ATOM3D SMP-U0AT: Small molecule properties, atomization energy
Small molecule properties, atomization energy. 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, atomization energy. 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.
Evaluation design
Benchmarks bring together tasks and protocols. A task describes the biological question; a protocol defines a particular test.
Benchmarks
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Recorded evaluations
Each evaluation records what was tested and under which conditions.
- 3DCNN on ATOM3D SMP-U0AT: Small molecule properties, atomization energy
- ENN on ATOM3D SMP-U0AT: Small molecule properties, atomization energy
- GNN on ATOM3D SMP-U0AT: Small molecule properties, atomization energy
- [Liu et al., 2019] on ATOM3D SMP-U0AT: Small molecule properties, atomization energy
- [Tsubaki et al., 2019] on ATOM3D SMP-U0AT: Small molecule properties, atomization energy
Run instructions
No runnable recipe has been reviewed for this task. Dataset access, model requirements, licences and compute requirements must be checked against its sources before execution.
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Published comparisons
Explore the results reported under one evaluation protocol. Each figure keeps its source, dataset and metric together; it is not a ranking across studies. The pooled view gathers every source table that reports the same metric and names what it does not hold constant.
ATOM3D SMP-U0AT: Small molecule properties, atomization energy
mae (error) · Lower values are better for this metric.
Every method ATOM3D reports on Small molecule properties, atomization energy, scored with MAE on ATOM3D SMP.
- 3DCNN · Method · Author-reported evaluation3.862
- GNN · Method · Author-reported evaluation1.424
- ENN · Method · Author-reported evaluation0.025
- [Tsubaki et al., 2019] · Configuration · Author-reported evaluation0.182
- [Liu et al., 2019] · Configuration · Author-reported evaluation0.218
Source order is preserved. Plotted marks show point estimates; uncertainty, where reported, is retained in the printed values and table. Differences do not establish statistical significance.
ATOM3D: Tasks On Molecules in Three Dimensions · Table 3, row(U0at [eV])Values, uncertainty and evidence
| Tested entity | Printed value | Uncertainty | Evidence |
|---|---|---|---|
| 3DCNN · Method | 3.862 error | Not reported | Author-reported evaluation · source checkedATOM3D: Tasks On Molecules in Three Dimensions · Table 3, row(U0at [eV]), column(3DCNN) |
| GNN · Method | 1.424 error | Not reported | Author-reported evaluation · source checkedATOM3D: Tasks On Molecules in Three Dimensions · Table 3, row(U0at [eV]), column(GNN) |
| ENN · Method | 0.025 error | Not reported | Author-reported evaluation · source checkedATOM3D: Tasks On Molecules in Three Dimensions · Table 3, row(U0at [eV]), column(ENN) |
| [Tsubaki et al., 2019] · Configuration | 0.182 error | Not reported | Author-reported evaluation · source checkedATOM3D: Tasks On Molecules in Three Dimensions · Table 3, row(U0at [eV]), column([Tsubaki et al., 2019]) |
| [Liu et al., 2019] · Configuration | 0.218 error | Not reported | Author-reported evaluation · source checkedATOM3D: Tasks On Molecules in Three Dimensions · Table 3, row(U0at [eV]), column([Liu et al., 2019]) |
Scope and limitations
- 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.
Source transcription and grouping reviewed by automated source review on 2026-09-18. These experiments were not independently reproduced by rewire.
Tested entities and results
Release 2026-09-17-134cd1815de8 · 5 evaluations · 5 metric rows. Different protocols are not a single leaderboard. Where several source tables report the same metric, the published comparisons above offer a pooled view that names what it does not hold constant.
