Molecular Property Prediction

Molecular property prediction is the task of predicting the properties of a molecule from its structure.

Papers

Recently Added Most Hyped Most Active Needs Verification Most Verified

Showing 101–150 of 354 papers

Title	Date	Tasks	Status	Hype
Uncertainty Quantification for Molecular Property Predictions with Graph Neural Architecture Search	Jul 19, 2023	Decision MakingDrug Discovery	CodeCode Available	1
Uncertainty Quantification Using Neural Networks for Molecular Property Prediction	May 20, 2020	Drug DiscoveryExperimental Design	CodeCode Available	1
Learning to Split for Automatic Bias Detection	Apr 28, 2022	Bias Detectionimage-classification	CodeCode Available	1
Improving Self-supervised Molecular Representation Learning using Persistent Homology	Nov 29, 2023	Molecular Property Predictionmolecular representation	CodeCode Available	1
MoleculeNet: A Benchmark for Molecular Machine Learning	Mar 2, 2017	BIG-bench Machine Learningimbalanced classification	CodeCode Available	1
Fast Quantum Property Prediction via Deeper 2D and 3D Graph Networks	Jun 16, 2021	Graph Neural NetworkMolecular Property Prediction	CodeCode Available	1
Learning 3D Representations of Molecular Chirality with Invariance to Bond Rotations	Oct 8, 2021	Contrastive LearningData Augmentation	CodeCode Available	1
Few-Shot Graph Learning for Molecular Property Prediction	Feb 16, 2021	AttributeDrug Discovery	CodeCode Available	1
Fine-Tuning Graph Neural Networks via Graph Topology induced Optimal Transport	Mar 20, 2022	Graph ClassificationGraph Learning	CodeCode Available	1
CACTUS: Chemistry Agent Connecting Tool-Usage to Science	May 2, 2024	Molecular Property PredictionPrompt Engineering	CodeCode Available	1
Hierarchical graph neural nets can capture long-range interactions	Jul 15, 2021	BenchmarkingMolecular Property Prediction	CodeCode Available	1
3D Infomax improves GNNs for Molecular Property Prediction	Oct 8, 2021	Contrastive LearningGraph Learning	CodeCode Available	1
FragNet: A Graph Neural Network for Molecular Property Prediction with Four Levels of Interpretability	Oct 16, 2024	Drug DiscoveryGraph Neural Network	CodeCode Available	1
Multi-channel learning for integrating structural hierarchies into context-dependent molecular representation	Nov 5, 2023	Drug DiscoveryMolecular Property Prediction	CodeCode Available	1
Learning Invariances in Neural Networks	Oct 22, 2020	image-classificationImage Classification	CodeCode Available	1
A new perspective on building efficient and expressive 3D equivariant graph neural networks	Apr 7, 2023	Graph Property PredictionMolecular Property Prediction	CodeCode Available	1
Lo-Hi: Practical ML Drug Discovery Benchmark	Oct 10, 2023	Drug DiscoveryMolecular Property Prediction	CodeCode Available	1
Molecule3D: A Benchmark for Predicting 3D Geometries from Molecular Graphs	Sep 30, 2021	3D Geometry PredictionMolecular Property Prediction	CodeCode Available	1
ChemBERTa-2: Towards Chemical Foundation Models	Sep 5, 2022	Molecular Property PredictionSelf-Supervised Learning	CodeCode Available	1
A community-powered search of machine learning strategy space to find NMR property prediction models	Aug 13, 2020	BIG-bench Machine LearningMolecular Property Prediction	CodeCode Available	1
ChemBERTa: Large-Scale Self-Supervised Pretraining for Molecular Property Prediction	Oct 19, 2020	Molecular Property Predictionmolecular representation	CodeCode Available	1
Optimal Transport Graph Neural Networks	Jun 8, 2020	Drug DiscoveryGraph Neural Network	CodeCode Available	1
Generative Pre-Training from Molecules	Sep 16, 2021	Feature EngineeringGeneral Knowledge	CodeCode Available	1
ChemLLM: A Chemical Large Language Model	Feb 10, 2024	Language ModelingLanguage Modelling	CodeCode Available	1
GPS++: An Optimised Hybrid MPNN/Transformer for Molecular Property Prediction	Nov 18, 2022	DenoisingMolecular Property Prediction	CodeCode Available	1
