Model type
Study-specific predictive method; this record is the paper-specific evaluated configuration.
Configuration
PlantCAD2
PlantCAD2 is a plant-specific, single-nucleotide genomic language model.
Sources
PlantCAD2: A Long-Context DNA Language Model for Cross-Species Functional Annotation in Angiosperms · Abstract (paragraph 1); Methods/Accessible chromatin region prediction (paragraph 3)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
PlantCAD2: A Long-Context DNA Language Model for Cross-Species Functional Annotation in Angiosperms · Methods/Zero-shot evaluation of Evo2 model (paragraph 2); Results/PlantCAD2: a long-context DNA language model for angiosperms (paragraph 1)At a glance
Biological inputs
Plant genomic DNA at single-nucleotide resolution
Sources
PlantCAD2: A Long-Context DNA Language Model for Cross-Species Functional Annotation in Angiosperms · Methods/Repeat annotation and loss re-weighting (paragraph 2); Introduction (paragraph 4)Outputs
Sequence representations, zero-shot scores and adapted regulatory predictions
Sources
PlantCAD2: A Long-Context DNA Language Model for Cross-Species Functional Annotation in Angiosperms · Results/Transcription factor binding sites revealed by high-confidence predictions of PlantCAD2 (paragraph 1); Methods/Evolutionary constraint prediction using the zero-shot strategy (paragraph 3)limited source coverage · Automated source review, 2026-09-16. All specifications and missing details
Evaluations and results
Release 2026-09-17-d277315f7d76 · 1 evaluation · 1 metric row. Different protocols are not a single leaderboard.
| Metric and finding | Coverage and uncertainty | Evidence |
|---|---|---|
| PlantCAD2: cross-species conservation prediction Configuration: PlantCAD2Task: cross-species conservation predictionDataset: Andropogoneae genome-wide conservation Zero-shot score for conserved versus non-conserved sites from alignments of 35 Andropogoneae genomes Author-reported evaluation · Evaluation metadata: needs review | ||
| 0.725 AUROC Unit: fraction · Direction: unknown | Uncertainty: not reported in legacy extract Scored: Not reported · Eligible: Not reported | source checkedPlantCAD2: 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. |
How it works
How the evaluated method works
A Caduceus-style bidirectional, reverse-complement-equivariant architecture uses Mamba2 blocks and masked-language pretraining.
Sources
PlantCAD2: A Long-Context DNA Language Model for Cross-Species Functional Annotation in Angiosperms · Methods/Zero-shot evaluation of Evo2 model (paragraph 2); Results/PlantCAD2: a long-context DNA language model for angiosperms (paragraph 1)What was evaluated
The linked evaluation record identifies PlantCAD2: cross-species conservation prediction. Its dataset, split, adaptation and evidence origin remain attached to the reported results.
Sources
PlantCAD2: A Long-Context DNA Language Model for Cross-Species Functional Annotation in Angiosperms · The named evaluation’s methods and comparison table; exact preserved evaluation IDs: evaluation-lit-b4-002Strengths and limitations
Strengths and considerations
- Combines plant-specific phylogenetic coverage with a longer context and strand-aware architecture.
Sources
PlantCAD2: A Long-Context DNA Language Model for Cross-Species Functional Annotation in Angiosperms · Discussions (paragraph 1); Results/Fine-tuning PlantCAD2 accurately predicts cross-species chromatin accessible regions and cell-type-specific accessible regions (paragraph 2)
Limitations and conditions
- Evidence concerns the paper’s plant benchmarks and adaptations; superiority in selected tasks does not imply superiority across all genomes or biological capabilities.
Sources
PlantCAD2: A Long-Context DNA Language Model for Cross-Species Functional Annotation in Angiosperms · Introduction (paragraph 6); Abstract (paragraph 1)
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-65059c3a806306Specifications
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.
