Datasets
The paper’s PRIME receptor-binding-domain variant collection; this is a paper-specific task, not a universal protein benchmark.
Task
Mutated RBD binding prediction
PRIME examines how protein representations generalise across a published viral-variant dataset. This record covers its binding-prediction endpoint.
Sources
PRIME: An evaluation framework for protein representation inference and generalization in viral mutation space · Abstract; Results: Benchmark data collection for viral phenotype prediction; Table 1 task and column headingsOverview
Metrics
R² for the linked binding-regression results; preserve the endpoint and split beside each value.
Allowed inputs
Protein-sequence representations associated with measured phenotype labels.
Sources
PRIME: An evaluation framework for protein representation inference and generalization in viral mutation space · Abstract; Results: Benchmark data collection for viral phenotype prediction; Table 1 task and column headingsEvaluation procedure diagram
How it worksConceptual assessment outline
Conceptual overview of the published statistical assessment.
Sources
PRIME: An evaluation framework for protein representation inference and generalization in viral mutation space · Abstract; Results: Benchmark data collection for viral phenotype prediction; Table 1 task and column headingslimited source coverage · Automated source review, 2026-09-16. All specifications and missing details
Results
Results are available, but no reviewed comparison panel is linked in this release.
All evaluations
2 evaluations · 2 results. Different protocols are not a single leaderboard.
Filter evaluations
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: ESM-2 | Task: Mutated RBD binding prediction Dataset: PRIME mutated RBD | 0.0248 R² unitless · unknown Uncertainty: ± 0.01 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceESM-2: Mutated RBD binding prediction Frozen mean-pooled representation with downstream regression; position-stratified split. Aggregation: Not reported PRIME: An evaluation framework for protein representation inference and generalization in viral mutation space · Table 1, ESM-2 8M / Mean / not fine-tuned row, Position-Stratified Split Binding R² column |
| Configuration: ESM-C | Task: Mutated RBD binding prediction Dataset: PRIME mutated RBD | -0.0162 R² unitless · unknown Uncertainty: ± 0.01 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceESM-C: Mutated RBD binding prediction Frozen mean-pooled representation with downstream regression; position-stratified split. Aggregation: Not reported PRIME: An evaluation framework for protein representation inference and generalization in viral mutation space · Table 1, ESM-C 300M / Mean / not fine-tuned row, Position-Stratified Split Binding R² column |
Source checking is not independent reproduction. Release 2026-09-29-06401fd5b220.
Methods and evaluation design
Procedure, tasks and evaluated configurations
How it works
What the evaluation establishes
The paper contrasts ordinary random assessment with assessment across withheld mutation positions. These settings ask different generalisation questions and their scores should not be pooled. Binding and expression are separate measured labels; neither is a direct measure of infection, transmission or clinical risk.
Sources
PRIME: An evaluation framework for protein representation inference and generalization in viral mutation space · Abstract; Results: Benchmark data collection for viral phenotype prediction; Table 1 task and column headingsRecorded evaluations
Each evaluation records what was tested and under which conditions.
Run instructions
No runnable recipe has been reviewed for this task. Dataset access, model requirements, licences and compute requirements must be checked against its sources before execution.
A task describes a biological question. Choose a linked protocol to obtain concrete split and scoring instructions.
Strengths, limitations and unresolved questions
Strengths and limitations
Strengths and considerations
- The contrasting assessment settings expose how a reported score depends on the generalisation question.
Sources
PRIME: An evaluation framework for protein representation inference and generalization in viral mutation space · Abstract; Results: Benchmark data collection for viral phenotype prediction; Table 1 task and column headings
Limitations and conditions
- Prediction of a measured binding label does not establish infectivity or clinical risk. A source-checked score alone does not verify the full dataset lineage or split manifest.
Sources
PRIME: An evaluation framework for protein representation inference and generalization in viral mutation space · Abstract; Results: Benchmark data collection for viral phenotype prediction; Table 1 task and column headings
Profile review details
Inspected the cited primary abstract and descriptive computational-evaluation sections. Review covers the descriptive claims shown; no executable protocol was reconstructed. Original numerical records retain their prior transcription review.
