Conservation prediction compares zero-shot sequence scores across genomic models with different context and prediction objectives.
Three conservation tasks use Sorghum bicolor with Andropogoneae alignments, a Poaceae coding-sequence alignment with Pharus latifolius as outgroup, and potato (Solanum tuberosum) with 95 Solanaceae genomes. Each uses its own alignment-derived conservation labels.
AUROC for conserved/non-conserved site classification in the cross-species conservation evaluations.
Plant DNA sequence.
Conceptual summary of the cited evaluation; exact task configuration and source version remain part of the protocol.
limited source coverage · Automated source review, 2026-09-16. All specifications and missing details
Results are available, but no reviewed comparison panel is linked in this release.
1 evaluation · 1 result. Different protocols are not a single leaderboard.
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: PlantCAD2 | Task: cross-species conservation prediction Dataset: Andropogoneae genome-wide conservation | 0.725 AUROC fraction · unknown Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourcePlantCAD2: cross-species conservation prediction Zero-shot score for conserved versus non-conserved sites from alignments of 35 Andropogoneae genomes Aggregation: Not reported PlantCAD2: A Long-Context DNA Language Model for Cross-Species Functional Annotation in Angiosperms · Table 1, Cross-species evolutionary conservation > Conservation within Andropogoneae (Genome-wide) row, PlantCAD2 AUROC entry |
Source checking is not independent reproduction. Release 2026-09-29-06401fd5b220.
Three conservation tasks use Sorghum bicolor with Andropogoneae alignments, a Poaceae coding-sequence alignment with Pharus latifolius as outgroup, and potato (Solanum tuberosum) with 95 Solanaceae genomes. Each uses its own alignment-derived conservation labels. This is zero-shot scoring rather than fitting on conservation labels. For the Andropogoneae and Poaceae tasks, the evaluated site is centered at position 4,096 in an 8,192-base window and its reference base is masked. Conservation thresholds and selected positions differ by task. AUROC for conserved/non-conserved site classification in the cross-species conservation evaluations. PlantCAD2, PlantCAD, GPN and Evo2. The paper explicitly states that Solanaceae species were absent from PlantCAD2 pretraining, while Evo 2 included multiple Solanum genomes. This supports a scoped distinction for the potato experiment, not a universal claim that every evaluated position or homolog was unseen.
Each evaluation records what was tested and under which conditions.
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No source-reviewed explanatory claims are recorded here yet.
Targeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change.
Stable record: reported-task-3109f8d0f2b7b5Explanatory 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.
| Property | Description and evidence |
|---|---|
| Datasets | Three conservation tasks use Sorghum bicolor with Andropogoneae alignments, a Poaceae coding-sequence alignment with Pharus latifolius as outgroup, and potato (Solanum tuberosum) with 95 Solanaceae genomes. Each uses its own alignment-derived conservation labels.SourcesPlantCAD2: A Long-Context DNA Language Model for Cross-Species Functional Annotation in Angiosperms · Methods: Evolutionary constraint prediction using the zero-shot strategy |
| Splits | This is zero-shot scoring rather than fitting on conservation labels. For the Andropogoneae and Poaceae tasks, the evaluated site is centered at position 4,096 in an 8,192-base window and its reference base is masked. Conservation thresholds and selected positions differ by task.SourcesPlantCAD2: A Long-Context DNA Language Model for Cross-Species Functional Annotation in Angiosperms · Methods: Evolutionary constraint prediction using the zero-shot strategy |
