Strengths and considerations
No source-reviewed explanatory claims are recorded here yet.
Configuration
PIDE‡
PIDE‡ as evaluated in the cited study. Paper-specific evaluated pipeline; exact checkpoint not inferred from label
Sources
LAMBDA: A Prophage Detection Benchmark for Genomic Language Models · Table 5., row PIDE‡, column Precision; XML row7 column2Overview
Key specifications have not been extracted for this record. See the linked evaluation and sources for the reported setup.
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.
Filter evaluations
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: PIDE‡ | Protocol: Genome-wide prophage detection (Genome-wide prophage detection) Dataset: LAMBDA genome-wide prophage test | 0.984 Specificity fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourcePIDE‡: 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 PIDE‡, column Specificity; XML row7 column4 |
| Configuration: PIDE‡ | Protocol: Genome-wide prophage detection (Genome-wide prophage detection) Dataset: LAMBDA genome-wide prophage test | 0.715 MCC unitless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourcePIDE‡: 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 PIDE‡, column MCC; XML row7 column7 |
| Configuration: PIDE‡ | Protocol: Genome-wide prophage detection (Genome-wide prophage detection) Dataset: LAMBDA genome-wide prophage test | 0.707 F1 fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourcePIDE‡: 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 PIDE‡, column F1; XML row7 column6 |
| Configuration: PIDE‡ | Protocol: Genome-wide prophage detection (Genome-wide prophage detection) Dataset: LAMBDA genome-wide prophage test | 0.647 Precision fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourcePIDE‡: 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 PIDE‡, column Precision; XML row7 column2 |
| Configuration: PIDE‡ | Protocol: Genome-wide prophage detection (Genome-wide prophage detection) Dataset: LAMBDA genome-wide prophage test | 0.844 Recall fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourcePIDE‡: 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 PIDE‡, column Recall; XML row7 column3 |
| Configuration: PIDE‡ | Protocol: Genome-wide prophage detection (Genome-wide prophage detection) Dataset: LAMBDA genome-wide prophage test | 0.016 FPR fraction · lower Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourcePIDE‡: 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 PIDE‡, column FPR; XML row7 column5 |
Source checking is not independent reproduction. Release 2026-09-29-06401fd5b220.
Use this model
How it works, versions and access
How it works
Evaluation in this paper
Paper-specific evaluated pipeline; exact checkpoint not inferred from label
Sources
LAMBDA: A Prophage Detection Benchmark for Genomic Language Models · Table 5., row PIDE‡, column Precision; XML row7 column2Strengths, limitations and unresolved questions
Strengths and limitations
Limitations and conditions
No source-reviewed explanatory claims are recorded here yet.
Profile review details
Primary-source transcription and separate automated review. No human sign-off or experimental reproduction.
Stable record: paper-model-77d8666610454c6842Specifications
Inputs, training, access and other details
Explanatory profile: limited source coverage · Automated source review, 2026-09-17. Review applies to the cited claims; unresolved fields are listed below. Numerical results retain their own review status.
| Property | Description and evidence |
|---|---|
| Model type | Not extracted or verified for this record. |
| Inputs | Not extracted or verified for this record. |
| Outputs | Not extracted or verified for this record. |
| Parameters | Not extracted or verified for this record. |
| Known versions | Not extracted or verified for this record. |
| Training data | Not extracted or verified for this record. |
| Context limits | Not extracted or verified for this record. |
| Access | Not extracted or verified for this record. |
| Code licence | Not extracted or verified for this record. |
| Weights licence | Not extracted or verified for this record. |
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 |
|---|---|---|
| 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 Table 5., row PIDE‡, column Precision; XML row7 column2 Version: PMC13041943.1 | source checked automated source review · 2026-09-17 Audit detailsPrimary-source transcription and separate automated review. No human sign-off or experimental reproduction. Field: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| Introduction PIDE‡ 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 Table 5., row PIDE‡, column Precision; XML row7 column2 Version: PMC13041943.1 | source checked automated source review · 2026-09-17 Audit detailsPrimary-source transcription and separate automated review. No human sign-off or experimental reproduction. Field: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
Sources and history
View linked audit checks and correction history
Release 2026-09-29-06401fd5b220 · Record review: needs review
1 source records and release history
- LAMBDA: A Prophage Detection Benchmark for Genomic Language Models · Original source · PMC13041943.1
Technical metadata and extraction receipts
Stable ID: paper-model-77d8666610454c6842
- 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 PIDE‡, column Precision; XML row7 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.