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 251–300 of 354 papers

Title	Date	Tasks	Status
Revisiting Graph Neural Networks on Graph-level Tasks: Comprehensive Experiments, Analysis, and Improvements	Jan 1, 2025	Contrastive LearningGraph Classification	—Unverified
Improved Uncertainty Estimation of Graph Neural Network Potentials Using Engineered Latent Space Distances	Jul 15, 2024	Graph Neural NetworkMolecular Property Prediction	—Unverified
Scaffold Splits Overestimate Virtual Screening Performance	Jun 2, 2024	BenchmarkingClustering	—Unverified
Scalable Multi-Task Transfer Learning for Molecular Property Prediction	Oct 1, 2024	Molecular Property PredictionPrediction	—Unverified
SE(3)-Invariant Multiparameter Persistent Homology for Chiral-Sensitive Molecular Property Prediction	Dec 12, 2023	Active LearningDrug Discovery	—Unverified
Self-supervised Learning and Graph Classification under Heterophily	Jun 14, 2023	ClassificationGraph Classification	—Unverified
Sheaf HyperNetworks for Personalized Federated Learning	May 31, 2024	Federated LearningMolecular Property Prediction	—Unverified
Simple GNN Regularisation for 3D Molecular Property Prediction and Beyond	Sep 29, 2021	Initial Structure to Relaxed Energy (IS2RE), DirectMolecular Property Prediction	—Unverified
Site-specific graph neural network for predicting protonation energy of oxygenate molecules	Sep 18, 2019	Graph Neural NetworkMolecular Property Prediction	—Unverified
Sliced Denoising: A Physics-Informed Molecular Pre-Training Method	Nov 3, 2023	DenoisingDrug Discovery	—Unverified
SMILES-Mamba: Chemical Mamba Foundation Models for Drug ADMET Prediction	Aug 11, 2024	Drug DiscoveryMamba	—Unverified
Smirk: An Atomically Complete Tokenizer for Molecular Foundation Models	Sep 19, 2024	DiversityMolecular Property Prediction	—Unverified
Sort & Slice: A Simple and Superior Alternative to Hash-Based Folding for Extended-Connectivity Fingerprints	Mar 10, 2024	Molecular Property PredictionProperty Prediction	—Unverified
Structure-based drug design with geometric deep learning	Oct 19, 2022	Deep LearningDrug Design	—Unverified
Substructure-Atom Cross Attention for Molecular Representation Learning	Oct 15, 2022	Drug DiscoveryGraph Neural Network	—Unverified
Supervised Pretraining for Molecular Force Fields and Properties Prediction	Nov 23, 2022	Molecular Property PredictionPrediction	—Unverified
Synergistic Fusion of Graph and Transformer Features for Enhanced Molecular Property Prediction	Aug 25, 2023	Drug DiscoveryMolecular Property Prediction	—Unverified
TapWeight: Reweighting Pretraining Objectives for Task-Adaptive Pretraining	Oct 13, 2024	Molecular Property PredictionNatural Language Understanding	—Unverified
Task Addition in Multi-Task Learning by Geometrical Alignment	Sep 25, 2024	Molecular Property PredictionMulti-Task Learning	—Unverified
Impact of Domain Knowledge and Multi-Modality on Intelligent Molecular Property Prediction: A Systematic Survey	Feb 11, 2024	Drug DiscoveryMolecular Property Prediction	—Unverified
Token-Mol 1.0: Tokenized drug design with large language model	Jul 10, 2024	Drug DesignDrug Discovery	—Unverified
Triangular Contrastive Learning on Molecular Graphs	May 26, 2022	Contrastive LearningData Augmentation	—Unverified
TRIDENT: Tri-Modal Molecular Representation Learning with Taxonomic Annotations and Local Correspondence	Jun 26, 2025	Molecular Property Predictionmolecular representation	—Unverified
Two-Stage Pretraining for Molecular Property Prediction in the Wild	Nov 5, 2024	DenoisingMolecular Property Prediction	—Unverified
Tyger: Task-Type-Generic Active Learning for Molecular Property Prediction	May 23, 2022	Active LearningDrug Discovery	—Unverified
Uncertainty quantification of molecular property prediction with Bayesian neural networks	Mar 20, 2019	Molecular Property PredictionProperty Prediction	—Unverified
