Drug Discovery

Drug discovery is the task of applying machine learning to discover new candidate drugs.

( Image credit: A Turing Test for Molecular Generators )

Papers

Recently Added Most Hyped Most Active Needs Verification Most Verified

Showing 1001–1050 of 1337 papers

Title	Date	Tasks	Status
Utilizing Edge Features in Graph Neural Networks via Variational Information Maximization	Jun 13, 2019	Drug DiscoveryQuantum Chemistry Regression	—Unverified
Utilizing Large Language Models in an iterative paradigm with domain feedback for zero-shot molecule optimization	Oct 17, 2024	Drug DiscoveryHallucination	—Unverified
Utilizing Low-Dimensional Molecular Embeddings for Rapid Chemical Similarity Search	Feb 12, 2024	CPUDrug Discovery	—Unverified
Variational Autoencoding Molecular Graphs with Denoising Diffusion Probabilistic Model	Jul 2, 2023	DenoisingDrug Discovery	—Unverified
Variational Quantum Algorithms for Chemical Simulation and Drug Discovery	Nov 15, 2022	Drug DiscoveryProtein Folding	—Unverified
VDDB: a comprehensive resource and machine learning platform for antiviral drug discovery	Sep 17, 2022	Activity PredictionDrug Discovery	—Unverified
ViDTA: Enhanced Drug-Target Affinity Prediction via Virtual Graph Nodes and Attention-based Feature Fusion	Dec 27, 2024	Drug DiscoveryGraph Neural Network	—Unverified
VIMPNN: A physics informed neural network for estimating potential energies of out-of-equilibrium systems	Sep 25, 2019	Drug Discovery	—Unverified
Viroinformatics-based investigation of SARS-CoV-2 core proteins for potential therapeutic targets	Sep 27, 2020	Drug Discovery	—Unverified
Virtual Cells: Predict, Explain, Discover	May 20, 2025	Drug Discovery	—Unverified
Virtual Screening of Pharmaceutical Compounds with hERG Inhibitory Activity (Cardiotoxicity) using Ensemble Learning	Jun 5, 2021	BIG-bench Machine LearningDrug Discovery	—Unverified
ViTally Consistent: Scaling Biological Representation Learning for Cell Microscopy	Nov 4, 2024	Drug DiscoveryRepresentation Learning	—Unverified
Weakly Supervised Learning of Single-Cell Feature Embeddings	Jun 1, 2018	Drug DiscoveryWeakly-supervised Learning	—Unverified
Weighted Tanimoto Coefficient for 3D Molecule Structure Similarity Measurement	Jun 10, 2018	Drug Discovery	—Unverified
WelQrate: Defining the Gold Standard in Small Molecule Drug Discovery Benchmarking	Nov 14, 2024	BenchmarkingDrug Discovery	—Unverified
Why Deep Models Often cannot Beat Non-deep Counterparts on Molecular Property Prediction?	Jun 30, 2023	Drug DiscoveryMolecular Property Prediction	—Unverified
Widely Used and Fast De Novo Drug Design by a Protein Sequence-Based Reinforcement Learning Model	Aug 14, 2022	Drug DesignDrug Discovery	—Unverified
XInsight: Revealing Model Insights for GNNs with Flow-based Explanations	Jun 7, 2023	Drug DiscoveryGraph Classification	—Unverified
XMOL: Explainable Multi-property Optimization of Molecules	Sep 12, 2024	Drug Discovery	—Unverified
Leveraging Latent Evolutionary Optimization for Targeted Molecule Generation	Jul 2, 2024	Drug DesignDrug Discovery	—Unverified
Leveraging Partial SMILES Validation Scheme for Enhanced Drug Design in Reinforcement Learning Frameworks	May 1, 2025	Deep Reinforcement LearningDrug Design	—Unverified
Leveraging Side Information for Ligand Conformation Generation using Diffusion-Based Approaches	Aug 2, 2023	DenoisingDrug Discovery	—Unverified
LIDDIA: Language-based Intelligent Drug Discovery Agent	Feb 19, 2025	Drug DiscoveryNavigate	—Unverified
Ligand-induced protein dynamics differences correlate with protein-ligand binding affinities: An unsupervised deep learning approach	Sep 3, 2021	Dimensionality ReductionDrug Discovery	—Unverified