Structure-Aware E(3)-Invariant Molecular Conformer Aggregation Networks	Feb 3, 2024	GPUMolecular Property Prediction	CodeCode Available	1
ChemRL-GEM: Geometry Enhanced Molecular Representation Learning for Property Prediction	Jun 11, 2021	Molecular Property Predictionmolecular representation	—Unverified	0
Geometry-aware Line Graph Transformer Pre-training for Molecular Property Prediction	Sep 1, 2023	3D geometryMolecular Property Prediction	—Unverified	0
In-Context Learning for Few-Shot Molecular Property Prediction	Oct 13, 2023	Few-Shot LearningIn-Context Learning	—Unverified	0
An In-depth Summary of Recent Artificial Intelligence Applications in Drug Design	Oct 10, 2021	Drug DesignGenerative Adversarial Network	—Unverified	0
An ensemble of VisNet, Transformer-M, and pretraining models for molecular property prediction in OGB Large-Scale Challenge @ NeurIPS 2022	Nov 23, 2022	Graph Neural NetworkGraph Regression	—Unverified	0
Gaussian Process Molecule Property Prediction with FlowMO	Oct 2, 2020	Active LearningGaussian Processes	—Unverified	0
Uncertainty quantification of molecular property prediction using Bayesian neural network models	Nov 19, 2018	Molecular Property PredictionProperty Prediction	—Unverified	0
Infusing Linguistic Knowledge of SMILES into Chemical Language Models	Apr 20, 2022	Molecular Property PredictionProperty Prediction	—Unverified	0
Gated Graph Recursive Neural Networks for Molecular Property Prediction	Aug 31, 2019	Drug DiscoveryMolecular Property Prediction	—Unverified	0
G^3: Representation Learning and Generation for Geometric Graphs	Sep 29, 2021	Drug DiscoveryMolecular Property Prediction	—Unverified	0
Can Molecular Evolution Mechanism Enhance Molecular Representation?	Jan 27, 2025	Molecular Property Predictionmolecular representation	—Unverified	0
FragmentNet: Adaptive Graph Fragmentation for Graph-to-Sequence Molecular Representation Learning	Feb 3, 2025	Graph-to-SequenceMolecular Property Prediction	—Unverified	0
FP-GNN: a versatile deep learning architecture for enhanced molecular property prediction	May 8, 2022	Deep LearningMolecular Property Prediction	—Unverified	0
Calibrated Uncertainty for Molecular Property Prediction using Ensembles of Message Passing Neural Networks	Jul 13, 2021	BIG-bench Machine LearningDecision Making	—Unverified	0
Integrating Chemical Language and Molecular Graph in Multimodal Fused Deep Learning for Drug Property Prediction	Dec 29, 2023	Deep LearningDrug Discovery	—Unverified	0
Accelerating Molecular Graph Neural Networks via Knowledge Distillation	Jun 26, 2023	Data AugmentationKnowledge Distillation	—Unverified	0
BOOM: Benchmarking Out-Of-distribution Molecular Property Predictions of Machine Learning Models	May 3, 2025	BenchmarkingHyperparameter Optimization	—Unverified	0
Extreme Acceleration of Graph Neural Network-based Prediction Models for Quantum Chemistry	Nov 25, 2022	Graph Neural NetworkMolecular Property Prediction	—Unverified	0
BioLangFusion: Multimodal Fusion of DNA, mRNA, and Protein Language Models	Jun 10, 2025	Inductive BiasMolecular Property Prediction	—Unverified	0
Explainable Molecular Property Prediction: Aligning Chemical Concepts with Predictions via Language Models	May 25, 2024	Drug DiscoveryMolecular Property Prediction	—Unverified	0
3D Graph Contrastive Learning for Molecular Property Prediction	May 31, 2022	Contrastive LearningMolecular Property Prediction	—Unverified	0
Improving Counterfactual Truthfulness for Molecular Property Prediction through Uncertainty Quantification	Apr 3, 2025	counterfactualMolecular Property Prediction	—Unverified	0
Evaluating Scalable Uncertainty Estimation Methods for DNN-Based Molecular Property Prediction	Oct 7, 2019	Bayesian InferenceMolecular Property Prediction	—Unverified	0
Evaluating multiple models using labeled and unlabeled data	Jan 21, 2025	Molecular Property PredictionProperty Prediction	—Unverified	0

