Configuration

EVO2

This configuration is evaluated for phage–bacterium discrimination and genome-wide prophage detection in LAMBDA.

Sources

LAMBDA: A Prophage Detection Benchmark for Genomic Language Models · Materials and Methods/LAMBDA Benchmark Dataset Construction. (paragraph 1); Abstract (paragraph 1)

1 evaluation · 6 metric rows

How it worksEvaluated procedure (conceptual)

Conceptual input–method–output guide. Check the procedure text and linked evaluation for fitted components, additional inputs and exact settings.

Sources

LAMBDA: A Prophage Detection Benchmark for Genomic Language Models · Abstract (paragraph 1); Results/Genome-Wide Prophage Detection./Extracting Prophage Signal from Raw Model Predictions. (paragraph 3)

At a glance

Model type

Autoregressive DNA model; this record is the paper-specific evaluated configuration.

Sources

ArcInstitute/evo2 README.md · README.md model description

Biological inputs

Bacterial/phage DNA sequences and genome windows

Sources

LAMBDA: A Prophage Detection Benchmark for Genomic Language Models · Materials and Methods/LAMBDA Benchmark Dataset Construction./Segment Subsampling. (paragraph 1); Materials and Methods/LAMBDA Benchmark Dataset Construction./Data Sources. (paragraph 1)

Outputs

Phage classification scores or candidate prophage regions

Sources

LAMBDA: A Prophage Detection Benchmark for Genomic Language Models · Results/Genome-Wide Prophage Detection./Scanning for Novel, Unannotated Prophage Regions. (paragraph 2); Materials and Methods/LAMBDA Benchmark Dataset Construction./Prophage Signal Extraction Algorithm. (paragraph 1)

limited source coverage · Automated source review, 2026-09-16. All specifications and missing details

Evaluations and results

Release 2026-09-17-d277315f7d76 · 1 evaluation · 6 metric rows. Different protocols are not a single leaderboard.

Evaluation setupMetricEvidence origin

Results grouped by the exact reported evaluation
Metric and finding	Coverage and uncertainty	Evidence
EVO2: Genome-wide prophage detection Configuration: EVO2Protocol: 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. Independent external evaluation · Evaluation metadata: needs review
0.680 MCC Unit: unitless · Direction: higher	Uncertainty: not reported in legacy extract Scored: Not reported · Eligible: Not reported	source checkedLAMBDA: A Prophage Detection Benchmark for Genomic Language Models; LAMBDA: A Prophage Detection Benchmark for Genomic Language Models · Table 5, EVO2 row, MCC column Source checking is not independent reproduction.
0.012 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 EVO2†, column FPR; XML row8 column5 Source checking is not independent reproduction.
0.694 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 EVO2†, column Precision; XML row8 column2 Source checking is not independent reproduction.
0.665 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 EVO2†, column F1; XML row8 column6 Source checking is not independent reproduction.
0.988 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 EVO2†, column Specificity; XML row8 column4 Source checking is not independent reproduction.
0.742 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 EVO2†, column Recall; XML row8 column3 Source checking is not independent reproduction.

How it works

How the evaluated method works

The benchmark separates embedding probes, fine-tuning, diagnostic tests and genome-wide scans; the associated result identifies which procedure is used.

Sources

Underlying method and version boundaries

Evo 2 uses the StripedHyena 2 architecture at single-nucleotide resolution. The official family documentation describes autoregressive training on 8.8 trillion OpenGenome2 tokens and context lengths up to one million bases; an exact evaluated checkpoint remains a separate identity.

Sources

ArcInstitute/evo2 README.md · README.md; introduction, model description, pretrained-model and usage sections at pinned revision

What was evaluated

The linked evaluation record identifies EVO2: Genome-wide prophage detection. Its dataset, split, adaptation and evidence origin remain attached to the reported results.

