Method

GNN

Graph convolutional network over atoms linked when within 4.5 Å, with one-hot atom-type node features, five graph convolution layers and two fully connected layers.

14 evaluations · 14 results

Overview

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Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.

Evaluations and results

14 evaluations · 14 results. Different protocols are not a single leaderboard.

Sorted by Spearman (higher 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	Protocol and dataset	Spearman	AUROC	MAE	Accuracy	Pearson	RMSE
GNNEvaluation	ATOM3D PSR-GLOBAL-RS: Protein structure ranking, global Spearman, ATOM3D PSR (ATOM3D split)	0.75 (best in column)	Not reported	Not reported	Not reported	Not reported	Not reported
GNNEvaluation	ATOM3D LBA-RS: Ligand binding affinity, global Spearman correlation, ATOM3D LBA (ATOM3D split)	0.533	Not reported	Not reported	Not reported	Not reported	Not reported
GNNEvaluation	ATOM3D RSR-GLOBAL-RS: RNA structure ranking, global Spearman, ATOM3D RSR (ATOM3D split)	0.512	Not reported	Not reported	Not reported	Not reported	Not reported
GNNEvaluation	ATOM3D PSR-MEAN-RS: Protein structure ranking, mean Spearman within a target, ATOM3D PSR (ATOM3D split)	0.411	Not reported	Not reported	Not reported	Not reported	Not reported
GNNEvaluation	ATOM3D RSR-MEAN-RS: RNA structure ranking, mean Spearman within a target, ATOM3D RSR (ATOM3D split)	0.234	Not reported	Not reported	Not reported	Not reported	Not reported
GNNEvaluation	ATOM3D LBA-RMSE: Ligand binding affinity, root mean squared error, ATOM3D LBA (ATOM3D split)	Not reported	Not reported	Not reported	Not reported	Not reported	1.6
GNNEvaluation	ATOM3D LBA-RP: Ligand binding affinity, global Pearson correlation, ATOM3D LBA (ATOM3D split)	Not reported	Not reported	Not reported	Not reported	0.545	Not reported
GNNEvaluation	ATOM3D LEP-AUROC: Ligand efficacy prediction, ATOM3D LEP (ATOM3D split)	Not reported	0.681 (best in column)	Not reported	Not reported	Not reported	Not reported
GNNEvaluation	ATOM3D MSP: Mutation stability prediction, ATOM3D MSP (ATOM3D split)	Not reported	0.609	Not reported	Not reported	Not reported	Not reported
GNNEvaluation	ATOM3D PIP: Protein interface prediction, ATOM3D PIP (ATOM3D split)	Not reported	0.669	Not reported	Not reported	Not reported	Not reported
GNNEvaluation	ATOM3D RES: Residue identity, ATOM3D RES (ATOM3D split)	Not reported	Not reported	Not reported	0.082	Not reported	Not reported
GNNEvaluation	ATOM3D SMP-EGAP: Small molecule properties, HOMO-LUMO gap, ATOM3D SMP (ATOM3D split)	Not reported	Not reported	0.137 (best in column)	Not reported	Not reported	Not reported
GNNEvaluation	ATOM3D SMP-MU: Small molecule properties, dipole moment, ATOM3D SMP (ATOM3D split)	Not reported	Not reported	0.501	Not reported	Not reported	Not reported
GNNEvaluation	ATOM3D SMP-U0AT: Small molecule properties, atomization energy, ATOM3D SMP (ATOM3D split)	Not reported	Not reported	1.42	Not reported	Not reported	Not reported

