Model type
Mobile-genetic-element detector; this record is the paper-specific evaluated configuration.
Configuration
geNomad
This configuration is evaluated for phage–bacterium discrimination and genome-wide prophage detection in LAMBDA.
Sources
LAMBDA: A Prophage Detection Benchmark for Genomic Language Models · Materials and Methods/LAMBDA Benchmark Dataset Construction. (paragraph 1); Abstract (paragraph 1)How it worksEvaluated procedure (conceptual)
Conceptual input–method–output guide. Check the procedure text and linked evaluation for fitted components, additional inputs and exact settings.
Sources
LAMBDA: A Prophage Detection Benchmark for Genomic Language Models · Abstract (paragraph 1); Results/Genome-Wide Prophage Detection./Extracting Prophage Signal from Raw Model Predictions. (paragraph 3)At a glance
Biological inputs
Bacterial/phage DNA sequences and genome windows
Sources
LAMBDA: A Prophage Detection Benchmark for Genomic Language Models · Materials and Methods/LAMBDA Benchmark Dataset Construction./Segment Subsampling. (paragraph 1); Materials and Methods/LAMBDA Benchmark Dataset Construction./Data Sources. (paragraph 1)Outputs
Phage classification scores or candidate prophage regions
Sources
LAMBDA: A Prophage Detection Benchmark for Genomic Language Models · Results/Genome-Wide Prophage Detection./Scanning for Novel, Unannotated Prophage Regions. (paragraph 2); Materials and Methods/LAMBDA Benchmark Dataset Construction./Prophage Signal Extraction Algorithm. (paragraph 1)limited source coverage · Automated source review, 2026-09-16. All specifications and missing details
Evaluations and results
Release 2026-09-17-d277315f7d76 · 1 evaluation · 6 metric rows. Different protocols are not a single leaderboard.
| Metric and finding | Coverage and uncertainty | Evidence |
|---|---|---|
| geNomad: Genome-wide prophage detection Configuration: geNomadProtocol: Genome-wide prophage detection (Genome-wide prophage detection)Dataset: LAMBDA genome-wide prophage test 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. Independent external evaluation · Evaluation metadata: needs review | ||
| 0.794 MCC Unit: unitless · Direction: higher | Uncertainty: not reported in legacy extract Scored: Not reported · Eligible: Not reported | 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 Source checking is not independent reproduction. |
| 0.786 F1 Unit: fraction · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedLAMBDA: A Prophage Detection Benchmark for Genomic Language Models · Table 5., row geNomad, column F1; XML row3 column6 Source checking is not independent reproduction. |
| 0.009 FPR Unit: fraction · Direction: lower | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedLAMBDA: A Prophage Detection Benchmark for Genomic Language Models · Table 5., row geNomad, column FPR; XML row3 column5 Source checking is not independent reproduction. |
| 0.873 Recall Unit: fraction · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedLAMBDA: A Prophage Detection Benchmark for Genomic Language Models · Table 5., row geNomad, column Recall; XML row3 column3 Source checking is not independent reproduction. |
| 0.991 Specificity Unit: fraction · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedLAMBDA: A Prophage Detection Benchmark for Genomic Language Models · Table 5., row geNomad, column Specificity; XML row3 column4 Source checking is not independent reproduction. |
| 0.761 Precision Unit: fraction · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedLAMBDA: A Prophage Detection Benchmark for Genomic Language Models · Table 5., row geNomad, column Precision; XML row3 column2 Source checking is not independent reproduction. |
How it works
How the evaluated method works
The benchmark separates embedding probes, fine-tuning, diagnostic tests and genome-wide scans; the associated result identifies which procedure is used.
Sources
LAMBDA: A Prophage Detection Benchmark for Genomic Language Models · Abstract (paragraph 1); Results/Genome-Wide Prophage Detection./Extracting Prophage Signal from Raw Model Predictions. (paragraph 3)Underlying method and version boundaries
geNomad identifies viral and plasmid sequences, including proviruses, and supplies viral taxonomy and protein-function annotations. These separate outputs have different evaluation definitions.
Sources
apcamargo/genomad README.md · README.md; introduction, model description, pretrained-model and usage sections at pinned revisionWhat was evaluated
The linked evaluation record identifies geNomad: Genome-wide prophage detection. Its dataset, split, adaptation and evidence origin remain attached to the reported results.
