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 151–200 of 354 papers

Title	Date	Tasks	Status	Hype
3D Denoisers are Good 2D Teachers: Molecular Pretraining via Denoising and Cross-Modal Distillation	Sep 8, 2023	DenoisingKnowledge Distillation	—Unverified	0
Hierarchical Grammar-Induced Geometry for Data-Efficient Molecular Property Prediction	Sep 4, 2023	Drug DiscoveryMolecular Property Prediction	CodeCode Available	1
Geometry-aware Line Graph Transformer Pre-training for Molecular Property Prediction	Sep 1, 2023	3D geometryMolecular Property Prediction	—Unverified	0
Synergistic Fusion of Graph and Transformer Features for Enhanced Molecular Property Prediction	Aug 25, 2023	Drug DiscoveryMolecular Property Prediction	—Unverified	0
On Data Imbalance in Molecular Property Prediction with Pre-training	Aug 17, 2023	Molecular Property PredictionProperty Prediction	—Unverified	0
Is Self-Supervised Pretraining Good for Extrapolation in Molecular Property Prediction?	Aug 16, 2023	Molecular Property PredictionProperty Prediction	—Unverified	0
Rotation-Invariant Random Features Provide a Strong Baseline for Machine Learning on 3D Point Clouds	Jul 27, 2023	3D Shape ClassificationInductive Bias	CodeCode Available	0
CTAGE: Curvature-Based Topology-Aware Graph Embedding for Learning Molecular Representations	Jul 25, 2023	Drug DesignGraph Embedding	—Unverified	0
Uncertainty Quantification for Molecular Property Predictions with Graph Neural Architecture Search	Jul 19, 2023	Decision MakingDrug Discovery	CodeCode Available	1
Can Large Language Models Empower Molecular Property Prediction?	Jul 14, 2023	Molecular Property PredictionPrediction	CodeCode Available	1
Predicting small molecules solubilities on endpoint devices using deep ensemble neural networks	Jul 11, 2023	Computational EfficiencyMolecular Property Prediction	CodeCode Available	1
ChiENN: Embracing Molecular Chirality with Graph Neural Networks	Jul 5, 2023	Drug DiscoveryMolecular Property Prediction	CodeCode Available	1
Variational Autoencoding Molecular Graphs with Denoising Diffusion Probabilistic Model	Jul 2, 2023	DenoisingDrug Discovery	—Unverified	0
Why Deep Models Often cannot Beat Non-deep Counterparts on Molecular Property Prediction?	Jun 30, 2023	Drug DiscoveryMolecular Property Prediction	—Unverified	0
Graph Sampling-based Meta-Learning for Molecular Property Prediction	Jun 29, 2023	Graph SamplingMeta-Learning	CodeCode Available	1
Tanimoto Random Features for Scalable Molecular Machine Learning	Jun 26, 2023	Molecular Property PredictionProperty Prediction	CodeCode Available	0
Accelerating Molecular Graph Neural Networks via Knowledge Distillation	Jun 26, 2023	Data AugmentationKnowledge Distillation	—Unverified	0
Beyond Chemical Language: A Multimodal Approach to Enhance Molecular Property Prediction	Jun 22, 2023	feature selectionLanguage Modeling	—Unverified	0
Molecular geometric deep learning	Jun 22, 2023	Deep LearningMolecular Property Prediction	CodeCode Available	0
MUBen: Benchmarking the Uncertainty of Molecular Representation Models	Jun 14, 2023	BenchmarkingDrug Discovery	CodeCode Available	0
Self-supervised Learning and Graph Classification under Heterophily	Jun 14, 2023	ClassificationGraph Classification	—Unverified	0
MolCAP: Molecular Chemical reActivity pretraining and prompted-finetuning enhanced molecular representation learning	Jun 13, 2023	DiversityDrug Discovery	—Unverified	0
Automated 3D Pre-Training for Molecular Property Prediction	Jun 13, 2023	Drug DiscoveryGraph Learning	CodeCode Available	1
Bi-level Contrastive Learning for Knowledge-Enhanced Molecule Representations	Jun 2, 2023	Contrastive LearningKnowledge Graphs	—Unverified	0
Atomic and Subgraph-aware Bilateral Aggregation for Molecular Representation Learning	May 22, 2023	Molecular Property Predictionmolecular representation	—Unverified	0