| Property | Description and evidence |
|---|---|
| Model type | Study-specific predictive method; this record is the paper-specific evaluated configuration.SourcesPlantCAD2: A Long-Context DNA Language Model for Cross-Species Functional Annotation in Angiosperms · Methods/Zero-shot evaluation of Evo2 model (paragraph 2); Results/PlantCAD2: a long-context DNA language model for angiosperms (paragraph 1) |
| Architecture / procedure | A Caduceus-style bidirectional, reverse-complement-equivariant architecture uses Mamba2 blocks and masked-language pretraining.SourcesPlantCAD2: A Long-Context DNA Language Model for Cross-Species Functional Annotation in Angiosperms · Methods/Zero-shot evaluation of Evo2 model (paragraph 2); Results/PlantCAD2: a long-context DNA language model for angiosperms (paragraph 1) |
| Biological inputs | Plant genomic DNA at single-nucleotide resolutionSourcesPlantCAD2: A Long-Context DNA Language Model for Cross-Species Functional Annotation in Angiosperms · Methods/Repeat annotation and loss re-weighting (paragraph 2); Introduction (paragraph 4) |
| Outputs | Sequence representations, zero-shot scores and adapted regulatory predictionsSourcesPlantCAD2: A Long-Context DNA Language Model for Cross-Species Functional Annotation in Angiosperms · Results/Transcription factor binding sites revealed by high-confidence predictions of PlantCAD2 (paragraph 1); Methods/Evolutionary constraint prediction using the zero-shot strategy (paragraph 3) |
| Parameters | An aggregate parameter total for this exact evaluated configuration is not established by the inspected sources. · Not reported in inspected sourcesSources (2)PlantCAD2: A Long-Context DNA Language Model for Cross-Species Functional Annotation in Angiosperms; plantcad/plantcad README.md · Methods/Preparing pre-training genomes; Methods/PlantCAD2 model architecture and pre-training; Methods/Repeat annotation and loss re-weighting; Methods/Evolutionary constraint prediction using the zero-shot strategy; Methods/Core and non-core gene classification using the zero-shot strategy; Methods/Accessible chromatin region prediction; Methods/Gene expression prediction in leaf; Methods/Leaf protein abundance prediction task; inspected for aggregate parameter count (component sizes are not added without an exact configuration); README.md at pinned repository revision |
| Known versions / configuration | PlantCAD2 is the comparison-table label; that label does not specify an immutable weight revision. · Not reported in inspected sourcesSourcesPlantCAD2: A Long-Context DNA Language Model for Cross-Species Functional Annotation in Angiosperms · Model identification in the comparison table and corresponding Methods; immutable checkpoint revision is not supplied by the table label. |
| Training data / fitting | 65 angiosperm genomesSourcesPlantCAD2: A Long-Context DNA Language Model for Cross-Species Functional Annotation in Angiosperms · Methods/Preparing pre-training genomes (paragraph 1); Methods/PlantCAD2 model architecture and pre-training (paragraph 3) |
| Context limits | 8,192 base pairsSourcesPlantCAD2: A Long-Context DNA Language Model for Cross-Species Functional Annotation in Angiosperms · Methods/PlantCAD2 model architecture and pre-training (paragraph 3); Introduction (paragraph 4) |
| Access | Official study implementation and usage documentation: https://github.com/plantcad/plantcad/blob/7240f0238f869b3ac25e4b5ad0996fad96ede9db/README.md. This pinned documentation revision is not automatically the evaluated weight revision.Sourcesplantcad/plantcad README.md · README.md; installation, model download and usage instructions |
| Code licence | Apache 2.0 (study repository code at the cited revision; this does not establish every dependency or historical checkpoint licence).Sourcesplantcad/plantcad 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 sourcesSourcesplantcad/plantcad 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
| 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 | PlantCAD2: A Long-Context DNA Language Model for Cross-Species Functional Annotation in Angiosperms Methods/Zero-shot evaluation of Evo2 model (paragraph 2); Results/PlantCAD2: a long-context DNA language model for angiosperms (paragraph 1) Version: preprint version in PMC | source checked automated source review · 2026-09-16 Audit detailsPrimary 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: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Diagram steps ["Plant genomic DNA at single-nucleotide resolution","PlantCAD2","Sequence representations, zero-shot scores and adapted regulatory predictions"] Individual claims | PlantCAD2: A Long-Context DNA Language Model for Cross-Species Functional Annotation in Angiosperms Methods/Zero-shot evaluation of Evo2 model (paragraph 2); Results/PlantCAD2: a long-context DNA language model for angiosperms (paragraph 1) Version: preprint version in PMC | source checked automated source review · 2026-09-16 Audit detailsPrimary 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: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Diagram title Evaluated procedure (conceptual) Individual claims | PlantCAD2: A Long-Context DNA Language Model for Cross-Species Functional Annotation in Angiosperms Methods/Zero-shot evaluation of Evo2 model (paragraph 2); Results/PlantCAD2: a long-context DNA language model for angiosperms (paragraph 1) Version: preprint version in PMC | source checked automated source review · 2026-09-16 Audit detailsPrimary 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: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Model type Study-specific predictive method; this record is the paper-specific