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
Acquiring and Adapting Priors for Novel Tasks via Neural Meta-Architectures	Jul 7, 2025	3D GenerationComputational chemistry	—Unverified	0
Combining Graph Neural Networks and Mixed Integer Linear Programming for Molecular Inference under the Two-Layered Model	Jul 5, 2025	Molecular Property PredictionProperty Prediction	—Unverified	0
TRIDENT: Tri-Modal Molecular Representation Learning with Taxonomic Annotations and Local Correspondence	Jun 26, 2025	Molecular Property Predictionmolecular representation	—Unverified	0
Descriptor-based Foundation Models for Molecular Property Prediction	Jun 18, 2025	Molecular Property PredictionPrediction	CodeCode Available	2
Robust Molecular Property Prediction via Densifying Scarce Labeled Data	Jun 13, 2025	Drug DiscoveryMeta-Learning	CodeCode Available	0
BioLangFusion: Multimodal Fusion of DNA, mRNA, and Protein Language Models	Jun 10, 2025	Inductive BiasMolecular Property Prediction	—Unverified	0
The Catechol Benchmark: Time-series Solvent Selection Data for Few-shot Machine Learning	Jun 9, 2025	Active LearningBenchmarking	CodeCode Available	0
Graph Neural Networks in Modern AI-aided Drug Discovery	Jun 7, 2025	Drug Discoverygraph construction	—Unverified	0
Recent Developments in GNNs for Drug Discovery	Jun 2, 2025	Drug DiscoveryMolecular Property Prediction	—Unverified	0
AdaptMol: Adaptive Fusion from Sequence String to Topological Structure for Few-shot Drug Discovery	May 17, 2025	Drug DiscoveryFew-Shot Learning	—Unverified	0
All You Need Is Synthetic Task Augmentation	May 15, 2025	AllMolecular Property Prediction	—Unverified	0
Impact of SMILES Notational Inconsistencies on Chemical Language Model Performance	May 11, 2025	feature selectionLanguage Modeling	CodeCode Available	0
34 Examples of LLM Applications in Materials Science and Chemistry: Towards Automation, Assistants, Agents, and Accelerated Scientific Discovery	May 5, 2025	Large Language ModelMolecular Property Prediction	—Unverified	0
BOOM: Benchmarking Out-Of-distribution Molecular Property Predictions of Machine Learning Models	May 3, 2025	BenchmarkingHyperparameter Optimization	—Unverified	0
Towards Faster and More Compact Foundation Models for Molecular Property Prediction	Apr 28, 2025	Model CompressionMolecular Property Prediction	CodeCode Available	0
Learning Hierarchical Interaction for Accurate Molecular Property Prediction	Apr 28, 2025	Drug DiscoveryMolecular Property Prediction	CodeCode Available	0
GraphATC: advancing multilevel and multi-label anatomical therapeutic chemical classification via atom-level graph learning	Apr 26, 2025	Drug ATC ClassificationGraph Classification	CodeCode Available	0
GotenNet: Rethinking Efficient 3D Equivariant Graph Neural Networks	Apr 24, 2025	Atomic ForcesComputational Efficiency	CodeCode Available	2
Improving Counterfactual Truthfulness for Molecular Property Prediction through Uncertainty Quantification	Apr 3, 2025	counterfactualMolecular Property Prediction	—Unverified	0
AugWard: Augmentation-Aware Representation Learning for Accurate Graph Classification	Mar 27, 2025	DiversityDrug Discovery	CodeCode Available	0
Ensemble Knowledge Distillation for Machine Learning Interatomic Potentials	Mar 18, 2025	Atomic ForcesKnowledge Distillation	—Unverified	0
A Generalist Cross-Domain Molecular Learning Framework for Structure-Based Drug Discovery	Mar 6, 2025	DenoisingDrug Discovery	—Unverified	0
Transformers for molecular property prediction: Domain adaptation efficiently improves performance	Mar 5, 2025	Domain AdaptationMolecular Property Prediction	CodeCode Available	0