Sources
LAMBDA: A Prophage Detection Benchmark for Genomic Language Models · The named evaluation’s methods and comparison table; exact preserved evaluation IDs: evaluation-lit-038Strengths and limitations
Strengths and considerations
- Extends genomic-model evaluation beyond eukaryotic regulatory-element labels.
Sources
LAMBDA: A Prophage Detection Benchmark for Genomic Language Models · Abstract (paragraph 1); Background (paragraph 1)
Limitations and conditions
- Candidate regions outside reference annotations are not automatically validated prophages; the paper uses additional gene-content screening.
Sources
LAMBDA: A Prophage Detection Benchmark for Genomic Language Models · Materials and Methods/LAMBDA Benchmark Dataset Construction./Candidate Prophage Screening. (paragraph 1); Results/Genome-Wide Prophage Detection./Scanning for Novel, Unannotated Prophage Regions. (paragraph 2)
Profile review details
Primary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction.
Stable record: reported-model-d0677d52d2b9fdSpecifications
Inputs, training, access and other details
Explanatory profile: limited source coverage · Automated source review, 2026-09-16. Review applies to the cited claims; unresolved fields are listed below. Numerical results retain their own review status.
| Property | Description and evidence |
|---|---|
| Model type | Mobile-genetic-element detector; this record is the paper-specific evaluated configuration.Sourcesapcamargo/genomad README.md · README.md model description |
| Architecture / procedure | The benchmark separates embedding probes, fine-tuning, diagnostic tests and genome-wide scans; the associated result identifies which procedure is used.SourcesLAMBDA: A Prophage Detection Benchmark for Genomic Language Models · Abstract (paragraph 1); Results/Genome-Wide Prophage Detection./Extracting Prophage Signal from Raw Model Predictions. (paragraph 3) |
| Biological inputs | Bacterial/phage DNA sequences and genome windowsSourcesLAMBDA: A Prophage Detection Benchmark for Genomic Language Models · Materials and Methods/LAMBDA Benchmark Dataset Construction./Segment Subsampling. (paragraph 1); Materials and Methods/LAMBDA Benchmark Dataset Construction./Data Sources. (paragraph 1) |
| Outputs | Phage classification scores or candidate prophage regionsSourcesLAMBDA: A Prophage Detection Benchmark for Genomic Language Models · Results/Genome-Wide Prophage Detection./Scanning for Novel, Unannotated Prophage Regions. (paragraph 2); Materials and Methods/LAMBDA Benchmark Dataset Construction./Prophage Signal Extraction Algorithm. (paragraph 1) |
| Parameters | An aggregate parameter total for this exact evaluated configuration is not established by the inspected sources. · Not reported in inspected sourcesSources (2)LAMBDA: A Prophage Detection Benchmark for Genomic Language Models; apcamargo/genomad README.md · Results/Evaluating the Power of Pretrained Sequence Representations.; Materials and Methods/LAMBDA Benchmark Dataset Construction.; Materials and Methods/LAMBDA Benchmark Dataset Construction./Data Sources.; Materials and Methods/LAMBDA Benchmark Dataset Construction./Bacterial contamination filtering via BLAST.; Materials and Methods/LAMBDA Benchmark Dataset Construction./Segment Subsampling.; Materials and Methods/LAMBDA Benchmark Dataset Construction./Data Splitting and Data Leakage Prevention.; Materials and Methods/LAMBDA Benchmark Dataset Construction./GC-Control Dataset.; Materials and Methods/LAMBDA Benchmark Dataset Construction./Class Prediction Control Datasets.; inspected for aggregate parameter count (component sizes are not added without an exact configuration); README.md at pinned repository revision |
| Known versions / configuration | geNomad is the comparison-table label; that label does not specify an immutable weight revision. · Not reported in inspected sourcesSourcesLAMBDA: A Prophage Detection Benchmark for Genomic Language Models · Model identification in the comparison table and corresponding Methods; immutable checkpoint revision is not supplied by the table label. |
| Training data / fitting | The benchmark runs the existing geNomad detector as a comparator to the fitted genomic-language-model probes. Its exact upstream training/reference-data release is not identified in the comparison methods.SourcesLAMBDA: A Prophage Detection Benchmark for Genomic Language Models · Materials and Methods / LAMBDA Benchmark Dataset Construction / Comparison with Traditional and Protein-based Models |
