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
Locally-Deployed Chain-of-Thought (CoT) Reasoning Model in Chemical Engineering: Starting from 30 Experimental Data	Feb 17, 2025	Gaussian ProcessesLanguage Modeling	—Unverified
CL-MFAP: A Contrastive Learning-Based Multimodal Foundation Model for Molecular Property Prediction and Antibiotic Screening	Feb 16, 2025	Contrastive LearningMolecular Property Prediction	CodeCode Available
Mol-LLM: Multimodal Generalist Molecular LLM with Improved Graph Utilization	Feb 5, 2025	Chemical Reaction PredictionMolecular Property Prediction	—Unverified
FragmentNet: Adaptive Graph Fragmentation for Graph-to-Sequence Molecular Representation Learning	Feb 3, 2025	Graph-to-SequenceMolecular Property Prediction	—Unverified
ReactEmbed: A Cross-Domain Framework for Protein-Molecule Representation Learning via Biochemical Reaction Networks	Jan 30, 2025	Contrastive LearningDrug Discovery	CodeCode Available
MolGraph-xLSTM: A graph-based dual-level xLSTM framework with multi-head mixture-of-experts for enhanced molecular representation and interpretability	Jan 30, 2025	Drug DiscoveryMixture-of-Experts	—Unverified
Can Molecular Evolution Mechanism Enhance Molecular Representation?	Jan 27, 2025	Molecular Property Predictionmolecular representation	—Unverified
Evaluating multiple models using labeled and unlabeled data	Jan 21, 2025	Molecular Property PredictionProperty Prediction	—Unverified
Molecular Graph Contrastive Learning with Line Graph	Jan 15, 2025	AttributeContrastive Learning	CodeCode Available
Dual-Modality Representation Learning for Molecular Property Prediction	Jan 11, 2025	Molecular Property PredictionPrediction	—Unverified
Revisiting Graph Neural Networks on Graph-level Tasks: Comprehensive Experiments, Analysis, and Improvements	Jan 1, 2025	Contrastive LearningGraph Classification	—Unverified
Multi-modal Contrastive Learning with Negative Sampling Calibration for Phenotypic Drug Discovery	Jan 1, 2025	Contrastive LearningDrug Discovery	—Unverified
RingFormer: A Ring-Enhanced Graph Transformer for Organic Solar Cell Property Prediction	Dec 12, 2024	Graph Representation LearningMolecular Property Prediction	CodeCode Available
Investigating Graph Neural Networks and Classical Feature-Extraction Techniques in Activity-Cliff and Molecular Property Prediction	Nov 20, 2024	Drug DiscoveryMolecular Property Prediction	—Unverified
GeomCLIP: Contrastive Geometry-Text Pre-training for Molecules	Nov 16, 2024	DenoisingMolecular Property Prediction	CodeCode Available
Two-Stage Pretraining for Molecular Property Prediction in the Wild	Nov 5, 2024	DenoisingMolecular Property Prediction	—Unverified
Pin-Tuning: Parameter-Efficient In-Context Tuning for Few-Shot Molecular Property Prediction	Nov 2, 2024	AttributeDrug Discovery	CodeCode Available
MolCap-Arena: A Comprehensive Captioning Benchmark on Language-Enhanced Molecular Property Prediction	Nov 1, 2024	Molecular Property PredictionProperty Prediction	CodeCode Available
Subgraph Aggregation for Out-of-Distribution Generalization on Graphs	Oct 29, 2024	Molecular Property PredictionOut-of-Distribution Generalization	CodeCode Available
Contextual Representation Anchor Network to Alleviate Selection Bias in Few-Shot Drug Discovery	Oct 28, 2024	Drug DiscoveryFew-Shot Learning	—Unverified
Homomorphism Counts as Structural Encodings for Graph Learning	Oct 24, 2024	Graph LearningMolecular Property Prediction	CodeCode Available
Explaining Graph Neural Networks with Large Language Models: A Counterfactual Perspective for Molecular Property Prediction	Oct 19, 2024	counterfactualCounterfactual Explanation	CodeCode Available
KA-GNN: Kolmogorov-Arnold Graph Neural Networks for Molecular Property Prediction	Oct 15, 2024	Drug DiscoveryGraph Attention	—Unverified
Large-Scale Knowledge Integration for Enhanced Molecular Property Prediction	Oct 15, 2024	Drug DiscoveryMolecular Property Prediction	CodeCode Available
UniGEM: A Unified Approach to Generation and Property Prediction for Molecules	Oct 14, 2024	Drug DiscoveryMolecular Property Prediction	—Unverified
