Papers › CHILI: Chemically-Informed Large-scale Inorganic Nanomaterials Dataset for Advancing...

CHILI: Chemically-Informed Large-scale Inorganic Nanomaterials Dataset for Advancing Graph Machine Learning

20 Feb 2024arXiv:2402.13221archive 2025-07-28

Ulrik Friis-Jensen, Frederik L. Johansen, Andy S. Anker, Erik B. Dam, Kirsten M. Ø. Jensen, Raghavendra Selvan

Advances in graph machine learning (ML) have been driven by applications in chemistry as graphs have remained the most expressive representations of molecules. While early graph ML methods focused primarily on small organic molecules, recently, the scope of graph ML has expanded to include inorganic materials. Modelling the periodicity and symmetry of inorganic crystalline materials poses unique challenges, which existing graph ML methods are unable to address. Moving to inorganic nanomaterials increases complexity as the scale of number of nodes within each graph can be broad ($10$ to 10⁵). The bulk of existing graph ML focuses on characterising molecules and materials by predicting target properties with graphs as input. However, the most exciting applications of graph ML will be in their generative capabilities, which is currently not at par with other domains such as images or text. We invite the graph ML community to address these open challenges by presenting two new chemically-informed large-scale inorganic (CHILI) nanomaterials datasets: A medium-scale dataset (with overall >6M nodes, >49M edges) of mono-metallic oxide nanomaterials generated from 12 selected crystal types (CHILI-3K) and a large-scale dataset (with overall >183M nodes, >1.2B edges) of nanomaterials generated from experimentally determined crystal structures (CHILI-100K). We define 11 property prediction tasks and 6 structure prediction tasks, which are of special interest for nanomaterial research. We benchmark the performance of a wide array of baseline methods and use these benchmarking results to highlight areas which need future work. To the best of our knowledge, CHILI-3K and CHILI-100K are the first open-source nanomaterial datasets of this scale -- both on the individual graph level and of the dataset as a whole -- and the only nanomaterials datasets with high structural and elemental diversity.

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UlrikFriisJensen/CHILI officialmentioned in papermentioned on GitHubpytorch report

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Tasks

Atomic number classificationBenchmarkingCrystal system classificationDistance regressionND regressionNeutron PDF regressionPosition regressionProperty PredictionSANS regressionSAXS regressionSpace group classificationX-ray PDF regressionXRD regression

Datasets

Introduced by this paper, per the archive.

