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
FedGraphNN: A Federated Learning System and Benchmark for Graph Neural Networks	Apr 14, 2021	Federated LearningGraph Neural Network	CodeCode Available	1
Assigning Confidence to Molecular Property Prediction	Feb 23, 2021	Drug DesignMolecular Docking	CodeCode Available	1
Molecular Contrastive Learning of Representations via Graph Neural Networks	Feb 19, 2021	BIG-bench Machine LearningContrastive Learning	CodeCode Available	1
Few-Shot Graph Learning for Molecular Property Prediction	Feb 16, 2021	AttributeDrug Discovery	CodeCode Available	1
Molecular machine learning with conformer ensembles	Dec 15, 2020	BIG-bench Machine LearningDeep Learning	CodeCode Available	1
Advanced Graph and Sequence Neural Networks for Molecular Property Prediction and Drug Discovery	Dec 2, 2020	BIG-bench Machine LearningDrug Discovery	CodeCode Available	1
Bayesian Graph Neural Networks for Molecular Property Prediction	Nov 25, 2020	Molecular Property PredictionPrediction	CodeCode Available	1
Comparison of Atom Representations in Graph Neural Networks for Molecular Property Prediction	Nov 23, 2020	Molecular Property PredictionProperty Prediction	CodeCode Available	1
TrimNet: learning molecular representation from triplet messages for biomedicine	Nov 4, 2020	Drug DiscoveryMolecular Property Prediction	CodeCode Available	1
Learning Invariances in Neural Networks	Oct 22, 2020	image-classificationImage Classification	CodeCode Available	1
ChemBERTa: Large-Scale Self-Supervised Pretraining for Molecular Property Prediction	Oct 19, 2020	Molecular Property Predictionmolecular representation	CodeCode Available	1
Relevance of Rotationally Equivariant Convolutions for Predicting Molecular Properties	Aug 19, 2020	Molecular Property PredictionProperty Prediction	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
ASGN: An Active Semi-supervised Graph Neural Network for Molecular Property Prediction	Jul 7, 2020	Active LearningGraph Neural Network	CodeCode Available	1
Self-Supervised Graph Transformer on Large-Scale Molecular Data	Jun 18, 2020	Drug DesignMolecular Property Prediction	CodeCode Available	1
Optimal Transport Graph Neural Networks	Jun 8, 2020	Drug DiscoveryGraph Neural Network	CodeCode Available	1
Uncertainty Quantification Using Neural Networks for Molecular Property Prediction	May 20, 2020	Drug DiscoveryExperimental Design	CodeCode Available	1
Principal Neighbourhood Aggregation for Graph Nets	Apr 12, 2020	Graph ClassificationGraph Regression	CodeCode Available	1
InfoGraph: Unsupervised and Semi-supervised Graph-Level Representation Learning via Mutual Information Maximization	Jul 31, 2019	Graph ClassificationMolecular Property Prediction	CodeCode Available	1
Strategies for Pre-training Graph Neural Networks	May 29, 2019	Graph ClassificationMolecular Property Prediction	CodeCode Available	1
GuacaMol: Benchmarking Models for De Novo Molecular Design	Nov 22, 2018	BenchmarkingDrug Discovery	CodeCode Available	1
How Powerful are Graph Neural Networks?	Oct 1, 2018	General ClassificationGraph Classification	CodeCode Available	1
Graph Attention Networks	Oct 30, 2017	Document ClassificationGraph Attention	CodeCode Available	1
Neural Message Passing for Quantum Chemistry	Apr 4, 2017	Drug DiscoveryFormation Energy	CodeCode Available	1
MoleculeNet: A Benchmark for Molecular Machine Learning	Mar 2, 2017	BIG-bench Machine Learningimbalanced classification	CodeCode Available	1
Semi-Supervised Classification with Graph Convolutional Networks	Sep 9, 2016	Document ClassificationDrug Discovery	CodeCode Available	1
Acquiring and Adapting Priors for Novel Tasks via Neural Meta-Architectures	Jul 7, 2025	3D GenerationComputational chemistry	—Unverified	0
