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 151–200 of 354 papers

Title	Date	Tasks	Status
Atom-Motif Contrastive Transformer for Molecular Property Prediction	Oct 11, 2023	Molecular Property PredictionPrediction	—Unverified
Attention-wise masked graph contrastive learning for predicting molecular property	May 2, 2022	Contrastive LearningGraph Attention	—Unverified
BBA: Bi-Modal Behavioral Alignment for Reasoning with Large Vision-Language Models	Feb 21, 2024	Geometry Problem SolvingMolecular Property Prediction	—Unverified
Beyond Chemical Language: A Multimodal Approach to Enhance Molecular Property Prediction	Jun 22, 2023	feature selectionLanguage Modeling	—Unverified
BioLangFusion: Multimodal Fusion of DNA, mRNA, and Protein Language Models	Jun 10, 2025	Inductive BiasMolecular Property Prediction	—Unverified
BOOM: Benchmarking Out-Of-distribution Molecular Property Predictions of Machine Learning Models	May 3, 2025	BenchmarkingHyperparameter Optimization	—Unverified
Calibrated Uncertainty for Molecular Property Prediction using Ensembles of Message Passing Neural Networks	Jul 13, 2021	BIG-bench Machine LearningDecision Making	—Unverified
Can Molecular Evolution Mechanism Enhance Molecular Representation?	Jan 27, 2025	Molecular Property Predictionmolecular representation	—Unverified
ChemRL-GEM: Geometry Enhanced Molecular Representation Learning for Property Prediction	Jun 11, 2021	Molecular Property Predictionmolecular representation	—Unverified
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
Contextual Representation Anchor Network to Alleviate Selection Bias in Few-Shot Drug Discovery	Oct 28, 2024	Drug DiscoveryFew-Shot Learning	—Unverified
Coordinating Cross-modal Distillation for Molecular Property Prediction	Nov 30, 2022	Graph RegressionGraph Representation Learning	—Unverified
CrysAtom: Distributed Representation of Atoms for Crystal Property Prediction	Sep 7, 2024	Formation EnergyGraph Neural Network	—Unverified
CTAGE: Curvature-Based Topology-Aware Graph Embedding for Learning Molecular Representations	Jul 25, 2023	Drug DesignGraph Embedding	—Unverified
Deep Learning Methods for Small Molecule Drug Discovery: A Survey	Mar 1, 2023	Deep LearningDrug Discovery	—Unverified
Directed Graph Attention Neural Network Utilizing 3D Coordinates for Molecular Property Prediction	Dec 1, 2020	Graph AttentionMolecular Property Prediction	—Unverified
Directional Message Passing on Molecular Graphs via Synthetic Coordinates	Nov 8, 2021	Graph Neural NetworkMolecular Property Prediction	—Unverified
Distribution Learning for Molecular Regression	Jul 30, 2024	Mixture-of-ExpertsMolecular Property Prediction	—Unverified
Enforcing Predictive Invariance across Structured Biomedical Domains	Jun 6, 2020	Domain GeneralizationMolecular Property Prediction	—Unverified
Multi-View Graph Neural Networks for Molecular Property Prediction	May 17, 2020	Drug DiscoveryGraph Neural Network	—Unverified
Dual-Modality Representation Learning for Molecular Property Prediction	Jan 11, 2025	Molecular Property PredictionPrediction	—Unverified
Dumpling GNN: Hybrid GNN Enables Better ADC Payload Activity Prediction Based on Chemical Structure	Sep 23, 2024	Activity PredictionDrug Discovery	—Unverified
Edge-Level Explanations for Graph Neural Networks by Extending Explainability Methods for Convolutional Neural Networks	Nov 1, 2021	Molecular Property PredictionProperty Prediction	—Unverified
Ensemble Knowledge Distillation for Machine Learning Interatomic Potentials	Mar 18, 2025	Atomic ForcesKnowledge Distillation	—Unverified
Ensemble Model With Bert,Roberta and Xlnet For Molecular property prediction	May 30, 2024	Ensemble LearningMolecular Property Prediction	—Unverified
