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 301–350 of 354 papers

Title	Date	Tasks	Status
Molecular Representation Learning by Leveraging Chemical Information	Mar 15, 2021	Drug DesignGraph Property Prediction	CodeCode Available
Molecular Property Prediction: A Multilevel Quantum Interactions Modeling Perspective	Jun 25, 2019	Graph Neural NetworkGraph Regression	CodeCode Available
Molecular Graph Representation Learning Integrating Large Language Models with Domain-specific Small Models	Aug 19, 2024	DescriptiveDrug Discovery	CodeCode Available
Cross-modal representation alignment of molecular structure and perturbation-induced transcriptional profiles	Nov 22, 2019	Cross-Modal Information RetrievalInformation Retrieval	CodeCode Available
GCI: A (G)raph (C)oncept (I)nterpretation Framework	Feb 9, 2023	Explainable Artificial Intelligence (XAI)Molecular Property Prediction	CodeCode Available
Flexible dual-branched message passing neural network for quantum mechanical property prediction with molecular conformation	Jun 14, 2021	Computational chemistryMolecular Property Prediction	CodeCode Available
CL-MFAP: A Contrastive Learning-Based Multimodal Foundation Model for Molecular Property Prediction and Antibiotic Screening	Feb 16, 2025	Contrastive LearningMolecular Property Prediction	CodeCode Available
Molecular Graph Contrastive Learning with Line Graph	Jan 15, 2025	AttributeContrastive Learning	CodeCode Available
MolPLA: A Molecular Pretraining Framework for Learning Cores, R-Groups and their Linker Joints	Jan 30, 2024	Contrastive LearningMolecular Property Prediction	CodeCode Available
MolXPT: Wrapping Molecules with Text for Generative Pre-training	May 18, 2023	Language ModelingLanguage Modelling	CodeCode Available
Motif-aware Attribute Masking for Molecular Graph Pre-training	Sep 8, 2023	AttributeDecoder	CodeCode Available
Molecular geometric deep learning	Jun 22, 2023	Deep LearningMolecular Property Prediction	CodeCode Available
MUBen: Benchmarking the Uncertainty of Molecular Representation Models	Jun 14, 2023	BenchmarkingDrug Discovery	CodeCode Available
Towards Faster and More Compact Foundation Models for Molecular Property Prediction	Apr 28, 2025	Model CompressionMolecular Property Prediction	CodeCode Available
Transformers for molecular property prediction: Lessons learned from the past five years	Apr 5, 2024	Drug DiscoveryMolecular Property Prediction	CodeCode Available
Multimodal Model with Text and Drug Embeddings for Adverse Drug Reaction Classification	Oct 21, 2022	ClassificationMolecular Property Prediction	CodeCode Available
MolCap-Arena: A Comprehensive Captioning Benchmark on Language-Enhanced Molecular Property Prediction	Nov 1, 2024	Molecular Property PredictionProperty Prediction	CodeCode Available
Transformers for molecular property prediction: Domain adaptation efficiently improves performance	Mar 5, 2025	Domain AdaptationMolecular Property Prediction	CodeCode Available
Sliceformer: Make Multi-head Attention as Simple as Sorting in Discriminative Tasks	Oct 26, 2023	image-classificationImage Classification	CodeCode Available
Learning Multi-view Molecular Representations with Structured and Unstructured Knowledge	Jun 14, 2024	Knowledge GraphsMolecular Property Prediction	CodeCode Available
Learning Hierarchical Interaction for Accurate Molecular Property Prediction	Apr 28, 2025	Drug DiscoveryMolecular Property Prediction	CodeCode Available
Unveiling Molecular Secrets: An LLM-Augmented Linear Model for Explainable and Calibratable Molecular Property Prediction	Oct 11, 2024	CPUDimensionality Reduction	CodeCode Available
N-Gram Graph: Simple Unsupervised Representation for Graphs, with Applications to Molecules	Jun 24, 2018	Drug DesignGraph Neural Network	CodeCode Available
Large-Scale Knowledge Integration for Enhanced Molecular Property Prediction	Oct 15, 2024	Drug DiscoveryMolecular Property Prediction	CodeCode Available
ApisTox: a new benchmark dataset for the classification of small molecules toxicity on honey bees	Apr 24, 2024	BenchmarkingMolecular Property Prediction	CodeCode Available