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Method: GNN	Task: ATOM3D LBA-RMSE: Ligand binding affinity, root mean squared error Dataset subset: ATOM3D LBA (ATOM3D split)	1.6 RMSE unit-unreported · lower Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GNN on ATOM3D LBA-RMSE: Ligand binding affinity, root mean squared error Trained and scored under the ATOM3D split for this task. Asterisks in the paper mark a run whose training data differed. Aggregation: Not reported ATOM3D: Tasks On Molecules in Three Dimensions · Table 5, row(LBA RMSE), column(GNN)
Method: GNN	Task: ATOM3D LBA-RP: Ligand binding affinity, global Pearson correlation Dataset subset: ATOM3D LBA (ATOM3D split)	0.545 Pearson unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GNN on ATOM3D LBA-RP: Ligand binding affinity, global Pearson correlation Trained and scored under the ATOM3D split for this task. Asterisks in the paper mark a run whose training data differed. Aggregation: Not reported ATOM3D: Tasks On Molecules in Three Dimensions · Table 5, row(glob. RP), column(GNN)
Method: GNN	Task: ATOM3D LBA-RS: Ligand binding affinity, global Spearman correlation Dataset subset: ATOM3D LBA (ATOM3D split)	0.533 Spearman unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GNN on ATOM3D LBA-RS: Ligand binding affinity, global Spearman correlation Trained and scored under the ATOM3D split for this task. Asterisks in the paper mark a run whose training data differed. Aggregation: Not reported ATOM3D: Tasks On Molecules in Three Dimensions · Table 5, row(glob. RS), column(GNN)
Method: GNN	Task: ATOM3D LEP-AUROC: Ligand efficacy prediction Dataset subset: ATOM3D LEP (ATOM3D split)	0.681 AUROC unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GNN on ATOM3D LEP-AUROC: Ligand efficacy prediction Trained and scored under the ATOM3D split for this task. Asterisks in the paper mark a run whose training data differed. Aggregation: Not reported ATOM3D: Tasks On Molecules in Three Dimensions · Table 5, row(LEP AUROC), column(GNN)
Method: GNN	Task: ATOM3D MSP: Mutation stability prediction Dataset subset: ATOM3D MSP (ATOM3D split)	0.609 AUROC unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GNN on ATOM3D MSP: Mutation stability prediction Trained and scored under the ATOM3D split for this task. Asterisks in the paper mark a run whose training data differed. Aggregation: Not reported ATOM3D: Tasks On Molecules in Three Dimensions · Table 4, row(MSP AUROC), column(GNN)
Method: GNN	Task: ATOM3D PIP: Protein interface prediction Dataset subset: ATOM3D PIP (ATOM3D split)	0.669 AUROC unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GNN on ATOM3D PIP: Protein interface prediction Trained and scored under the ATOM3D split for this task. Asterisks in the paper mark a run whose training data differed. Aggregation: Not reported ATOM3D: Tasks On Molecules in Three Dimensions · Table 4, row(PIP AUROC), column(GNN)
Method: GNN	Task: ATOM3D PSR-GLOBAL-RS: Protein structure ranking, global Spearman Dataset subset: ATOM3D PSR (ATOM3D split)	0.75 Spearman unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GNN on ATOM3D PSR-GLOBAL-RS: Protein structure ranking, global Spearman Trained and scored under the ATOM3D split for this task. Asterisks in the paper mark a run whose training data differed. Aggregation: Not reported ATOM3D: Tasks On Molecules in Three Dimensions · Table 6, row(glob. RS), column(GNN)
Method: GNN	Task: ATOM3D PSR-MEAN-RS: Protein structure ranking, mean Spearman within a target Dataset subset: ATOM3D PSR (ATOM3D split)	0.411 Spearman unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GNN on ATOM3D PSR-MEAN-RS: Protein structure ranking, mean Spearman within a target Trained and scored under the ATOM3D split for this task. Asterisks in the paper mark a run whose training data differed. Aggregation: Not reported ATOM3D: Tasks On Molecules in Three Dimensions · Table 6, row(PSR mean RS), column(GNN)
Method: GNN	Task: ATOM3D RES: Residue identity Dataset subset: ATOM3D RES (ATOM3D split)	0.082 Accuracy fraction · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GNN on ATOM3D RES: Residue identity Trained and scored under the ATOM3D split for this task. Asterisks in the paper mark a run whose training data differed. Aggregation: Not reported ATOM3D: Tasks On Molecules in Three Dimensions · Table 4, row(RES accuracy), column(GNN)
Method: GNN	Task: ATOM3D RSR-GLOBAL-RS: RNA structure ranking, global Spearman Dataset subset: ATOM3D RSR (ATOM3D split)	0.512 Spearman unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GNN on ATOM3D RSR-GLOBAL-RS: RNA structure ranking, global Spearman Trained and scored under the ATOM3D split for this task. Asterisks in the paper mark a run whose training data differed. Aggregation: Not reported ATOM3D: Tasks On Molecules in Three Dimensions · Table 6, row(glob. RS), column(GNN)
Method: GNN	Task: ATOM3D RSR-MEAN-RS: RNA structure ranking, mean Spearman within a target Dataset subset: ATOM3D RSR (ATOM3D split)	0.234 Spearman unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GNN on ATOM3D RSR-MEAN-RS: RNA structure ranking, mean Spearman within a target Trained and scored under the ATOM3D split for this task. Asterisks in the paper mark a run whose training data differed. Aggregation: Not reported ATOM3D: Tasks On Molecules in Three Dimensions · Table 6, row(RSR mean RS), column(GNN)
Method: GNN	Task: ATOM3D SMP-EGAP: Small molecule properties, HOMO-LUMO gap Dataset subset: ATOM3D SMP (ATOM3D split)	0.137 MAE unit-unreported · lower Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GNN on ATOM3D SMP-EGAP: Small molecule properties, HOMO-LUMO gap Trained and scored under the ATOM3D split for this task. Asterisks in the paper mark a run whose training data differed. Aggregation: Not reported ATOM3D: Tasks On Molecules in Three Dimensions · Table 3, row(SMP εgap [eV]), column(GNN)
Method: GNN	Task: ATOM3D SMP-MU: Small molecule properties, dipole moment Dataset subset: ATOM3D SMP (ATOM3D split)	0.501 MAE unit-unreported · lower Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GNN on ATOM3D SMP-MU: Small molecule properties, dipole moment Trained and scored under the ATOM3D split for this task. Asterisks in the paper mark a run whose training data differed. Aggregation: Not reported ATOM3D: Tasks On Molecules in Three Dimensions · Table 3, row(µ [D]), column(GNN)
Method: GNN	Task: ATOM3D SMP-U0AT: Small molecule properties, atomization energy Dataset subset: ATOM3D SMP (ATOM3D split)	1.42 MAE unit-unreported · lower Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GNN on ATOM3D SMP-U0AT: Small molecule properties, atomization energy Trained and scored under the ATOM3D split for this task. Asterisks in the paper mark a run whose training data differed. Aggregation: Not reported ATOM3D: Tasks On Molecules in Three Dimensions · Table 3, row(U0at [eV]), column(GNN)

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Stable ID: atom3d-method-gnn

areas: molecular-interactions
source locator: Table 3, column(GNN)
missing metadata: checkpoint revision: reason: unreported; parameters: reason: unextracted
provenance note: Implemented and trained by the ATOM3D authors.

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