rewirebio.iobenchmarks
Evaluation

N-Gram Graph XGB (ATOM3D baseline) on ATOM3D SMP-U0AT: Small molecule properties, atomization energy

ATOM3D evaluation of N-Gram Graph XGB (ATOM3D baseline), cited as [Liu et al., 2019], on Small molecule properties, atomization energy, scored with MAE.

The source table prints the tested method as [Liu et al., 2019]. Evidence for this identity: N-Gram Graph XGB (ATOM3D baseline)

Evaluation results

1 evaluation · 1 result. Different protocols are not a single leaderboard.

Filter evaluations

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configurationProtocol and datasetFindingEvidence and details
Configuration: N-Gram Graph XGB (ATOM3D baseline) (cited as [Liu et al., 2019])Task: ATOM3D SMP-U0AT: Small molecule properties, atomization energy
Dataset subset: ATOM3D SMP (ATOM3D split)
0.218 MAE
unit-unreported · lower

Uncertainty: Not yet extracted

Coverage: Not reported scored / Not reported eligible

Author-reported evaluation · Source checked
Methods, coverage and source

N-Gram Graph XGB (ATOM3D baseline) 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([Liu et al., 2019])

Source checking is not independent reproduction. Release 2026-11-02-a7f03c9e55a5.

Research readiness

0 of 4 readiness checks met. These checks assess whether the evidence supports a reproducible investigation; a source-checked score alone does not meet them.

Readiness checks, gaps and artifacts

Release 2026-11-02-a7f03c9e55a5 · Evidence verified: Not verified

Evidence incomplete

Replay metrics

Exact outcomes, predictions, identifiers and evaluator are connected.

Missing or unresolved evidence

  • No verified artifact manifest is linked to this exact record.
  • File checksums match the recorded files: not yet verified
  • Predictions are matched to the right samples: not yet verified
  • Score meaning and direction are confirmed: not yet verified
  • Metrics are recomputed from the saved predictions: not yet verified

Verified: Not verified

Evidence incomplete

Investigate discrepancies

Replay evidence includes annotations and an assessment of dependence. Unknown independence permits descriptive analysis only.

Missing or unresolved evidence

  • No verified artifact manifest is linked to this exact record.
  • File checksums match the recorded files: not yet verified
  • Predictions are matched to the right samples: not yet verified
  • Score meaning and direction are confirmed: not yet verified
  • Metrics are recomputed from the saved predictions: not yet verified
  • Sample annotations are recorded: not yet verified
  • Dependence between samples is assessed: not yet verified

Verified: Not verified

Evidence incomplete

Run locally

A pinned recipe describes the inputs, environment and resource requirements.

Missing or unresolved evidence

  • No verified artifact manifest is linked to this exact record.
  • File checksums match the recorded files: not yet verified
  • Predictions are matched to the right samples: not yet verified
  • Score meaning and direction are confirmed: not yet verified
  • A pinned run recipe exists: not yet verified
  • Compute requirements are estimated: not yet verified

Verified: Not verified

Evidence incomplete

Validate independently

Separate data and exposure records support an independent test.

Missing or unresolved evidence

  • No verified artifact manifest is linked to this exact record.
  • File checksums match the recorded files: not yet verified
  • Predictions are matched to the right samples: not yet verified
  • Score meaning and direction are confirmed: not yet verified
  • Independent validation data exist: not yet verified
  • Overlap with training data is checked: not yet verified

Verified: Not verified

Readiness describes the evidence in this release. Availability on your computer is checked separately when an investigation runs. Existing data exposure can prevent independent validation even when files are available.

Artifacts and reproduction

No verified artifact manifest is connected to this record yet. The gaps above identify what is needed before analysis can begin.

Evaluation procedure

Trained and scored under the ATOM3D split for this task. Asterisks in the paper mark a run whose training data differed.

Configuration
N-Gram Graph XGB (ATOM3D baseline)
Task
ATOM3D SMP-U0AT: Small molecule properties, atomization energy
Dataset subset
ATOM3D SMP (ATOM3D split)
origin
Author-reported evaluation
configuration
Not reported
protocol id
atom3d-task-smp-u0at
metric implementation
MAE

Metadata review: source checked. Unreported conditions prevent automatic comparisons.

Reproduction

Split
Not reported
Adaptation
Not reported
Scoring implementation
MAE

No execution recipe has been verified for this exact configuration and evaluation. A benchmark's general instructions may use different inputs, splits or model settings.