Linear to Neural Networks Regression: QSPR of Drugs via Degree-Distance Indices	Mar 18, 2025	Drug DesignDrug Discovery	—Unverified
Link Mining for Kernel-based Compound-Protein Interaction Predictions Using a Chemogenomics Approach	May 4, 2017	Drug DiscoveryPrediction	—Unverified
Low Data Drug Discovery with One-shot Learning	Nov 10, 2016	Drug DiscoveryMolecular Property Prediction	—Unverified
Lung tumor segmentation in MRI mice scans using 3D nnU-Net with minimum annotations	Nov 1, 2024	Drug DiscoverySegmentation	—Unverified
Machine Learning and Deep Learning Methods for Building Intelligent Systems in Medicine and Drug Discovery: A Comprehensive Survey	Jul 19, 2021	BIG-bench Machine LearningDeep Learning	—Unverified
Machine Learning-Based Prediction of Key Genes Correlated to the Subretinal Lesion Severity in a Mouse Model of Age-Related Macular Degeneration	Sep 8, 2024	Dimensionality ReductionDrug Discovery	—Unverified
Machine Learning-enhanced Efficient Spectroscopic Ellipsometry Modeling	Jan 1, 2022	BIG-bench Machine LearningDrug Discovery	—Unverified
Machine learning for the prediction of safe and biologically active organophosphorus molecules	Feb 21, 2023	Drug DesignDrug Discovery	—Unverified
Machine Learning Modeling Of SiRNA Structure-Potency Relationship With Applications Against Sars-Cov-2 Spike Gene	Jan 18, 2024	Drug Discovery	—Unverified
Machine Learning Models to Predict Inhibition of the Bile Salt Export Pump	Feb 28, 2020	BIG-bench Machine LearningDrug Discovery	—Unverified
Machine learning prediction errors better than DFT accuracy	Feb 17, 2017	BIG-bench Machine LearningDrug Discovery	—Unverified
Machine Learning Scoring Functions for Drug Discoveries from Experimental and Computer-Generated Protein-Ligand Structures: Towards Per-Target Scoring Functions	Dec 6, 2022	Drug Discovery	—Unverified
Machine Learning Small Molecule Properties in Drug Discovery	Aug 2, 2023	Decision MakingDrug Discovery	—Unverified
MADE: Graph Backdoor Defense with Masked Unlearning	Nov 26, 2024	backdoor defenseDrug Discovery	—Unverified
MAGNet: Motif-Agnostic Generation of Molecules from Shapes	May 30, 2023	Drug Discovery	—Unverified
Mapping Evolution of Molecules Across Biochemistry with Assembly Theory	Sep 9, 2024	Drug Discovery	—Unverified
MARS: A Motif-based Autoregressive Model for Retrosynthesis Prediction	Sep 27, 2022	Drug DiscoveryGraph Generation	—Unverified
MaskMol: Knowledge-guided Molecular Image Pre-Training Framework for Activity Cliffs	Sep 2, 2024	Drug DiscoveryRepresentation Learning	—Unverified
Mass Balance Approximation of Unfolding Improves Potential-Like Methods for Protein Stability Predictions	Apr 9, 2025	Drug Discovery	—Unverified
MATE-Pred: Multimodal Attention-based TCR-Epitope interaction Predictor	Dec 5, 2023	Drug Discovery	—Unverified
Meaningful machine learning models and machine-learned pharmacophores from fragment screening campaigns	Mar 25, 2022	BIG-bench Machine LearningDrug Discovery	—Unverified
Medical Imaging with Deep Learning for COVID- 19 Diagnosis: A Comprehensive Review	Jul 13, 2021	Computed Tomography (CT)COVID-19 Diagnosis	—Unverified
MEGADOCK-GUI: a GUI-based complete cross-docking tool for exploring protein-protein interactions	May 8, 2021	Drug Discovery	—Unverified
Meta-Learning GNN Initializations for Low-Resource Molecular Property Prediction	Jun 12, 2020	Drug DiscoveryFew-Shot Learning	—Unverified
Meta-Learning with Graph Neural Networks: Methods and Applications	Feb 27, 2021	Drug DiscoveryMeta-Learning	—Unverified
MetaMolGen: A Neural Graph Motif Generation Model for De Novo Molecular Design	Apr 22, 2025	Drug DiscoveryMeta-Learning	—Unverified