evaluated configuration. Individual claims | PlantCAD2: A Long-Context DNA Language Model for Cross-Species Functional Annotation in Angiosperms Methods/Zero-shot evaluation of Evo2 model (paragraph 2); Results/PlantCAD2: a long-context DNA language model for angiosperms (paragraph 1) Version: preprint version in PMC | source checked automated source review · 2026-09-16 Audit detailsPrimary 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: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Architecture / procedure A Caduceus-style bidirectional, reverse-complement-equivariant architecture uses Mamba2 blocks and masked-language pretraining. Individual claims | PlantCAD2: A Long-Context DNA Language Model for Cross-Species Functional Annotation in Angiosperms Methods/Zero-shot evaluation of Evo2 model (paragraph 2); Results/PlantCAD2: a long-context DNA language model for angiosperms (paragraph 1) Version: preprint version in PMC | source checked automated source review · 2026-09-16 Audit detailsPrimary 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: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| 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 | plantcad/plantcad README.md README.md; checkpoint/access documentation and licence scope Version: 7240f0238f869b3ac25e4b5ad0996fad96ede9db | unreported automated source review · 2026-09-16 Audit detailsPrimary 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: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Biological inputs Plant genomic DNA at single-nucleotide resolution Individual claims | PlantCAD2: A Long-Context DNA Language Model for Cross-Species Functional Annotation in Angiosperms Methods/Repeat annotation and loss re-weighting (paragraph 2); Introduction (paragraph 4) Version: preprint version in PMC | source checked automated source review · 2026-09-16 Audit detailsPrimary 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: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Outputs Sequence representations, zero-shot scores and adapted regulatory predictions Individual claims | PlantCAD2: A Long-Context DNA Language Model for Cross-Species Functional Annotation in Angiosperms Results/Transcription factor binding sites revealed by high-confidence predictions of PlantCAD2 (paragraph 1); Methods/Evolutionary constraint prediction using the zero-shot strategy (paragraph 3) Version: preprint version in PMC | source checked automated source review · 2026-09-16 Audit detailsPrimary 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: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Parameters An aggregate parameter total for this exact evaluated configuration is not established by the inspected sources. Individual claims | plantcad/plantcad README.md Methods/Preparing pre-training genomes; Methods/PlantCAD2 model architecture and pre-training; Methods/Repeat annotation and loss re-weighting; Methods/Evolutionary constraint prediction using the zero-shot strategy; Methods/Core and non-core gene classification using the zero-shot strategy; Methods/Accessible chromatin region prediction; Methods/Gene expression prediction in leaf; Methods/Leaf protein abundance prediction task; inspected for aggregate parameter count (component sizes are not added without an exact configuration); README.md at pinned repository revision Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 7240f0238f869b3ac25e4b5ad0996fad96ede9db | unreported automated source review · 2026-09-16 Audit detailsPrimary 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: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Parameters An aggregate parameter total for this exact evaluated configuration is not established by the inspected sources. Individual claims | PlantCAD2: A Long-Context DNA Language Model for Cross-Species Functional Annotation in Angiosperms Methods/Preparing pre-training genomes; Methods/PlantCAD2 model architecture and pre-training; Methods/Repeat annotation and loss re-weighting; Methods/Evolutionary constraint prediction using the zero-shot strategy; Methods/Core and non-core gene classification using the zero-shot strategy; Methods/Accessible chromatin region prediction; Methods/Gene expression prediction in leaf; Methods/Leaf protein abundance prediction task; inspected for aggregate parameter count (component sizes are not added without an exact configuration); README.md at pinned repository revision Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: preprint version in PMC | unreported automated source review · 2026-09-16 Audit detailsPrimary 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: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Sources and history
Release 2026-09-17-d277315f7d76 · Record review: needs review
3 source records and release history
- PlantCAD2: A Long-Context DNA Language Model for Cross-Species Functional Annotation in Angiosperms · Original source · preprint version in PMC
- plantcad/plantcad README.md · Original source · 7240f0238f869b3ac25e4b5ad0996fad96ede9db
- plantcad/plantcad LICENSE · Original source · 7240f0238f869b3ac25e4b5ad0996fad96ede9db
Technical metadata and extraction receipts
Stable ID: reported-model-65059c3a806306
- areas
- dna-genomes
- entity level
- method
- version
- Not reported
- reported name
- PlantCAD2
- 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: plantcad2-2025; source locator: Methods/Zero-shot evaluation of Evo2 model (paragraph 2); Results/PlantCAD2: a long-context DNA language model for angiosperms (paragraph 1) | Abstract (paragraph 1); Methods/Accessible chromatin region prediction (paragraph 3); 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.