Published comparison transcribed from the pinned source; not reproduced.
1 evaluation · 10 results. Different protocols are not a single leaderboard.
Protocol: FEP+ benchmark four-target subset, affinity ranking and cost · Dataset: Four-target subset of the public FEP benchmark
Sorted by Accelerator time (per-method cost as printed beside the accuracy columns) (lower is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.
| Tested configuration | Accelerator time (per-method cost as printed beside the accuracy columns) | Kendall tau (target average as printed, computed per assay and weighted by compound count) | MAE (centered, computed per assay and averaged across assays weighted by compound count) | MAE (non-centered, computed per assay and averaged across assays weighted by compound count) | MAE (pairwise, target average as printed, computed per assay and weighted by compound count) | Pearson (target average as printed, computed per assay and weighted by compound count) | Proportion (within 1 kcal/mol, centered, computed per assay and averaged across assays weighted by compound count) | Proportion (within 1 kcal/mol, non-centered, computed per assay and averaged across assays weighted by compound count) | Proportion (within 2 kcal/mol, centered, computed per assay and averaged across assays weighted by compound count) | Proportion (within 2 kcal/mol, non-centered, computed per assay and averaged across assays weighted by compound count) |
|---|---|---|---|---|---|---|---|---|---|---|
| BACPI ligand-only ablation (GAT)Evaluation | 0.18 GPU ms | 0.28 | 0.71 | 1.19 | 1.07 | 0.4 | 0.72 | 0.43 | 0.95 | 0.86 |
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: BACPI ligand-only ablation (GAT) | Protocol: FEP+ benchmark four-target subset, affinity ranking and cost Dataset: Four-target subset of the public FEP benchmark | 0.28 Kendall tau (target average as printed, computed per assay and weighted by compound count) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceGAT on the FEP+ benchmark four-target subset uc-leadopt-20261022-protocol-boltz2-fep-4target Aggregation: Not reported Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix · Table 12, row "GAT", column "Kendall tau", sub-column "target avg." (text-layer line 1709) |
| Configuration: BACPI ligand-only ablation (GAT) | Protocol: FEP+ benchmark four-target subset, affinity ranking and cost Dataset: Four-target subset of the public FEP benchmark | 0.71 MAE (centered, computed per assay and averaged across assays weighted by compound count) kilocalorie-per-mole · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceGAT on the FEP+ benchmark four-target subset uc-leadopt-20261022-protocol-boltz2-fep-4target Aggregation: Not reported Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix · Table 12, row "GAT", column "MAE", sub-column "cent." (text-layer line 1709) |
| Configuration: BACPI ligand-only ablation (GAT) | Protocol: FEP+ benchmark four-target subset, affinity ranking and cost Dataset: Four-target subset of the public FEP benchmark | 1.19 MAE (non-centered, computed per assay and averaged across assays weighted by compound count) kilocalorie-per-mole · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceGAT on the FEP+ benchmark four-target subset uc-leadopt-20261022-protocol-boltz2-fep-4target Aggregation: Not reported Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix · Table 12, row "GAT", column "MAE", sub-column "non-cent." (text-layer line 1709) |
| Configuration: BACPI ligand-only ablation (GAT) | Protocol: FEP+ benchmark four-target subset, affinity ranking and cost Dataset: Four-target subset of the public FEP benchmark | 0.4 Pearson (target average as printed, computed per assay and weighted by compound count) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceGAT on the FEP+ benchmark four-target subset uc-leadopt-20261022-protocol-boltz2-fep-4target Aggregation: Not reported Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix · Table 12, row "GAT", column "Pearson R", sub-column "target avg." (text-layer line 1709) |
| Configuration: BACPI ligand-only ablation (GAT) | Protocol: FEP+ benchmark four-target subset, affinity ranking and cost Dataset: Four-target subset of the public FEP benchmark | 1.07 MAE (pairwise, target average as printed, computed per assay and weighted by compound count) kilocalorie-per-mole · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceGAT on the FEP+ benchmark four-target subset uc-leadopt-20261022-protocol-boltz2-fep-4target Aggregation: Not reported Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix · Table 12, row "GAT", column "PMAE", sub-column "target avg." (text-layer line 1709) |
| Configuration: BACPI ligand-only ablation (GAT) | Protocol: FEP+ benchmark four-target subset, affinity ranking and cost Dataset: Four-target subset of the public FEP benchmark | 0.18 GPU ms Accelerator time (per-method cost as printed beside the accuracy columns) millisecond · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceGAT on the FEP+ benchmark four-target subset uc-leadopt-20261022-protocol-boltz2-fep-4target Aggregation: Not reported Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix · Table 12, row "GAT", column "time" (text-layer line 1709) |
| Configuration: BACPI ligand-only ablation (GAT) | Protocol: FEP+ benchmark four-target subset, affinity ranking and cost Dataset: Four-target subset of the public FEP benchmark | 0.72 Proportion (within 1 kcal/mol, centered, computed per assay and averaged across assays weighted by compound count) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceGAT on the FEP+ benchmark four-target subset uc-leadopt-20261022-protocol-boltz2-fep-4target Aggregation: Not reported Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix · Table 12, row "GAT", column "Perc. within 1", sub-column "cent." (text-layer line 1709) |
| Configuration: BACPI ligand-only ablation (GAT) | Protocol: FEP+ benchmark four-target subset, affinity ranking and cost Dataset: Four-target subset of the public FEP benchmark | 0.43 Proportion (within 1 kcal/mol, non-centered, computed per assay and averaged across assays weighted by compound count) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceGAT on the FEP+ benchmark four-target subset uc-leadopt-20261022-protocol-boltz2-fep-4target Aggregation: Not reported Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix · Table 12, row "GAT", column "Perc. within 1", sub-column "non-cent." (text-layer line 1709) |