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All datasets QM9 Tox21 BACE HIV dataset MUV ToxCast BBBP BindingDB clintox DAVIS-DTA KIBA LIT-PCBA(ALDH1)

Benchmark Results

#	Model	Metric	Claimed	Verified	Status
1	Molecular Graph Convolutions	Error ratio	2.59	—	Unverified
2	Gated Graph Sequence NN	Error ratio	1.36	—	Unverified
3	MPNNs	Error ratio	0.68	—	Unverified
4	DeepMoleNet	Error ratio	0.53	—	Unverified
5	DimeNet	Error ratio	0.44	—	Unverified
6	PaiNN	Error ratio	0.41	—	Unverified
7	DimeNet++	Error ratio	0.41	—	Unverified
8	ComENet	Error ratio	0.4	—	Unverified
9	SphereNet	Error ratio	0.39	—	Unverified
10	MXMNet	Error ratio	0.38	—	Unverified

#	Model	Metric	Claimed	Verified	Status
1	elEmBERT-V1	AUC	0.96	—	Unverified
2	TrimNet + Perforated Backpropagation	AUC	0.89	—	Unverified
3	SSVAE with multiple SMILES	AUC	0.87	—	Unverified
4	Ensemble predictor	AUC	0.86	—	Unverified
5	TrimNet	AUC	0.86	—	Unverified
6	GraphConv + dummy super node	AUC	0.85	—	Unverified
7	GraphConv	AUC	0.85	—	Unverified
8	SNN (SELU Network)	AUC	0.85	—	Unverified
9	ContextPred	AUC	0.78	—	Unverified
10	GIT-Mol(G+S)	AUC	0.76	—	Unverified

#	Model	Metric	Claimed	Verified	Status
1	TrimNet	AUC	0.88	—	Unverified
2	Ensemble locally constant network	AUC	0.87	—	Unverified
3	ProtoW-L2	AUC	0.87	—	Unverified
4	elEmBERT-V1	AUC	0.86	—	Unverified
5	ContextPred	AUC	0.85	—	Unverified
6	GIT-Mol(G+S)	AUC	0.81	—	Unverified

#	Model	Metric	Claimed	Verified	Status
1	GraphConv + dummy super node + focal loss	AUC	0.85	—	Unverified
2	GraphConv	AUC	0.82	—	Unverified
3	TrimNet	AUC	0.8	—	Unverified
4	ContextPred	AUC	0.8	—	Unverified
5	RNN-DFS	AUC	0.63	—	Unverified

#	Model	Metric	Claimed	Verified	Status
1	TrimNet	AUC	0.85	—	Unverified
2	GraphConv + dummy super node	AUC	0.85	—	Unverified
3	GraphConv	AUC	0.84	—	Unverified
4	ContextPred	AUC	0.81	—	Unverified
5	RNN-DFS	AUC	0.65	—	Unverified

#	Model	Metric	Claimed	Verified	Status
1	TrimNet	AUC	0.78	—	Unverified
2	GraphConv + dummy super node	AUC	0.77	—	Unverified
3	GraphConv	AUC	0.75	—	Unverified
4	GIT-Mol(G+S)	AUC	0.67	—	Unverified
5	ContextPred	AUC	0.66	—	Unverified

#	Model	Metric	Claimed	Verified	Status
1	ProtoW-L2	AUC	0.92	—	Unverified
2	elEmBERT-V1	AUC	0.91	—	Unverified
3	GIT-Mol(G+S)	AUC	0.74	—	Unverified
4	ContextPred	AUC	0.69	—	Unverified