MolXPT: Wrapping Molecules with Text for Generative Pre-training	May 18, 2023	Language ModelingLanguage Modelling	CodeCode Available	0
Knowledge graph-enhanced molecular contrastive learning with functional prompt	May 4, 2023	Contrastive LearningDrug Design	—Unverified	0
MolKD: Distilling Cross-Modal Knowledge in Chemical Reactions for Molecular Property Prediction	May 3, 2023	Drug DiscoveryMolecular Property Prediction	—Unverified	0
O-GNN: Incorporating Ring Priors into Molecular Modeling	May 1, 2023	Drug DesignGraph Regression	CodeCode Available	1
Molecule-Morphology Contrastive Pretraining for Transferable Molecular Representation	Apr 27, 2023	Molecular Property Predictionmolecular representation	CodeCode Available	1
Uni-QSAR: an Auto-ML Tool for Molecular Property Prediction	Apr 24, 2023	Drug DiscoveryModel Selection	CodeCode Available	3
SELFormer: Molecular Representation Learning via SELFIES Language Models	Apr 10, 2023	Dimensionality ReductionDrug Discovery	CodeCode Available	1
A new perspective on building efficient and expressive 3D equivariant graph neural networks	Apr 7, 2023	Graph Property PredictionMolecular Property Prediction	CodeCode Available	1
HD-Bind: Encoding of Molecular Structure with Low Precision, Hyperdimensional Binary Representations	Mar 27, 2023	Molecular DockingMolecular Property Prediction	—Unverified	0
Molecular Property Prediction by Semantic-invariant Contrastive Learning	Mar 13, 2023	Contrastive LearningDrug Design	—Unverified	0
Deep Learning Methods for Small Molecule Drug Discovery: A Survey	Mar 1, 2023	Deep LearningDrug Discovery	—Unverified	0
Learning Topology-Specific Experts for Molecular Property Prediction	Feb 27, 2023	Molecular Property PredictionPrediction	CodeCode Available	1
GCI: A (G)raph (C)oncept (I)nterpretation Framework	Feb 9, 2023	Explainable Artificial Intelligence (XAI)Molecular Property Prediction	CodeCode Available	0
GPS++: Reviving the Art of Message Passing for Molecular Property Prediction	Feb 6, 2023	Molecular Property PredictionProperty Prediction	CodeCode Available	1
Implicit Geometry and Interaction Embeddings Improve Few-Shot Molecular Property Prediction	Feb 4, 2023	Few-Shot LearningMolecular Docking	CodeCode Available	0
MolCPT: Molecule Continuous Prompt Tuning to Generalize Molecular Representation Learning	Dec 20, 2022	Molecular Property Predictionmolecular representation	—Unverified	0
Pushing the boundaries of molecular property prediction for drug discovery with multitask learning BERT enhanced by SMILES enumeration	Dec 15, 2022	Drug DiscoveryFeature Engineering	CodeCode Available	1
Implicit Convolutional Kernels for Steerable CNNs	Dec 12, 2022	Molecular Property PredictionPoint Cloud Classification	CodeCode Available	1
An open unified deep graph learning framework for discovering drug leads	Dec 6, 2022	BenchmarkingDrug Discovery	CodeCode Available	0
Coordinating Cross-modal Distillation for Molecular Property Prediction	Nov 30, 2022	Graph RegressionGraph Representation Learning	—Unverified	0
BatmanNet: Bi-branch Masked Graph Transformer Autoencoder for Molecular Representation	Nov 25, 2022	Drug DiscoveryMolecular Property Prediction	CodeCode Available	0
Invariance-Aware Randomized Smoothing Certificates	Nov 25, 2022	Molecular Property PredictionProperty Prediction	—Unverified	0
Extreme Acceleration of Graph Neural Network-based Prediction Models for Quantum Chemistry	Nov 25, 2022	Graph Neural NetworkMolecular Property Prediction	—Unverified	0
Supervised Pretraining for Molecular Force Fields and Properties Prediction	Nov 23, 2022	Molecular Property PredictionPrediction	—Unverified	0
An ensemble of VisNet, Transformer-M, and pretraining models for molecular property prediction in OGB Large-Scale Challenge @ NeurIPS 2022	Nov 23, 2022	Graph Neural NetworkGraph Regression	—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