Sources

LAMBDA: A Prophage Detection Benchmark for Genomic Language Models · The named evaluation’s methods and comparison table; exact preserved evaluation IDs: evaluation-lit-037

Strengths and limitations

Strengths and considerations

Extends genomic-model evaluation beyond eukaryotic regulatory-element labels.
Sources
LAMBDA: A Prophage Detection Benchmark for Genomic Language Models · Abstract (paragraph 1); Background (paragraph 1)

Limitations and conditions

Candidate regions outside reference annotations are not automatically validated prophages; the paper uses additional gene-content screening.
Sources
LAMBDA: A Prophage Detection Benchmark for Genomic Language Models · Materials and Methods/LAMBDA Benchmark Dataset Construction./Candidate Prophage Screening. (paragraph 1); Results/Genome-Wide Prophage Detection./Scanning for Novel, Unannotated Prophage Regions. (paragraph 2)

Profile review details

Primary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction.

Stable record: reported-model-aa763db2cfdeff

Specifications

Inputs, training, access and other details

Explanatory profile: limited source coverage · Automated source review, 2026-09-16. 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
Model type	Autoregressive DNA model; this record is the paper-specific evaluated configuration. Sources ArcInstitute/evo2 README.md · README.md model description
Architecture / procedure	The benchmark separates embedding probes, fine-tuning, diagnostic tests and genome-wide scans; the associated result identifies which procedure is used. Sources LAMBDA: A Prophage Detection Benchmark for Genomic Language Models · Abstract (paragraph 1); Results/Genome-Wide Prophage Detection./Extracting Prophage Signal from Raw Model Predictions. (paragraph 3)
Biological inputs	Bacterial/phage DNA sequences and genome windows Sources LAMBDA: A Prophage Detection Benchmark for Genomic Language Models · Materials and Methods/LAMBDA Benchmark Dataset Construction./Segment Subsampling. (paragraph 1); Materials and Methods/LAMBDA Benchmark Dataset Construction./Data Sources. (paragraph 1)
Outputs	Phage classification scores or candidate prophage regions Sources LAMBDA: A Prophage Detection Benchmark for Genomic Language Models · Results/Genome-Wide Prophage Detection./Scanning for Novel, Unannotated Prophage Regions. (paragraph 2); Materials and Methods/LAMBDA Benchmark Dataset Construction./Prophage Signal Extraction Algorithm. (paragraph 1)
Parameters	7B parameters in the benchmark model inventory. Sources LAMBDA: A Prophage Detection Benchmark for Genomic Language Models · Table1; EVO2 row
Known versions / configuration	EVO2 7B as identified by Table 1; exact checkpoint hash is not supplied in that inventory. Sources LAMBDA: A Prophage Detection Benchmark for Genomic Language Models · Results/Genome-Wide Prophage Detection./Probing EVO2 Latent Space with Sparse Autoencoders. (paragraph 1); Table T2 (paragraph 1)
Training data / fitting	OpenGenome2 multispecies pretraining, as identified in Table 1; LAMBDA trains separate linear or three-layer neural probes on frozen embeddings. Sources LAMBDA: A Prophage Detection Benchmark for Genomic Language Models · Results/Evaluating the Power of Pretrained Sequence Representations. (paragraph 2); Materials and Methods/LAMBDA Benchmark Dataset Construction./Comparison with Traditional and Protein-based Models. (paragraph 1)
Context limits	The source lists a 1M-base model limit; the actual LAMBDA experiments evaluate 2-kb,4-kb and 8-kb windows. Sources LAMBDA: A Prophage Detection Benchmark for Genomic Language Models · Table1 EVO2 row; Tables2–3 window lengths
Access	Official upstream implementation and usage documentation: https://github.com/ArcInstitute/evo2/blob/53f195997257c56c00e5ef8d33a54f5baad143a6/README.md. This pinned documentation revision is not automatically the evaluated weight revision. Sources ArcInstitute/evo2 README.md · README.md; installation, model download and usage instructions
Code licence	Apache 2.0 (upstream repository code at the cited revision; this does not establish every dependency or historical checkpoint licence). Sources ArcInstitute/evo2 LICENSE · LICENSE; complete licence text
Weights licence	The inspected model-access documentation does not explicitly identify terms for this exact evaluated checkpoint or fitted head; repository code terms are shown separately. · Not reported in inspected sources Sources ArcInstitute/evo2 README.md · README.md; checkpoint/access documentation and licence scope

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.