UniGEM: A Unified Approach to Generation and Property Prediction for Molecules	Oct 14, 2024	Drug DiscoveryMolecular Property Prediction	—Unverified
Unsupervised Learning of Molecular Embeddings for Enhanced Clustering and Emergent Properties for Chemical Compounds	Oct 25, 2023	Molecular Property PredictionProperty Prediction	—Unverified
Variational Autoencoding Molecular Graphs with Denoising Diffusion Probabilistic Model	Jul 2, 2023	DenoisingDrug Discovery	—Unverified
Which Hyperparameters to Optimise? An Investigation of Evolutionary Hyperparameter Optimisation in Graph Neural Network For Molecular Property Prediction	Apr 13, 2021	Graph Neural NetworkHyperparameter Optimization	—Unverified
Uncertainty quantification of molecular property prediction using Bayesian neural network models	Nov 19, 2018	Molecular Property PredictionProperty Prediction	—Unverified
Ranking Structured Objects with Graph Neural Networks	Apr 18, 2021	Graph RankingGraph Regression	CodeCode Available
ReactEmbed: A Cross-Domain Framework for Protein-Molecule Representation Learning via Biochemical Reaction Networks	Jan 30, 2025	Contrastive LearningDrug Discovery	CodeCode Available
AugWard: Augmentation-Aware Representation Learning for Accurate Graph Classification	Mar 27, 2025	DiversityDrug Discovery	CodeCode Available
GraphATC: advancing multilevel and multi-label anatomical therapeutic chemical classification via atom-level graph learning	Apr 26, 2025	Drug ATC ClassificationGraph Classification	CodeCode Available
Attentive Walk-Aggregating Graph Neural Networks	Oct 6, 2021	Molecular Property PredictionPrediction	CodeCode Available
Graph Anisotropic Diffusion	Apr 30, 2022	Molecular Property PredictionProperty Prediction	CodeCode Available
Global Human-guided Counterfactual Explanations for Molecular Properties via Reinforcement Learning	Jun 19, 2024	counterfactualCounterfactual Explanation	CodeCode Available
testRNN: Coverage-guided Testing on Recurrent Neural Networks	Jun 20, 2019	Molecular Property PredictionProperty Prediction	CodeCode Available
RingFormer: A Ring-Enhanced Graph Transformer for Organic Solar Cell Property Prediction	Dec 12, 2024	Graph Representation LearningMolecular Property Prediction	CodeCode Available
Robust Molecular Property Prediction via Densifying Scarce Labeled Data	Jun 13, 2025	Drug DiscoveryMeta-Learning	CodeCode Available
The Catechol Benchmark: Time-series Solvent Selection Data for Few-shot Machine Learning	Jun 9, 2025	Active LearningBenchmarking	CodeCode Available
Rotation-Invariant Random Features Provide a Strong Baseline for Machine Learning on 3D Point Clouds	Jul 27, 2023	3D Shape ClassificationInductive Bias	CodeCode Available
Advancing Drug Discovery with Enhanced Chemical Understanding via Asymmetric Contrastive Multimodal Learning	Nov 11, 2023	Contrastive LearningDrug Discovery	CodeCode Available
Data-Efficient Molecular Generation with Hierarchical Textual Inversion	May 5, 2024	Drug DiscoveryImage Generation	CodeCode Available
GeoT: A Geometry-aware Transformer for Reliable Molecular Property Prediction and Chemically Interpretable Representation Learning	Jun 29, 2021	Molecular Property Predictionmolecular representation	CodeCode Available
The Role of Model Architecture and Scale in Predicting Molecular Properties: Insights from Fine-Tuning RoBERTa, BART, and LLaMA	May 2, 2024	BenchmarkingDrug Discovery	CodeCode Available
GeomCLIP: Contrastive Geometry-Text Pre-training for Molecules	Nov 16, 2024	DenoisingMolecular Property Prediction	CodeCode Available
GEM-2: Next Generation Molecular Property Prediction Network by Modeling Full-range Many-body Interactions	Aug 11, 2022	Computational chemistryDrug Discovery	CodeCode Available
MoleculeCLA: Rethinking Molecular Benchmark via Computational Ligand-Target Binding Analysis	Jun 13, 2024	Drug DiscoveryMolecular Property Prediction	CodeCode Available

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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