ATOM3D SMP-EGAP: Small molecule properties, HOMO-LUMO gap
Small molecule properties, HOMO-LUMO gap. Scored with MAE on ATOM3D SMP. Trained and scored under the ATOM3D split for this task. Asterisks in the paper mark a run whose training data differed.
Overview
Small molecule properties, HOMO-LUMO gap. Scored with MAE on ATOM3D SMP. Trained and scored under the ATOM3D split for this task. Asterisks in the paper mark a run whose training data differed.
Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.
Results
Each comparison retains its reviewed evaluation scope, dataset and metric. Results are shown without a pooled ranking.
ATOM3D SMP-EGAP: Small molecule properties, HOMO-LUMO gap
mae (error) · Lower values are better.
ATOM3D SMP-EGAP: Small molecule properties, HOMO-LUMO gap · ATOM3D SMP (ATOM3D split)
Evidence origin: Author-reported evaluation.
ATOM3D: Tasks On Molecules in Three Dimensions · Table 3, row(SMP εgap [eV])- The paper marks some runs with an asterisk to say their training data differed, though the splitting criteria were the same.
Comparison details and limitations
Every method ATOM3D reports on Small molecule properties, HOMO-LUMO gap, scored with MAE on ATOM3D SMP.
- Author-reported numbers, source checked but not independently reproduced.
- MAE and RMSE are errors, better when lower. The other metrics are better when higher.
- Comparison methods are named by the citation the table prints; the paper's text says which method each is.
Automated source review: 2026-09-18. Numerical source review does not establish independent reproduction.
Dots show point estimates. Whiskers show only explicitly defined uncertainty (standard deviation, standard error or a labelled interval); their definitions remain in Table. Unresolved uncertainty is not plotted. Differences do not establish statistical significance.
Showing 5 of 5 matching rows.
- 3DCNN0.58
- N-Gram Graph XGB (ATOM3D baseline) (cited as [Liu et al., 2019])0.184
- Molecular GNN, SMILES implementation (ATOM3D baseline) (cited as [Tsubaki et al., 2019])0.154
- GNN0.137
- ENN0.095
Methods and evaluation design
Procedure, tasks and evaluated configurations
Evaluation design
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Benchmarks
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Recorded evaluations
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- 3DCNN on ATOM3D SMP-EGAP: Small molecule properties, HOMO-LUMO gap
- ENN on ATOM3D SMP-EGAP: Small molecule properties, HOMO-LUMO gap
- GNN on ATOM3D SMP-EGAP: Small molecule properties, HOMO-LUMO gap
- N-Gram Graph XGB (ATOM3D baseline) on ATOM3D SMP-EGAP: Small molecule properties, HOMO-LUMO gap
- Molecular GNN, SMILES implementation (ATOM3D baseline) on ATOM3D SMP-EGAP: Small molecule properties, HOMO-LUMO gap
Run instructions
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Strengths, limitations and unresolved questions
Evidence
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Evidence table
Inspect claims, sources and review details
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One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.
1 evidence row matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Relationship: part of discovery-benchmark-atom3d Individual claims | ATOM3D: Tasks On Molecules in Three Dimensions Table 3, row(SMP εgap [eV]) Version: Primary full-text snapshot retrieved 2026-09-17; exact bytes pinned by SHA-256 | source checked automated source review · 2026-09-18 Audit detailsPrimary-source transcription with no human sign-off and no independent reproduction. Field: Claim: atom3d-association-smp-egap Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
Sources and history
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Release 2026-09-29-06401fd5b220 · Record review: source checked
1 source records and release history
- ATOM3D: Tasks On Molecules in Three Dimensions · Original source · Primary full-text snapshot retrieved 2026-09-17; exact bytes pinned by SHA-256
Technical metadata and extraction receipts
Stable ID: atom3d-task-smp-egap
- areas
- molecular-interactions
- tasks
- Small molecule properties, HOMO-LUMO gap
- metric
- MAE
- metric direction
- lower
- dataset
- ATOM3D SMP
- protocol
- Trained and scored under the ATOM3D split for this task. Asterisks in the paper mark a run whose training data differed.
- source locator
- Table 3, row(SMP εgap [eV])
- comparison panels
- id: atom3d-panel-smp-egap; title: ATOM3D SMP-EGAP: Small molecule properties, HOMO-LUMO gap; protocol id: atom3d-task-smp-egap; dataset id: atom3d-dataset-atom3d-smp; metric: mae; unit: error; direction: lower; result ids: atom3d-result-3dcnn-smp-egap-mae; atom3d-result-gnn-smp-egap-mae; atom3d-result-enn-smp-egap-mae; atom3d-result-tsubaki-et-al-2019-smp-egap-mae; atom3d-result-liu-et-al-2019-smp-egap-mae; source ids: evidence-expansion-atom3d-92656c20; source locator: Table 3, row(SMP εgap [eV]); context: Every method ATOM3D reports on Small molecule properties, HOMO-LUMO gap, scored with MAE on ATOM3D SMP.; caveats: Author-reported numbers, source checked but not independently reproduced.; MAE and RMSE are errors, better when lower. The other metrics are better when higher.; Comparison methods are named by the citation the table prints; the paper's text says which method each is.; The paper marks some runs with an asterisk to say their training data differed, though the splitting criteria were the same.; review: method: automated_source_review; date: 2026-09-18
Related records
- part of: ATOM3D
- subject: ATOM3D SMP-EGAP: part of discovery-benchmark-atom3d
- benchmark: 3DCNN on ATOM3D SMP-EGAP: Small molecule properties, HOMO-LUMO gap
- benchmark: ENN on ATOM3D SMP-EGAP: Small molecule properties, HOMO-LUMO gap
- benchmark: GNN on ATOM3D SMP-EGAP: Small molecule properties, HOMO-LUMO gap
- benchmark: N-Gram Graph XGB (ATOM3D baseline) on ATOM3D SMP-EGAP: Small molecule properties, HOMO-LUMO gap
- benchmark: Molecular GNN, SMILES implementation (ATOM3D baseline) on ATOM3D SMP-EGAP: Small molecule properties, HOMO-LUMO gap