Combining Graph Neural Networks and Mixed Integer Linear Programming for Molecular Inference under the Two-Layered Model	Jul 5, 2025	Molecular Property PredictionProperty Prediction	—Unverified	0
TRIDENT: Tri-Modal Molecular Representation Learning with Taxonomic Annotations and Local Correspondence	Jun 26, 2025	Molecular Property Predictionmolecular representation	—Unverified	0
Robust Molecular Property Prediction via Densifying Scarce Labeled Data	Jun 13, 2025	Drug DiscoveryMeta-Learning	CodeCode Available	0
BioLangFusion: Multimodal Fusion of DNA, mRNA, and Protein Language Models	Jun 10, 2025	Inductive BiasMolecular Property Prediction	—Unverified	0
The Catechol Benchmark: Time-series Solvent Selection Data for Few-shot Machine Learning	Jun 9, 2025	Active LearningBenchmarking	CodeCode Available	0
Graph Neural Networks in Modern AI-aided Drug Discovery	Jun 7, 2025	Drug Discoverygraph construction	—Unverified	0
Recent Developments in GNNs for Drug Discovery	Jun 2, 2025	Drug DiscoveryMolecular Property Prediction	—Unverified	0
AdaptMol: Adaptive Fusion from Sequence String to Topological Structure for Few-shot Drug Discovery	May 17, 2025	Drug DiscoveryFew-Shot Learning	—Unverified	0
All You Need Is Synthetic Task Augmentation	May 15, 2025	AllMolecular Property Prediction	—Unverified	0
Impact of SMILES Notational Inconsistencies on Chemical Language Model Performance	May 11, 2025	feature selectionLanguage Modeling	CodeCode Available	0
34 Examples of LLM Applications in Materials Science and Chemistry: Towards Automation, Assistants, Agents, and Accelerated Scientific Discovery	May 5, 2025	Large Language ModelMolecular Property Prediction	—Unverified	0
BOOM: Benchmarking Out-Of-distribution Molecular Property Predictions of Machine Learning Models	May 3, 2025	BenchmarkingHyperparameter Optimization	—Unverified	0
Towards Faster and More Compact Foundation Models for Molecular Property Prediction	Apr 28, 2025	Model CompressionMolecular Property Prediction	CodeCode Available	0
Learning Hierarchical Interaction for Accurate Molecular Property Prediction	Apr 28, 2025	Drug DiscoveryMolecular Property Prediction	CodeCode Available	0
GraphATC: advancing multilevel and multi-label anatomical therapeutic chemical classification via atom-level graph learning	Apr 26, 2025	Drug ATC ClassificationGraph Classification	CodeCode Available	0
Improving Counterfactual Truthfulness for Molecular Property Prediction through Uncertainty Quantification	Apr 3, 2025	counterfactualMolecular Property Prediction	—Unverified	0
AugWard: Augmentation-Aware Representation Learning for Accurate Graph Classification	Mar 27, 2025	DiversityDrug Discovery	CodeCode Available	0
Ensemble Knowledge Distillation for Machine Learning Interatomic Potentials	Mar 18, 2025	Atomic ForcesKnowledge Distillation	—Unverified	0
A Generalist Cross-Domain Molecular Learning Framework for Structure-Based Drug Discovery	Mar 6, 2025	DenoisingDrug Discovery	—Unverified	0
Transformers for molecular property prediction: Domain adaptation efficiently improves performance	Mar 5, 2025	Domain AdaptationMolecular Property Prediction	CodeCode Available	0
Integrating convolutional layers and biformer network with forward-forward and backpropagation training	Feb 28, 2025	Computational chemistryDrug Discovery	CodeCode Available	0
Position: Graph Learning Will Lose Relevance Due To Poor Benchmarks	Feb 20, 2025	BenchmarkingCombinatorial Optimization	—Unverified	0
Locally-Deployed Chain-of-Thought (CoT) Reasoning Model in Chemical Engineering: Starting from 30 Experimental Data	Feb 17, 2025	Gaussian ProcessesLanguage Modeling	—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	ChemRL-GEM	ROC-AUC	78.1	—	Unverified
6	PretrainGNN	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