Integrating convolutional layers and biformer network with forward-forward and backpropagation training	Feb 28, 2025	Computational chemistryDrug Discovery	CodeCode Available	0
Position: Graph Learning Will Lose Relevance Due To Poor Benchmarks	Feb 20, 2025	BenchmarkingCombinatorial Optimization	—Unverified	0
Pre-training Graph Neural Networks on Molecules by Using Subgraph-Conditioned Graph Information Bottleneck	Feb 20, 2025	Graph ClassificationGraph Neural Network	CodeCode Available	1
Locally-Deployed Chain-of-Thought (CoT) Reasoning Model in Chemical Engineering: Starting from 30 Experimental Data	Feb 17, 2025	Gaussian ProcessesLanguage Modeling	—Unverified	0
Knowledge-aware contrastive heterogeneous molecular graph learning	Feb 17, 2025	BenchmarkingContrastive Learning	—Unverified	0
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	0
Mol-LLM: Multimodal Generalist Molecular LLM with Improved Graph Utilization	Feb 5, 2025	Chemical Reaction PredictionMolecular Property Prediction	—Unverified	0
FragmentNet: Adaptive Graph Fragmentation for Graph-to-Sequence Molecular Representation Learning	Feb 3, 2025	Graph-to-SequenceMolecular Property Prediction	—Unverified	0
ReactEmbed: A Cross-Domain Framework for Protein-Molecule Representation Learning via Biochemical Reaction Networks	Jan 30, 2025	Contrastive LearningDrug Discovery	CodeCode Available	0
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	0
Can Molecular Evolution Mechanism Enhance Molecular Representation?	Jan 27, 2025	Molecular Property Predictionmolecular representation	—Unverified	0
Evaluating multiple models using labeled and unlabeled data	Jan 21, 2025	Molecular Property PredictionProperty Prediction	—Unverified	0
Molecular Graph Contrastive Learning with Line Graph	Jan 15, 2025	AttributeContrastive Learning	CodeCode Available	0
Dual-Modality Representation Learning for Molecular Property Prediction	Jan 11, 2025	Molecular Property PredictionPrediction	—Unverified	0
Multi-modal Contrastive Learning with Negative Sampling Calibration for Phenotypic Drug Discovery	Jan 1, 2025	Contrastive LearningDrug Discovery	—Unverified	0
Revisiting Graph Neural Networks on Graph-level Tasks: Comprehensive Experiments, Analysis, and Improvements	Jan 1, 2025	Contrastive LearningGraph Classification	—Unverified	0
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
RingFormer: A Ring-Enhanced Graph Transformer for Organic Solar Cell Property Prediction	Dec 12, 2024	Graph Representation LearningMolecular Property Prediction	CodeCode Available	0
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
Investigating Graph Neural Networks and Classical Feature-Extraction Techniques in Activity-Cliff and Molecular Property Prediction	Nov 20, 2024	Drug DiscoveryMolecular Property Prediction	—Unverified	0
GeomCLIP: Contrastive Geometry-Text Pre-training for Molecules	Nov 16, 2024	DenoisingMolecular Property Prediction	CodeCode Available	0
Two-Stage Pretraining for Molecular Property Prediction in the Wild	Nov 5, 2024	DenoisingMolecular Property Prediction	—Unverified	0
Pin-Tuning: Parameter-Efficient In-Context Tuning for Few-Shot Molecular Property Prediction	Nov 2, 2024	AttributeDrug Discovery	CodeCode Available	0
MolCap-Arena: A Comprehensive Captioning Benchmark on Language-Enhanced Molecular Property Prediction	Nov 1, 2024	Molecular Property PredictionProperty Prediction	CodeCode Available	0
Subgraph Aggregation for Out-of-Distribution Generalization on Graphs	Oct 29, 2024	Molecular Property PredictionOut-of-Distribution Generalization	CodeCode Available	0
Contextual Representation Anchor Network to Alleviate Selection Bias in Few-Shot Drug Discovery	Oct 28, 2024	Drug DiscoveryFew-Shot Learning	—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