Equilibrium Aggregation: Encoding Sets via Optimization	Feb 25, 2022	Molecular Property PredictionProperty Prediction	—Unverified
Equivariant Graph Attention Networks for Molecular Property Prediction	Feb 20, 2022	Drug DiscoveryGraph Attention	—Unverified
An Equivariant Pretrained Transformer for Unified 3D Molecular Representation Learning	Feb 20, 2024	DenoisingDrug Discovery	—Unverified
Evaluating multiple models using labeled and unlabeled data	Jan 21, 2025	Molecular Property PredictionProperty Prediction	—Unverified
Evaluating Scalable Uncertainty Estimation Methods for DNN-Based Molecular Property Prediction	Oct 7, 2019	Bayesian InferenceMolecular Property Prediction	—Unverified
Explainable Molecular Property Prediction: Aligning Chemical Concepts with Predictions via Language Models	May 25, 2024	Drug DiscoveryMolecular Property Prediction	—Unverified
Extreme Acceleration of Graph Neural Network-based Prediction Models for Quantum Chemistry	Nov 25, 2022	Graph Neural NetworkMolecular Property Prediction	—Unverified
FP-GNN: a versatile deep learning architecture for enhanced molecular property prediction	May 8, 2022	Deep LearningMolecular Property Prediction	—Unverified
FragmentNet: Adaptive Graph Fragmentation for Graph-to-Sequence Molecular Representation Learning	Feb 3, 2025	Graph-to-SequenceMolecular Property Prediction	—Unverified
G^3: Representation Learning and Generation for Geometric Graphs	Sep 29, 2021	Drug DiscoveryMolecular Property Prediction	—Unverified
Gated Graph Recursive Neural Networks for Molecular Property Prediction	Aug 31, 2019	Drug DiscoveryMolecular Property Prediction	—Unverified
Gaussian Process Molecule Property Prediction with FlowMO	Oct 2, 2020	Active LearningGaussian Processes	—Unverified
Geometry-aware Line Graph Transformer Pre-training for Molecular Property Prediction	Sep 1, 2023	3D geometryMolecular Property Prediction	—Unverified
GLaD: Synergizing Molecular Graphs and Language Descriptors for Enhanced Power Conversion Efficiency Prediction in Organic Photovoltaic Devices	May 23, 2024	Decision MakingEfficient Exploration	—Unverified
GL-Disen: Global-Local disentanglement for unsupervised learning of graph-level representations	Jan 1, 2021	DisentanglementGraph Representation Learning	—Unverified
Bi-level Contrastive Learning for Knowledge-Enhanced Molecule Representations	Jun 2, 2023	Contrastive LearningKnowledge Graphs	—Unverified
GPT-MolBERTa: GPT Molecular Features Language Model for molecular property prediction	Sep 20, 2023	Language ModelingLanguage Modelling	—Unverified
Graph Multi-Similarity Learning for Molecular Property Prediction	Jan 31, 2024	AttributeContrastive Learning	—Unverified
Graph Networks with Spectral Message Passing	Dec 31, 2020	Molecular Property PredictionProperty Prediction	—Unverified
Graph Neural Network Architecture Search for Molecular Property Prediction	Aug 27, 2020	Graph Neural NetworkMolecular Property Prediction	—Unverified
Graph Neural Networks for Molecules	Sep 12, 2022	Molecular Property PredictionProperty Prediction	—Unverified
Graph neural networks for the prediction of molecular structure-property relationships	Jul 25, 2022	Drug DiscoveryMolecular Property Prediction	—Unverified
Graph Neural Networks in Modern AI-aided Drug Discovery	Jun 7, 2025	Drug Discoverygraph construction	—Unverified
Graph Residual based Method for Molecular Property Prediction	Jul 27, 2024	Graph Neural NetworkMolecular Property Prediction	—Unverified
Grouping-matrix based Graph Pooling with Adaptive Number of Clusters	Sep 7, 2022	Binary ClassificationMolecular Property Prediction	—Unverified

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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