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	Hype
Knowledge-informed Molecular Learning: A Survey on Paradigm Transfer	Feb 17, 2022	Molecular Property PredictionProperty Prediction	—Unverified	0
TorchDrug: A Powerful and Flexible Machine Learning Platform for Drug Discovery	Feb 16, 2022	BIG-bench Machine LearningDrug Discovery	CodeCode Available	3
Improving Molecular Representation Learning with Metric Learning-enhanced Optimal Transport	Feb 13, 2022	Domain AdaptationMetric Learning	CodeCode Available	1
Graph Self-supervised Learning with Accurate Discrepancy Learning	Feb 7, 2022	Contrastive LearningLink Prediction	CodeCode Available	1
GRPE: Relative Positional Encoding for Graph Transformer	Jan 30, 2022	Graph ClassificationGraph Regression	CodeCode Available	1
Graph-wise Common Latent Factor Extraction for Unsupervised Graph Representation Learning	Dec 16, 2021	Graph EmbeddingGraph Generation	CodeCode Available	0
Molecular Contrastive Learning with Chemical Element Knowledge Graph	Dec 1, 2021	Contrastive LearningDrug Design	CodeCode Available	1
Image-Like Graph Representations for Improved Molecular Property Prediction	Nov 20, 2021	Graph Neural NetworkMolecular Property Prediction	—Unverified	0
DropGNN: Random Dropouts Increase the Expressiveness of Graph Neural Networks	Nov 11, 2021	Graph ClassificationGraph Regression	CodeCode Available	1
Directional Message Passing on Molecular Graphs via Synthetic Coordinates	Nov 8, 2021	Graph Neural NetworkMolecular Property Prediction	—Unverified	0
Edge-Level Explanations for Graph Neural Networks by Extending Explainability Methods for Convolutional Neural Networks	Nov 1, 2021	Molecular Property PredictionProperty Prediction	—Unverified	0
An In-depth Summary of Recent Artificial Intelligence Applications in Drug Design	Oct 10, 2021	Drug DesignGenerative Adversarial Network	—Unverified	0
Learning 3D Representations of Molecular Chirality with Invariance to Bond Rotations	Oct 8, 2021	Contrastive LearningData Augmentation	CodeCode Available	1
3D Infomax improves GNNs for Molecular Property Prediction	Oct 8, 2021	Contrastive LearningGraph Learning	CodeCode Available	1
Attentive Walk-Aggregating Graph Neural Networks	Oct 6, 2021	Molecular Property PredictionPrediction	CodeCode Available	0
Motif-based Graph Self-Supervised Learning for Molecular Property Prediction	Oct 3, 2021	Molecular Property PredictionProperty Prediction	CodeCode Available	1
Molecule3D: A Benchmark for Predicting 3D Geometries from Molecular Graphs	Sep 30, 2021	3D Geometry PredictionMolecular Property Prediction	CodeCode Available	1
3D Pre-training improves GNNs for Molecular Property Prediction	Sep 29, 2021	Graph Neural NetworkMolecular Property Prediction	—Unverified	0
Simple GNN Regularisation for 3D Molecular Property Prediction and Beyond	Sep 29, 2021	Initial Structure to Relaxed Energy (IS2RE), DirectMolecular Property Prediction	—Unverified	0
G^3: Representation Learning and Generation for Geometric Graphs	Sep 29, 2021	Drug DiscoveryMolecular Property Prediction	—Unverified	0
Multi-task Learning with Domain Knowledge for Molecular Property Prediction	Sep 24, 2021	Drug DiscoveryMolecular Property Prediction	—Unverified	0
GeomGCL: Geometric Graph Contrastive Learning for Molecular Property Prediction	Sep 24, 2021	Contrastive LearningData Augmentation	CodeCode Available	1
Multilingual Molecular Representation Learning via Contrastive Pre-training	Sep 18, 2021	Contrastive LearningLanguage Modeling	—Unverified	0
Generative Pre-Training from Molecules	Sep 16, 2021	Feature EngineeringGeneral Knowledge	CodeCode Available	1