Stable record: reported-task-00e594df6a182dSpecifications
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 |
|---|---|
| Entity type | Paper-specific evaluation task; this profile is a descriptive evidence summary.SourcesPRIME: An evaluation framework for protein representation inference and generalization in viral mutation space · Abstract; Results: Benchmark data collection for viral phenotype prediction; Table 1 task and column headings |
| Datasets | The paper’s PRIME receptor-binding-domain variant collection; this is a paper-specific task, not a universal protein benchmark.SourcesPRIME: An evaluation framework for protein representation inference and generalization in viral mutation space · Abstract; Results: Benchmark data collection for viral phenotype prediction; Table 1 task and column headings |
| Organisms | SARS-CoV-2 in the reported variant dataset.SourcesPRIME: An evaluation framework for protein representation inference and generalization in viral mutation space · Abstract; Results: Benchmark data collection for viral phenotype prediction; Table 1 task and column headings |
| Assays | Previously published binding and expression measurements provide phenotype labels; this record concerns binding prediction.SourcesPRIME: An evaluation framework for protein representation inference and generalization in viral mutation space · Abstract; Results: Benchmark data collection for viral phenotype prediction; Table 1 task and column headings |
| Splits | Random and position-stratified settings are distinct. The linked results retain the reported setting; this profile does not supply an executable split manifest.SourcesPRIME: An evaluation framework for protein representation inference and generalization in viral mutation space · Abstract; Results: Benchmark data collection for viral phenotype prediction; Table 1 task and column headings |
| Allowed inputs | Protein-sequence representations associated with measured phenotype labels.SourcesPRIME: An evaluation framework for protein representation inference and generalization in viral mutation space · Abstract; Results: Benchmark data collection for viral phenotype prediction; Table 1 task and column headings |
| Adaptation | The paper distinguishes frozen representations from adapted models. Individual evaluation records retain that distinction.SourcesPRIME: An evaluation framework for protein representation inference and generalization in viral mutation space · Abstract; Results: Benchmark data collection for viral phenotype prediction; Table 1 task and column headings |
| Metrics | R² for the linked binding-regression results; preserve the endpoint and split beside each value.SourcesPRIME: An evaluation framework for protein representation inference and generalization in viral mutation space · Abstract; Results: Benchmark data collection for viral phenotype prediction; Table 1 task and column headings |
| Baselines | The paper compares pretrained encoder configurations. The exact method named in each retained result remains its identity; no model recommendation follows from this summary.SourcesPRIME: An evaluation framework for protein representation inference and generalization in viral mutation space · Abstract; Results: Benchmark data collection for viral phenotype prediction; Table 1 task and column headings |
Evidence
Source checking verifies the cited claim or transcription. It does not establish independent reproduction.
Papers and result coverage
Last literature check: 2026-09-17. Dated primary-source discovery and protocol/table screening. Source checking does not mean experimental reproduction. Only separately extracted and independently reviewed numeric batches are publishable.
| Paper or primary resource | Version | Reference |
|---|---|---|
| PRIME: An evaluation framework for protein representation inference and generalization in viral mutation space | version of record | Read source |
Historical gaps recorded on 2026-09-17
The catalogue now holds 2 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.
- complete numerical transcription and independent cell review: Full primary artifact and table inventory preserved; no new numeric row is published from this audit alone.
- exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size.
Search and extraction details
primary comparison tables located
Searches
- PRIME: An evaluation framework for protein representation inference and generalization in viral mutation space 10.1186/s12864-026-12976-5
Evidence locations
- Table 1; XML table Tab1
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.
16 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Diagram caption Conceptual overview of the published statistical assessment. Individual claims | PRIME: An evaluation framework for protein representation inference and generalization in viral mutation space Abstract; Results: Benchmark data collection for viral phenotype prediction; Table 1 task and column headings Version: version of record | source checked automated source review · 2026-09-16 Audit detailsInspected the cited primary abstract and descriptive computational-evaluation sections. Review covers the descriptive claims shown; no executable protocol was reconstructed. Original numerical records retain their prior transcription review. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Diagram steps
| PRIME: An evaluation framework for protein representation inference and generalization in viral mutation space Abstract; Results: Benchmark data collection for viral phenotype prediction; Table 1 task and column headings Version: version of record | source checked automated source review · 2026-09-16 Audit detailsInspected the cited primary abstract and descriptive computational-evaluation sections. Review covers the descriptive claims shown; no executable protocol was reconstructed. Original numerical records retain their prior transcription review. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Diagram title Conceptual assessment outline Individual claims | PRIME: An evaluation framework for protein representation inference and generalization in viral mutation space Abstract; Results: Benchmark data collection for viral phenotype prediction; Table 1 task and column headings Version: version of record | source checked automated source review · 2026-09-16 Audit detailsInspected the cited primary abstract and descriptive computational-evaluation sections. Review covers the descriptive claims shown; no executable protocol was reconstructed. Original numerical records retain their prior transcription review. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Entity type Paper-specific evaluation task; this profile is a descriptive evidence summary. Individual claims | PRIME: An evaluation framework for protein representation inference and generalization in viral mutation space Abstract; Results: Benchmark data collection for viral phenotype prediction; Table 1 task and column headings Version: version of record | source checked automated source review · 2026-09-16 Audit detailsInspected the cited primary abstract and descriptive computational-evaluation sections. Review covers the descriptive claims shown; no executable protocol was reconstructed. Original numerical records retain their prior transcription review. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Datasets The paper’s PRIME receptor-binding-domain variant collection; this is a paper-specific task, not a universal protein benchmark. Individual claims | PRIME: An evaluation framework for protein representation inference and generalization in viral mutation space Abstract; Results: Benchmark data collection for viral phenotype prediction; Table 1 task and column headings Version: version of record | source checked automated source review · 2026-09-16 Audit detailsInspected the cited primary abstract and descriptive computational-evaluation sections. Review covers the descriptive claims shown; no executable protocol was reconstructed. Original numerical records retain their prior transcription review. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Organisms SARS-CoV-2 in the reported variant dataset. Individual claims | PRIME: An evaluation framework for protein representation inference and generalization in viral mutation space Abstract; Results: Benchmark data collection for viral phenotype prediction; Table 1 task and column headings Version: version of record | source checked automated source review · 2026-09-16 Audit detailsInspected the cited primary abstract and descriptive computational-evaluation sections. Review covers the descriptive claims shown; no executable protocol was reconstructed. Original numerical records retain their prior transcription review. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Assays Previously published binding and expression measurements provide phenotype labels; this record concerns binding prediction. Individual claims | PRIME: An evaluation framework for protein representation inference and generalization in viral mutation space Abstract; Results: Benchmark data collection for viral phenotype prediction; Table 1 task and column headings Version: version of record | source checked automated source review · 2026-09-16 Audit detailsInspected the cited primary abstract and descriptive computational-evaluation sections. Review covers the descriptive claims shown; no executable protocol was reconstructed. Original numerical records retain their prior transcription review. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Splits Random and position-stratified settings are distinct. The linked results retain the reported setting; this profile does not supply an executable split manifest. Individual claims | PRIME: An evaluation framework for protein representation inference and generalization in viral mutation space Abstract; Results: Benchmark data collection for viral phenotype prediction; Table 1 task and column headings Version: version of record | source checked automated source review · 2026-09-16 Audit detailsInspected the cited primary abstract and descriptive computational-evaluation sections. Review covers the descriptive claims shown; no executable protocol was reconstructed. Original numerical records retain their prior transcription review. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Allowed inputs Protein-sequence representations associated with measured phenotype labels. Individual claims | PRIME: An evaluation framework for protein representation inference and generalization in viral mutation space Abstract; Results: Benchmark data collection for viral phenotype prediction; Table 1 task and column headings Version: version of record | source checked automated source review · 2026-09-16 Audit detailsInspected the cited primary abstract and descriptive computational-evaluation sections. Review covers the descriptive claims shown; no executable protocol was reconstructed. Original numerical records retain their prior transcription review. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Adaptation The paper distinguishes frozen representations from adapted models. Individual evaluation records retain that distinction. Individual claims | PRIME: An evaluation framework for protein representation inference and generalization in viral mutation space Abstract; Results: Benchmark data collection for viral phenotype prediction; Table 1 task and column headings Version: version of record | source checked automated source review · 2026-09-16 Audit detailsInspected the cited primary abstract and descriptive computational-evaluation sections. Review covers the descriptive claims shown; no executable protocol was reconstructed. Original numerical records retain their prior transcription review. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Sources and history
View linked audit checks and correction history
Release 2026-09-29-06401fd5b220 · Record review: needs review
2 source records and release history
- PRIME: An evaluation framework for protein representation inference and generalization in viral mutation space · Original source · version of record
- PRIME: An evaluation framework for protein representation inference and generalization in viral mutation space · Original source · version of record
Technical metadata and extraction receipts
Stable ID: reported-task-00e594df6a182d
- areas
- proteins-complexes
- tasks
- Mutated RBD binding prediction
- entity level
- task
- version
- Not reported
- task
- Mutated RBD binding prediction
- scope note
- Paper-specific evaluation task; protocol completeness requires further extraction.
- benchmark research
- review date: 2026-09-17; status: primary_comparison_tables_located; primary sources: evidence-expansion-prime-2026-f6aac4c2; inspected locators: Table 1; XML table Tab1; searched queries: PRIME: An evaluation framework for protein representation inference and generalization in viral mutation space 10.1186/s12864-026-12976-5; gaps: complete numerical transcription and independent cell review: Full primary artifact and table inventory preserved; no new numeric row is published from this audit alone.; exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size.; claim scope: Dated primary-source discovery and protocol/table screening. Source checking does not mean experimental reproduction. Only separately extracted and independently reviewed numeric batches are publishable.
- historical missing metadata
- protocol version: 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
- benchmark
- entity classification
- review date: 2026-09-17; rationale: This source-scoped record identifies the biological prediction task and holds its paper context. Preserve the existing task identity; exact split, model adaptation and scoring remain in linked evaluations or separate protocol records.; source ids: prime-2026; source locator: Abstract; Results: Benchmark data collection for viral phenotype prediction; Table 1 task and column headings; ambiguities: A paper- or suite-specific task may constrain some inputs or metrics; that alone does not make it interchangeable with a complete versioned protocol. No protocol equivalence is inferred.; Some legacy profile Entity type facts use the generic phrase computational evaluation protocol. That boilerplate is not sufficient to establish a single fixed protocol identity or to merge this task with another protocol record.
Related records
- dataset: PRIME mutated RBD
- benchmark: ESM-2: Mutated RBD binding prediction
- benchmark: ESM-C: Mutated RBD binding prediction