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
ApisTox: a new benchmark dataset for the classification of small molecules toxicity on honey bees	Apr 24, 2024	BenchmarkingMolecular Property Prediction	CodeCode Available	0
Transformers for molecular property prediction: Lessons learned from the past five years	Apr 5, 2024	Drug DiscoveryMolecular Property Prediction	CodeCode Available	0
Generalizable, Fast, and Accurate DeepQSPR with fastprop	Apr 2, 2024	Molecular Property PredictionProperty Prediction	CodeCode Available	2
A Python library for efficient computation of molecular fingerprints	Mar 27, 2024	Drug DiscoveryMolecular Property Prediction	CodeCode Available	3
Sort & Slice: A Simple and Superior Alternative to Hash-Based Folding for Extended-Connectivity Fingerprints	Mar 10, 2024	Molecular Property PredictionProperty Prediction	—Unverified	0
Self-Guided Masked Autoencoders for Domain-Agnostic Self-Supervised Learning	Feb 22, 2024	Molecular Property PredictionProperty Prediction	CodeCode Available	1
BBA: Bi-Modal Behavioral Alignment for Reasoning with Large Vision-Language Models	Feb 21, 2024	Geometry Problem SolvingMolecular Property Prediction	—Unverified	0
An Equivariant Pretrained Transformer for Unified 3D Molecular Representation Learning	Feb 20, 2024	DenoisingDrug Discovery	—Unverified	0
An end-to-end attention-based approach for learning on graphs	Feb 16, 2024	Graph ClassificationGraph Regression	CodeCode Available	2
Impact of Domain Knowledge and Multi-Modality on Intelligent Molecular Property Prediction: A Systematic Survey	Feb 11, 2024	Drug DiscoveryMolecular Property Prediction	—Unverified	0
ChemLLM: A Chemical Large Language Model	Feb 10, 2024	Language ModelingLanguage Modelling	CodeCode Available	1
Triplet Interaction Improves Graph Transformers: Accurate Molecular Graph Learning with Triplet Graph Transformers	Feb 7, 2024	Drug DiscoveryGraph Learning	CodeCode Available	2
Structure-Aware E(3)-Invariant Molecular Conformer Aggregation Networks	Feb 3, 2024	GPUMolecular Property Prediction	CodeCode Available	1
Diverse Explanations From Data-Driven and Domain-Driven Perspectives in the Physical Sciences	Feb 1, 2024	DiversityExplainable artificial intelligence	CodeCode Available	0
Graph Multi-Similarity Learning for Molecular Property Prediction	Jan 31, 2024	AttributeContrastive Learning	—Unverified	0
MolPLA: A Molecular Pretraining Framework for Learning Cores, R-Groups and their Linker Joints	Jan 30, 2024	Contrastive LearningMolecular Property Prediction	CodeCode Available	0
Enhancing Molecular Property Prediction with Auxiliary Learning and Task-Specific Adaptation	Jan 29, 2024	Auxiliary LearningMolecular Property Prediction	CodeCode Available	0
TwinBooster: Synergising Large Language Models with Barlow Twins and Gradient Boosting for Enhanced Molecular Property Prediction	Jan 9, 2024	Drug DiscoveryLanguage Modeling	CodeCode Available	0
Multi-Modal Representation Learning for Molecular Property Prediction: Sequence, Graph, Geometry	Jan 7, 2024	Data AugmentationDrug Discovery	CodeCode Available	2
Can Large Language Models Understand Molecules?	Jan 5, 2024	Drug DiscoveryLanguage Modelling	CodeCode Available	1
Integrating Chemical Language and Molecular Graph in Multimodal Fused Deep Learning for Drug Property Prediction	Dec 29, 2023	Deep LearningDrug Discovery	—Unverified	0
AdaMR: Adaptable Molecular Representation for Unified Pre-training Strategy	Dec 28, 2023	AttributeMolecular Property Prediction	—Unverified	0
Molecular Property Prediction Based on Graph Structure Learning	Dec 28, 2023	Drug DiscoveryGraph Neural Network	—Unverified	0
Pre-training of Molecular GNNs via Conditional Boltzmann Generator	Dec 20, 2023	Molecular Property PredictionProperty Prediction	—Unverified	0