| Context limits | A maximum input/context length for this exact evaluated configuration is not established by the inspected sources. · Not reported in inspected sourcesSources (2)LAMBDA: A Prophage Detection Benchmark for Genomic Language Models; apcamargo/genomad README.md · Results/Evaluating the Power of Pretrained Sequence Representations.; Materials and Methods/LAMBDA Benchmark Dataset Construction.; Materials and Methods/LAMBDA Benchmark Dataset Construction./Data Sources.; Materials and Methods/LAMBDA Benchmark Dataset Construction./Bacterial contamination filtering via BLAST.; Materials and Methods/LAMBDA Benchmark Dataset Construction./Segment Subsampling.; Materials and Methods/LAMBDA Benchmark Dataset Construction./Data Splitting and Data Leakage Prevention.; Materials and Methods/LAMBDA Benchmark Dataset Construction./GC-Control Dataset.; Materials and Methods/LAMBDA Benchmark Dataset Construction./Class Prediction Control Datasets.; inspected for explicit maximum input length (dataset lengths and family-wide limits are not substituted); README.md at pinned repository revision |
| Access | Official upstream implementation and usage documentation: https://github.com/apcamargo/genomad/blob/8c5fd0d1722d458a3e8ff50278cdc00ed4a514fc/README.md. This pinned documentation revision is not automatically the evaluated weight revision.Sourcesapcamargo/genomad README.md · README.md; installation, model download and usage instructions |
| Code licence | Repository-specific licence text is available; a standard SPDX label has not been established. (upstream repository code at the cited revision; this does not establish every dependency or historical checkpoint licence).Sourcesapcamargo/genomad LICENSE · LICENSE; complete licence text |
| Weights licence | The inspected model-access documentation does not explicitly identify terms for this exact evaluated checkpoint or fitted head; repository code terms are shown separately. · Not reported in inspected sourcesSourcesapcamargo/genomad README.md · README.md; checkpoint/access documentation and licence scope |
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.
22 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Diagram caption Conceptual input–method–output guide. Check the procedure text and linked evaluation for fitted components, additional inputs and exact settings. Individual claims | LAMBDA: A Prophage Detection Benchmark for Genomic Language Models Abstract (paragraph 1); Results/Genome-Wide Prophage Detection./Extracting Prophage Signal from Raw Model Predictions. (paragraph 3) Version: PMC13041943.1 | source checked automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Diagram steps ["Bacterial/phage DNA sequences and genome windows","geNomad","Phage classification scores or candidate prophage regions"] Individual claims | LAMBDA: A Prophage Detection Benchmark for Genomic Language Models Abstract (paragraph 1); Results/Genome-Wide Prophage Detection./Extracting Prophage Signal from Raw Model Predictions. (paragraph 3) Version: PMC13041943.1 | source checked automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Diagram title Evaluated procedure (conceptual) Individual claims | LAMBDA: A Prophage Detection Benchmark for Genomic Language Models Abstract (paragraph 1); Results/Genome-Wide Prophage Detection./Extracting Prophage Signal from Raw Model Predictions. (paragraph 3) Version: PMC13041943.1 | source checked automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Model type Mobile-genetic-element detector; this record is the paper-specific evaluated configuration. Individual claims | apcamargo/genomad README.md README.md model description Version: 8c5fd0d1722d458a3e8ff50278cdc00ed4a514fc | source checked automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Architecture / procedure The benchmark separates embedding probes, fine-tuning, diagnostic tests and genome-wide scans; the associated result identifies which procedure is used. Individual claims | LAMBDA: A Prophage Detection Benchmark for Genomic Language Models Abstract (paragraph 1); Results/Genome-Wide Prophage Detection./Extracting Prophage Signal from Raw Model Predictions. (paragraph 3) Version: PMC13041943.1 | source checked automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Weights licence The inspected model-access documentation does not explicitly identify terms for this exact evaluated checkpoint or fitted head; repository code terms are shown separately. Individual claims | apcamargo/genomad README.md README.md; checkpoint/access documentation and licence scope Version: 8c5fd0d1722d458a3e8ff50278cdc00ed4a514fc | unreported automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Biological inputs Bacterial/phage DNA sequences and genome windows