Evidence claim

ProteinBench against ProteinGym on ESM3 and ProteinMPNN: different tasks

Discrepancy review of ESM3 · ProteinBench IF-DE-NOVO-BACKBONES-BASED-SEQUENCE-DESIGN-LENGTH-100-PLDDT · pLDDT

explained

Review of discrepancy-d586dd34b17efa52, revision 2: explained. Discrepancy rules version 4 gave discrepancy-f82ed80f71c6f0bd a new ID (two-study-conflict); the state and resolution are carried forward unchanged.

Evidence

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Evidence table

Inspect claims, sources and review details

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31 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-11-02-a7f03c9e55a5
Property and statement	Original source and location	Review and provenance
Date 2026-10-24 Context-only references	proteinbench primary benchmark evidence Original source ↗ The outlier and consensus results of discrepancy-f82ed80f71c6f0bd as published at https://benchmarks.rewirebio.io/contested/discrepancy-f82ed80f71c6f0bd/ (release 2026-10-23-968c8720eea6) Version: 2409.06744v1 Retrieved: 2026-09-16T21:07:13.231727+00:00	not individually reviewed No individual claim review recorded Audit details Field: `attributes.date` Source artifact SHA-256: `4334d636223ad42bfb9ae68aae03f5a255c29ba1cebe7b8f9588fb3b9b5453b2` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
Discrepancy id discrepancy-d586dd34b17efa52 Context-only references	proteinbench primary benchmark evidence Original source ↗ The outlier and consensus results of discrepancy-f82ed80f71c6f0bd as published at https://benchmarks.rewirebio.io/contested/discrepancy-f82ed80f71c6f0bd/ (release 2026-10-23-968c8720eea6) Version: 2409.06744v1 Retrieved: 2026-09-16T21:07:13.231727+00:00	not individually reviewed No individual claim review recorded Audit details Field: `attributes.discrepancy_id` Source artifact SHA-256: `4334d636223ad42bfb9ae68aae03f5a255c29ba1cebe7b8f9588fb3b9b5453b2` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
Claimed field discrepancy_review Context-only references	proteinbench primary benchmark evidence Original source ↗ The outlier and consensus results of discrepancy-f82ed80f71c6f0bd as published at https://benchmarks.rewirebio.io/contested/discrepancy-f82ed80f71c6f0bd/ (release 2026-10-23-968c8720eea6) Version: 2409.06744v1 Retrieved: 2026-09-16T21:07:13.231727+00:00	not individually reviewed No individual claim review recorded Audit details Field: `attributes.field` Source artifact SHA-256: `4334d636223ad42bfb9ae68aae03f5a255c29ba1cebe7b8f9588fb3b9b5453b2` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
Investigation url https://github.com/rewire-bio/rewire-benchmark-data/issues/205 Context-only references	proteinbench primary benchmark evidence Original source ↗ The outlier and consensus results of discrepancy-f82ed80f71c6f0bd as published at https://benchmarks.rewirebio.io/contested/discrepancy-f82ed80f71c6f0bd/ (release 2026-10-23-968c8720eea6) Version: 2409.06744v1 Retrieved: 2026-09-16T21:07:13.231727+00:00	not individually reviewed No individual claim review recorded Audit details Field: `attributes.investigation_url` Source artifact SHA-256: `4334d636223ad42bfb9ae68aae03f5a255c29ba1cebe7b8f9588fb3b9b5453b2` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
Previous ids 1 values discrepancy-f82ed80f71c6f0bd Context-only references	proteinbench primary benchmark evidence Original source ↗ The outlier and consensus results of discrepancy-f82ed80f71c6f0bd as published at https://benchmarks.rewirebio.io/contested/discrepancy-f82ed80f71c6f0bd/ (release 2026-10-23-968c8720eea6) Version: 2409.06744v1 Retrieved: 2026-09-16T21:07:13.231727+00:00	not individually reviewed No individual claim review recorded Audit details Field: `attributes.previous_ids` Source artifact SHA-256: `4334d636223ad42bfb9ae68aae03f5a255c29ba1cebe7b8f9588fb3b9b5453b2` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
Rationale ProteinBench ranks ProteinMPNN above ESM3 on de novo backbone sequence design (pLDDT and scTM after refolding); the consensus is ProteinGym zero-shot variant effect prediction, where ESM3 leads. Different endpoints; both kept as reported. The same pair also fires the other way round as discrepancy-fed245c475fd08dc, with ProteinGym as the outlier (issue 205). Context-only references	proteinbench primary benchmark evidence Original source ↗ The outlier and consensus results of discrepancy-f82ed80f71c6f0bd as published at https://benchmarks.rewirebio.io/contested/discrepancy-f82ed80f71c6f0bd/ (release 2026-10-23-968c8720eea6) Version: 2409.06744v1 Retrieved: 2026-09-16T21:07:13.231727+00:00	not individually reviewed No individual claim review recorded Audit details Field: `attributes.rationale` Source artifact SHA-256: `4334d636223ad42bfb9ae68aae03f5a255c29ba1cebe7b8f9588fb3b9b5453b2` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
Revision 2 Context-only references	proteinbench primary benchmark evidence Original source ↗ The outlier and consensus results of discrepancy-f82ed80f71c6f0bd as published at https://benchmarks.rewirebio.io/contested/discrepancy-f82ed80f71c6f0bd/ (release 2026-10-23-968c8720eea6) Version: 2409.06744v1 Retrieved: 2026-09-16T21:07:13.231727+00:00	not individually reviewed No individual claim review recorded Audit details Field: `attributes.revision` Source artifact SHA-256: `4334d636223ad42bfb9ae68aae03f5a255c29ba1cebe7b8f9588fb3b9b5453b2` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
Source location The outlier and consensus results of discrepancy-f82ed80f71c6f0bd as published at https://benchmarks.rewirebio.io/contested/discrepancy-f82ed80f71c6f0bd/ (release 2026-10-23-968c8720eea6) Context-only references	proteinbench primary benchmark evidence Original source ↗ The outlier and consensus results of discrepancy-f82ed80f71c6f0bd as published at https://benchmarks.rewirebio.io/contested/discrepancy-f82ed80f71c6f0bd/ (release 2026-10-23-968c8720eea6) Version: 2409.06744v1 Retrieved: 2026-09-16T21:07:13.231727+00:00	not individually reviewed No individual claim review recorded Audit details Field: `attributes.source_locator` Source artifact SHA-256: `4334d636223ad42bfb9ae68aae03f5a255c29ba1cebe7b8f9588fb3b9b5453b2` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
Claimed value explained Context-only references	proteinbench primary benchmark evidence Original source ↗ The outlier and consensus results of discrepancy-f82ed80f71c6f0bd as published at https://benchmarks.rewirebio.io/contested/discrepancy-f82ed80f71c6f0bd/ (release 2026-10-23-968c8720eea6) Version: 2409.06744v1 Retrieved: 2026-09-16T21:07:13.231727+00:00	not individually reviewed No individual claim review recorded Audit details Field: `attributes.value` Source artifact SHA-256: `4334d636223ad42bfb9ae68aae03f5a255c29ba1cebe7b8f9588fb3b9b5453b2` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
Description Review of discrepancy-d586dd34b17efa52, revision 2: explained. Discrepancy rules version 4 gave discrepancy-f82ed80f71c6f0bd a new ID (two-study-conflict); the state and resolution are carried forward unchanged. Context-only references	proteinbench primary benchmark evidence Original source ↗ The outlier and consensus results of discrepancy-f82ed80f71c6f0bd as published at https://benchmarks.rewirebio.io/contested/discrepancy-f82ed80f71c6f0bd/ (release 2026-10-23-968c8720eea6) Version: 2409.06744v1 Retrieved: 2026-09-16T21:07:13.231727+00:00	not individually reviewed No individual claim review recorded Audit details Field: `description` Source artifact SHA-256: `4334d636223ad42bfb9ae68aae03f5a255c29ba1cebe7b8f9588fb3b9b5453b2` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact

How to read the evidence

Sources and history

Release 2026-11-02-a7f03c9e55a5 · Record review: source checked

1 source record and release history

proteinbench primary benchmark evidence · Original source · 2409.06744v1

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Technical metadata and extraction receipts

Stable ID: discrepancy-review-20261023-proteinbench-esm3-proteinmpnn-r2

areas: proteins-complexes
contexts: research
field: discrepancy_review
discrepancy id: discrepancy-d586dd34b17efa52
revision: 2
value: explained
date: 2026-10-24
rationale: ProteinBench ranks ProteinMPNN above ESM3 on de novo backbone sequence design (pLDDT and scTM after refolding); the consensus is ProteinGym zero-shot variant effect prediction, where ESM3 leads. Different endpoints; both kept as reported. The same pair also fires the other way round as discrepancy-fed245c475fd08dc, with ProteinGym as the outlier (issue 205).
investigation url: https://github.com/rewire-bio/rewire-benchmark-data/issues/205
source locator: The outlier and consensus results of discrepancy-f82ed80f71c6f0bd as published at https://benchmarks.rewirebio.io/contested/discrepancy-f82ed80f71c6f0bd/ (release 2026-10-23-968c8720eea6)
review: method: automated-source-review; ai-assisted-source-review; reviewer: claude; reviewer note: Recorded by a Claude agent; no human review claimed.; date: 2026-10-24; method note: Read every outlier and consensus result of the finding, with its protocol, metric, configuration and source, from the published contested-result page, and compared the tasks, settings and configurations on each side. The original papers were not re-opened.; note: Carried forward by scripts/kg/migrate-discrepancy-ids.py when rules version 4 re-keyed the finding; the evidence and decision are those of discrepancy-review-20261023-proteinbench-esm3-proteinmpnn.
previous ids: discrepancy-f82ed80f71c6f0bd

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