CHILI-100KCHILI-3K

Results from the paper archive 2025-07-28

TaskDatasetModelMetricValueRank at snapshotLeaderboardReport
Atomic number classification CHILI-100K EdgeCNN F1-score (Weighted) 0.572 +/- 0.017 #1 of 9 Archive leaderboard report
Atomic number classification CHILI-100K GIN F1-score (Weighted) 0.336 +/- 0.005 #2 of 9 Archive leaderboard report
Atomic number classification CHILI-100K GraphUNet F1-score (Weighted) 0.287 +/- 0.004 #3 of 9 Archive leaderboard report
Atomic number classification CHILI-100K GCN F1-score (Weighted) 0.275 +/- 0.002 #4 of 9 Archive leaderboard report
Atomic number classification CHILI-100K GraphSAGE F1-score (Weighted) 0.195 +/- 0.007 #5 of 9 Archive leaderboard report
Atomic number classification CHILI-100K Most Frequent Class F1-score (Weighted) 0.192 #6 of 9 Archive leaderboard report
Atomic number classification CHILI-100K GAT F1-score (Weighted) 0.192 +/- 0.000 #7 of 9 Archive leaderboard report
Atomic number classification CHILI-100K PMLP F1-score (Weighted) 0.191 +/- 0.000 #8 of 9 Archive leaderboard report
Atomic number classification CHILI-100K Random F1-score (Weighted) 0.015 +/- 0.000 #9 of 9 Archive leaderboard report
Atomic number classification CHILI-3K EdgeCNN F1-score (Weighted) 0.632 +/- 0.009 #1 of 9 Archive leaderboard report
Atomic number classification CHILI-3K GIN F1-score (Weighted) 0.587 +/- 0.002 #2 of 9 Archive leaderboard report
Atomic number classification CHILI-3K GraphUNet F1-score (Weighted) 0.552 +/- 0.079 #3 of 9 Archive leaderboard report
Atomic number classification CHILI-3K GCN F1-score (Weighted) 0.496 +/- 0.001 #4 of 9 Archive leaderboard report
Atomic number classification CHILI-3K GraphSAGE F1-score (Weighted) 0.491 +/- 0.004 #5 of 9 Archive leaderboard report
Atomic number classification CHILI-3K Most Frequent Class F1-score (Weighted) 0.461 #6 of 9 Archive leaderboard report
Atomic number classification CHILI-3K PMLP F1-score (Weighted) 0.461 +/- 0.000 #7 of 9 Archive leaderboard report
Atomic number classification CHILI-3K GAT F1-score (Weighted) 0.461 +/- 0.000 #8 of 9 Archive leaderboard report
Atomic number classification CHILI-3K Random F1-score (Weighted) 0.016 +/- 0.000 #9 of 9 Archive leaderboard report
Crystal system classification CHILI-100K Random F1-score (Weighted) 0.168 +/- 0.014 #1 of 9 Archive leaderboard report
Crystal system classification CHILI-100K PMLP F1-score (Weighted) 0.124 +/- 0.036 #2 of 9 Archive leaderboard report
Crystal system classification CHILI-100K GAT F1-score (Weighted) 0.110 +/- 0.029 #3 of 9 Archive leaderboard report
Crystal system classification CHILI-100K EdgeCNN F1-score (Weighted) 0.072 +/- 0.047 #4 of 9 Archive leaderboard report
Crystal system classification CHILI-100K GCN F1-score (Weighted) 0.069 +/- 0.023 #5 of 9 Archive leaderboard report
Crystal system classification CHILI-100K GIN F1-score (Weighted) 0.069 +/- 0.040 #6 of 9 Archive leaderboard report
Crystal system classification CHILI-100K GraphUNet F1-score (Weighted) 0.068 +/- 0.006 #7 of 9 Archive leaderboard report
Crystal system classification CHILI-100K GraphSAGE F1-score (Weighted) 0.061 +/- 0.019 #8 of 9 Archive leaderboard report
Crystal system classification CHILI-100K Most Frequent Class F1-score (Weighted) 0.046 #9 of 9 Archive leaderboard report
Crystal system classification CHILI-3K EdgeCNN F1-score (Weighted) 0.657 +/- 0.196 #1 of 9 Archive leaderboard report
