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	Score
Molecule-Morphology Contrastive Pretraining for Transferable Molecular Representation	Apr 27, 2023	Molecular Property Predictionmolecular representation	CodeCode Available	1	5
Advanced Graph and Sequence Neural Networks for Molecular Property Prediction and Drug Discovery	Dec 2, 2020	BIG-bench Machine LearningDrug Discovery	CodeCode Available	1	5
Strategies for Pre-training Graph Neural Networks	May 29, 2019	Graph ClassificationMolecular Property Prediction	CodeCode Available	1	5
Graph Sampling-based Meta-Learning for Molecular Property Prediction	Jun 29, 2023	Graph SamplingMeta-Learning	CodeCode Available	1	5
Pre-training Graph Neural Networks on Molecules by Using Subgraph-Conditioned Graph Information Bottleneck	Feb 20, 2025	Graph ClassificationGraph Neural Network	CodeCode Available	1	5
Implicit Convolutional Kernels for Steerable CNNs	Dec 12, 2022	Molecular Property PredictionPoint Cloud Classification	CodeCode Available	1	5
FedGraphNN: A Federated Learning System and Benchmark for Graph Neural Networks	Apr 14, 2021	Federated LearningGraph Neural Network	CodeCode Available	1	5
Few-Shot Graph Learning for Molecular Property Prediction	Feb 16, 2021	AttributeDrug Discovery	CodeCode Available	1	5
Fine-Tuning Graph Neural Networks via Graph Topology induced Optimal Transport	Mar 20, 2022	Graph ClassificationGraph Learning	CodeCode Available	1	5
CACTUS: Chemistry Agent Connecting Tool-Usage to Science	May 2, 2024	Molecular Property PredictionPrompt Engineering	CodeCode Available	1	5
Self-Supervised Graph Transformer on Large-Scale Molecular Data	Jun 18, 2020	Drug DesignMolecular Property Prediction	CodeCode Available	1	5
Learning 3D Representations of Molecular Chirality with Invariance to Bond Rotations	Oct 8, 2021	Contrastive LearningData Augmentation	CodeCode Available	1	5
FragNet: A Graph Neural Network for Molecular Property Prediction with Four Levels of Interpretability	Oct 16, 2024	Drug DiscoveryGraph Neural Network	CodeCode Available	1	5
Multi-channel learning for integrating structural hierarchies into context-dependent molecular representation	Nov 5, 2023	Drug DiscoveryMolecular Property Prediction	CodeCode Available	1	5
FunQG: Molecular Representation Learning Via Quotient Graphs	Jul 18, 2022	Molecular Property Predictionmolecular representation	CodeCode Available	1	5
A new perspective on building efficient and expressive 3D equivariant graph neural networks	Apr 7, 2023	Graph Property PredictionMolecular Property Prediction	CodeCode Available	1	5
Pre-training via Denoising for Molecular Property Prediction	May 31, 2022	DenoisingMolecular Property Prediction	CodeCode Available	1	5
ChemBERTa-2: Fine-Tuning for Molecule’s HIV Replication Inhibition Prediction	Sep 15, 2023	Molecular Property Prediction	CodeCode Available	1	5
ChemBERTa-2: Towards Chemical Foundation Models	Sep 5, 2022	Molecular Property PredictionSelf-Supervised Learning	CodeCode Available	1	5
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	5
Relevance of Rotationally Equivariant Convolutions for Predicting Molecular Properties	Aug 19, 2020	Molecular Property PredictionProperty Prediction	CodeCode Available	1	5
Structured Multi-task Learning for Molecular Property Prediction	Feb 22, 2022	Drug DiscoveryGraph Neural Network	CodeCode Available	1	5
Generative Pre-Training from Molecules	Sep 16, 2021	Feature EngineeringGeneral Knowledge	CodeCode Available	1	5
ChemLLM: A Chemical Large Language Model	Feb 10, 2024	Language ModelingLanguage Modelling	CodeCode Available	1	5
Optimal Transport Graph Neural Networks	Jun 8, 2020	Drug DiscoveryGraph Neural Network	CodeCode Available	1	5
Simple GNN Regularisation for 3D Molecular Property Prediction & Beyond	Jun 15, 2021	DenoisingDiversity	CodeCode Available	1	5
GeoT: A Geometry-aware Transformer for Reliable Molecular Property Prediction and Chemically Interpretable Representation Learning	Jun 29, 2021	Molecular Property Predictionmolecular representation	CodeCode Available	0	5