| Metrics | AUROC for conserved/non-conserved site classification in the cross-species conservation evaluations.SourcesPlantCAD2: A Long-Context DNA Language Model for Cross-Species Functional Annotation in Angiosperms · Methods: Zero-shot evaluation of PlantCAD2, PlantCAD and GPN; Evo2 evaluation; cached text lines 110–115; task metric definitions and corresponding results table |
| Baselines | PlantCAD2, PlantCAD, GPN and Evo2.SourcesPlantCAD2: A Long-Context DNA Language Model for Cross-Species Functional Annotation in Angiosperms · Methods: Zero-shot evaluation of PlantCAD2, PlantCAD and GPN; Evo2 evaluation; cached text lines 110–115; task metric definitions and corresponding results table |
| Leakage controls | The paper explicitly states that Solanaceae species were absent from PlantCAD2 pretraining, while Evo 2 included multiple Solanum genomes. This supports a scoped distinction for the potato experiment, not a universal claim that every evaluated position or homolog was unseen.SourcesPlantCAD2: A Long-Context DNA Language Model for Cross-Species Functional Annotation in Angiosperms · Results: PlantCAD2 accurately predicts evolutionary conservation with a zero-shot strategy; Methods: Evolutionary constraint prediction using the zero-shot strategy |
| Uncertainty | Supplemental Table 2 supplies task-, model- and context-specific AUROC point estimates, without uncertainty columns. Figure S2 varies context length; that variation is not a confidence interval or repeated-seed error estimate. · Not reported in inspected sourcesSources (2)PlantCAD2: A Long-Context DNA Language Model for Cross-Species Functional Annotation in Angiosperms; plantcad2-2025__media-1.xlsx · Supplemental Table 2 worksheet: Task, Model, Context and AUROC columns; Figure S2 |
| Entity type | Paper-specific computational evaluation protocol.SourcesPlantCAD2: A Long-Context DNA Language Model for Cross-Species Functional Annotation in Angiosperms · Methods: Zero-shot evaluation of PlantCAD2, PlantCAD and GPN; Evo2 evaluation; cached text lines 110–115; task metric definitions and corresponding results table |
| Organisms | Plant genomic sequences.SourcesPlantCAD2: A Long-Context DNA Language Model for Cross-Species Functional Annotation in Angiosperms · Methods: Zero-shot evaluation of PlantCAD2, PlantCAD and GPN; Evo2 evaluation; cached text lines 110–115; task metric definitions and corresponding results table |
| Assays | Conservation/evolutionary-constraint annotations.SourcesPlantCAD2: A Long-Context DNA Language Model for Cross-Species Functional Annotation in Angiosperms · Methods: Zero-shot evaluation of PlantCAD2, PlantCAD and GPN; Evo2 evaluation; cached text lines 110–115; task metric definitions and corresponding results table |
| Allowed inputs | Plant DNA sequence.SourcesPlantCAD2: A Long-Context DNA Language Model for Cross-Species Functional Annotation in Angiosperms · Methods: Zero-shot evaluation of PlantCAD2, PlantCAD and GPN; Evo2 evaluation; cached text lines 110–115; task metric definitions and corresponding results table |
| Adaptation | Zero-shot scoring compared across PlantCAD2, PlantCAD, GPN and Evo2.SourcesPlantCAD2: A Long-Context DNA Language Model for Cross-Species Functional Annotation in Angiosperms · Methods: Zero-shot evaluation of PlantCAD2, PlantCAD and GPN; Evo2 evaluation; cached text lines 110–115; task metric definitions and corresponding results table |
Source checking verifies the cited claim or transcription. It does not establish independent reproduction.
Last literature check: 2026-09-17. Primary-paper discovery and source inspection. Source-checked results are not independently reproduced experiments.
| Paper or primary resource | Version | Reference |
|---|---|---|
| PlantCAD2: A Long-Context DNA Language Model for Cross-Species Functional Annotation in Angiosperms | preprint version in PMC | Read source DOI: 10.1101/2025.08.27.672609 |
The catalogue now holds 1 result rows for this benchmark. A note below about pending extraction describes the state on 2026-09-17 and may since have been answered by a later batch. The result rows and their sources are the current record.
primary comparison table screened
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One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.