Reproducing this published result requires matching its model configuration, data, split and scorer. Source checking or a successful smoke test does not establish score reproduction.

Evidence

Source checking verifies the cited claim or transcription. It does not establish 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.

16 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-11-02-a7f03c9e55a5
Property and statementOriginal source and locationReview and provenance
Comparison: metric implementation
MAE
Context-only references
ATOM3D: Tasks On Molecules in Three Dimensions

Original source ↗

Table 3, row(U0at [eV]), column([Liu et al., 2019])

Version: Primary full-text snapshot retrieved 2026-09-17; exact bytes pinned by SHA-256
Retrieved: 2026-09-17T08:06:28.182997+00:00

not individually reviewed

No individual claim review recorded

author reported

Audit details

Field: attributes.comparison.metric_implementation

Source artifact SHA-256: 92656c20a15311c32bed9edc7f465bb26eb30338f40324fe43bec4b1fc6a7890

Hash scope: Exact retrieved primary paper artifact bytes.

Inspected artifact

Comparison: protocol id
atom3d-task-smp-u0at
Context-only references
ATOM3D: Tasks On Molecules in Three Dimensions

Original source ↗

Table 3, row(U0at [eV]), column([Liu et al., 2019])

Version: Primary full-text snapshot retrieved 2026-09-17; exact bytes pinned by SHA-256
Retrieved: 2026-09-17T08:06:28.182997+00:00

not individually reviewed

No individual claim review recorded

author reported

Audit details

Field: attributes.comparison.protocol_id

Source artifact SHA-256: 92656c20a15311c32bed9edc7f465bb26eb30338f40324fe43bec4b1fc6a7890

Hash scope: Exact retrieved primary paper artifact bytes.

Inspected artifact

Origin
author_reported
Context-only references
ATOM3D: Tasks On Molecules in Three Dimensions

Original source ↗

Table 3, row(U0at [eV]), column([Liu et al., 2019])

Version: Primary full-text snapshot retrieved 2026-09-17; exact bytes pinned by SHA-256
Retrieved: 2026-09-17T08:06:28.182997+00:00

not individually reviewed

No individual claim review recorded

author reported

Audit details

Field: attributes.origin

Source artifact SHA-256: 92656c20a15311c32bed9edc7f465bb26eb30338f40324fe43bec4b1fc6a7890

Hash scope: Exact retrieved primary paper artifact bytes.

Inspected artifact

Protocol
Trained and scored under the ATOM3D split for this task. Asterisks in the paper mark a run whose training data differed.
Context-only references
ATOM3D: Tasks On Molecules in Three Dimensions

Original source ↗

Table 3, row(U0at [eV]), column([Liu et al., 2019])

Version: Primary full-text snapshot retrieved 2026-09-17; exact bytes pinned by SHA-256
Retrieved: 2026-09-17T08:06:28.182997+00:00

not individually reviewed

No individual claim review recorded

author reported

Audit details

Field: attributes.protocol

Source artifact SHA-256: 92656c20a15311c32bed9edc7f465bb26eb30338f40324fe43bec4b1fc6a7890

Hash scope: Exact retrieved primary paper artifact bytes.

Inspected artifact

Source identity: display name
N-Gram Graph XGB (ATOM3D baseline) on ATOM3D SMP-U0AT: Small molecule properties, atomization energy
Context-only references
ATOM3D: Tasks On Molecules in Three Dimensions

Original source ↗

Table 3, row(U0at [eV]), column([Liu et al., 2019])

Version: Primary full-text snapshot retrieved 2026-09-17; exact bytes pinned by SHA-256
Retrieved: 2026-09-17T08:06:28.182997+00:00

not individually reviewed

No individual claim review recorded

author reported

Audit details

Field: attributes.source_identity.display_name

Source artifact SHA-256: 92656c20a15311c32bed9edc7f465bb26eb30338f40324fe43bec4b1fc6a7890

Hash scope: Exact retrieved primary paper artifact bytes.

Inspected artifact

Source identity: original description
ATOM3D evaluation of [Liu et al., 2019] on Small molecule properties, atomization energy, scored with MAE.
Context-only references
ATOM3D: Tasks On Molecules in Three Dimensions

Original source ↗

Table 3, row(U0at [eV]), column([Liu et al., 2019])

Version: Primary full-text snapshot retrieved 2026-09-17; exact bytes pinned by SHA-256
Retrieved: 2026-09-17T08:06:28.182997+00:00

not individually reviewed

No individual claim review recorded

author reported

Audit details

Field: attributes.source_identity.original_description

Source artifact SHA-256: 92656c20a15311c32bed9edc7f465bb26eb30338f40324fe43bec4b1fc6a7890

Hash scope: Exact retrieved primary paper artifact bytes.

