Datasets
Reviewed human and vertebrate-host viral protein records from Swiss-Prot/UniProtKB, with redundancy filtering described in Methods 2.1.
Task
human-versus-viral protein classification
This evaluation asks whether protein representations distinguish human and viral sequence labels. It is a classification task, not a direct test of immune function.
Sources
Protein Language Models Expose Viral Immune Mimicry · Abstract; Methods 2.1 Protein Datasets and 2.6 Model Performance; Table 1Overview
Metrics
AUROC, log loss, accuracy, precision and recall are described; precision and recall use macro averaging. The linked result retains its original percentage unit.
Allowed inputs
Protein sequence representations paired with the study’s human/viral labels.
Sources
Protein Language Models Expose Viral Immune Mimicry · Abstract; Methods 2.1 Protein Datasets and 2.6 Model Performance; Table 1Evaluation procedure diagram
How it worksConceptual assessment outline
Conceptual overview of the published statistical assessment.
Sources
Protein Language Models Expose Viral Immune Mimicry · Abstract; Methods 2.1 Protein Datasets and 2.6 Model Performance; Table 1limited source coverage · Automated source review, 2026-09-16. All specifications and missing details
Results
Each comparison retains its reviewed evaluation scope, dataset and metric. Results are shown without a pooled ranking.
Held-out human-versus-virus protein classification · Table 1
AUROC (percent) · Higher values are better.
Held-out human-versus-virus protein classification (human-versus-viral protein classification) · human and viral proteins
Evidence origin: Author-reported evaluation.
Protein Language Models Expose Viral Immune Mimicry · Table 1: AUC (%), Held-out human-versus-virus protein classification- Origin classification does not establish immune mimicry.
- Table footnote says all values are percent but log-loss values are dimensionless; log-loss units quarantined.
- Narrative n-gram AUC91.9 differs from Table1 value91.5; preserve table value.
Comparison details and limitations
Compare protein origin classifiers; T 5 embeddings plus linear/tree models vs ESM 2 fine-tuning and simple controls. UniRef90 deduplication; proteins longer than1,600 residues excluded; UniRef50 clusters assigned80% training and20% test with no cluster shared. Separate four-fold error-analysis experiment not assigned toTable1.
- No interval assigned unless printed in source cell.
Automated source review: 2026-09-17. Numerical source review does not establish independent reproduction.
Dots show point estimates. Whiskers show only explicitly defined uncertainty (standard deviation, standard error or a labelled interval); their definitions remain in Table. Unresolved uncertainty is not plotted. Differences do not establish statistical significance.
Showing 8 of 8 matching rows.
Methods and evaluation design
Procedure, tasks and evaluated configurations
How it works
What the evaluation establishes
The source uses reviewed protein records and separates training and test data by sequence clusters. That reduces direct overlap between related examples under the stated clustering rule. It reports classification metrics for different representations; classification errors and biological explanations of those errors are separate claims.
Sources
Protein Language Models Expose Viral Immune Mimicry · Abstract; Methods 2.1 Protein Datasets and 2.6 Model Performance; Table 1Evaluation design
Benchmarks bring together tasks and protocols. A task describes the biological question; a protocol defines a particular test.
Protocols
These source-backed links do not make different protocols or scores interchangeable.
Run this benchmark
Choose a concrete protocol before running an evaluation. Its inputs, split and scoring rules determine which results can be compared.
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
- Cluster separation makes the treatment of related sequences visible when interpreting classification accuracy.
Sources
Protein Language Models Expose Viral Immune Mimicry · Abstract; Methods 2.1 Protein Datasets and 2.6 Model Performance; Table 1
Limitations and conditions
- Distinguishing sequence origin does not establish an immune mechanism. Database selection, similarity filtering and label composition constrain generalisation.