#	Model	Metric	Claimed	Verified	Status
1	AttentionSiteDTI	AUC	0.97	—	Unverified
2	GLAM	AUC	0.95	—	Unverified
3	TransformerCPI	AUC	0.94	—	Unverified
4	DGraphDTA	AUC	0.92	—	Unverified

#	Model	Metric	Claimed	Verified	Status
1	BiLSTM	AUC	0.97	—	Unverified
2	TrimNet	AUC	0.95	—	Unverified
3	GIT-Mol(G+S)	AUC	0.88	—	Unverified
4	ContextPred	AUC	0.73	—	Unverified

#	Model	Metric	Claimed	Verified	Status
1	SMT-DTA	CI	0.89	—	Unverified
2	DeepPurpose	CI	0.88	—	Unverified
3	DeepDTA	CI	0.87	—	Unverified
4	GraphDTA	CI	0.86	—	Unverified

#	Model	Metric	Claimed	Verified	Status
1	SMT-DTA	CI	0.89	—	Unverified
2	DeepPurpose	CI	0.87	—	Unverified
3	DeepDTA	CI	0.86	—	Unverified
4	GraphDTA	CI	0.86	—	Unverified

#	Model	Metric	Claimed	Verified	Status
1	EGT+TGT-At-DP	AUC	0.81	—	Unverified
2	GLAM	AUC	0.76	—	Unverified
3	TransformerCPI	AUC	0.69	—	Unverified
4	DGraphDTA	AUC	0.68	—	Unverified

#	Model	Metric	Claimed	Verified	Status
1	EGT+TGT-At-DP	AUC	0.75	—	Unverified
2	GLAM	AUC	0.71	—	Unverified
3	TransformerCPI	AUC	0.65	—	Unverified
4	DGraphDTA	AUC	0.63	—	Unverified

#	Model	Metric	Claimed	Verified	Status
1	EGT+TGT-At-DP	AUC	0.74	—	Unverified
2	GLAM	AUC	0.73	—	Unverified
3	TransformerCPI	AUC	0.68	—	Unverified
4	DGraphDTA	AUC	0.67	—	Unverified

#	Model	Metric	Claimed	Verified	Status
1	elEmBERT-V1	AUC	0.78	—	Unverified
2	Ensemble locally constant networks	AUC	0.69	—	Unverified
3	GIT-Mol(G+S)	AUC	0.63	—	Unverified
4	ContextPred	AUC	0.63	—	Unverified

#	Model	Metric	Claimed	Verified	Status
1	GLAM	AUC	0.67	—	Unverified
2	TransformerCPI	AUC	0.62	—	Unverified
3	DGraphDTA	AUC	0.61	—	Unverified

#	Model	Metric	Claimed	Verified	Status
1	DeepDTA	Pearson Correlation	0.85	—	Unverified
2	DeepAffinity	Pearson Correlation	0.84	—	Unverified

#	Model	Metric	Claimed	Verified	Status
1	GraphConv + dummy super node	AUC	0.87	—	Unverified
2	GraphConv	AUC	0.86	—	Unverified

#	Model	Metric	Claimed	Verified	Status
1	GLAM	AUC	0.89	—	Unverified

#	Model	Metric	Claimed	Verified	Status
1	GLAM	AUC	0.93	—	Unverified

#	Model	Metric	Claimed	Verified	Status
1	HierG2G	Diversity	0.19	—	Unverified

#	Model	Metric	Claimed	Verified	Status
1	Multi-input Neural network with Attention	AUC	0.91	—	Unverified

#	Model	Metric	Claimed	Verified	Status
1	GLAM	RMSE	0.59	—	Unverified

#	Model	Metric	Claimed	Verified	Status
1	GLAM	RMSE	1.32	—	Unverified

#	Model	Metric	Claimed	Verified	Status
1	GLAM	RMSE	0.6	—	Unverified

#	Model	Metric	Claimed	Verified	Status
1	Ensemble locally constant networks	RMSE	1.22	—	Unverified

#	Model	Metric	Claimed	Verified	Status
1	HierG2G	Diversity	0.48	—	Unverified

#	Model	Metric	Claimed	Verified	Status
1	GLAM	AUC	0.74	—	Unverified