Leakage control applied to the four-target subset
Leakage control of FEP+ benchmark four-target subset, affinity ranking and cost
Training proteins with at least 90% sequence similarity to a validation or test protein were removed, by clustering all affinity-dataset protein sequences with 'mmseqs easy-cluster ... --min-seq-id 0.9 --cov-mode 0 -c 0.01' and dropping any training protein sharing a cluster with a validation or test protein (appendix D.2.1, 'Data leakage control'). Compound-level dependence was checked in Figure 10 and no strong dependence was observed; that figure prints no values.
The training-data filtering the Boltz-2 supplement applied before scoring the four-target subset.
Evidence
Source checking verifies the cited claim or transcription. It does not establish independent reproduction.
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.
6 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Claimed field leakage_control Context-only references | Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix Appendix D.2.1, 'Data leakage control'; Figure 10 Version: bioRxiv v1 posted 2025-06-18; supplement PDF as deposited in Europe PMC PMC12262699 (PPR1038344) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: The recorded hash is of the supplement PDF itself, extracted from the Europe PMC supplementaryFiles ZIP (ZIP SHA-256 25050dabd9c66fdb955704095023037f1bbabc3a93b7b61f00344c75df8bdb70 on 2026-10-22; the ZIP is rebuilt per request and its hash is not stable). Archive member: NIHPP2025.06.14.659707v1-supplement-1.pdf |
| Source location Appendix D.2.1, 'Data leakage control'; Figure 10 Context-only references | Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix Appendix D.2.1, 'Data leakage control'; Figure 10 Version: bioRxiv v1 posted 2025-06-18; supplement PDF as deposited in Europe PMC PMC12262699 (PPR1038344) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: The recorded hash is of the supplement PDF itself, extracted from the Europe PMC supplementaryFiles ZIP (ZIP SHA-256 25050dabd9c66fdb955704095023037f1bbabc3a93b7b61f00344c75df8bdb70 on 2026-10-22; the ZIP is rebuilt per request and its hash is not stable). Archive member: NIHPP2025.06.14.659707v1-supplement-1.pdf |
| Claimed value Training proteins with at least 90% sequence similarity to a validation or test protein were removed, by clustering all affinity-dataset protein sequences with 'mmseqs easy-cluster ... --min-seq-id 0.9 --cov-mode 0 -c 0.01' and dropping any training protein sharing a cluster with a validation or test protein (appendix D.2.1, 'Data leakage control'). Compound-level dependence was checked in Figure 10 and no strong dependence was observed; that figure prints no values. Context-only references | Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix Appendix D.2.1, 'Data leakage control'; Figure 10 Version: bioRxiv v1 posted 2025-06-18; supplement PDF as deposited in Europe PMC PMC12262699 (PPR1038344) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: The recorded hash is of the supplement PDF itself, extracted from the Europe PMC supplementaryFiles ZIP (ZIP SHA-256 25050dabd9c66fdb955704095023037f1bbabc3a93b7b61f00344c75df8bdb70 on 2026-10-22; the ZIP is rebuilt per request and its hash is not stable). Archive member: NIHPP2025.06.14.659707v1-supplement-1.pdf |
| Description The training-data filtering the Boltz-2 supplement applied before scoring the four-target subset. Context-only references | Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix Appendix D.2.1, 'Data leakage control'; Figure 10 Version: bioRxiv v1 posted 2025-06-18; supplement PDF as deposited in Europe PMC PMC12262699 (PPR1038344) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: The recorded hash is of the supplement PDF itself, extracted from the Europe PMC supplementaryFiles ZIP (ZIP SHA-256 25050dabd9c66fdb955704095023037f1bbabc3a93b7b61f00344c75df8bdb70 on 2026-10-22; the ZIP is rebuilt per request and its hash is not stable). Archive member: NIHPP2025.06.14.659707v1-supplement-1.pdf |
| Relationship: subject uc-leadopt-20261022-protocol-boltz2-fep-4target Context-only references | Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix Appendix D.2.1, 'Data leakage control'; Figure 10 Version: bioRxiv v1 posted 2025-06-18; supplement PDF as deposited in Europe PMC PMC12262699 (PPR1038344) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: The recorded hash is of the supplement PDF itself, extracted from the Europe PMC supplementaryFiles ZIP (ZIP SHA-256 25050dabd9c66fdb955704095023037f1bbabc3a93b7b61f00344c75df8bdb70 on 2026-10-22; the ZIP is rebuilt per request and its hash is not stable). Archive member: NIHPP2025.06.14.659707v1-supplement-1.pdf |
| Name Leakage control applied to the four-target subset Context-only references | Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix Appendix D.2.1, 'Data leakage control'; Figure 10 Version: bioRxiv v1 posted 2025-06-18; supplement PDF as deposited in Europe PMC PMC12262699 (PPR1038344) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: The recorded hash is of the supplement PDF itself, extracted from the Europe PMC supplementaryFiles ZIP (ZIP SHA-256 25050dabd9c66fdb955704095023037f1bbabc3a93b7b61f00344c75df8bdb70 on 2026-10-22; the ZIP is rebuilt per request and its hash is not stable). Archive member: NIHPP2025.06.14.659707v1-supplement-1.pdf |
Sources and history
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
1 source record and release history
- Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix · Original source · bioRxiv v1 posted 2025-06-18; supplement PDF as deposited in Europe PMC PMC12262699 (PPR1038344)
Technical metadata and extraction receipts
Stable ID: uc-leadopt-20261022-claim-leakage-4target
- field
- leakage_control
- value
- Training proteins with at least 90% sequence similarity to a validation or test protein were removed, by clustering all affinity-dataset protein sequences with 'mmseqs easy-cluster ... --min-seq-id 0.9 --cov-mode 0 -c 0.01' and dropping any training protein sharing a cluster with a validation or test protein (appendix D.2.1, 'Data leakage control'). Compound-level dependence was checked in Figure 10 and no strong dependence was observed; that figure prints no values.
- source locator
- Appendix D.2.1, 'Data leakage control'; Figure 10
- review
- method: source-hash-verification; pdf-text-parse; independent-cell-check; rendered-source-visual-check; ai-assisted-source-review; method note: Re-retrieved all three sources and matched each pinned SHA-256. Re-rendered the Boltz-2 supplement with pdftotext -layout (poppler 26.08.0) and matched the text layer's recorded SHA-256. Re-read all 256 cells with a parser written for this review that does not import the extraction script, matching each result to its cell through its own source_locator, and separately read appendix tables 11, 12 and 14 from PNG renderings of PDF pages 29 and 30 at 160 dpi, and Ross Table 3 from the pinned XML markup. Checked printed value, numeric value, locator, metric concept, qualifier, direction, unit, uncertainty and the linked configuration, protocol and dataset, and that every N/A or '-' cell is recorded as missing with a reason.; reviewer: claude; reviewer note: Claude review agent, independent of the extraction agent; no human review claimed; reviewed at: 2026-10-22T13:40:00Z; artifact sha256: be867a5d92add8b223d47d882a4213ad489741f3e4d5081a0901a54370342569; retrieval url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12262699/supplementaryFiles; note: Independent review 2026-10-22: the quoted wording was matched against the pinned artifact and the locator checked.