Sources
Protein Language Models Expose Viral Immune Mimicry · Abstract; Methods 2.1 Protein Datasets and 2.6 Model Performance; Table 1
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-53506fe386e4a1Specifications
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.SourcesProtein Language Models Expose Viral Immune Mimicry · Abstract; Methods 2.1 Protein Datasets and 2.6 Model Performance; Table 1 |
| Datasets | Reviewed human and vertebrate-host viral protein records from Swiss-Prot/UniProtKB, with redundancy filtering described in Methods 2.1.SourcesProtein Language Models Expose Viral Immune Mimicry · Abstract; Methods 2.1 Protein Datasets and 2.6 Model Performance; Table 1 |
| Organisms | Human proteins and proteins from viruses with a known vertebrate host.SourcesProtein Language Models Expose Viral Immune Mimicry · Abstract; Methods 2.1 Protein Datasets and 2.6 Model Performance; Table 1 |
| Assays | Sequence-origin labels from curated database records. This classification endpoint is not an experimental immune-response assay.SourcesProtein Language Models Expose Viral Immune Mimicry · Abstract; Methods 2.1 Protein Datasets and 2.6 Model Performance; Table 1 |
| Splits | Methods 2.1 assigns whole UniRef50 clusters to training or test sets. This profile records the split principle, not a verified membership manifest.SourcesProtein Language Models Expose Viral Immune Mimicry · Abstract; Methods 2.1 Protein Datasets and 2.6 Model Performance; Table 1 |
| Allowed inputs | Protein sequence representations paired with the study’s human/viral labels.SourcesProtein Language Models Expose Viral Immune Mimicry · Abstract; Methods 2.1 Protein Datasets and 2.6 Model Performance; Table 1 |
| Adaptation | Pretrained protein representations are evaluated through a study-specific classifier; a backbone name alone does not identify the full fitted pipeline.SourcesProtein Language Models Expose Viral Immune Mimicry · Abstract; Methods 2.1 Protein Datasets and 2.6 Model Performance; Table 1 |
| Metrics | AUROC, log loss, accuracy, precision and recall are described; precision and recall use macro averaging. The linked result retains its original percentage unit.SourcesProtein Language Models Expose Viral Immune Mimicry · Abstract; Methods 2.1 Protein Datasets and 2.6 Model Performance; Table 1 |
| Baselines | Table 1 compares the reported protein-representation configurations. They are classification comparators, not experimental immune-function controls.SourcesProtein Language Models Expose Viral Immune Mimicry · Abstract; Methods 2.1 Protein Datasets and 2.6 Model Performance; Table 1 |
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. Primary-source discovery and table/protocol screening; source checked is not independently reproduced. Raw acquisitions not automatically numerical publication approval.
| Paper or primary resource | Version | Reference |
|---|---|---|
| Protein Language Models Expose Viral Immune Mimicry | version of record | Read source DOI: 10.3390/v17091199 |
Historical gaps recorded on 2026-09-17
The catalogue now holds 32 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.
- Independent batch review before import; preserve existing observation identities.
Search and extraction details
complete comparison tables extracted pending publication review
Searches
- Protein Language Models Expose Viral Immune Mimicry primary paper benchmark results
Evidence locations
- Table1; held-out protein-origin classification; separate error-analysis CV
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 | Protein Language Models Expose Viral Immune Mimicry Abstract; Methods 2.1 Protein Datasets and 2.6 Model Performance; Table 1 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
