Strengths and considerations
No source-reviewed explanatory claims are recorded here yet.
Pipeline
megaDNA†
megaDNA† as evaluated in the cited study. Paper genome-scanning gLM pipeline, including filtered region postprocessing; exact encoder checkpoint not inferred from the label
Sources
LAMBDA: A Prophage Detection Benchmark for Genomic Language Models · Table 5., row megaDNA†, column Precision; XML row12 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 |
|---|---|---|---|
| Pipeline: megaDNA† | Protocol: Genome-wide prophage detection (Genome-wide prophage detection) Dataset: LAMBDA genome-wide prophage test | 0.595 F1 fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourcemegaDNA†: 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 megaDNA†, column F1; XML row12 column6 |
| Pipeline: megaDNA† | Protocol: Genome-wide prophage detection (Genome-wide prophage detection) Dataset: LAMBDA genome-wide prophage test | 0.671 Recall fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourcemegaDNA†: 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 megaDNA†, column Recall; XML row12 column3 |
| Pipeline: megaDNA† | Protocol: Genome-wide prophage detection (Genome-wide prophage detection) Dataset: LAMBDA genome-wide prophage test | 0.012 FPR fraction · lower Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourcemegaDNA†: 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 megaDNA†, column FPR; XML row12 column5 |
| Pipeline: megaDNA† | Protocol: Genome-wide prophage detection (Genome-wide prophage detection) Dataset: LAMBDA genome-wide prophage test | 0.988 Specificity fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourcemegaDNA†: 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 megaDNA†, column Specificity; XML row12 column4 |
| Pipeline: megaDNA† | Protocol: Genome-wide prophage detection (Genome-wide prophage detection) Dataset: LAMBDA genome-wide prophage test | 0.609 MCC unitless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourcemegaDNA†: 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 megaDNA†, column MCC; XML row12 column7 |
| Pipeline: megaDNA† | Protocol: Genome-wide prophage detection (Genome-wide prophage detection) Dataset: LAMBDA genome-wide prophage test | 0.627 Precision fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourcemegaDNA†: 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 megaDNA†, column Precision; XML row12 column2 |
Source checking is not independent reproduction. Release 2026-09-29-06401fd5b220.
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How it works, versions and access
How it works
Evaluation in this paper
Paper genome-scanning gLM pipeline, including filtered region postprocessing; exact encoder checkpoint not inferred from the label
Sources
LAMBDA: A Prophage Detection Benchmark for Genomic Language Models · Table 5., row megaDNA†, column Precision; XML row12 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-235cc7b07d37f90c0cSpecifications
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 |
|---|---|
| Components | Not extracted or verified for this record. |
| Inputs | Not extracted or verified for this record. |
| Outputs | Not extracted or verified for this record. |
| Adaptation | Not extracted or verified for this record. |
| Implementation | Not extracted or verified for this record. |
Evidence
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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 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 megaDNA†, column Precision; XML row12 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 megaDNA† 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 megaDNA†, column Precision; XML row12 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-235cc7b07d37f90c0c
- 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 megaDNA†, column Precision; XML row12 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.