Pipeline

NTv2†

NTv2† 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 NTv2†, column Precision; XML row10 column2

1 evaluation · 6 results

Overview

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.

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Pipeline: NTv2†	Protocol: Genome-wide prophage detection (Genome-wide prophage detection) Dataset: LAMBDA genome-wide prophage test	0.995 Specificity fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source NTv2†: 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 NTv2†, column Specificity; XML row10 column4
Pipeline: NTv2†	Protocol: Genome-wide prophage detection (Genome-wide prophage detection) Dataset: LAMBDA genome-wide prophage test	0.644 F1 fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source NTv2†: 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 NTv2†, column F1; XML row10 column6
Pipeline: NTv2†	Protocol: Genome-wide prophage detection (Genome-wide prophage detection) Dataset: LAMBDA genome-wide prophage test	0.627 Recall fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source NTv2†: 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 NTv2†, column Recall; XML row10 column3
Pipeline: NTv2†	Protocol: Genome-wide prophage detection (Genome-wide prophage detection) Dataset: LAMBDA genome-wide prophage test	0.756 Precision fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source NTv2†: 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 NTv2†, column Precision; XML row10 column2
Pipeline: NTv2†	Protocol: Genome-wide prophage detection (Genome-wide prophage detection) Dataset: LAMBDA genome-wide prophage test	0.005 FPR fraction · lower Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source NTv2†: 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 NTv2†, column FPR; XML row10 column5
Pipeline: NTv2†	Protocol: Genome-wide prophage detection (Genome-wide prophage detection) Dataset: LAMBDA genome-wide prophage test	0.658 MCC unitless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source NTv2†: 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 NTv2†, column MCC; XML row10 column7

Source checking is not independent reproduction. Release 2026-09-29-06401fd5b220.

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How it works, versions and access

Underlying model: Nucleotide Transformer. Results on this page belong to this pipeline and its evaluated settings.

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 NTv2†, column Precision; XML row10 column2

Strengths, limitations and unresolved questions

Strengths and limitations

Strengths and considerations

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Profile review details

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Stable record: paper-model-984c6b7cbb3e92f1d0

Specifications

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.

Inputs, outputs and configuration
Property	Description and evidence
Components	Not extracted or verified for this record.
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Adaptation	Not extracted or verified for this record.
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Evidence

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Evidence table

Inspect claims, sources and review details

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One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.

4 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-09-29-06401fd5b220
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 Original source ↗ Table 5., row NTv2†, column Precision; XML row10 column2 Version: PMC13041943.1 Retrieved: 2026-09-17T07:56:21.006973+00:00	source checked automated source review · 2026-09-17 Audit details Primary-source transcription and separate automated review. No human sign-off or experimental reproduction. Field: `attributes.profile.sections.0.body` Source artifact SHA-256: `22c2e218e87dce757907f6086a0e2ad37c13f785b34fff5bea7cfa1a6c276b16` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
Introduction NTv2† 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 Original source ↗ Table 5., row NTv2†, column Precision; XML row10 column2 Version: PMC13041943.1 Retrieved: 2026-09-17T07:56:21.006973+00:00	source checked automated source review · 2026-09-17 Audit details Primary-source transcription and separate automated review. No human sign-off or experimental reproduction. Field: `attributes.profile.summary` Source artifact SHA-256: `22c2e218e87dce757907f6086a0e2ad37c13f785b34fff5bea7cfa1a6c276b16` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
Relationship: uses model discovery-model-nucleotide-transformer Individual claims	instadeepai/nucleotide-transformer: docs/nucleotide_transformer.md Original source ↗ LAMBDA Table 1 Nucleotide Transformer v2 500M and Table 5 NTv2 dagger \| Existing reviewed locator: Table 5., row NTv2†, column Precision; XML row10 column2 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 2dc37b86e16a6970fbc731751f7719d9f676f7f9 Retrieved: 2026-09-16T19:46:19.364532+00:00	source checked automated source review · 2026-09-23 Audit details Source review establishes this relationship only. Exact evaluated configurations and original numerical review status remain unchanged. Composite genome scanner uses NT-v2 500M; do not link catalog 50M variant. Field: `links:uses_model:discovery-model-nucleotide-transformer` Claim: model-evaluation-identity-5ec38bd15b70ef29b212 Source artifact SHA-256: `ab16d582de98652526b5cebb120eec969328f9db29dc741826bcd81c397e0672` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Relationship: uses model discovery-model-nucleotide-transformer Individual claims	LAMBDA: A Prophage Detection Benchmark for Genomic Language Models Original source ↗ LAMBDA Table 1 Nucleotide Transformer v2 500M and Table 5 NTv2 dagger \| Existing reviewed locator: Table 5., row NTv2†, column Precision; XML row10 column2 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: PMC13041943.1 Retrieved: 2026-09-17T07:56:21.006973+00:00	source checked automated source review · 2026-09-23 Audit details Source review establishes this relationship only. Exact evaluated configurations and original numerical review status remain unchanged. Composite genome scanner uses NT-v2 500M; do not link catalog 50M variant. Field: `links:uses_model:discovery-model-nucleotide-transformer` Claim: model-evaluation-identity-5ec38bd15b70ef29b212 Source artifact SHA-256: `22c2e218e87dce757907f6086a0e2ad37c13f785b34fff5bea7cfa1a6c276b16` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact

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Sources and history

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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

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Technical metadata and extraction receipts

Stable ID: paper-model-984c6b7cbb3e92f1d0

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 NTv2†, column Precision; XML row10 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.

Related records

uses model: Nucleotide Transformer
subject: NTv2†: uses model Nucleotide Transformer
model: NTv2†: Genome-wide prophage detection

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