Inspected artifact

Source identity: original name
[Liu et al., 2019] on ATOM3D SMP-U0AT: Small molecule properties, atomization energy
Context-only references
ATOM3D: Tasks On Molecules in Three Dimensions

Original source ↗

Table 3, row(U0at [eV]), column([Liu et al., 2019])

Version: Primary full-text snapshot retrieved 2026-09-17; exact bytes pinned by SHA-256
Retrieved: 2026-09-17T08:06:28.182997+00:00

not individually reviewed

No individual claim review recorded

author reported

Audit details

Field: attributes.source_identity.original_name

Source artifact SHA-256: 92656c20a15311c32bed9edc7f465bb26eb30338f40324fe43bec4b1fc6a7890

Hash scope: Exact retrieved primary paper artifact bytes.

Inspected artifact

Source identity: status
resolved
Context-only references
ATOM3D: Tasks On Molecules in Three Dimensions

Original source ↗

Table 3, row(U0at [eV]), column([Liu et al., 2019])

Version: Primary full-text snapshot retrieved 2026-09-17; exact bytes pinned by SHA-256
Retrieved: 2026-09-17T08:06:28.182997+00:00

not individually reviewed

No individual claim review recorded

author reported

Audit details

Field: attributes.source_identity.status

Source artifact SHA-256: 92656c20a15311c32bed9edc7f465bb26eb30338f40324fe43bec4b1fc6a7890

Hash scope: Exact retrieved primary paper artifact bytes.

Inspected artifact

Source identity: subject id
atom3d-method-liu-et-al-2019
Context-only references
ATOM3D: Tasks On Molecules in Three Dimensions

Original source ↗

Table 3, row(U0at [eV]), column([Liu et al., 2019])

Version: Primary full-text snapshot retrieved 2026-09-17; exact bytes pinned by SHA-256
Retrieved: 2026-09-17T08:06:28.182997+00:00

not individually reviewed

No individual claim review recorded

author reported

Audit details

Field: attributes.source_identity.subject_id

Source artifact SHA-256: 92656c20a15311c32bed9edc7f465bb26eb30338f40324fe43bec4b1fc6a7890

Hash scope: Exact retrieved primary paper artifact bytes.

Inspected artifact

Source label
[Liu et al., 2019]
Context-only references
ATOM3D: Tasks On Molecules in Three Dimensions

Original source ↗

Table 3, row(U0at [eV]), column([Liu et al., 2019])

Version: Primary full-text snapshot retrieved 2026-09-17; exact bytes pinned by SHA-256
Retrieved: 2026-09-17T08:06:28.182997+00:00

not individually reviewed

No individual claim review recorded

author reported

Audit details

Field: attributes.source_label

Source artifact SHA-256: 92656c20a15311c32bed9edc7f465bb26eb30338f40324fe43bec4b1fc6a7890

Hash scope: Exact retrieved primary paper artifact bytes.

Inspected artifact

How to read the evidence

Sources and history

Release 2026-11-02-a7f03c9e55a5 · Record review: source checked

1 source record and release historyDownload this release (gzip)
Technical metadata and extraction receipts

Stable ID: atom3d-evaluation-liu-et-al-2019-smp-u0at

areas
molecular-interactions
tasks
Small molecule properties, atomization energy
origin
author_reported
protocol
Trained and scored under the ATOM3D split for this task. Asterisks in the paper mark a run whose training data differed.
comparison
protocol id: atom3d-task-smp-u0at; metric implementation: MAE
missing metadata
budget: reason: unreported; checkpoint revision: reason: unreported; seeds: reason: unreported; split manifest: reason: unextracted
source locator
Table 3, row(U0at [eV]), column([Liu et al., 2019])
source label
[Liu et al., 2019]
source identity
status: resolved; display name: N-Gram Graph XGB (ATOM3D baseline) on ATOM3D SMP-U0AT: Small molecule properties, atomization energy; subject id: atom3d-method-liu-et-al-2019; original name: [Liu et al., 2019] on ATOM3D SMP-U0AT: Small molecule properties, atomization energy; original description: ATOM3D evaluation of [Liu et al., 2019] on Small molecule properties, atomization energy, scored with MAE.
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