SE(3)-Invariant Multiparameter Persistent Homology for Chiral-Sensitive Molecular Property Prediction	Dec 12, 2023	Active LearningDrug Discovery	—Unverified	0
Enhancing Molecular Property Prediction via Mixture of Collaborative Experts	Dec 6, 2023	Decision MakingDiversity	CodeCode Available	0
Provable Adversarial Robustness for Group Equivariant Tasks: Graphs, Point Clouds, Molecules, and More	Dec 5, 2023	Adversarial RobustnessMolecular Property Prediction	—Unverified	0
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
MultiModal-Learning for Predicting Molecular Properties: A Framework Based on Image and Graph Structures	Nov 28, 2023	Drug DiscoveryGraph Neural Network	—Unverified	0
Multiparameter Persistent Homology for Molecular Property Prediction	Nov 17, 2023	Molecular Property PredictionPrediction	—Unverified	0
Advancing Drug Discovery with Enhanced Chemical Understanding via Asymmetric Contrastive Multimodal Learning	Nov 11, 2023	Contrastive LearningDrug Discovery	CodeCode Available	0
Identifying Semantic Component for Robust Molecular Property Prediction	Nov 8, 2023	Molecular Property PredictionPrediction	CodeCode Available	0
Multi-channel learning for integrating structural hierarchies into context-dependent molecular representation	Nov 5, 2023	Drug DiscoveryMolecular Property Prediction	CodeCode Available	1
Sliced Denoising: A Physics-Informed Molecular Pre-Training Method	Nov 3, 2023	DenoisingDrug Discovery	—Unverified	0
Sliceformer: Make Multi-head Attention as Simple as Sorting in Discriminative Tasks	Oct 26, 2023	image-classificationImage Classification	CodeCode Available	0
Unsupervised Learning of Molecular Embeddings for Enhanced Clustering and Emergent Properties for Chemical Compounds	Oct 25, 2023	Molecular Property PredictionProperty Prediction	—Unverified	0
UniMAP: Universal SMILES-Graph Representation Learning	Oct 22, 2023	Graph MatchingGraph Representation Learning	CodeCode Available	1
Improving Molecular Properties Prediction Through Latent Space Fusion	Oct 20, 2023	Molecular Property PredictionPrediction	CodeCode Available	2
BioAct-Het: A Heterogeneous Siamese Neural Network for Bioactivity Prediction Using Novel Bioactivity Representatio	Oct 15, 2023	Drug DiscoveryMeta-Learning	CodeCode Available	0
In-Context Learning for Few-Shot Molecular Property Prediction	Oct 13, 2023	Few-Shot LearningIn-Context Learning	—Unverified	0
Atom-Motif Contrastive Transformer for Molecular Property Prediction	Oct 11, 2023	Molecular Property PredictionPrediction	—Unverified	0
Lo-Hi: Practical ML Drug Discovery Benchmark	Oct 10, 2023	Drug DiscoveryMolecular Property Prediction	CodeCode Available	1
PointGAT: A quantum chemical property prediction model integrating graph attention and 3D geometry	Oct 8, 2023	3D geometryComputational chemistry	—Unverified	0
On the Stability of Expressive Positional Encodings for Graphs	Oct 4, 2023	Molecular Property PredictionOut-of-Distribution Generalization	CodeCode Available	1
PACIA: Parameter-Efficient Adapter for Few-Shot Molecular Property Prediction	Oct 1, 2023	Few-Shot LearningGraph Neural Network	CodeCode Available	0
3D-Mol: A Novel Contrastive Learning Framework for Molecular Property Prediction with 3D Information	Sep 28, 2023	Contrastive LearningMolecular Property Prediction	—Unverified	0
GPT-MolBERTa: GPT Molecular Features Language Model for molecular property prediction	Sep 20, 2023	Language ModelingLanguage Modelling	—Unverified	0
ChemBERTa-2: Fine-Tuning for Molecule’s HIV Replication Inhibition Prediction	Sep 15, 2023	Molecular Property Prediction	CodeCode Available	1
Motif-aware Attribute Masking for Molecular Graph Pre-training	Sep 8, 2023	AttributeDecoder	CodeCode Available	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