18 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Diagram caption Conceptual summary of the cited evaluation; exact task configuration and source version remain part of the protocol. Individual claims | PlantCAD2: A Long-Context DNA Language Model for Cross-Species Functional Annotation in Angiosperms Methods: Zero-shot evaluation of PlantCAD2, PlantCAD and GPN; Evo2 evaluation; cached text lines 110–115; task metric definitions and corresponding results table; Methods: Evolutionary constraint prediction using the zero-shot strategy Version: preprint version in PMC | source checked automated source review · 2026-09-16 Audit detailsTargeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Diagram steps
| PlantCAD2: A Long-Context DNA Language Model for Cross-Species Functional Annotation in Angiosperms Methods: Zero-shot evaluation of PlantCAD2, PlantCAD and GPN; Evo2 evaluation; cached text lines 110–115; task metric definitions and corresponding results table; Methods: Evolutionary constraint prediction using the zero-shot strategy Version: preprint version in PMC | source checked automated source review · 2026-09-16 Audit detailsTargeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Diagram title Computational evaluation flow Individual claims | PlantCAD2: A Long-Context DNA Language Model for Cross-Species Functional Annotation in Angiosperms Methods: Zero-shot evaluation of PlantCAD2, PlantCAD and GPN; Evo2 evaluation; cached text lines 110–115; task metric definitions and corresponding results table; Methods: Evolutionary constraint prediction using the zero-shot strategy Version: preprint version in PMC | source checked automated source review · 2026-09-16 Audit detailsTargeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Datasets Three conservation tasks use Sorghum bicolor with Andropogoneae alignments, a Poaceae coding-sequence alignment with Pharus latifolius as outgroup, and potato (Solanum tuberosum) with 95 Solanaceae genomes. Each uses its own alignment-derived conservation labels. Individual claims | PlantCAD2: A Long-Context DNA Language Model for Cross-Species Functional Annotation in Angiosperms Methods: Evolutionary constraint prediction using the zero-shot strategy Version: preprint version in PMC | source checked automated source review · 2026-09-16 Audit detailsTargeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Splits This is zero-shot scoring rather than fitting on conservation labels. For the Andropogoneae and Poaceae tasks, the evaluated site is centered at position 4,096 in an 8,192-base window and its reference base is masked. Conservation thresholds and selected positions differ by task. Individual claims | PlantCAD2: A Long-Context DNA Language Model for Cross-Species Functional Annotation in Angiosperms Methods: Evolutionary constraint prediction using the zero-shot strategy Version: preprint version in PMC | source checked automated source review · 2026-09-16 Audit detailsTargeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Adaptation Zero-shot scoring compared across PlantCAD2, PlantCAD, GPN and Evo2. Individual claims | PlantCAD2: A Long-Context DNA Language Model for Cross-Species Functional Annotation in Angiosperms Methods: Zero-shot evaluation of PlantCAD2, PlantCAD and GPN; Evo2 evaluation; cached text lines 110–115; task metric definitions and corresponding results table Version: preprint version in PMC | source checked automated source review · 2026-09-16 Audit detailsTargeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Metrics AUROC for conserved/non-conserved site classification in the cross-species conservation evaluations. Individual claims | PlantCAD2: A Long-Context DNA Language Model for Cross-Species Functional Annotation in Angiosperms Methods: Zero-shot evaluation of PlantCAD2, PlantCAD and GPN; Evo2 evaluation; cached text lines 110–115; task metric definitions and corresponding results table Version: preprint version in PMC | source checked automated source review · 2026-09-16 Audit detailsTargeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Baselines PlantCAD2, PlantCAD, GPN and Evo2. Individual claims | PlantCAD2: A Long-Context DNA Language Model for Cross-Species Functional Annotation in Angiosperms Methods: Zero-shot evaluation of PlantCAD2, PlantCAD and GPN; Evo2 evaluation; cached text lines 110–115; task metric definitions and corresponding results table Version: preprint version in PMC | source checked automated source review · 2026-09-16 Audit detailsTargeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Leakage controls The paper explicitly states that Solanaceae species were absent from PlantCAD2 pretraining, while Evo 2 included multiple Solanum genomes. This supports a scoped distinction for the potato experiment, not a universal claim that every evaluated position or homolog was unseen. Individual claims | PlantCAD2: A Long-Context DNA Language Model for Cross-Species Functional Annotation in Angiosperms Results: PlantCAD2 accurately predicts evolutionary conservation with a zero-shot strategy; Methods: Evolutionary constraint prediction using the zero-shot strategy Version: preprint version in PMC | source checked automated source review · 2026-09-16 Audit detailsTargeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Uncertainty Supplemental Table 2 supplies task-, model- and context-specific AUROC point estimates, without uncertainty columns. Figure S2 varies context length; that variation is not a confidence interval or repeated-seed error estimate. Individual claims | plantcad2-2025__media-1.xlsx Supplemental Table 2 worksheet: Task, Model, Context and AUROC columns; Figure S2 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Retrieved 2026-09-16; sha256:f551e80bf044a0ea8ccc2e6f443fdf3690ca5e4a54d0e4bb4b2e6470ffc944be | unreported automated source review · 2026-09-16 Audit detailsTargeted full-paper and supplement review of the outstanding task fields, with original dataset metadata checked where accessible. Source-scoped omissions are explicit; no independent benchmark reproduction or numerical-result change. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record Archive member: media-1.xlsx |
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Release 2026-09-29-06401fd5b220 · Record review: needs review
Stable ID: reported-task-3109f8d0f2b7b5