different inputs, splits or model settings.
Reproducing this published result requires matching its model configuration, data, split and scorer. Source checking or a successful smoke test does not establish score reproduction.
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.
2 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| attributes.metric_direction higher Individual claims | LAMBDA: A Prophage Detection Benchmark for Genomic Language Models Table 5., row geNomad, column MCC; XML row3 column7 Version: PMC13041943.1 | source checked automated source review · 2026-09-17 independent paper Audit detailsField: Claim: paper-claim-37b8fa6a5341083053 Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| attributes.printed_value 0.794 Individual claims | LAMBDA: A Prophage Detection Benchmark for Genomic Language Models Table 5, geNomad row, MCC column Version: PMC13041943.1 | source checked primary xml exact label cell check · 2026-09-16T10:33:36.240Z independent paper Audit detailsExact row/header labels and numeric cell matched. Check verifies transcription, not experimental correctness. Field: Claim: claim-lit-038 Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record Extraction artifact SHA-256: |
Sources and history
View linked audit checks and correction history
Release 2026-09-29-06401fd5b220 · Record review: source checked
2 source records and release history
- LAMBDA: A Prophage Detection Benchmark for Genomic Language Models · Original source · PMC13041943.1
- LAMBDA: A Prophage Detection Benchmark for Genomic Language Models · Original source · PMC13041943.1
Technical metadata and extraction receipts
Stable ID: lit-038
- areas
- microbes-communities
- tasks
- Genome-wide prophage detection
- printed value
- 0.794
- numeric value
- 0.794
- metric
- MCC
- metric direction
- higher
- unit
- unitless
- uncertainty
- Not reported
- source locator
- Table 5, geNomad row, MCC column
- review
- method: primary_xml_exact_label_cell_check; reviewer: rewire deterministic table checker v1; reviewed at: 2026-09-16T10:33:36.240Z; notes: Exact row/header labels and numeric cell matched. Check verifies transcription, not experimental correctness.; evidence: Table 5, geNomad row, MCC column; cell: 0.794; artifact sha256: 22c2e218e87dce757907f6086a0e2ad37c13f785b34fff5bea7cfa1a6c276b16; retrieval url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC13041943/fullTextXML
- legacy id
- lit-038
- legacy row
- id: lit-038; paper id: lambda-prophage-2026; domain id: microbes-communities; task: Genome-wide prophage detection; model: geNomad; model version: Not reported; dataset: LAMBDA genome-wide prophage test; dataset version: Not reported; split: Not reported; metric: MCC; value: 0.794; unit: unitless; uncertainty: Not reported; protocol: Traditional specialist comparator; genome-wide evaluation.; source locator: Table 5, geNomad row, MCC column; source url: https://pmc.ncbi.nlm.nih.gov/articles/PMC13041943/; evaluation origin: independent_paper; reviewed utc: 2026-09-15T23:25:00Z
- missing metadata
- model version: not_reported_in_legacy_extract; dataset version: not_reported_in_legacy_extract; split: not_reported_in_legacy_extract; uncertainty: not_reported_in_legacy_extract