On Graph Neural Network Ensembles for Large-Scale Molecular Property Prediction	Jun 29, 2021	Active LearningGraph Neural Network	CodeCode Available
Knowledge-enhanced Relation Graph and Task Sampling for Few-shot Molecular Property Prediction	May 24, 2024	Meta-LearningMolecular Property Prediction	CodeCode Available
Isotropic Gaussian Processes on Finite Spaces of Graphs	Nov 3, 2022	Gaussian ProcessesMolecular Property Prediction	CodeCode Available
Path-Augmented Graph Transformer Network	May 29, 2019	Molecular Property PredictionProperty Prediction	CodeCode Available
BioAct-Het: A Heterogeneous Siamese Neural Network for Bioactivity Prediction Using Novel Bioactivity Representatio	Oct 15, 2023	Drug DiscoveryMeta-Learning	CodeCode Available
Explaining Graph Neural Networks with Large Language Models: A Counterfactual Perspective for Molecular Property Prediction	Oct 19, 2024	counterfactualCounterfactual Explanation	CodeCode Available
Pin-Tuning: Parameter-Efficient In-Context Tuning for Few-Shot Molecular Property Prediction	Nov 2, 2024	AttributeDrug Discovery	CodeCode Available
Enhancing Molecular Property Prediction with Auxiliary Learning and Task-Specific Adaptation	Jan 29, 2024	Auxiliary LearningMolecular Property Prediction	CodeCode Available
BatmanNet: Bi-branch Masked Graph Transformer Autoencoder for Molecular Representation	Nov 25, 2022	Drug DiscoveryMolecular Property Prediction	CodeCode Available
Enhancing Molecular Property Prediction via Mixture of Collaborative Experts	Dec 6, 2023	Decision MakingDiversity	CodeCode Available
Predicting molecular dipole moments by combining atomic partial charges and atomic dipoles	Mar 27, 2020	GPRMolecular Property Prediction	CodeCode Available
Structure-Enhanced Meta-Learning For Few-Shot Graph Classification	Mar 5, 2021	ClassificationGeneral Classification	CodeCode Available
Integrating convolutional layers and biformer network with forward-forward and backpropagation training	Feb 28, 2025	Computational chemistryDrug Discovery	CodeCode Available
Independent Vector Analysis for Data Fusion Prior to Molecular Property Prediction with Machine Learning	Nov 1, 2018	BIG-bench Machine LearningDrug Discovery	CodeCode Available
Improving Molecular Pretraining with Complementary Featurizations	Sep 29, 2022	Computational chemistryDrug Discovery	CodeCode Available
Subgraph Aggregation for Out-of-Distribution Generalization on Graphs	Oct 29, 2024	Molecular Property PredictionOut-of-Distribution Generalization	CodeCode Available
TwinBooster: Synergising Large Language Models with Barlow Twins and Gradient Boosting for Enhanced Molecular Property Prediction	Jan 9, 2024	Drug DiscoveryLanguage Modeling	CodeCode Available
Impact of SMILES Notational Inconsistencies on Chemical Language Model Performance	May 11, 2025	feature selectionLanguage Modeling	CodeCode Available
Uni-Mol: A Universal 3D Molecular Representation Learning Framework	Sep 8, 2022	3D geometry3D Geometry Prediction	CodeCode Available
Identifying the kind behind SMILES—anatomical therapeutic chemical classification using structure-only representations	Aug 26, 2022	Drug ATC ClassificationMolecular Property Prediction	CodeCode Available
ProGReST: Prototypical Graph Regression Soft Trees for Molecular Property Prediction	Oct 7, 2022	Graph RegressionMolecular Property Prediction	CodeCode Available
An open unified deep graph learning framework for discovering drug leads	Dec 6, 2022	BenchmarkingDrug Discovery	CodeCode Available
Identifying Semantic Component for Robust Molecular Property Prediction	Nov 8, 2023	Molecular Property PredictionPrediction	CodeCode Available
Diverse Explanations From Data-Driven and Domain-Driven Perspectives in the Physical Sciences	Feb 1, 2024	DiversityExplainable artificial intelligence	CodeCode Available
Homomorphism Counts as Structural Encodings for Graph Learning	Oct 24, 2024	Graph LearningMolecular 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