Strengths and considerations
No source-reviewed explanatory claims are recorded here yet.
Protocol
Held-out human-versus-virus protein classification (human-versus-viral protein classification)
Held-out human-versus-virus protein classification · Table 1. 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.
Sources
Protein Language Models Expose Viral Immune Mimicry · Table 1: AUC (%), Held-out human-versus-virus protein classificationOverview
Key specifications have not been extracted for this record. See the linked evaluation and sources for the reported setup.
limited source coverage · Automated source review, 2026-09-17. 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
Evaluation in this paper
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.
Sources
Protein Language Models Expose Viral Immune Mimicry · Table 1: AUC (%), Held-out human-versus-virus protein classificationEvaluation design
Benchmarks bring together tasks and protocols. A task describes the biological question; a protocol defines a particular test.
These source-backed links do not make different protocols or scores interchangeable.
Recorded evaluations
Each evaluation records what was tested and under which conditions.
- ESM2 650M: human-versus-viral protein classification
- Tree-T5: Held-out human-versus-virus protein classification
- BL Length: Held-out human-versus-virus protein classification
- AA n-grams: Held-out human-versus-virus protein classification
- ESM2 8M: Held-out human-versus-virus protein classification
- ESM2 35M: Held-out human-versus-virus protein classification
- ESM2 150M: Held-out human-versus-virus protein classification
- Linear-T5: Held-out human-versus-virus protein classification
Baseline coverage
Reference methods help show what a model adds beyond simple controls. We track a null control and a conventional method for each protocol.
0 of 2 active baseline roles have published Rewire measurements in this release. Measurements on a selected protocol do not establish coverage of an entire suite.
No execution recipe linked to this protocol. Recipe availability does not establish a completed evaluation.
No reviewed evaluations with results linked in this release.
Literature evidence is not a Rewire measurement. Executed but unpublished runs and private review status are not included.
Null control
Proposed control: requires review
Training-set class prior where supervised fitting is permitted
Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.
This is a suggested selection rule, not a validated method or a measured score.
Conventional reference
Proposed control: requires review
Regularised classifier on simple permitted features, or protocol's conventional reference
Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.
This is a suggested selection rule, not a validated method or a measured score.
Protocol coverage CSV · Model evaluation matrix · Source table · Release and checksums
Coverage is derived from release 2026-09-29-06401fd5b220. Source citations describe the original records; they do not validate an unreviewed baseline proposal. No results have been generated by this audit.
Run instructions
No runnable recipe has been reviewed for this protocol. Dataset access, model requirements, licences and compute requirements must be checked against its sources before execution.
Strengths, limitations and unresolved questions
Strengths and limitations
Limitations and conditions
No source-reviewed explanatory claims are recorded here yet.
Profile review details
Primary-source transcription and separate automated review. No human sign-off or experimental reproduction.
Stable record: paper-protocol-1352834b9391c1dacbSpecifications
Inputs, training, access and other details
Explanatory profile: limited source coverage · Automated source review, 2026-09-17. Review applies to the cited claims; unresolved fields are listed below. Numerical results retain their own review status.
| Property | Description and evidence |
|---|---|
| Datasets | Not extracted or verified for this record. |
| Organisms | Not extracted or verified for this record. |
| Assays | Not extracted or verified for this record. |
| Splits | Not extracted or verified for this record. |
| Allowed inputs | Not extracted or verified for this record. |
| Adaptation | Not extracted or verified for this record. |
| Metrics | Not extracted or verified for this record. |
| Baselines | Not extracted or verified for this record. |
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
- Table 1: AUC (%), Held-out human-versus-virus protein classification
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.
3 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Evaluation in this paper 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. Individual claims | Protein Language Models Expose Viral Immune Mimicry Table 1: AUC (%), Held-out human-versus-virus protein classification Version: version of record | source checked automated source review · 2026-09-17 Audit detailsPrimary-source transcription and separate automated review. No human sign-off or experimental reproduction. Field: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| Introduction Held-out human-versus-virus protein classification · Table 1. 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. Individual claims | Protein Language Models Expose Viral Immune Mimicry Table 1: AUC (%), Held-out human-versus-virus protein classification Version: version of record | source checked automated source review · 2026-09-17 Audit detailsPrimary-source transcription and separate automated review. No human sign-off or experimental reproduction. Field: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| Relationship: evaluates task reported-task-53506fe386e4a1 Individual claims | Protein Language Models Expose Viral Immune Mimicry Table 1: AUC (%), Held-out human-versus-virus protein classification Version: version of record | source checked automated source review · 2026-09-17 Audit detailsField: Claim: paper-claim-91e8ca5ec38f180326 Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
Sources and history
View linked audit checks and correction history
Release 2026-09-29-06401fd5b220 · Record review: needs review
1 source records and release history
- Protein Language Models Expose Viral Immune Mimicry · Original source · version of record
Technical metadata and extraction receipts
Stable ID: paper-protocol-1352834b9391c1dacb
- areas
- proteins-complexes
- tasks
- human-versus-viral protein classification
- entity level
- protocol
- protocol
- 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.
- 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: Table 1: AUC (%), Held-out human-versus-virus protein classification; 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.
- legacy kinds
- benchmark
- entity classification
- review date: 2026-09-17; rationale: The source-backed record identifies a specified evaluated procedure and its dataset/split/scoring context. Classify it as a protocol while preserving version and comparison restrictions.; source ids: part2-viral-immune-mimicry-2025; source locator: Table 1: AUC (%), Held-out human-versus-virus protein classification; ambiguities: None recorded
Related records
- evaluates task: human-versus-viral protein classification
- benchmark: ESM2 650M: human-versus-viral protein classification
- subject: Held-out human-versus-virus protein classification (human-versus-viral protein classification): links:evaluates_task:reported-task-53506fe386e4a1
- benchmark: Tree-T5: Held-out human-versus-virus protein classification
- benchmark: BL Length: Held-out human-versus-virus protein classification
- benchmark: AA n-grams: Held-out human-versus-virus protein classification
- benchmark: ESM2 8M: Held-out human-versus-virus protein classification
- benchmark: ESM2 35M: Held-out human-versus-virus protein classification
- benchmark: ESM2 150M: Held-out human-versus-virus protein classification
- benchmark: Linear-T5: Held-out human-versus-virus protein classification