Crystal system classification CHILI-3K GAT F1-score (Weighted) 0.504 +/- 0.076 #2 of 9 Archive leaderboard report
Crystal system classification CHILI-3K Most Frequent Class F1-score (Weighted) 0.440 #3 of 9 Archive leaderboard report
Crystal system classification CHILI-3K PMLP F1-score (Weighted) 0.440 +/- 0.036 #4 of 9 Archive leaderboard report
Crystal system classification CHILI-3K GIN F1-score (Weighted) 0.438 +/- 0.004 #5 of 9 Archive leaderboard report
Crystal system classification CHILI-3K GraphUNet F1-score (Weighted) 0.431 +/- 0.014 #6 of 9 Archive leaderboard report
Crystal system classification CHILI-3K GraphSAGE F1-score (Weighted) 0.422 +/- 0.037 #7 of 9 Archive leaderboard report
Crystal system classification CHILI-3K GCN F1-score (Weighted) 0.367 +/- 0.127 #8 of 9 Archive leaderboard report
Crystal system classification CHILI-3K Random F1-score (Weighted) 0.191 +/- 0.008 #9 of 9 Archive leaderboard report
Distance regression CHILI-100K EdgeCNN MSE 0.030 +/- 0.001 #1 of 8 Archive leaderboard report
Distance regression CHILI-100K GraphSAGE MSE 0.064 +/- 0.001 #2 of 8 Archive leaderboard report
Distance regression CHILI-100K GraphUNet MSE 0.085 +/- 0.002 #3 of 8 Archive leaderboard report
Distance regression CHILI-100K GCN MSE 0.090 +/- 0.002 #4 of 8 Archive leaderboard report
Distance regression CHILI-100K GAT MSE 0.252 +/- 0.003 #5 of 8 Archive leaderboard report
Distance regression CHILI-100K Mean MSE 0.307 #6 of 8 Archive leaderboard report
Distance regression CHILI-100K PMLP MSE 0.486 +/- 0.014 #7 of 8 Archive leaderboard report
Distance regression CHILI-100K GIN MSE 0.491 +/- 0.038 #8 of 8 Archive leaderboard report
Distance regression CHILI-3K EdgeCNN MSE 0.015 +/- 0.001 #1 of 8 Archive leaderboard report
Distance regression CHILI-3K GraphSAGE MSE 0.055 +/- 0.002 #2 of 8 Archive leaderboard report
Distance regression CHILI-3K GraphUNet MSE 0.055 +/- 0.001 #3 of 8 Archive leaderboard report
Distance regression CHILI-3K GCN MSE 0.056 +/- 0.006 #4 of 8 Archive leaderboard report
Distance regression CHILI-3K Mean MSE 0.265 #5 of 8 Archive leaderboard report
Distance regression CHILI-3K GAT MSE 0.342 +/- 0.117 #6 of 8 Archive leaderboard report
Distance regression CHILI-3K PMLP MSE 0.359 +/- 0.017 #7 of 8 Archive leaderboard report
Distance regression CHILI-3K GIN MSE 0.464 +/- 0.005 #8 of 8 Archive leaderboard report
Position regression CHILI-100K GraphUNet Positional MAE 14.824 +/- 0.315 #1 of 8 Archive leaderboard report
Position regression CHILI-100K Mean Positional MAE 16.336 #2 of 8 Archive leaderboard report
Position regression CHILI-100K GCN Positional MAE 16.336 +/- 0.000 #3 of 8 Archive leaderboard report
Position regression CHILI-100K PMLP Positional MAE 16.336 +/- 0.000 #4 of 8 Archive leaderboard report
Position regression CHILI-100K GAT Positional MAE 16.336 +/- 0.000 #5 of 8 Archive leaderboard report
Position regression CHILI-100K GIN Positional MAE 16.336 +/- 0.000 #6 of 8 Archive leaderboard report
Position regression CHILI-100K EdgeCNN Positional MAE 16.336 +/- 0.000 #7 of 8 Archive leaderboard report
Position regression CHILI-100K GraphSAGE Positional MAE 16.337 +/- 0.000 #8 of 8 Archive leaderboard report
Position regression CHILI-3K GraphUNet Positional MAE 14.765 +/- 0.395 #1 of 8 Archive leaderboard report
Position regression CHILI-3K Mean Positional MAE 16.575 #2 of 8 Archive leaderboard report