| Protein Language Models Expose Viral Immune Mimicry Abstract; Methods 2.1 Protein Datasets and 2.6 Model Performance; Table 1 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 | Protein Language Models Expose Viral Immune Mimicry Abstract; Methods 2.1 Protein Datasets and 2.6 Model Performance; Table 1 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 | Protein Language Models Expose Viral Immune Mimicry Abstract; Methods 2.1 Protein Datasets and 2.6 Model Performance; Table 1 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 Reviewed human and vertebrate-host viral protein records from Swiss-Prot/UniProtKB, with redundancy filtering described in Methods 2.1. Individual claims | Protein Language Models Expose Viral Immune Mimicry Abstract; Methods 2.1 Protein Datasets and 2.6 Model Performance; Table 1 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 Human proteins and proteins from viruses with a known vertebrate host. Individual claims | Protein Language Models Expose Viral Immune Mimicry Abstract; Methods 2.1 Protein Datasets and 2.6 Model Performance; Table 1 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 Sequence-origin labels from curated database records. This classification endpoint is not an experimental immune-response assay. Individual claims | Protein Language Models Expose Viral Immune Mimicry Abstract; Methods 2.1 Protein Datasets and 2.6 Model Performance; Table 1 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 Methods 2.1 assigns whole UniRef50 clusters to training or test sets. This profile records the split principle, not a verified membership manifest. Individual claims | Protein Language Models Expose Viral Immune Mimicry Abstract; Methods 2.1 Protein Datasets and 2.6 Model Performance; Table 1 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 paired with the study’s human/viral labels. Individual claims | Protein Language Models Expose Viral Immune Mimicry Abstract; Methods 2.1 Protein Datasets and 2.6 Model Performance; Table 1 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 Pretrained protein representations are evaluated through a study-specific classifier; a backbone name alone does not identify the full fitted pipeline. Individual claims | Protein Language Models Expose Viral Immune Mimicry Abstract; Methods 2.1 Protein Datasets and 2.6 Model Performance; Table 1 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
- Protein Language Models Expose Viral Immune Mimicry · Original source · version of record
- Protein Language Models Expose Viral Immune Mimicry · Original source · version of record
Technical metadata and extraction receipts
Stable ID: reported-task-53506fe386e4a1
- areas
- proteins-complexes
- tasks
- human-versus-viral protein classification
- entity level
- task
- version
- Not reported
- task
- human-versus-viral protein classification
- scope note
- Paper-specific evaluation task; protocol completeness requires further extraction.
- comparison panels
- id: part2-viral-immune-mimicry-2025-viruses-17-01199-t001-3a83e9bebb; title: Held-out human-versus-virus protein classification · Table 1; protocol id: paper-protocol-1352834b9391c1dacb; dataset id: reported-dataset-43f24c4dfb7351; metric: AUROC; unit: percent; direction: higher; result ids: paper-result-e2941183edbcf0f806; paper-result-088aaf71a44cdc5709; paper-result-a19e0533c00420b50c; paper-result-13ca62957ffa02eef1; paper-result-a541b9f3a77eec62e2; lit-b4-009; paper-result-b740d08b806206779f; paper-result-6536626a03a3ef62f0; source ids: part2-viral-immune-mimicry-2025; source locator: Table 1: AUC (%), Held-out human-versus-virus protein classification; context: Compare protein origin classifiers; T 5 embeddings plus linear/tree models vs ESM 2 fine-tuning and simple controls. UniRef90 deduplication; proteins longer than1,600 residues excluded; UniRef50 clusters assigned80% training and20% test with no cluster shared. Separate four-fold error-analysis experiment not assigned toTable1.; caveats: Origin classification does not establish immune mimicry.; Table footnote says all values are percent but log-loss values are dimensionless; log-loss units quarantined.; Narrative n-gram AUC91.9 differs from Table1 value91.5; preserve table value.; No interval assigned unless printed in source cell.; review: method: automated_source_review; date: 2026-09-17; id: part2-viral-immune-mimicry-2025-viruses-17-01199-t001-668a472b03; title: Held-out human-versus-virus protein classification · Table 1; protocol id: paper-protocol-1352834b9391c1dacb; dataset id: reported-dataset-43f24c4dfb7351; metric: Accur.; unit: percent; direction: higher; result ids: paper-result-91e7ac901444849ecd; paper-result-ca12e3e749c612d6d8; paper-result-ee7f4e8a864f523eaf; paper-result-544d2c1cd2bd46af9b; paper-result-32da435487ad9e4e7b; paper-result-7ffc4775000c61b1e4; paper-result-87b3b45c365edc42f3; paper-result-439ed50c8779070823; source ids: part2-viral-immune-mimicry-2025; source locator: Table 1: Accur., Held-out human-versus-virus protein classification; context: Compare protein origin