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All datasets BBBP BACE SIDER Tox21 clintox Lipophilicity FreeSolv HIV dataset ESOL QM7 QM8 QM9

Benchmark Results

#	Model	Metric	Claimed	Verified	Status
1	DumplingGNN	ROC-AUC	96.4	—	Unverified
2	ChemBFN	ROC-AUC	95.74	—	Unverified
3	MTL-BERT	ROC-AUC	93	—	Unverified
4	XGBoost	ROC-AUC	90.5	—	Unverified
5	SELFormer	ROC-AUC	90.2	—	Unverified
6	STL-BERT	ROC-AUC	89.6	—	Unverified
7	Cano-BERT	ROC-AUC	89.2	—	Unverified
8	AttrMasking	ROC-AUC	89.2	—	Unverified
9	AttentiveFP	ROC-AUC	85.5	—	Unverified
10	Deep-CBN	ROC-AUC	75.8	—	Unverified

#	Model	Metric	Claimed	Verified	Status
1	MolXPT	ROC-AUC	88.4	—	Unverified
2	Uni-Mol	ROC-AUC	85.7	—	Unverified
3	ChemRL-GEM	ROC-AUC	85.6	—	Unverified
4	PretrainGNN	ROC-AUC	84.5	—	Unverified
5	SMA	ROC-AUC	84.3	—	Unverified
6	Deep-CBN	ROC-AUC	83.6	—	Unverified
7	SPMM	ROC-AUC	83	—	Unverified
8	GROVER (base)	ROC-AUC	82.6	—	Unverified
9	GROVER (large)	ROC-AUC	81	—	Unverified
10	D-MPNN	ROC-AUC	80.9	—	Unverified

#	Model	Metric	Claimed	Verified	Status
1	BioAct-Het	ROC-AUC	91.11	—	Unverified
2	Deep-CBN	ROC-AUC	78.2	—	Unverified
3	MolXPT	ROC-AUC	71.7	—	Unverified
4	IterRefLSTM	ROC-AUC	70.4	—	Unverified
5	ChemRL-GEM	ROC-AUC	67.2	—	Unverified
6	N-GramRF	ROC-AUC	66.8	—	Unverified
7	Uni-Mol	ROC-AUC	65.9	—	Unverified
8	N-GramXGB	ROC-AUC	65.5	—	Unverified
9	GROVER (large)	ROC-AUC	65.4	—	Unverified
10	GROVER (base)	ROC-AUC	64.8	—	Unverified

#	Model	Metric	Claimed	Verified	Status
1	Deep-CBN	ROC-AUC	92.4	—	Unverified
2	BioAct-Het	ROC-AUC	89.8	—	Unverified
3	IterRefLSTM	ROC-AUC	83	—	Unverified
4	Uni-Mol	ROC-AUC	79.6	—	Unverified
5	PretrainGNN	ROC-AUC	78.1	—	Unverified
6	ChemRL-GEM	ROC-AUC	78.1	—	Unverified
7	Autogluon	ROC-AUC	77.84	—	Unverified
8	MolXPT	ROC-AUC	77.1	—	Unverified
9	D-MPNN	ROC-AUC	75.9	—	Unverified
10	N-GramXGB	ROC-AUC	75.8	—	Unverified

#	Model	Metric	Claimed	Verified	Status
1	Deep-CBN	ROC-AUC	99.2	—	Unverified
2	ChemBFN	ROC-AUC	99.18	—	Unverified
3	Uni-Mol	ROC-AUC	91.9	—	Unverified
4	SPMM	ROC-AUC	91	—	Unverified
5	D-MPNN	ROC-AUC	90.6	—	Unverified
6	ChemRL-GEM	ROC-AUC	90.1	—	Unverified
7	N-GramXGB	ROC-AUC	87.5	—	Unverified
8	GAL 120B	ROC-AUC	82.6	—	Unverified
9	GAL 30B	ROC-AUC	82.2	—	Unverified
10	GROVER (base)	ROC-AUC	81.2	—	Unverified

#	Model	Metric	Claimed	Verified	Status
1	N-GramXGB	RMSE	2.07	—	Unverified
2	GROVER (large)	RMSE	0.82	—	Unverified
3	GROVER (base)	RMSE	0.82	—	Unverified
4	N-GramRF	RMSE	0.81	—	Unverified
5	ChemBERTa-2 (MTR-77M)	RMSE	0.8	—	Unverified
6	ChemBFN	RMSE	0.75	—	Unverified
7	PretrainGNN	RMSE	0.74	—	Unverified
8	SPMM	RMSE	0.71	—	Unverified
9	D-MPNN	RMSE	0.68	—	Unverified
10	ChemRL-GEM	RMSE	0.66	—	Unverified

#	Model	Metric	Claimed	Verified	Status
1	N-GramXGB	RMSE	5.06	—	Unverified
2	PretrainGNN	RMSE	2.76	—	Unverified
3	N-GramRF	RMSE	2.69	—	Unverified
4	GROVER (large)	RMSE	2.27	—	Unverified
5	GROVER (base)	RMSE	2.18	—	Unverified
6	D-MPNN	RMSE	2.08	—	Unverified
7	ChemRL-GEM	RMSE	1.88	—	Unverified
8	SPMM	RMSE	1.86	—	Unverified
9	Uni-Mol	RMSE	1.62	—	Unverified
10	ChemBFN	RMSE	1.42	—	Unverified

