Evidence claim

S3F: description

Description of S3F

Sequence-Structure-Surface Fitness model that combines protein language model sequence representations with Geometric Vector Perceptron encoders of the backbone and surface to predict protein fitness zero-shot, scored in ProteinGym as a substitution baseline.

Replace a placeholder or provenance description with a sourced functional description (issue #88a). Historical releases retain the original value.

Evidence

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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.

28 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
Property and statement	Original source and location	Review and provenance
Claimed field description Context-only references	Abstract: Multi-Scale Representation Learning for Protein Fitness Prediction Original source ↗ uc20260930-source-proteingym-amfr-spearman: Benchmark CSV header (model scored in the zero-shot DMS substitution benchmark); run-doc-proteingym-readme-md-144fe22b: README 'Leaderboard' baseline table (model name, input modalities, reference); qa-descriptions-20261010-source-s3f: abstract; qa-descriptions-20261010-source-s3f-html: Section 4 experimental setup (S2F, S2F-MSA, S3F-MSA definitions) Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: arXiv API entry for 2412.01108v1 (title and abstract) Retrieved: 2026-10-10T06:44:48Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.field` Source artifact SHA-256: `2fdfced916db0418fdbe0188747b1c8e3c1b0832aec6569642ffcdc97b4ae551` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Claimed field description Context-only references	Multi-Scale Representation Learning for Protein Fitness Prediction (arXiv HTML full text) Original source ↗ uc20260930-source-proteingym-amfr-spearman: Benchmark CSV header (model scored in the zero-shot DMS substitution benchmark); run-doc-proteingym-readme-md-144fe22b: README 'Leaderboard' baseline table (model name, input modalities, reference); qa-descriptions-20261010-source-s3f: abstract; qa-descriptions-20261010-source-s3f-html: Section 4 experimental setup (S2F, S2F-MSA, S3F-MSA definitions) Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: arXiv 2412.01108v1 HTML Retrieved: 2026-10-10T06:46:14Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.field` Source artifact SHA-256: `9906e21b676729f27185a9554001d06455ceb588e889520f8b9a52f010048dda` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Claimed field description Context-only references	OATML-Markslab/ProteinGym / README.md Original source ↗ uc20260930-source-proteingym-amfr-spearman: Benchmark CSV header (model scored in the zero-shot DMS substitution benchmark); run-doc-proteingym-readme-md-144fe22b: README 'Leaderboard' baseline table (model name, input modalities, reference); qa-descriptions-20261010-source-s3f: abstract; qa-descriptions-20261010-source-s3f-html: Section 4 experimental setup (S2F, S2F-MSA, S3F-MSA definitions) Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Git commit 144fe22b07dfaeec2b366f2346203a9838a55b4c Retrieved: 2026-09-17T09:32:03.517591+00:00	not individually reviewed No individual claim review recorded Audit details Field: `attributes.field` Source artifact SHA-256: `321487a8de52c6cfa647a658f61150dd72e0acb0125470524fb94d1f8b23321a` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Claimed field description Context-only references	ProteinGym AMFR assay-level Spearman comparison Original source ↗ uc20260930-source-proteingym-amfr-spearman: Benchmark CSV header (model scored in the zero-shot DMS substitution benchmark); run-doc-proteingym-readme-md-144fe22b: README 'Leaderboard' baseline table (model name, input modalities, reference); qa-descriptions-20261010-source-s3f: abstract; qa-descriptions-20261010-source-s3f-html: Section 4 experimental setup (S2F, S2F-MSA, S3F-MSA definitions) Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 144fe22b07dfaeec2b366f2346203a9838a55b4c Retrieved: 2026-09-30	not individually reviewed No individual claim review recorded Audit details Field: `attributes.field` Source artifact SHA-256: `f432423b87f79ac9778dfac86e3d95be041d246bc618dc0a406b35b0b7466437` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Previous value Named prediction model family identified in the cited primary source. Exact fitted configurations and scores are separate records. Context-only references	Abstract: Multi-Scale Representation Learning for Protein Fitness Prediction Original source ↗ uc20260930-source-proteingym-amfr-spearman: Benchmark CSV header (model scored in the zero-shot DMS substitution benchmark); run-doc-proteingym-readme-md-144fe22b: README 'Leaderboard' baseline table (model name, input modalities, reference); qa-descriptions-20261010-source-s3f: abstract; qa-descriptions-20261010-source-s3f-html: Section 4 experimental setup (S2F, S2F-MSA, S3F-MSA definitions) Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: arXiv API entry for 2412.01108v1 (title and abstract) Retrieved: 2026-10-10T06:44:48Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.previous_value` Source artifact SHA-256: `2fdfced916db0418fdbe0188747b1c8e3c1b0832aec6569642ffcdc97b4ae551` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Previous value Named prediction model family identified in the cited primary source. Exact fitted configurations and scores are separate records. Context-only references	Multi-Scale Representation