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	Hype
Heterogenous Ensemble of Models for Molecular Property Prediction	Nov 20, 2022	Molecular Property PredictionPrediction	CodeCode Available	1
Bidirectional Generation of Structure and Properties Through a Single Molecular Foundation Model	Nov 19, 2022	Molecular Property PredictionProperty Prediction	CodeCode Available	1
GPS++: An Optimised Hybrid MPNN/Transformer for Molecular Property Prediction	Nov 18, 2022	DenoisingMolecular Property Prediction	CodeCode Available	1
Galactica: A Large Language Model for Science	Nov 16, 2022	AnachronismsBias Detection	CodeCode Available	4
A 3D-Shape Similarity-based Contrastive Approach to Molecular Representation Learning	Nov 3, 2022	Contrastive LearningMolecular Property Prediction	—Unverified	0
Isotropic Gaussian Processes on Finite Spaces of Graphs	Nov 3, 2022	Gaussian ProcessesMolecular Property Prediction	CodeCode Available	0
Multimodal Model with Text and Drug Embeddings for Adverse Drug Reaction Classification	Oct 21, 2022	ClassificationMolecular Property Prediction	CodeCode Available	0
Structure-based drug design with geometric deep learning	Oct 19, 2022	Deep LearningDrug Design	—Unverified	0
PEMP: Leveraging Physics Properties to Enhance Molecular Property Prediction	Oct 18, 2022	Drug DiscoveryMolecular Property Prediction	—Unverified	0
Substructure-Atom Cross Attention for Molecular Representation Learning	Oct 15, 2022	Drug DiscoveryGraph Neural Network	—Unverified	0
ProGReST: Prototypical Graph Regression Soft Trees for Molecular Property Prediction	Oct 7, 2022	Graph RegressionMolecular Property Prediction	CodeCode Available	0
Improving Molecular Pretraining with Complementary Featurizations	Sep 29, 2022	Computational chemistryDrug Discovery	CodeCode Available	0
Unraveling Key Elements Underlying Molecular Property Prediction: A Systematic Study	Sep 26, 2022	Drug DiscoveryMolecular Property Prediction	CodeCode Available	1
A Molecular Multimodal Foundation Model Associating Molecule Graphs with Natural Language	Sep 12, 2022	Contrastive LearningCross-Modal Retrieval	CodeCode Available	1
Graph Neural Networks for Molecules	Sep 12, 2022	Molecular Property PredictionProperty Prediction	—Unverified	0
Uni-Mol: A Universal 3D Molecular Representation Learning Framework	Sep 8, 2022	3D geometry3D Geometry Prediction	—Unverified	0
Grouping-matrix based Graph Pooling with Adaptive Number of Clusters	Sep 7, 2022	Binary ClassificationMolecular Property Prediction	—Unverified	0
ChemBERTa-2: Towards Chemical Foundation Models	Sep 5, 2022	Molecular Property PredictionSelf-Supervised Learning	CodeCode Available	1
HiGNN: Hierarchical Informative Graph Neural Networks for Molecular Property Prediction Equipped with Feature-Wise Attention	Aug 30, 2022	Drug DesignDrug Discovery	CodeCode Available	1
Identifying the kind behind SMILES—anatomical therapeutic chemical classification using structure-only representations	Aug 26, 2022	Drug ATC ClassificationMolecular Property Prediction	CodeCode Available	0
GEM-2: Next Generation Molecular Property Prediction Network by Modeling Full-range Many-body Interactions	Aug 11, 2022	Computational chemistryDrug Discovery	—Unverified	0
Semi-Supervised Junction Tree Variational Autoencoder for Molecular Property Prediction	Aug 10, 2022	Computational chemistryDrug Discovery	CodeCode Available	1
Physical Pooling Functions in Graph Neural Networks for Molecular Property Prediction	Jul 27, 2022	Molecular Property PredictionProperty Prediction	—Unverified	0
Graph neural networks for the prediction of molecular structure-property relationships	Jul 25, 2022	Drug DiscoveryMolecular Property Prediction	—Unverified	0
FunQG: Molecular Representation Learning Via Quotient Graphs	Jul 18, 2022	Molecular Property Predictionmolecular representation	CodeCode Available	1
