Configuration

N-Gram Graph XGB (ATOM3D baseline)

N-gram graph method on the chemical bond graph, as the ATOM3D text describes it.

Identified as N-Gram Graph with XGBoost. The source table prints [Liu et al., 2019].

Configuration: 2D baseline for SMP: N-gram graph representation of the chemical bond graph with XGBoost.

ATOM3D App. F.1 compares to 'N-Gram Graph XGB [Liu et al., 2019]': the unsupervised N-gram graph representation combined with XGBoost, with a link to the public repository. The cited paper introduces the N-gram graph and evaluates it with XGBoost.

Not established: Who produced the values. ATOM3D does not say whether it retrained N-Gram Graph XGB or reused published values. Table 8 has no row for it. Checkpoint and settings. No hyperparameters, checkpoint or implementation revision are identified.

ATOM3D: Tasks On Molecules in Three Dimensions; N-Gram Graph: Simple Unsupervised Representation for Graphs, with Applications to Molecules (arXiv:1806.09206v2); N-gram graph repository README (chao1224/n_gram_graph) · ATOM3D arXiv:2012.04035v4 §5.1 and Table 3, p.7; App. F.1, p.23, and footnote 8, p.24. N-Gram Graph arXiv:1806.09206v2 title, p.1; RF and XGB models, p.6. github.com/chao1224/n_gram_graph README at 3acf580fe4b5835409abcbd566aadcba6f63fdb8.. AI-assisted source review on 2026-09-24; no human scientific review.

3 evaluations · 3 results

Overview

N-gram graph method on the chemical bond graph, as the ATOM3D text describes it.

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

Evaluations and results

3 evaluations · 3 results. Different protocols are not a single leaderboard.

Filter evaluations

Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: N-Gram Graph XGB (ATOM3D baseline) (cited as [Liu et al., 2019])	Task: ATOM3D SMP-EGAP: Small molecule properties, HOMO-LUMO gap Dataset subset: ATOM3D SMP (ATOM3D split)	0.184 mae error · lower Uncertainty: Not reported 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-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([Liu et al., 2019])
Configuration: N-Gram Graph XGB (ATOM3D baseline) (cited as [Liu et al., 2019])	Task: ATOM3D SMP-MU: Small molecule properties, dipole moment Dataset subset: ATOM3D SMP (ATOM3D split)	0.52 mae error · lower Uncertainty: Not reported 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-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([Liu et al., 2019])
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 error · lower Uncertainty: Not reported 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 2026-09-29-06401fd5b220.

Use this model

How it works, versions and access

Strengths, limitations and unresolved questions

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.

0 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-09-29-06401fd5b220
Property and statement	Original source and location	Review and provenance

No evidence rows match these filters. Choose another scope or clear the search.

All evidence (CSV)All evidence (JSONL)How to read the evidence

Sources and history

View linked audit checks and correction history

Release 2026-09-29-06401fd5b220 · Record review: source checked

3 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
N-Gram Graph: Simple Unsupervised Representation for Graphs, with Applications to Molecules (arXiv:1806.09206v2) · Original source · 1806.09206v2
N-gram graph repository README (chao1224/n_gram_graph) · Original source · 3acf580fe4b5835409abcbd566aadcba6f63fdb8

Download this release

Technical metadata and extraction receipts

Stable ID: atom3d-method-liu-et-al-2019

areas: molecular-interactions
source locator: Table 3, column([Liu et al., 2019])
missing metadata: checkpoint revision: unreported; parameters: unextracted
source label: [Liu et al., 2019]
source identity: status: resolved; label form: bracketed_citation; display name: N-Gram Graph XGB (ATOM3D baseline); identity: N-Gram Graph with XGBoost; configuration: 2D baseline for SMP: N-gram graph representation of the chemical bond graph with XGBoost.; basis: ATOM3D App. F.1 compares to 'N-Gram Graph XGB [Liu et al., 2019]': the unsupervised N-gram graph representation combined with XGBoost, with a link to the public repository. The cited paper introduces the N-gram graph and evaluates it with XGBoost.; source ids: evidence-expansion-atom3d-92656c20; source-label-ngram-graph-arxiv-fa329cdc; source-label-ngram-graph-readme-3acf580f; source locator: ATOM3D arXiv:2012.04035v4 §5.1 and Table 3, p.7; App. F.1, p.23, and footnote 8, p.24. N-Gram Graph arXiv:1806.09206v2 title, p.1; RF and XGB models, p.6. github.com/chao1224/n_gram_graph README at 3acf580fe4b5835409abcbd566aadcba6f63fdb8.; known details: None recorded; unknown: label: Who produced the values; note: ATOM3D does not say whether it retrained N-Gram Graph XGB or reused published values. Table 8 has no row for it.; label: Checkpoint and settings; note: No hyperparameters, checkpoint or implementation revision are identified.; original name: [Liu et al., 2019]; original description: N-gram graph method on the chemical bond graph, as the ATOM3D text describes it.; review: method: automated_source_review; date: 2026-09-24; note: AI-assisted review against the cited primary sources. No human scientific review. Values, locators and comparison conditions are unchanged.

Related records

Suggest a correction