Learning for Protein Fitness Prediction (arXiv HTML full text) Original source ↗ uc20260930-source-proteingym-amfr-spearman: Benchmark CSV header (model scored in the zero-shot DMS substitution benchmark); run-doc-proteingym-readme-md-144fe22b: README 'Leaderboard' baseline table (model name, input modalities, reference); qa-descriptions-20261010-source-s3f: abstract; qa-descriptions-20261010-source-s3f-html: Section 4 experimental setup (S2F, S2F-MSA, S3F-MSA definitions) Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: arXiv 2412.01108v1 HTML Retrieved: 2026-10-10T06:46:14Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.previous_value` Source artifact SHA-256: `9906e21b676729f27185a9554001d06455ceb588e889520f8b9a52f010048dda` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Previous value Named prediction model family identified in the cited primary source. Exact fitted configurations and scores are separate records. Context-only references	OATML-Markslab/ProteinGym / README.md Original source ↗ uc20260930-source-proteingym-amfr-spearman: Benchmark CSV header (model scored in the zero-shot DMS substitution benchmark); run-doc-proteingym-readme-md-144fe22b: README 'Leaderboard' baseline table (model name, input modalities, reference); qa-descriptions-20261010-source-s3f: abstract; qa-descriptions-20261010-source-s3f-html: Section 4 experimental setup (S2F, S2F-MSA, S3F-MSA definitions) Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Git commit 144fe22b07dfaeec2b366f2346203a9838a55b4c Retrieved: 2026-09-17T09:32:03.517591+00:00	not individually reviewed No individual claim review recorded Audit details Field: `attributes.previous_value` Source artifact SHA-256: `321487a8de52c6cfa647a658f61150dd72e0acb0125470524fb94d1f8b23321a` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Previous value Named prediction model family identified in the cited primary source. Exact fitted configurations and scores are separate records. Context-only references	ProteinGym AMFR assay-level Spearman comparison Original source ↗ uc20260930-source-proteingym-amfr-spearman: Benchmark CSV header (model scored in the zero-shot DMS substitution benchmark); run-doc-proteingym-readme-md-144fe22b: README 'Leaderboard' baseline table (model name, input modalities, reference); qa-descriptions-20261010-source-s3f: abstract; qa-descriptions-20261010-source-s3f-html: Section 4 experimental setup (S2F, S2F-MSA, S3F-MSA definitions) Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 144fe22b07dfaeec2b366f2346203a9838a55b4c Retrieved: 2026-09-30	not individually reviewed No individual claim review recorded Audit details Field: `attributes.previous_value` Source artifact SHA-256: `f432423b87f79ac9778dfac86e3d95be041d246bc618dc0a406b35b0b7466437` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Source location uc20260930-source-proteingym-amfr-spearman: Benchmark CSV header (model scored in the zero-shot DMS substitution benchmark); run-doc-proteingym-readme-md-144fe22b: README 'Leaderboard' baseline table (model name, input modalities, reference); qa-descriptions-20261010-source-s3f: abstract; qa-descriptions-20261010-source-s3f-html: Section 4 experimental setup (S2F, S2F-MSA, S3F-MSA definitions) Context-only references	Abstract: Multi-Scale Representation Learning for Protein Fitness Prediction Original source ↗ uc20260930-source-proteingym-amfr-spearman: Benchmark CSV header (model scored in the zero-shot DMS substitution benchmark); run-doc-proteingym-readme-md-144fe22b: README 'Leaderboard' baseline table (model name, input modalities, reference); qa-descriptions-20261010-source-s3f: abstract; qa-descriptions-20261010-source-s3f-html: Section 4 experimental setup (S2F, S2F-MSA, S3F-MSA definitions) Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: arXiv API entry for 2412.01108v1 (title and abstract) Retrieved: 2026-10-10T06:44:48Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.source_locator` Source artifact SHA-256: `2fdfced916db0418fdbe0188747b1c8e3c1b0832aec6569642ffcdc97b4ae551` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Source location uc20260930-source-proteingym-amfr-spearman: Benchmark CSV header (model scored in the zero-shot DMS substitution benchmark); run-doc-proteingym-readme-md-144fe22b: README 'Leaderboard' baseline table (model name, input modalities, reference); qa-descriptions-20261010-source-s3f: abstract; qa-descriptions-20261010-source-s3f-html: Section 4 experimental setup (S2F, S2F-MSA, S3F-MSA definitions) Context-only references	Multi-Scale Representation Learning for Protein Fitness Prediction (arXiv HTML full text) Original source ↗ uc20260930-source-proteingym-amfr-spearman: Benchmark CSV header (model scored in the zero-shot DMS substitution benchmark); run-doc-proteingym-readme-md-144fe22b: README 'Leaderboard' baseline table (model name, input modalities, reference); qa-descriptions-20261010-source-s3f: abstract; qa-descriptions-20261010-source-s3f-html: Section 4 experimental setup (S2F, S2F-MSA, S3F-MSA definitions) Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: arXiv 2412.01108v1 HTML Retrieved: 2026-10-10T06:46:14Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.source_locator` Source artifact SHA-256: `9906e21b676729f27185a9554001d06455ceb588e889520f8b9a52f010048dda` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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Sources and history