An open unified deep graph learning framework for discovering drug leads	Dec 6, 2022	BenchmarkingDrug Discovery	CodeCode Available	0	5
GeomCLIP: Contrastive Geometry-Text Pre-training for Molecules	Nov 16, 2024	DenoisingMolecular Property Prediction	CodeCode Available	0	5
Path-Augmented Graph Transformer Network	May 29, 2019	Molecular Property PredictionProperty Prediction	CodeCode Available	0	5
GEM-2: Next Generation Molecular Property Prediction Network by Modeling Full-range Many-body Interactions	Aug 11, 2022	Computational chemistryDrug Discovery	CodeCode Available	0	5
GCI: A (G)raph (C)oncept (I)nterpretation Framework	Feb 9, 2023	Explainable Artificial Intelligence (XAI)Molecular Property Prediction	CodeCode Available	0	5
Pin-Tuning: Parameter-Efficient In-Context Tuning for Few-Shot Molecular Property Prediction	Nov 2, 2024	AttributeDrug Discovery	CodeCode Available	0	5
N-Gram Graph: Simple Unsupervised Representation for Graphs, with Applications to Molecules	Jun 24, 2018	Drug DesignGraph Neural Network	CodeCode Available	0	5
On Graph Neural Network Ensembles for Large-Scale Molecular Property Prediction	Jun 29, 2021	Active LearningGraph Neural Network	CodeCode Available	0	5
Predicting molecular dipole moments by combining atomic partial charges and atomic dipoles	Mar 27, 2020	GPRMolecular Property Prediction	CodeCode Available	0	5
Flexible dual-branched message passing neural network for quantum mechanical property prediction with molecular conformation	Jun 14, 2021	Computational chemistryMolecular Property Prediction	CodeCode Available	0	5
Attentive Walk-Aggregating Graph Neural Networks	Oct 6, 2021	Molecular Property PredictionPrediction	CodeCode Available	0	5
BioAct-Het: A Heterogeneous Siamese Neural Network for Bioactivity Prediction Using Novel Bioactivity Representatio	Oct 15, 2023	Drug DiscoveryMeta-Learning	CodeCode Available	0	5
MolXPT: Wrapping Molecules with Text for Generative Pre-training	May 18, 2023	Language ModelingLanguage Modelling	CodeCode Available	0	5
Explaining Graph Neural Networks with Large Language Models: A Counterfactual Perspective for Molecular Property Prediction	Oct 19, 2024	counterfactualCounterfactual Explanation	CodeCode Available	0	5
MolPLA: A Molecular Pretraining Framework for Learning Cores, R-Groups and their Linker Joints	Jan 30, 2024	Contrastive LearningMolecular Property Prediction	CodeCode Available	0	5
Motif-aware Attribute Masking for Molecular Graph Pre-training	Sep 8, 2023	AttributeDecoder	CodeCode Available	0	5
MUBen: Benchmarking the Uncertainty of Molecular Representation Models	Jun 14, 2023	BenchmarkingDrug Discovery	CodeCode Available	0	5
MoleculeCLA: Rethinking Molecular Benchmark via Computational Ligand-Target Binding Analysis	Jun 13, 2024	Drug DiscoveryMolecular Property Prediction	CodeCode Available	0	5
Molecular Property Prediction: A Multilevel Quantum Interactions Modeling Perspective	Jun 25, 2019	Graph Neural NetworkGraph Regression	CodeCode Available	0	5
BatmanNet: Bi-branch Masked Graph Transformer Autoencoder for Molecular Representation	Nov 25, 2022	Drug DiscoveryMolecular Property Prediction	CodeCode Available	0	5
Molecular Representation Learning by Leveraging Chemical Information	Mar 15, 2021	Drug DesignGraph Property Prediction	CodeCode Available	0	5
Multimodal Model with Text and Drug Embeddings for Adverse Drug Reaction Classification	Oct 21, 2022	ClassificationMolecular Property Prediction	CodeCode Available	0	5
Enhancing Molecular Property Prediction with Auxiliary Learning and Task-Specific Adaptation	Jan 29, 2024	Auxiliary LearningMolecular Property Prediction	CodeCode Available	0	5

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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	PretrainGNN	ROC-AUC	78.1	—	Unverified
6	ChemRL-GEM	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