Position regression CHILI-3K GCN Positional MAE 16.575 +/- 0.000 #3 of 8 Archive leaderboard report
Position regression CHILI-3K PMLP Positional MAE 16.575 +/- 0.000 #4 of 8 Archive leaderboard report
Position regression CHILI-3K GraphSAGE Positional MAE 16.575 +/- 0.000 #5 of 8 Archive leaderboard report
Position regression CHILI-3K GAT Positional MAE 16.575 +/- 0.000 #6 of 8 Archive leaderboard report
Position regression CHILI-3K GIN Positional MAE 16.575 +/- 0.000 #7 of 8 Archive leaderboard report
Position regression CHILI-3K EdgeCNN Positional MAE 16.575 +/- 0.000 #8 of 8 Archive leaderboard report
SAXS regression CHILI-100K PMLP MSE 0.003 +/- 0.000 #1 of 8 Archive leaderboard report
SAXS regression CHILI-100K EdgeCNN MSE 0.007 +/- 0.009 #2 of 8 Archive leaderboard report
SAXS regression CHILI-100K GAT MSE 0.009 +/- 0.000 #3 of 8 Archive leaderboard report
SAXS regression CHILI-100K GraphUNet MSE 0.009 +/- 0.000 #4 of 8 Archive leaderboard report
SAXS regression CHILI-100K GIN MSE 0.009 +/- 0.000 #5 of 8 Archive leaderboard report
SAXS regression CHILI-100K GCN MSE 0.010 +/- 0.000 #6 of 8 Archive leaderboard report
SAXS regression CHILI-100K GraphSAGE MSE 0.011 +/- 0.002 #7 of 8 Archive leaderboard report
SAXS regression CHILI-100K Mean MSE 0.038 #8 of 8 Archive leaderboard report
SAXS regression CHILI-3K EdgeCNN MSE 0.006 +/- 0.004 #1 of 8 Archive leaderboard report
SAXS regression CHILI-3K GCN MSE 0.008 +/- 0.000 #2 of 8 Archive leaderboard report
SAXS regression CHILI-3K GraphSAGE MSE 0.008 +/- 0.001 #3 of 8 Archive leaderboard report
SAXS regression CHILI-3K GAT MSE 0.008 +/- 0.000 #4 of 8 Archive leaderboard report
SAXS regression CHILI-3K GraphUNet MSE 0.008 +/- 0.000 #5 of 8 Archive leaderboard report
SAXS regression CHILI-3K GIN MSE 0.008 +/- 0.000 #6 of 8 Archive leaderboard report
SAXS regression CHILI-3K PMLP MSE 0.022 +/- 0.025 #7 of 8 Archive leaderboard report
SAXS regression CHILI-3K Mean MSE 0.037 #8 of 8 Archive leaderboard report
Space group classification CHILI-100K EdgeCNN F1-score (Weighted) 0.158 +/- 0.035 #1 of 9 Archive leaderboard report
Space group classification CHILI-100K PMLP F1-score (Weighted) 0.047 +/- 0.012 #2 of 9 Archive leaderboard report
Space group classification CHILI-100K GraphSAGE F1-score (Weighted) 0.044 +/- 0.002 #3 of 9 Archive leaderboard report
Space group classification CHILI-100K GAT F1-score (Weighted) 0.044 +/- 0.001 #4 of 9 Archive leaderboard report
Space group classification CHILI-100K GCN F1-score (Weighted) 0.043 +/- 0.001 #5 of 9 Archive leaderboard report
Space group classification CHILI-100K GraphUNet F1-score (Weighted) 0.043 +/- 0.000 #6 of 9 Archive leaderboard report
Space group classification CHILI-100K GIN F1-score (Weighted) 0.043 +/- 0.000 #7 of 9 Archive leaderboard report
Space group classification CHILI-100K Most Frequent Class F1-score (Weighted) 0.010 #8 of 9 Archive leaderboard report
Space group classification CHILI-100K Random F1-score (Weighted) 0.002 +/- 0.001 #9 of 9 Archive leaderboard report
Space group classification CHILI-3K EdgeCNN F1-score (Weighted) 0.733 +/- 0.207 #1 of 9 Archive leaderboard report
Space group classification CHILI-3K GraphSAGE F1-score (Weighted) 0.151 +/- 0.045 #2 of 9 Archive leaderboard report
Space group classification CHILI-3K PMLP F1-score (Weighted) 0.135 +/- 0.006 #3 of 9 Archive leaderboard report