#	Model	Metric	Claimed	Verified	Status
1	DVMP	AUC	0.81	—	Unverified
2	Uni-Mol	AUC	0.81	—	Unverified
3	ChemBFN	AUC	0.79	—	Unverified
4	ChemBERTa-2 Fine-tuned	AUC	0.79	—	Unverified
5	SMA	AUC	0.79	—	Unverified
6	MolXPT	AUC	0.78	—	Unverified
7	GAL 30B	AUC	0.76	—	Unverified
8	GAL 120B	AUC	0.75	—	Unverified
9	GAL 1.3B	AUC	0.72	—	Unverified
10	GAL 6.7B	AUC	0.72	—	Unverified

#	Model	Metric	Claimed	Verified	Status
1	D-MPNN	RMSE	1.05	—	Unverified
2	XGBoost	RMSE	0.99	—	Unverified
3	ChemBERTa-2 (MTR-77M)	RMSE	0.89	—	Unverified
4	ChemBFN	RMSE	0.88	—	Unverified
5	SPMM	RMSE	0.81	—	Unverified
6	ChemRL-GEM	RMSE	0.8	—	Unverified
7	Uni-Mol	RMSE	0.79	—	Unverified
8	SMA	RMSE	0.62	—	Unverified
9	MPNN	RMSE	0.58	—	Unverified

#	Model	Metric	Claimed	Verified	Status
1	PretrainGNN	MAE	113.2	—	Unverified
2	D-MPNN	MAE	103.5	—	Unverified
3	GROVER (base)	MAE	94.5	—	Unverified
4	N-GramRF	MAE	92.8	—	Unverified
5	GROVER (large)	MAE	92	—	Unverified
6	N-GramXGB	MAE	81.9	—	Unverified
7	ChemRL-GEM	MAE	58.9	—	Unverified
8	Uni-Mol	MAE	41.8	—	Unverified

#	Model	Metric	Claimed	Verified	Status
1	N-GramRF	MAE	0.02	—	Unverified
2	GROVER (large)	MAE	0.02	—	Unverified
3	GROVER (base)	MAE	0.02	—	Unverified
4	N-GramXGB	MAE	0.02	—	Unverified
5	PretrainGNN	MAE	0.02	—	Unverified
6	D-MPNN	MAE	0.02	—	Unverified
7	ChemRL-GEM	MAE	0.02	—	Unverified
8	Uni-Mol	MAE	0.02	—	Unverified

#	Model	Metric	Claimed	Verified	Status
1	N-GramRF	MAE	0.01	—	Unverified
2	GROVER (large)	MAE	0.01	—	Unverified
3	GROVER (base)	MAE	0.01	—	Unverified
4	N-GramXGB	MAE	0.01	—	Unverified
5	PretrainGNN	MAE	0.01	—	Unverified
6	D-MPNN	MAE	0.01	—	Unverified
7	ChemRL-GEM	MAE	0.01	—	Unverified
8	Uni-Mol	MAE	0	—	Unverified

#	Model	Metric	Claimed	Verified	Status
1	DumplingGNN	ROC-AUC	78.2	—	Unverified
2	Uni-Mol	ROC-AUC	69.6	—	Unverified
3	ChemRL-GEM	ROC-AUC	69.2	—	Unverified
4	PretrainGNN	ROC-AUC	65.7	—	Unverified
5	D-MPNN	ROC-AUC	65.5	—	Unverified
6	GROVER (base)	ROC-AUC	65.4	—	Unverified
7	GROVER (large)	ROC-AUC	65.3	—	Unverified

#	Model	Metric	Claimed	Verified	Status
1	Uni-Mol	AUC	0.77	—	Unverified
2	GAL 30B	AUC	0.69	—	Unverified
3	GAL 6.7B	AUC	0.64	—	Unverified
4	GAL 1.3B	AUC	0.62	—	Unverified
5	GAL 125M	AUC	0.58	—	Unverified

#	Model	Metric	Claimed	Verified	Status
1	Deep-CBN	ROC-AUC	99.8	—	Unverified
2	Uni-Mol	ROC-AUC	82.1	—	Unverified
3	BioAct-Het	ROC-AUC	69.47	—	Unverified
4	IterRefLSTM	ROC-AUC	67	—	Unverified

#	Model	Metric	Claimed	Verified	Status
1	Deep-CBN	ROC-AUC	97.3	—	Unverified
2	Uni-Mol	ROC-AUC	80.8	—	Unverified
3	ChemBFN	ROC-AUC	79.37	—	Unverified

#	Model	Metric	Claimed	Verified	Status
1	ChemBERTa-2 (MTR-77M)	RMSE	48.52	—	Unverified
2	SPMM	RMSE	44.75	—	Unverified

#	Model	Metric	Claimed	Verified	Status
1	DumplingGNN	ROC-AUC	88.87	—	Unverified
2	Uni-Mol	ROC-AUC	88.5	—	Unverified