Latent Tree Decomposition Parsers for AMR-to-Text Generation	Aug 27, 2021	AMR-to-Text GenerationClustering	—Unverified	0
Property-Aware Relation Networks for Few-Shot Molecular Property Prediction	Jul 16, 2021	Drug DiscoveryGraph Learning	—Unverified	0
Hierarchical graph neural nets can capture long-range interactions	Jul 15, 2021	BenchmarkingMolecular Property Prediction	CodeCode Available	1
Calibrated Uncertainty for Molecular Property Prediction using Ensembles of Message Passing Neural Networks	Jul 13, 2021	BIG-bench Machine LearningDecision Making	—Unverified	0
Quantitative Evaluation of Explainable Graph Neural Networks for Molecular Property Prediction	Jul 1, 2021	Drug DiscoveryExplainable artificial intelligence	CodeCode Available	1
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
On Graph Neural Network Ensembles for Large-Scale Molecular Property Prediction	Jun 29, 2021	Active LearningGraph Neural Network	CodeCode Available	0
DGL-LifeSci: An Open-Source Toolkit for Deep Learning on Graphs in Life Science	Jun 27, 2021	Deep LearningMolecular Property Prediction	CodeCode Available	1
Dual-view Molecule Pre-training	Jun 17, 2021	Molecular Property PredictionProperty Prediction	CodeCode Available	1
Large-Scale Chemical Language Representations Capture Molecular Structure and Properties	Jun 17, 2021	Drug DiscoveryMolecular Property Prediction	CodeCode Available	1
Fast Quantum Property Prediction via Deeper 2D and 3D Graph Networks	Jun 16, 2021	Graph Neural NetworkMolecular Property Prediction	CodeCode Available	1
Simple GNN Regularisation for 3D Molecular Property Prediction & Beyond	Jun 15, 2021	DenoisingDiversity	CodeCode Available	1
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
ChemRL-GEM: Geometry Enhanced Molecular Representation Learning for Property Prediction	Jun 11, 2021	Molecular Property Predictionmolecular representation	—Unverified	0
Artificial Intelligence in Drug Discovery: Applications and Techniques	Jun 9, 2021	Drug DesignDrug Discovery	CodeCode Available	1
Do Transformers Really Perform Bad for Graph Representation?	Jun 9, 2021	Graph ClassificationGraph Property Prediction	CodeCode Available	2
MoleHD: Ultra-Low-Cost Drug Discovery using Hyperdimensional Computing	Jun 5, 2021	Drug DiscoveryMolecular Property Prediction	—Unverified	0
SpreadGNN: Serverless Multi-task Federated Learning for Graph Neural Networks	Jun 4, 2021	BIG-bench Machine LearningFederated Learning	CodeCode Available	1
How Attentive are Graph Attention Networks?	May 30, 2021	Graph AttentionGraph Classification	CodeCode Available	1
Ranking Structured Objects with Graph Neural Networks	Apr 18, 2021	Graph RankingGraph Regression	CodeCode Available	0
FedGraphNN: A Federated Learning System and Benchmark for Graph Neural Networks	Apr 14, 2021	Federated LearningGraph Neural Network	CodeCode Available	1
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	0
Molecular Representation Learning by Leveraging Chemical Information	Mar 15, 2021	Drug DesignGraph Property Prediction	CodeCode Available	0
Structure-Enhanced Meta-Learning For Few-Shot Graph Classification	Mar 5, 2021	ClassificationGeneral Classification	CodeCode Available	0
Assigning Confidence to Molecular Property Prediction	Feb 23, 2021	Drug DesignMolecular Docking	CodeCode Available	1
Molecular Contrastive Learning of Representations via Graph Neural Networks	Feb 19, 2021	BIG-bench Machine LearningContrastive Learning	CodeCode Available	1

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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