Strengths and considerations
No source-reviewed explanatory claims are recorded here yet.
Pipeline
Caduceus†
Caduceus† as evaluated in the cited study. Paper genome-scanning gLM pipeline, including filtered region postprocessing; exact encoder checkpoint not inferred from the label
LAMBDA: A Prophage Detection Benchmark for Genomic Language Models · Table 5., row Caduceus†, column Precision; XML row15 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 genome-scanning gLM pipeline, including filtered region postprocessing; exact encoder checkpoint not inferred from the label
LAMBDA: A Prophage Detection Benchmark for Genomic Language Models · Table 5., row Caduceus†, column Precision; XML row15 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 |
|---|---|---|
| Caduceus†: Genome-wide prophage detection Pipeline: Caduceus†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 | ||
| 0.616 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 Caduceus†, column Precision; XML row15 column2 Source checking is not independent reproduction. |
| 0.010 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 Caduceus†, column FPR; XML row15 column5 Source checking is not independent reproduction. |
| 0.625 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 Caduceus†, column Recall; XML row15 column3 Source checking is not independent reproduction. |
| 0.567 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 Caduceus†, column F1; XML row15 column6 Source checking is not independent reproduction. |
| 0.990 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 Caduceus†, column Specificity; XML row15 column4 Source checking is not independent reproduction. |
| 0.583 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 Caduceus†, column MCC; XML row15 column7 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-53f00fb44417cec450Evidence 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 genome-scanning gLM pipeline, including filtered region postprocessing; exact encoder checkpoint not inferred from the label Individual claims | LAMBDA: A Prophage Detection Benchmark for Genomic Language Models Table 5., row Caduceus†, column Precision; XML row15 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 Caduceus† as evaluated in the cited study. Paper genome-scanning gLM pipeline, including filtered region postprocessing; exact encoder checkpoint not inferred from the label Individual claims | LAMBDA: A Prophage Detection Benchmark for Genomic Language Models Table 5., row Caduceus†, column Precision; XML row15 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-53f00fb44417cec450
- areas
- microbes-communities
- tasks
- Genome-wide prophage detection
- entity level
- method
- configuration type
- reported_configuration
- version
- Paper genome-scanning gLM pipeline, including filtered region postprocessing; exact encoder checkpoint not inferred from the label
- legacy kinds
- model
- entity classification
- review date: 2026-09-17; rationale: Genome scanning with overlapping windows is followed by per-genome score normalization, smoothing, clustering/merging and size/score filtering to identify prophage regions. The reported row evaluates that complete workflow, not the unprocessed encoder. Preserve the exact source-scoped composition and its results; no additional checkpoint or family equivalence is inferred.; source ids: part2-lambda-prophage-2026; source locator: Table 5., row Caduceus†, column Precision; XML row15 column2 | Table 5 dagger-labelled genome-scanning rows; genome-wide detection Methods; Figure 2 caption; raw versus filtered region evaluation; ambiguities: This is the paper-specific pipeline identity. Missing component versions or checkpoint hashes remain unknown; a shared upstream name does not establish equivalent pipelines.