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 1–50 of 354 papers

Title	Date	Tasks	Status	Hype
Galactica: A Large Language Model for Science	Nov 16, 2022	AnachronismsBias Detection	CodeCode Available	4
Scikit-fingerprints: easy and efficient computation of molecular fingerprints in Python	Jul 18, 2024	Molecular Property PredictionProperty Prediction	CodeCode Available	3
^2DFT: A Universal Quantum Chemistry Dataset of Drug-Like Molecules and a Benchmark for Neural Network Potentials	Jun 20, 2024	Drug DiscoveryMolecular Property Prediction	CodeCode Available	3
A Python library for efficient computation of molecular fingerprints	Mar 27, 2024	Drug DiscoveryMolecular Property Prediction	CodeCode Available	3
Uni-QSAR: an Auto-ML Tool for Molecular Property Prediction	Apr 24, 2023	Drug DiscoveryModel Selection	CodeCode Available	3
TorchDrug: A Powerful and Flexible Machine Learning Platform for Drug Discovery	Feb 16, 2022	BIG-bench Machine LearningDrug Discovery	CodeCode Available	3
AutoGluon-Tabular: Robust and Accurate AutoML for Structured Data	Mar 13, 2020	AutoMLMolecular Property Prediction	CodeCode Available	3
Descriptor-based Foundation Models for Molecular Property Prediction	Jun 18, 2025	Molecular Property PredictionPrediction	CodeCode Available	2
GotenNet: Rethinking Efficient 3D Equivariant Graph Neural Networks	Apr 24, 2025	Atomic ForcesComputational Efficiency	CodeCode Available	2
M^3-20M: A Large-Scale Multi-Modal Molecule Dataset for AI-driven Drug Design and Discovery	Dec 8, 2024	Drug DesignMolecular Property Prediction	CodeCode Available	2
Generalizable, Fast, and Accurate DeepQSPR with fastprop	Apr 2, 2024	Molecular Property PredictionProperty Prediction	CodeCode Available	2
An end-to-end attention-based approach for learning on graphs	Feb 16, 2024	Graph ClassificationGraph Regression	CodeCode Available	2
Triplet Interaction Improves Graph Transformers: Accurate Molecular Graph Learning with Triplet Graph Transformers	Feb 7, 2024	Drug DiscoveryGraph Learning	CodeCode Available	2
Multi-Modal Representation Learning for Molecular Property Prediction: Sequence, Graph, Geometry	Jan 7, 2024	Data AugmentationDrug Discovery	CodeCode Available	2
Improving Molecular Properties Prediction Through Latent Space Fusion	Oct 20, 2023	Molecular Property PredictionPrediction	CodeCode Available	2
Equiformer: Equivariant Graph Attention Transformer for 3D Atomistic Graphs	Jun 23, 2022	Graph AttentionGraph Neural Network	CodeCode Available	2
Recipe for a General, Powerful, Scalable Graph Transformer	May 25, 2022	Graph ClassificationGraph Property Prediction	CodeCode Available	2
Do Transformers Really Perform Bad for Graph Representation?	Jun 9, 2021	Graph ClassificationGraph Property Prediction	CodeCode Available	2
Therapeutics Data Commons: Machine Learning Datasets and Tasks for Drug Discovery and Development	Feb 18, 2021	BIG-bench Machine LearningDrug Discovery	CodeCode Available	2
Analyzing Learned Molecular Representations for Property Prediction	Apr 2, 2019	Molecular Property Predictionmolecular representation	CodeCode Available	2
Pre-training Graph Neural Networks on Molecules by Using Subgraph-Conditioned Graph Information Bottleneck	Feb 20, 2025	Graph ClassificationGraph Neural Network	CodeCode Available	1
Property Enhanced Instruction Tuning for Multi-task Molecule Generation with Large Language Models	Dec 24, 2024	Machine TranslationMolecular Property Prediction	CodeCode Available	1