Unified 2D and 3D Pre-Training of Molecular Representations	Jul 14, 2022	Graph GenerationMolecular Property Prediction	CodeCode Available	1
Pre-training Transformers for Molecular Property Prediction Using Reaction Prediction	Jul 6, 2022	Drug DiscoveryMolecular Property Prediction	—Unverified	0
Pure Transformers are Powerful Graph Learners	Jul 6, 2022	Graph ClassificationGraph Learning	CodeCode Available	1
An adaptive graph learning method for automated molecular interactions and properties predictions	Jun 23, 2022	Drug DiscoveryGraph Learning	CodeCode Available	1
Equiformer: Equivariant Graph Attention Transformer for 3D Atomistic Graphs	Jun 23, 2022	Graph AttentionGraph Neural Network	CodeCode Available	2
Efficient and Accurate Physics-aware Multiplex Graph Neural Networks for 3D Small Molecules and Macromolecule Complexes	Jun 6, 2022	Graph Neural NetworkMolecular Property Prediction	CodeCode Available	1
KPGT: Knowledge-Guided Pre-training of Graph Transformer for Molecular Property Prediction	Jun 2, 2022	Graph Representation LearningMolecular Property Prediction	CodeCode Available	1
3D Graph Contrastive Learning for Molecular Property Prediction	May 31, 2022	Contrastive LearningMolecular Property Prediction	—Unverified	0
Pre-training via Denoising for Molecular Property Prediction	May 31, 2022	DenoisingMolecular Property Prediction	CodeCode Available	1
Triangular Contrastive Learning on Molecular Graphs	May 26, 2022	Contrastive LearningData Augmentation	—Unverified	0
Recipe for a General, Powerful, Scalable Graph Transformer	May 25, 2022	Graph ClassificationGraph Property Prediction	CodeCode Available	2
Tyger: Task-Type-Generic Active Learning for Molecular Property Prediction	May 23, 2022	Active LearningDrug Discovery	—Unverified	0
Discovering and Explaining the Representation Bottleneck of Graph Neural Networks from Multi-order Interactions	May 15, 2022	graph constructionGraph Learning	CodeCode Available	1
FP-GNN: a versatile deep learning architecture for enhanced molecular property prediction	May 8, 2022	Deep LearningMolecular Property Prediction	—Unverified	0
Meta-learning Adaptive Deep Kernel Gaussian Processes for Molecular Property Prediction	May 5, 2022	Bilevel OptimizationDrug Discovery	CodeCode Available	1
Attention-wise masked graph contrastive learning for predicting molecular property	May 2, 2022	Contrastive LearningGraph Attention	—Unverified	0
Graph Anisotropic Diffusion	Apr 30, 2022	Molecular Property PredictionProperty Prediction	CodeCode Available	0
Learning to Split for Automatic Bias Detection	Apr 28, 2022	Bias Detectionimage-classification	CodeCode Available	1
Infusing Linguistic Knowledge of SMILES into Chemical Language Models	Apr 20, 2022	Molecular Property PredictionProperty Prediction	—Unverified	0
Accurate ADMET Prediction with XGBoost	Apr 15, 2022	Drug DiscoveryMolecular Property Prediction	CodeCode Available	1
Fine-Tuning Graph Neural Networks via Graph Topology induced Optimal Transport	Mar 20, 2022	Graph ClassificationGraph Learning	CodeCode Available	1
A photonic chip-based machine learning approach for the prediction of molecular properties	Mar 3, 2022	BIG-bench Machine LearningComputational chemistry	—Unverified	0
Equilibrium Aggregation: Encoding Sets via Optimization	Feb 25, 2022	Molecular Property PredictionProperty Prediction	—Unverified	0
Structured Multi-task Learning for Molecular Property Prediction	Feb 22, 2022	Drug DiscoveryGraph Neural Network	CodeCode Available	1
Equivariant Graph Attention Networks for Molecular Property Prediction	Feb 20, 2022	Drug DiscoveryGraph Attention	—Unverified	0

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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