| Metric and finding | Coverage and uncertainty | Evidence |
|---|---|---|
| 3DCNN on ATOM3D SMP-U0AT: Small molecule properties, atomization energy Method: 3DCNNTask: ATOM3D SMP-U0AT: Small molecule properties, atomization energyDataset subset: ATOM3D SMP (ATOM3D split) Trained and scored under the ATOM3D split for this task. Asterisks in the paper mark a run whose training data differed. Author-reported evaluation · Evaluation metadata: source checked | ||
| 3.862 mae Unit: error · Direction: lower | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedATOM3D: Tasks On Molecules in Three Dimensions · Table 3, row(U0at [eV]), column(3DCNN) Source checking is not independent reproduction. |
| ENN on ATOM3D SMP-U0AT: Small molecule properties, atomization energy Method: ENNTask: ATOM3D SMP-U0AT: Small molecule properties, atomization energyDataset subset: ATOM3D SMP (ATOM3D split) Trained and scored under the ATOM3D split for this task. Asterisks in the paper mark a run whose training data differed. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.025 mae Unit: error · Direction: lower | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedATOM3D: Tasks On Molecules in Three Dimensions · Table 3, row(U0at [eV]), column(ENN) Source checking is not independent reproduction. |
| GNN on ATOM3D SMP-U0AT: Small molecule properties, atomization energy Method: GNNTask: ATOM3D SMP-U0AT: Small molecule properties, atomization energyDataset subset: ATOM3D SMP (ATOM3D split) Trained and scored under the ATOM3D split for this task. Asterisks in the paper mark a run whose training data differed. Author-reported evaluation · Evaluation metadata: source checked | ||
| 1.424 mae Unit: error · Direction: lower | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedATOM3D: Tasks On Molecules in Three Dimensions · Table 3, row(U0at [eV]), column(GNN) Source checking is not independent reproduction. |
| [Liu et al., 2019] on ATOM3D SMP-U0AT: Small molecule properties, atomization energy Configuration: [Liu et al., 2019]Task: ATOM3D SMP-U0AT: Small molecule properties, atomization energyDataset subset: ATOM3D SMP (ATOM3D split) Trained and scored under the ATOM3D split for this task. Asterisks in the paper mark a run whose training data differed. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.218 mae Unit: error · Direction: lower | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedATOM3D: Tasks On Molecules in Three Dimensions · Table 3, row(U0at [eV]), column([Liu et al., 2019]) Source checking is not independent reproduction. |
| [Tsubaki et al., 2019] on ATOM3D SMP-U0AT: Small molecule properties, atomization energy Configuration: [Tsubaki et al., 2019]Task: ATOM3D SMP-U0AT: Small molecule properties, atomization energyDataset subset: ATOM3D SMP (ATOM3D split) Trained and scored under the ATOM3D split for this task. Asterisks in the paper mark a run whose training data differed. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.182 mae Unit: error · Direction: lower | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedATOM3D: Tasks On Molecules in Three Dimensions · Table 3, row(U0at [eV]), column([Tsubaki et al., 2019]) Source checking is not 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.
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(U0at [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-u0at Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
Sources and history
Release 2026-09-17-134cd1815de8 · 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-u0at
- areas
- molecular-interactions
- tasks
- Small molecule properties, atomization energy
- 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(U0at [eV])
- comparison panels
- id: atom3d-panel-smp-u0at; title: ATOM3D SMP-U0AT: Small molecule properties, atomization energy; protocol id: atom3d-task-smp-u0at; dataset id: atom3d-dataset-atom3d-smp; metric: mae; unit: error; direction: lower; result ids: atom3d-result-3dcnn-smp-u0at-mae; atom3d-result-gnn-smp-u0at-mae; atom3d-result-enn-smp-u0at-mae; atom3d-result-tsubaki-et-al-2019-smp-u0at-mae; atom3d-result-liu-et-al-2019-smp-u0at-mae; source ids: evidence-expansion-atom3d-92656c20; source locator: Table 3, row(U0at [eV]); context: Every method ATOM3D reports on Small molecule properties, atomization energy, 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-U0AT: part of discovery-benchmark-atom3d
- benchmark: 3DCNN on ATOM3D SMP-U0AT: Small molecule properties, atomization energy
- benchmark: ENN on ATOM3D SMP-U0AT: Small molecule properties, atomization energy
- benchmark: GNN on ATOM3D SMP-U0AT: Small molecule properties, atomization energy
- benchmark: [Liu et al., 2019] on ATOM3D SMP-U0AT: Small molecule properties, atomization energy
- benchmark: [Tsubaki et al., 2019] on ATOM3D SMP-U0AT: Small molecule properties, atomization energy