Individual claims | LAMBDA: A Prophage Detection Benchmark for Genomic Language Models Materials and Methods/LAMBDA Benchmark Dataset Construction./Segment Subsampling. (paragraph 1); Materials and Methods/LAMBDA Benchmark Dataset Construction./Data Sources. (paragraph 1) Version: PMC13041943.1 | source checked automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Outputs Phage classification scores or candidate prophage regions Individual claims | LAMBDA: A Prophage Detection Benchmark for Genomic Language Models Results/Genome-Wide Prophage Detection./Scanning for Novel, Unannotated Prophage Regions. (paragraph 2); Materials and Methods/LAMBDA Benchmark Dataset Construction./Prophage Signal Extraction Algorithm. (paragraph 1) Version: PMC13041943.1 | source checked automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Parameters An aggregate parameter total for this exact evaluated configuration is not established by the inspected sources. Individual claims | apcamargo/genomad README.md Results/Evaluating the Power of Pretrained Sequence Representations.; Materials and Methods/LAMBDA Benchmark Dataset Construction.; Materials and Methods/LAMBDA Benchmark Dataset Construction./Data Sources.; Materials and Methods/LAMBDA Benchmark Dataset Construction./Bacterial contamination filtering via BLAST.; Materials and Methods/LAMBDA Benchmark Dataset Construction./Segment Subsampling.; Materials and Methods/LAMBDA Benchmark Dataset Construction./Data Splitting and Data Leakage Prevention.; Materials and Methods/LAMBDA Benchmark Dataset Construction./GC-Control Dataset.; Materials and Methods/LAMBDA Benchmark Dataset Construction./Class Prediction Control Datasets.; inspected for aggregate parameter count (component sizes are not added without an exact configuration); README.md at pinned repository revision Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 8c5fd0d1722d458a3e8ff50278cdc00ed4a514fc | unreported automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Parameters An aggregate parameter total for this exact evaluated configuration is not established by the inspected sources. Individual claims | LAMBDA: A Prophage Detection Benchmark for Genomic Language Models Results/Evaluating the Power of Pretrained Sequence Representations.; Materials and Methods/LAMBDA Benchmark Dataset Construction.; Materials and Methods/LAMBDA Benchmark Dataset Construction./Data Sources.; Materials and Methods/LAMBDA Benchmark Dataset Construction./Bacterial contamination filtering via BLAST.; Materials and Methods/LAMBDA Benchmark Dataset Construction./Segment Subsampling.; Materials and Methods/LAMBDA Benchmark Dataset Construction./Data Splitting and Data Leakage Prevention.; Materials and Methods/LAMBDA Benchmark Dataset Construction./GC-Control Dataset.; Materials and Methods/LAMBDA Benchmark Dataset Construction./Class Prediction Control Datasets.; inspected for aggregate parameter count (component sizes are not added without an exact configuration); README.md at pinned repository revision Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: PMC13041943.1 | unreported automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Sources and history
Release 2026-09-17-d277315f7d76 · Record review: needs review
3 source records and release history
- LAMBDA: A Prophage Detection Benchmark for Genomic Language Models · Original source · PMC13041943.1
- apcamargo/genomad README.md · Original source · 8c5fd0d1722d458a3e8ff50278cdc00ed4a514fc
- apcamargo/genomad LICENSE · Original source · 8c5fd0d1722d458a3e8ff50278cdc00ed4a514fc
Technical metadata and extraction receipts
Stable ID: reported-model-d0677d52d2b9fd
- areas
- microbes-communities
- entity level
- method
- version
- Not reported
- reported name
- geNomad
- historical missing metadata
- version: not_reported_in_legacy_extract; checkpoint revision: not_reported_in_legacy_extract; training data: not_reported_in_legacy_extract; licence: not_reported_in_legacy_extract
- metadata review scope
- historical_missing_metadata preserves the original discovery state. Current descriptive evidence and missingness are recorded in profile.facts; numerical-result review is separate.
- 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: lambda-prophage-2026; evidence-reported-base-genomad-readme-md; source locator: Abstract (paragraph 1); Results/Genome-Wide Prophage Detection./Extracting Prophage Signal from Raw Model Predictions. (paragraph 3) | README.md model description | Materials and Methods/LAMBDA Benchmark Dataset Construction. (paragraph 1); Abstract (paragraph 1); 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.