WGFormer: An SE(3)-Transformer Driven by Wasserstein Gradient Flows for Molecular Ground-State Conformation Prediction	Oct 13, 2024	Computational EfficiencyMolecular Docking	—Unverified
TapWeight: Reweighting Pretraining Objectives for Task-Adaptive Pretraining	Oct 13, 2024	Molecular Property PredictionNatural Language Understanding	—Unverified
Unveiling Molecular Secrets: An LLM-Augmented Linear Model for Explainable and Calibratable Molecular Property Prediction	Oct 11, 2024	CPUDimensionality Reduction	CodeCode Available
Scalable Multi-Task Transfer Learning for Molecular Property Prediction	Oct 1, 2024	Molecular Property PredictionPrediction	—Unverified
Task Addition in Multi-Task Learning by Geometrical Alignment	Sep 25, 2024	Molecular Property PredictionMulti-Task Learning	—Unverified
Quantum Machine Learning in Drug Discovery: Applications in Academia and Pharmaceutical Industries	Sep 24, 2024	Drug DiscoveryMolecular Property Prediction	—Unverified
Dumpling GNN: Hybrid GNN Enables Better ADC Payload Activity Prediction Based on Chemical Structure	Sep 23, 2024	Activity PredictionDrug Discovery	—Unverified
Smirk: An Atomically Complete Tokenizer for Molecular Foundation Models	Sep 19, 2024	DiversityMolecular Property Prediction	—Unverified
Regression with Large Language Models for Materials and Molecular Property Prediction	Sep 9, 2024	Language ModelingLanguage Modelling	—Unverified
CrysAtom: Distributed Representation of Atoms for Crystal Property Prediction	Sep 7, 2024	Formation EnergyGraph Neural Network	—Unverified
Leveraging Chemistry Foundation Models to Facilitate Structure Focused Retrieval Augmented Generation in Multi-Agent Workflows for Catalyst and Materials Design	Aug 21, 2024	Cross-Modal RetrievalInformation Retrieval	—Unverified
Molecular Graph Representation Learning Integrating Large Language Models with Domain-specific Small Models	Aug 19, 2024	DescriptiveDrug Discovery	CodeCode Available
Advancements in Molecular Property Prediction: A Survey of Single and Multimodal Approaches	Aug 18, 2024	Drug DiscoveryMolecular Property Prediction	—Unverified
SMILES-Mamba: Chemical Mamba Foundation Models for Drug ADMET Prediction	Aug 11, 2024	Drug DiscoveryMamba	—Unverified
Advancing Molecular Machine Learning Representations with Stereoelectronics-Infused Molecular Graphs	Aug 8, 2024	Graph Neural NetworkMolecular Property Prediction	—Unverified
GNN-SKAN: Harnessing the Power of SwallowKAN to Advance Molecular Representation Learning with GNNs	Aug 2, 2024	Computational EfficiencyDrug Design	—Unverified
Distribution Learning for Molecular Regression	Jul 30, 2024	Mixture-of-ExpertsMolecular Property Prediction	—Unverified
Graph Residual based Method for Molecular Property Prediction	Jul 27, 2024	Graph Neural NetworkMolecular Property Prediction	—Unverified
Improved Uncertainty Estimation of Graph Neural Network Potentials Using Engineered Latent Space Distances	Jul 15, 2024	Graph Neural NetworkMolecular Property Prediction	—Unverified
Pre-training with Fractional Denoising to Enhance Molecular Property Prediction	Jul 14, 2024	DenoisingDrug Discovery	—Unverified
Token-Mol 1.0: Tokenized drug design with large language model	Jul 10, 2024	Drug DesignDrug Discovery	—Unverified
MolTRES: Improving Chemical Language Representation Learning for Molecular Property Prediction	Jul 9, 2024	Molecular Property PredictionProperty Prediction	—Unverified
Global Human-guided Counterfactual Explanations for Molecular Properties via Reinforcement Learning	Jun 19, 2024	counterfactualCounterfactual Explanation	CodeCode Available
Learning Multi-view Molecular Representations with Structured and Unstructured Knowledge	Jun 14, 2024	Knowledge GraphsMolecular Property Prediction	CodeCode Available
MoleculeCLA: Rethinking Molecular Benchmark via Computational Ligand-Target Binding Analysis	Jun 13, 2024	Drug DiscoveryMolecular Property Prediction	CodeCode Available

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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	PretrainGNN	ROC-AUC	78.1	—	Unverified
6	ChemRL-GEM	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