| Configuration: BACPI ligand-only ablation (GAT) | Protocol: FEP+ benchmark four-target subset, affinity ranking and cost Dataset: Four-target subset of the public FEP benchmark | 0.95 Proportion (within 2 kcal/mol, centered, computed per assay and averaged across assays weighted by compound count) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceGAT on the FEP+ benchmark four-target subset uc-leadopt-20261022-protocol-boltz2-fep-4target Aggregation: Not reported Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix · Table 12, row "GAT", column "Perc. within 2", sub-column "cent." (text-layer line 1709) |
| Configuration: BACPI ligand-only ablation (GAT) | Protocol: FEP+ benchmark four-target subset, affinity ranking and cost Dataset: Four-target subset of the public FEP benchmark | 0.86 Proportion (within 2 kcal/mol, non-centered, computed per assay and averaged across assays weighted by compound count) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceGAT on the FEP+ benchmark four-target subset uc-leadopt-20261022-protocol-boltz2-fep-4target Aggregation: Not reported Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix · Table 12, row "GAT", column "Perc. within 2", sub-column "non-cent." (text-layer line 1709) |
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FEP+ benchmark four-target subset, affinity ranking and cost
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18 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Comparison: adaptation Retrained on the Boltz-2 affinity training data with the protein network switched off Context-only references | Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix Table 12, row 'GAT' (text-layer line 1709) Version: bioRxiv v1 posted 2025-06-18; supplement PDF as deposited in Europe PMC PMC12262699 (PPR1038344) | not individually reviewed No individual claim review recorded author reported 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 |
| Comparison: aggregation Calculated per assay and averaged across assays with weight proportional to the number of compounds in each assay (appendix D.2.2, 'Evaluation metrics'). The Pearson R, Kendall tau and PMAE columns are printed under the label 'target avg.'; assays and targets are not the same unit, and the source does not reconcile the printed label with the stated computation. Context-only references | Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix Table 12, row 'GAT' (text-layer line 1709) Version: bioRxiv v1 posted 2025-06-18; supplement PDF as deposited in Europe PMC PMC12262699 (PPR1038344) | not individually reviewed No individual claim review recorded author reported 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 |
| Comparison: budget 0.18 GPU ms Context-only references | Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix Table 12, row 'GAT' (text-layer line 1709) Version: bioRxiv v1 posted 2025-06-18; supplement PDF as deposited in Europe PMC PMC12262699 (PPR1038344) | not individually reviewed No individual claim review recorded author reported 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 |
| Comparison: dataset version the FEP+ benchmark four-target subset Context-only references | Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix Table 12, row 'GAT' (text-layer line 1709) Version: bioRxiv v1 posted 2025-06-18; supplement PDF as deposited in Europe PMC PMC12262699 (PPR1038344) | not individually reviewed No individual claim review recorded author reported 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 |
| Comparison: inputs Protein sequence and ligand structure Context-only references | Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix Table 12, row 'GAT' (text-layer line 1709) Version: bioRxiv v1 posted 2025-06-18; supplement PDF as deposited in Europe PMC PMC12262699 (PPR1038344) | not individually reviewed No individual claim review recorded author reported 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 |
| Comparison: metric implementation Appendix D.2.2 'Evaluation metrics': Pearson R, Kendall tau, pairwise MAE (PMAE), MAE and the fraction of predictions within 1 and 2 kcal/mol, each computed per assay and averaged across assays weighted by compound count, with predictions converted to kcal/mol first; the centered variants translate each assay's predictions to the ground-truth mean Context-only references | Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix Table 12, row 'GAT' (text-layer line 1709) Version: bioRxiv v1 posted 2025-06-18; supplement PDF as deposited in Europe PMC PMC12262699 (PPR1038344) | not individually reviewed No individual claim review recorded author reported 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 |
| Comparison: population 87 neutral compounds over 4 targets (CDK2, TYK2, JNK1, P38) Context-only references | Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix Table 12, row 'GAT' (text-layer line 1709) Version: bioRxiv v1 posted 2025-06-18; supplement PDF as deposited in Europe PMC PMC12262699 (PPR1038344) | not individually reviewed No individual claim review recorded author reported 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 |
| Comparison: protocol id uc-leadopt-20261022-protocol-boltz2-fep-4target Context-only references | Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix Table 12, row 'GAT' (text-layer line 1709) Version: bioRxiv v1 posted 2025-06-18; supplement PDF as deposited in Europe PMC PMC12262699 (PPR1038344) | not individually reviewed No individual claim review recorded author reported 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 |
| Comparison: split Held-out affinity test set Context-only references | Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix Table 12, row 'GAT' (text-layer line 1709) Version: bioRxiv v1 posted 2025-06-18; supplement PDF as deposited in Europe PMC PMC12262699 (PPR1038344) | not individually reviewed No individual claim review recorded author reported 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 |
| Origin author_reported Context-only references | Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction, supplementary appendix Table 12, row 'GAT' (text-layer line 1709) Version: bioRxiv v1 posted 2025-06-18; supplement PDF as deposited in Europe PMC PMC12262699 (PPR1038344) | not individually reviewed No individual claim review recorded author reported 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 |
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
Stable ID: uc-leadopt-20261022-eval-t12-gat