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
LAMBDA: A Prophage Detection Benchmark for Genomic Language Models · Table 5., row PIDE‡, column Precision; XML row7 column2At a glance
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.
How it works
Evaluation in this paper
Paper-specific evaluated pipeline; exact checkpoint not inferred from label
LAMBDA: A Prophage Detection Benchmark for Genomic Language Models · Table 5., row PIDE‡, column Precision; XML row7 column2Evaluations 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 |
|---|---|---|
| PIDE‡: Genome-wide prophage detection Configuration: PIDE‡Protocol: 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. Author-reported evaluation · Evaluation metadata: needs review | ||
| 0.984 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 PIDE‡, column Specificity; XML row7 column4 Source checking is not independent reproduction. |
| 0.715 MCC Unit: unitless · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedLAMBDA: A Prophage Detection Benchmark for Genomic Language Models · Table 5., row PIDE‡, column MCC; XML row7 column7 Source checking is not independent reproduction. |
| 0.707 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 PIDE‡, column F1; XML row7 column6 Source checking is not independent reproduction. |
| 0.647 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 PIDE‡, column Precision; XML row7 column2 Source checking is not independent reproduction. |
| 0.844 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 PIDE‡, column Recall; XML row7 column3 Source checking is not independent reproduction. |
| 0.016 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 PIDE‡, column FPR; XML row7 column5 Source checking is not independent reproduction. |
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-77d8666610454c6842Evidence table
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
Release 2026-09-17-d277315f7d76 · Record review: needs review
- 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.