Release 2026-10-22-1b7cf027e4f6 · Record review: source checked

4 source records and release history

ProteinGym AMFR assay-level Spearman comparison · Original source · 144fe22b07dfaeec2b366f2346203a9838a55b4c
OATML-Markslab/ProteinGym / README.md · Original source · Git commit 144fe22b07dfaeec2b366f2346203a9838a55b4c
Abstract: Multi-Scale Representation Learning for Protein Fitness Prediction · Original source · arXiv API entry for 2412.01108v1 (title and abstract)
Multi-Scale Representation Learning for Protein Fitness Prediction (arXiv HTML full text) · Original source · arXiv 2412.01108v1 HTML

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Technical metadata and extraction receipts

Stable ID: metadata-correction-7b52813f1b702eada378

areas: proteins-complexes
field: description
previous value: Named prediction model family identified in the cited primary source. Exact fitted configurations and scores are separate records.
value: Sequence-Structure-Surface Fitness model that combines protein language model sequence representations with Geometric Vector Perceptron encoders of the backbone and surface to predict protein fitness zero-shot, scored in ProteinGym as a substitution baseline.
source locator: uc20260930-source-proteingym-amfr-spearman: Benchmark CSV header (model scored in the zero-shot DMS substitution benchmark); run-doc-proteingym-readme-md-144fe22b: README 'Leaderboard' baseline table (model name, input modalities, reference); qa-descriptions-20261010-source-s3f: abstract; qa-descriptions-20261010-source-s3f-html: Section 4 experimental setup (S2F, S2F-MSA, S3F-MSA definitions)
review: method: automated-source-review; ai-assisted-source-review; reviewer: claude; reviewer note: Extractor: Claude research agent for issue #88a. Reviewer: separate Claude review agent, independent of the extractor; no human review claimed; date: 2026-10-10; method note: Compared the description with the cited source text (abstract, README row, benchmark CSV header or full-text section) of re-downloaded artifacts, and previous_value with origin/main.; note: Description written from the cited source text; provenance text was generic and is kept here as previous_value. Independent review 2026-10-10: every stated fact is supported by the cited text.

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