20 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-09-17-d277315f7d76
Property and statement	Original source and location	Review and provenance
Diagram caption Conceptual input–method–output guide. Check the procedure text and linked evaluation for fitted components, additional inputs and exact settings. Individual claims	LAMBDA: A Prophage Detection Benchmark for Genomic Language Models Original source ↗ Abstract (paragraph 1); Results/Genome-Wide Prophage Detection./Extracting Prophage Signal from Raw Model Predictions. (paragraph 3) Version: PMC13041943.1 Retrieved: 2026-09-16T10:33:36.240Z	source checked automated source review · 2026-09-16 Audit details Primary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: `attributes.profile.diagram.caption` Source artifact SHA-256: `22c2e218e87dce757907f6086a0e2ad37c13f785b34fff5bea7cfa1a6c276b16` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Diagram steps ["Bacterial/phage DNA sequences and genome windows","EVO2","Phage classification scores or candidate prophage regions"] Individual claims	LAMBDA: A Prophage Detection Benchmark for Genomic Language Models Original source ↗ Abstract (paragraph 1); Results/Genome-Wide Prophage Detection./Extracting Prophage Signal from Raw Model Predictions. (paragraph 3) Version: PMC13041943.1 Retrieved: 2026-09-16T10:33:36.240Z	source checked automated source review · 2026-09-16 Audit details Primary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: `attributes.profile.diagram.steps` Source artifact SHA-256: `22c2e218e87dce757907f6086a0e2ad37c13f785b34fff5bea7cfa1a6c276b16` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Diagram title Evaluated procedure (conceptual) Individual claims	LAMBDA: A Prophage Detection Benchmark for Genomic Language Models Original source ↗ Abstract (paragraph 1); Results/Genome-Wide Prophage Detection./Extracting Prophage Signal from Raw Model Predictions. (paragraph 3) Version: PMC13041943.1 Retrieved: 2026-09-16T10:33:36.240Z	source checked automated source review · 2026-09-16 Audit details Primary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: `attributes.profile.diagram.title` Source artifact SHA-256: `22c2e218e87dce757907f6086a0e2ad37c13f785b34fff5bea7cfa1a6c276b16` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Model type Autoregressive DNA model; this record is the paper-specific evaluated configuration. Individual claims	ArcInstitute/evo2 README.md Original source ↗ README.md model description Version: 53f195997257c56c00e5ef8d33a54f5baad143a6 Retrieved: 2026-09-16T20:00:02.431871+00:00	source checked automated source review · 2026-09-16 Audit details Primary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: `attributes.profile.facts.0.value` Source artifact SHA-256: `58787c8ef5cb4fba4c04322a4ceb9f174e2233ec22d4193622fb6bc67d651d89` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Architecture / procedure The benchmark separates embedding probes, fine-tuning, diagnostic tests and genome-wide scans; the associated result identifies which procedure is used. Individual claims	LAMBDA: A Prophage Detection Benchmark for Genomic Language Models Original source ↗ Abstract (paragraph 1); Results/Genome-Wide Prophage Detection./Extracting Prophage Signal from Raw Model Predictions. (paragraph 3) Version: PMC13041943.1 Retrieved: 2026-09-16T10:33:36.240Z	source checked automated source review · 2026-09-16 Audit details Primary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: `attributes.profile.facts.1.value` Source artifact SHA-256: `22c2e218e87dce757907f6086a0e2ad37c13f785b34fff5bea7cfa1a6c276b16` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Weights licence The inspected model-access documentation does not explicitly identify terms for this exact evaluated checkpoint or fitted head; repository code terms are shown separately. Individual claims	ArcInstitute/evo2 README.md Original source ↗ README.md; checkpoint/access documentation and licence scope Version: 53f195997257c56c00e5ef8d33a54f5baad143a6 Retrieved: 2026-09-16T20:00:02.431871+00:00	unreported automated source review · 2026-09-16 Audit details Primary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: `attributes.profile.facts.10.value` Source artifact SHA-256: `58787c8ef5cb4fba4c04322a4ceb9f174e2233ec22d4193622fb6bc67d651d89` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Biological inputs Bacterial/phage DNA sequences and genome windows Individual claims	LAMBDA: A Prophage Detection Benchmark for Genomic Language Models Original source ↗ Materials and Methods/LAMBDA Benchmark Dataset Construction./Segment Subsampling. (paragraph 1); Materials and Methods/LAMBDA Benchmark Dataset Construction./Data Sources. (paragraph 1) Version: PMC13041943.1 Retrieved: 2026-09-16T10:33:36.240Z	source checked automated source review · 2026-09-16 Audit details Primary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: `attributes.profile.facts.2.value` Source artifact SHA-256: `22c2e218e87dce757907f6086a0e2ad37c13f785b34fff5bea7cfa1a6c276b16` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Outputs Phage classification scores or candidate prophage regions Individual claims	LAMBDA: A Prophage Detection Benchmark for Genomic Language Models Original source ↗ Results/Genome-Wide Prophage Detection./Scanning for Novel, Unannotated Prophage Regions. (paragraph 2); Materials and Methods/LAMBDA Benchmark Dataset Construction./Prophage Signal Extraction Algorithm. (paragraph 1) Version: PMC13041943.1 Retrieved: 2026-09-16T10:33:36.240Z	source checked automated source review · 2026-09-16 Audit details Primary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: `attributes.profile.facts.3.value` Source artifact SHA-256: `22c2e218e87dce757907f6086a0e2ad37c13f785b34fff5bea7cfa1a6c276b16` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Parameters 7B parameters in the benchmark model inventory. Individual claims	LAMBDA: A Prophage Detection Benchmark for Genomic Language Models Original source ↗ Table1; EVO2 row Version: PMC13041943.1 Retrieved: 2026-09-16T10:33:36.240Z	source checked automated source review · 2026-09-16 Audit details Primary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: `attributes.profile.facts.4.value` Source artifact SHA-256: `22c2e218e87dce757907f6086a0e2ad37c13f785b34fff5bea7cfa1a6c276b16` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Known versions / configuration EVO2 7B as identified by Table 1; exact checkpoint hash is not supplied in that inventory. Individual claims	LAMBDA: A Prophage Detection Benchmark for Genomic Language Models Original source ↗ Results/Genome-Wide Prophage Detection./Probing EVO2 Latent Space with Sparse Autoencoders. (paragraph 1); Table T2 (paragraph 1) Version: PMC13041943.1 Retrieved: 2026-09-16T10:33:36.240Z	source checked automated source review · 2026-09-16 Audit details Primary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: `attributes.profile.facts.5.value` Source artifact SHA-256: `22c2e218e87dce757907f6086a0e2ad37c13f785b34fff5bea7cfa1a6c276b16` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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Sources and history

