paper · benchmark creator

ATOM3D: Tasks On Molecules in Three Dimensions

Stanford University · 2021-12-07

Relationship layer

Benchmark usage

This table records what the work did with each benchmark before attempting to normalize a run. Partial claims remain visible without being treated as comparable evaluations.

No BenchmarkUse relation is normalized for this legacy work yet. Existing EvaluationRuns remain available below.

Normalized evaluation runs

ATOM3D1 run

Open benchmark record →

Evaluation run

atom3d-creator-full

From ATOM3D: Tasks On Molecules in Three Dimensions

atom3d-creator-task-nativevv0.2.6
Scopefull · n=8
ShotsNot applicable
TurnsNot applicable
System prompt publicNot applicable
Reasoning / effortNot applicable
BrowserNot applicable
InternetNot applicable
DatabasesNot applicable
Code executionNot applicable
ContainerNot reported
External toolstask-specific 3D CNN, graph neural network, and equivariant neural network pipelines
Token budgetNot applicable
Time / cost budgetNot reported
TemperatureNot applicable
SeedNot reported
Repeats3
Graderdeterministic task-specific scorer · human review: no
StatisticsNative per-task metrics with standard deviations over three replicates; structure-ranking correlations are computed per target before summary.
ContaminationTask-specific sequence-identity, time, target, or scaffold splits.
Metrics, results, and full protocol

Metrics

MetricKind / baselineUnitAggregationThreshold / tolerance
MAEabsolutetask-specificheld-out examplesNot reported
RMSEabsolutetask-specificheld-out examplesNot reported
AUROCabsoluteareaheld-out examplesNot reported
Accuracyabsoluteproportionheld-out examplesNot reported
Pearson correlationabsolutecorrelationtask-specificNot reported
Spearman correlationabsolutecorrelationtarget-level structure rankingNot reported

No numeric result rows are published yet; the verified protocol remains useful.

Evidence

  • table: Sections 2-5 and Tables 1-8; Appendix D (Defines all eight datasets, official splits, model classes, native metrics, three-replicate aggregation, and creator baseline results.) — supports /scope, /protocol, /metrics