Space group classification CHILI-3K GIN F1-score (Weighted) 0.125 +/- 0.026 #4 of 9 Archive leaderboard report
Space group classification CHILI-3K GAT F1-score (Weighted) 0.113 +/- 0.013 #5 of 9 Archive leaderboard report
Space group classification CHILI-3K Most Frequent Class F1-score (Weighted) 0.108 #6 of 9 Archive leaderboard report
Space group classification CHILI-3K GCN F1-score (Weighted) 0.099 +/- 0.019 #7 of 9 Archive leaderboard report
Space group classification CHILI-3K GraphUNet F1-score (Weighted) 0.095 +/- 0.036 #8 of 9 Archive leaderboard report
Space group classification CHILI-3K Random F1-score (Weighted) 0.009 +/- 0.008 #9 of 9 Archive leaderboard report
X-ray PDF regression CHILI-100K Mean MSE 0.007 #1 of 8 Archive leaderboard report
X-ray PDF regression CHILI-100K EdgeCNN MSE 0.012 +/- 0.000 #2 of 8 Archive leaderboard report
X-ray PDF regression CHILI-100K PMLP MSE 0.013 +/- 0.000 #3 of 8 Archive leaderboard report
X-ray PDF regression CHILI-100K GAT MSE 0.013 +/- 0.000 #4 of 8 Archive leaderboard report
X-ray PDF regression CHILI-100K GraphUNet MSE 0.013 +/- 0.000 #5 of 8 Archive leaderboard report
X-ray PDF regression CHILI-100K GIN MSE 0.013 +/- 0.000 #6 of 8 Archive leaderboard report
X-ray PDF regression CHILI-100K GCN MSE 0.014 +/- 0.000 #7 of 8 Archive leaderboard report
X-ray PDF regression CHILI-100K GraphSAGE MSE 0.037 +/- 0.026 #8 of 8 Archive leaderboard report
X-ray PDF regression CHILI-3K Mean MSE 0.008 #1 of 7 Archive leaderboard report
X-ray PDF regression CHILI-3K EdgeCNN MSE 0.011 +/- 0.000 #2 of 7 Archive leaderboard report
X-ray PDF regression CHILI-3K GCN MSE 0.012 +/- 0.000 #3 of 7 Archive leaderboard report
X-ray PDF regression CHILI-3K PMLP MSE 0.012 +/- 0.000 #4 of 7 Archive leaderboard report
X-ray PDF regression CHILI-3K GraphSAGE MSE 0.012 +/- 0.000 #5 of 7 Archive leaderboard report
X-ray PDF regression CHILI-3K GraphUNet MSE 0.012 +/- 0.000 #6 of 7 Archive leaderboard report
X-ray PDF regression CHILI-3K GAT MSE 0.029 +/- 0.030 #7 of 7 Archive leaderboard report
XRD regression CHILI-100K EdgeCNN MSE 0.006 +/- 0.000 #1 of 8 Archive leaderboard report
XRD regression CHILI-100K PMLP MSE 0.008 +/- 0.001 #2 of 8 Archive leaderboard report
XRD regression CHILI-100K GCN MSE 0.009 +/- 0.000 #3 of 8 Archive leaderboard report
XRD regression CHILI-100K GraphUNet MSE 0.009 +/- 0.000 #4 of 8 Archive leaderboard report
XRD regression CHILI-100K GIN MSE 0.009 +/- 0.000 #5 of 8 Archive leaderboard report
XRD regression CHILI-100K GraphSAGE MSE 0.018 +/- 0.014 #6 of 8 Archive leaderboard report
XRD regression CHILI-100K Mean MSE 0.021 #7 of 8 Archive leaderboard report
XRD regression CHILI-100K GAT MSE 0.108 +/- 0.172 #8 of 8 Archive leaderboard report
XRD regression CHILI-3K EdgeCNN MSE 0.008 +/- 0.001 #1 of 7 Archive leaderboard report
XRD regression CHILI-3K GCN MSE 0.010 +/- 0.000 #2 of 7 Archive leaderboard report
XRD regression CHILI-3K PMLP MSE 0.010 +/- 0.000 #3 of 7 Archive leaderboard report
XRD regression CHILI-3K GraphSAGE MSE 0.010 +/- 0.000 #4 of 7 Archive leaderboard report
XRD regression CHILI-3K GAT MSE 0.010 +/- 0.000 #5 of 7 Archive leaderboard report
XRD regression CHILI-3K GraphUNet MSE 0.010 +/- 0.000 #6 of 7 Archive leaderboard report
XRD regression CHILI-3K Mean MSE 0.017 #7 of 7 Archive leaderboard report

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