Release 2026-09-17-d277315f7d76 · Record review: needs review

3 source records and release history

LAMBDA: A Prophage Detection Benchmark for Genomic Language Models · Original source · PMC13041943.1
ArcInstitute/evo2 README.md · Original source · 53f195997257c56c00e5ef8d33a54f5baad143a6
ArcInstitute/evo2 LICENSE · Original source · 53f195997257c56c00e5ef8d33a54f5baad143a6

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Technical metadata and extraction receipts

Stable ID: reported-model-aa763db2cfdeff

areas: microbes-communities
entity level: method
version: Not reported
reported name: EVO2
historical missing metadata: version: not_reported_in_legacy_extract; checkpoint revision: not_reported_in_legacy_extract; training data: not_reported_in_legacy_extract; licence: not_reported_in_legacy_extract
metadata review scope: historical_missing_metadata preserves the original discovery state. Current descriptive evidence and missingness are recorded in profile.facts; numerical-result review is separate.
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: lambda-prophage-2026; evidence-reported-base-evo2-readme-md; source locator: Abstract (paragraph 1); Results/Genome-Wide Prophage Detection./Extracting Prophage Signal from Raw Model Predictions. (paragraph 3) | README.md model description | Materials and Methods/LAMBDA Benchmark Dataset Construction. (paragraph 1); Abstract (paragraph 1); 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.

Related records

model: EVO2: Genome-wide prophage detection

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