Pseudo-perplexity in One Fell Swoop for Protein Fitness Estimation
2025 · PRX Life 2025 journal article · Peer-reviewed
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Results
Values as the source printed them. Compare results only under compatible protocols, datasets and metrics.
| Model or configuration | Metric | Value | Dataset | Evaluation |
|---|---|---|---|---|
| ESM2 OFS pseudo-perplexity | Spearman | 0.403 unitless | ProteinGym substitutions | ESM2 OFS pseudo-perplexity: protein variant fitness prediction |
Claims
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- ESM2 OFS pseudo-perplexity: description: Description Estimates protein fitness from the negative pseudo-perplexity of a sequence, approximated in a single unmasked forward pass by an ensemble of eight multilayer perceptrons that predict the ESM-2 650M masked residue profiles. (Reviewed profile (2026-09-16): summary at Section III, One Fell Swoop; Figure 1; Section IV fitness evaluation; architecture fact at Section III, One Fell Swoop; Figure 1; Section IV fitness evaluation; description text also read at Abstract; Section III Pseudo-perplexity in one fell swoop)
- ESM2 OFS pseudo-perplexity: uses model ESM-2: Uses model ESM-2 (One Fell Swoop sequence-profile procedure; ESM2 650M unmasked residue embeddings)
- Reported Spearman rho for ESM2 OFS pseudo-perplexity: Printed value 0.403 (Published PDF page 6 (033014-6), Table I, ESM2: OFS PP row, Aggregate mean column)
Models, benchmarks and other records
Pipelines (1)
Tasks (1)
Datasets (1)
Evaluations (1)
Evidence
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Evidence table
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18 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Artifact retrieved at 2026-09-16T10:45:41.099916+00:00 Source metadata | Pseudo-perplexity in One Fell Swoop for Protein Fitness Estimation No field-specific location recorded Version: PRX Life 2025 journal article | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Artifact SHA-256 085ef646f11b8e5335c4b3d86b15fb6c7bf5edf4a80a8b622753ac69d9991a67 Source metadata | Pseudo-perplexity in One Fell Swoop for Protein Fitness Estimation No field-specific location recorded Version: PRX Life 2025 journal article | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Artifact url https://harvest.aps.org/v2/journals/articles/10.1103/zhx7-hcmm/fulltext Source metadata | Pseudo-perplexity in One Fell Swoop for Protein Fitness Estimation No field-specific location recorded Version: PRX Life 2025 journal article | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Doi 10.1103/zhx7-hcmm Source metadata | Pseudo-perplexity in One Fell Swoop for Protein Fitness Estimation No field-specific location recorded Version: PRX Life 2025 journal article | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Missing metadata: licence: reason unextracted Source metadata | Pseudo-perplexity in One Fell Swoop for Protein Fitness Estimation No field-specific location recorded Version: PRX Life 2025 journal article | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Publication status peer_reviewed Source metadata | Pseudo-perplexity in One Fell Swoop for Protein Fitness Estimation No field-specific location recorded Version: PRX Life 2025 journal article | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Retrieved at 2026-09-15T23:33:26Z Source metadata | Pseudo-perplexity in One Fell Swoop for Protein Fitness Estimation No field-specific location recorded Version: PRX Life 2025 journal article | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Scope decision included Source metadata | Pseudo-perplexity in One Fell Swoop for Protein Fitness Estimation No field-specific location recorded Version: PRX Life 2025 journal article | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Url https://journals.aps.org/prxlife/pdf/10.1103/zhx7-hcmm Source metadata | Pseudo-perplexity in One Fell Swoop for Protein Fitness Estimation No field-specific location recorded Version: PRX Life 2025 journal article | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Version PRX Life 2025 journal article Source metadata | Pseudo-perplexity in One Fell Swoop for Protein Fitness Estimation No field-specific location recorded Version: PRX Life 2025 journal article | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Sources and history
Release 2026-11-02-a7f03c9e55a5 · Record review: discovered
Primary paper retained with its original identifier. Metadata inherited from the literature collection; individual result checks are separate.
Technical metadata and extraction receipts
Stable ID: esm2-ofs-fitness-2025
- areas
- proteins-complexes
- url
- https://journals.aps.org/prxlife/pdf/10.1103/zhx7-hcmm
- version
- PRX Life 2025 journal article
- retrieved at
- 2026-09-15T23:33:26Z
- doi
- 10.1103/zhx7-hcmm
- publication status
- peer_reviewed
- year
- 2025
- artifact sha256
- 085ef646f11b8e5335c4b3d86b15fb6c7bf5edf4a80a8b622753ac69d9991a67
- artifact url
- https://harvest.aps.org/v2/journals/articles/10.1103/zhx7-hcmm/fulltext
- artifact retrieved at
- 2026-09-16T10:45:41.099916+00:00
- scope decision
- included
- missing metadata
- licence: reason: unextracted