classifiers; T 5 embeddings plus linear/tree models vs ESM 2 fine-tuning and simple controls. UniRef90 deduplication; proteins longer than1,600 residues excluded; UniRef50 clusters assigned80% training and20% test with no cluster shared. Separate four-fold error-analysis experiment not assigned toTable1.; caveats: Origin classification does not establish immune mimicry.; Table footnote says all values are percent but log-loss values are dimensionless; log-loss units quarantined.; Narrative n-gram AUC91.9 differs from Table1 value91.5; preserve table value.; No interval assigned unless printed in source cell.; review: method: automated_source_review; date: 2026-09-17; id: part2-viral-immune-mimicry-2025-viruses-17-01199-t001-e488608662; title: Held-out human-versus-virus protein classification · Table 1; protocol id: paper-protocol-1352834b9391c1dacb; dataset id: reported-dataset-43f24c4dfb7351; metric: Prec.; unit: percent; direction: higher; result ids: paper-result-a950e05fb8768ed4e8; paper-result-0c1a3836d475c5a506; paper-result-00f7697f28c706f26b; paper-result-1f9cd7bc0d3be4259f; paper-result-24e80b6223e7bd1109; paper-result-0c5e3578112cc7247a; paper-result-c583dfa48d139dadc8; paper-result-f67a4402bb1e2c96ba; source ids: part2-viral-immune-mimicry-2025; source locator: Table 1: Prec., Held-out human-versus-virus protein classification; context: Compare protein origin classifiers; T 5 embeddings plus linear/tree models vs ESM 2 fine-tuning and simple controls. UniRef90 deduplication; proteins longer than1,600 residues excluded; UniRef50 clusters assigned80% training and20% test with no cluster shared. Separate four-fold error-analysis experiment not assigned toTable1.; caveats: Origin classification does not establish immune mimicry.; Table footnote says all values are percent but log-loss values are dimensionless; log-loss units quarantined.; Narrative n-gram AUC91.9 differs from Table1 value91.5; preserve table value.; No interval assigned unless printed in source cell.; review: method: automated_source_review; date: 2026-09-17; id: part2-viral-immune-mimicry-2025-viruses-17-01199-t001-a4943fb2ad; title: Held-out human-versus-virus protein classification · Table 1; protocol id: paper-protocol-1352834b9391c1dacb; dataset id: reported-dataset-43f24c4dfb7351; metric: Recall; unit: percent; direction: higher; result ids: paper-result-b36e1a943ebc5dfb9a; paper-result-ccac699408a1229570; paper-result-4f2c34cb0e09f0167a; paper-result-4014edf9066fc226f1; paper-result-9d9d31080b47613e46; paper-result-a42799c550a1ae61e7; paper-result-67bb8fdb6692f4336f; paper-result-2aafdf0e911ae9cff5; source ids: part2-viral-immune-mimicry-2025; source locator: Table 1: Recall, Held-out human-versus-virus protein classification; context: Compare protein origin classifiers; T 5 embeddings plus linear/tree models vs ESM 2 fine-tuning and simple controls. UniRef90 deduplication; proteins longer than1,600 residues excluded; UniRef50 clusters assigned80% training and20% test with no cluster shared. Separate four-fold error-analysis experiment not assigned toTable1.; caveats: Origin classification does not establish immune mimicry.; Table footnote says all values are percent but log-loss values are dimensionless; log-loss units quarantined.; Narrative n-gram AUC91.9 differs from Table1 value91.5; preserve table value.; No interval assigned unless printed in source cell.; review: method: automated_source_review; date: 2026-09-17
- benchmark research
- review date: 2026-09-17; status: complete_comparison_tables_extracted_pending_publication_review; primary sources: part2-viral-immune-mimicry-2025; inspected locators: Table1; held-out protein-origin classification; separate error-analysis CV; searched queries: Protein Language Models Expose Viral Immune Mimicry primary paper benchmark results; gaps: Independent batch review before import; preserve existing observation identities.; claim scope: Primary-source discovery and table/protocol screening; source checked is not independently reproduced. Raw acquisitions not automatically numerical publication approval.
- historical missing metadata
- protocol version: not_reported_in_legacy_extract; split: 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: viral-immune-mimicry-2025; source locator: Abstract; Methods 2.1 Protein Datasets and 2.6 Model Performance; Table 1; 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.