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 201–250 of 354 papers

Title	Date	Tasks	Status
GNN-SKAN: Harnessing the Power of SwallowKAN to Advance Molecular Representation Learning with GNNs	Aug 2, 2024	Computational EfficiencyDrug Design	—Unverified
MolTRES: Improving Chemical Language Representation Learning for Molecular Property Prediction	Jul 9, 2024	Molecular Property PredictionProperty Prediction	—Unverified
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
3D Denoisers are Good 2D Teachers: Molecular Pretraining via Denoising and Cross-Modal Distillation	Sep 8, 2023	DenoisingKnowledge Distillation	—Unverified
3D Graph Contrastive Learning for Molecular Property Prediction	May 31, 2022	Contrastive LearningMolecular Property Prediction	—Unverified
3D-Mol: A Novel Contrastive Learning Framework for Molecular Property Prediction with 3D Information	Sep 28, 2023	Contrastive LearningMolecular Property Prediction	—Unverified
3D Pre-training improves GNNs for Molecular Property Prediction	Sep 29, 2021	Graph Neural NetworkMolecular Property Prediction	—Unverified
A 3D-Shape Similarity-based Contrastive Approach to Molecular Representation Learning	Nov 3, 2022	Contrastive LearningMolecular Property Prediction	—Unverified
Accelerating Molecular Graph Neural Networks via Knowledge Distillation	Jun 26, 2023	Data AugmentationKnowledge Distillation	—Unverified
Acquiring and Adapting Priors for Novel Tasks via Neural Meta-Architectures	Jul 7, 2025	3D GenerationComputational chemistry	—Unverified
AdaptMol: Adaptive Fusion from Sequence String to Topological Structure for Few-shot Drug Discovery	May 17, 2025	Drug DiscoveryFew-Shot Learning	—Unverified
AdaMR: Adaptable Molecular Representation for Unified Pre-training Strategy	Dec 28, 2023	AttributeMolecular Property Prediction	—Unverified
Advancements in Molecular Property Prediction: A Survey of Single and Multimodal Approaches	Aug 18, 2024	Drug DiscoveryMolecular Property Prediction	—Unverified
Advancing Molecular Machine Learning Representations with Stereoelectronics-Infused Molecular Graphs	Aug 8, 2024	Graph Neural NetworkMolecular Property Prediction	—Unverified
A Generalist Cross-Domain Molecular Learning Framework for Structure-Based Drug Discovery	Mar 6, 2025	DenoisingDrug Discovery	—Unverified
All SMILES Variational Autoencoder for Molecular Property Prediction and Optimization	Sep 25, 2019	AllMolecular Property Prediction	—Unverified
All You Need Is Synthetic Task Augmentation	May 15, 2025	AllMolecular Property Prediction	—Unverified
A Multiscale Graph Convolutional Network Using Hierarchical Clustering	Jun 22, 2020	ClusteringMolecular Property Prediction	—Unverified
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
An In-depth Summary of Recent Artificial Intelligence Applications in Drug Design	Oct 10, 2021	Drug DesignGenerative Adversarial Network	—Unverified
A photonic chip-based machine learning approach for the prediction of molecular properties	Mar 3, 2022	BIG-bench Machine LearningComputational chemistry	—Unverified
A Systematic Comparison Study on Hyperparameter Optimisation of Graph Neural Networks for Molecular Property Prediction	Feb 8, 2021	Hyperparameter OptimizationMolecular Property Prediction	—Unverified
Atomic and Subgraph-aware Bilateral Aggregation for Molecular Representation Learning	May 22, 2023	Molecular Property Predictionmolecular representation	—Unverified
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

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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