MOL-Mamba: Enhancing Molecular Representation with Structural & Electronic Insights	Dec 21, 2024	Drug DesignMamba	CodeCode Available	1
Publishing Neural Networks in Drug Discovery Might Compromise Training Data Privacy	Oct 22, 2024	Drug DiscoveryMolecular Property Prediction	CodeCode Available	1
FragNet: A Graph Neural Network for Molecular Property Prediction with Four Levels of Interpretability	Oct 16, 2024	Drug DiscoveryGraph Neural Network	CodeCode Available	1
A Bayesian Flow Network Framework for Chemistry Tasks	Jul 28, 2024	DiversityLanguage Modeling	CodeCode Available	1
MolecularGPT: Open Large Language Model (LLM) for Few-Shot Molecular Property Prediction	Jun 18, 2024	Drug DiscoveryGraph Neural Network	CodeCode Available	1
Learning Molecular Representation in a Cell	Jun 17, 2024	Molecular Property Predictionmolecular representation	CodeCode Available	1
3D-MolT5: Leveraging Discrete Structural Information for Molecule-Text Modeling	Jun 9, 2024	Molecular Property PredictionMolecule Captioning	CodeCode Available	1
E(n) Equivariant Topological Neural Networks	May 24, 2024	Inductive BiasMolecular Property Prediction	CodeCode Available	1
Contrastive Dual-Interaction Graph Neural Network for Molecular Property Prediction	May 4, 2024	Drug DiscoveryGraph Neural Network	CodeCode Available	1
CACTUS: Chemistry Agent Connecting Tool-Usage to Science	May 2, 2024	Molecular Property PredictionPrompt Engineering	CodeCode Available	1
Self-Guided Masked Autoencoders for Domain-Agnostic Self-Supervised Learning	Feb 22, 2024	Molecular Property PredictionProperty Prediction	CodeCode Available	1
ChemLLM: A Chemical Large Language Model	Feb 10, 2024	Language ModelingLanguage Modelling	CodeCode Available	1
Structure-Aware E(3)-Invariant Molecular Conformer Aggregation Networks	Feb 3, 2024	GPUMolecular Property Prediction	CodeCode Available	1
Can Large Language Models Understand Molecules?	Jan 5, 2024	Drug DiscoveryLanguage Modelling	CodeCode Available	1
Removing Biases from Molecular Representations via Information Maximization	Dec 1, 2023	FairnessMolecular Property Prediction	CodeCode Available	1
Improving Self-supervised Molecular Representation Learning using Persistent Homology	Nov 29, 2023	Molecular Property Predictionmolecular representation	CodeCode Available	1
Multi-channel learning for integrating structural hierarchies into context-dependent molecular representation	Nov 5, 2023	Drug DiscoveryMolecular Property Prediction	CodeCode Available	1
UniMAP: Universal SMILES-Graph Representation Learning	Oct 22, 2023	Graph MatchingGraph Representation Learning	CodeCode Available	1
Lo-Hi: Practical ML Drug Discovery Benchmark	Oct 10, 2023	Drug DiscoveryMolecular Property Prediction	CodeCode Available	1
On the Stability of Expressive Positional Encodings for Graphs	Oct 4, 2023	Molecular Property PredictionOut-of-Distribution Generalization	CodeCode Available	1
ChemBERTa-2: Fine-Tuning for Molecule’s HIV Replication Inhibition Prediction	Sep 15, 2023	Molecular Property Prediction	CodeCode Available	1
Hierarchical Grammar-Induced Geometry for Data-Efficient Molecular Property Prediction	Sep 4, 2023	Drug DiscoveryMolecular Property Prediction	CodeCode Available	1
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
Graph Sampling-based Meta-Learning for Molecular Property Prediction	Jun 29, 2023	Graph SamplingMeta-Learning	CodeCode Available	1
Automated 3D Pre-Training for Molecular Property Prediction	Jun 13, 2023	Drug DiscoveryGraph 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