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 251–300 of 1337 papers

Title	Date	Tasks	Status	Hype
Forward Learning of Graph Neural Networks	Mar 16, 2024	Drug DiscoveryGraph Learning	CodeCode Available	1
Equivariant message passing for the prediction of tensorial properties and molecular spectra	Feb 5, 2021	Drug Discovery	CodeCode Available	1
A hybrid quantum-classical fusion neural network to improve protein-ligand binding affinity predictions for drug discovery	Sep 6, 2023	Drug DiscoveryPrediction	CodeCode Available	1
DEEPScreen: high performance drug–target interaction prediction with convolutional neural networks using 2-D structural compound representations	Jan 8, 2020	Drug DiscoveryMolecular Docking	CodeCode Available	1
EquiPocket: an E(3)-Equivariant Geometric Graph Neural Network for Ligand Binding Site Prediction	Feb 23, 2023	Drug DiscoveryGraph Neural Network	CodeCode Available	1
EquiCPI: SE(3)-Equivariant Geometric Deep Learning for Structure-Aware Prediction of Compound-Protein Interactions	Apr 7, 2025	Drug DiscoveryRe-Ranking	CodeCode Available	1
Enhancing Uncertainty Quantification in Drug Discovery with Censored Regression Labels	Sep 6, 2024	Drug Discoveryregression	CodeCode Available	1
Context-enriched molecule representations improve few-shot drug discovery	Apr 24, 2023	Drug DiscoveryFew-Shot Learning	CodeCode Available	1
End-to-End Differentiable Molecular Mechanics Force Field Construction	Oct 2, 2020	Computational chemistryDrug Discovery	CodeCode Available	1
Evening the Score: Targeting SARS-CoV-2 Protease Inhibition in Graph Generative Models for Therapeutic Candidates	May 7, 2021	Drug DesignDrug Discovery	CodeCode Available	1
Fractional Denoising for 3D Molecular Pre-training	Jul 20, 2023	DenoisingDrug Discovery	CodeCode Available	1
DTIAM: A unified framework for predicting drug-target interactions, binding affinities and activation/inhibition mechanisms	Dec 23, 2023	Drug Discovery	CodeCode Available	1
Artificial Intelligence in Drug Discovery: Applications and Techniques	Jun 9, 2021	Drug DesignDrug Discovery	CodeCode Available	1
Coarse-to-Fine: a Hierarchical Diffusion Model for Molecule Generation in 3D	May 5, 2023	Drug Discovery	CodeCode Available	1
DrugGen: Advancing Drug Discovery with Large Language Models and Reinforcement Learning Feedback	Nov 20, 2024	Drug DesignDrug Discovery	CodeCode Available	1
EDBench: Large-Scale Electron Density Data for Molecular Modeling	May 14, 2025	Drug Discovery	CodeCode Available	1
DrugCLIP: Contrastive Protein-Molecule Representation Learning for Virtual Screening	Oct 10, 2023	Contrastive LearningData Augmentation	CodeCode Available	1
DrugAssist: A Large Language Model for Molecule Optimization	Dec 28, 2023	Drug DiscoveryLanguage Modeling	CodeCode Available	1
DrugPilot: LLM-based Parameterized Reasoning Agent for Drug Discovery	May 20, 2025	Drug Discovery	CodeCode Available	1
Drug–target affinity prediction using graph neural network and contact maps	Jun 1, 2020	Drug DesignDrug Discovery	CodeCode Available	1
Drug Discovery under Covariate Shift with Domain-Informed Prior Distributions over Functions	Jul 14, 2023	Domain AdaptationDrug Discovery	CodeCode Available	1
Context-Guided Diffusion for Out-of-Distribution Molecular and Protein Design	Jul 16, 2024	Drug DiscoveryOut-of-Distribution Generalization	CodeCode Available	1
Transition Path Sampling with Improved Off-Policy Training of Diffusion Path Samplers	May 30, 2024	Drug Discovery	CodeCode Available	1
Enhancing Activity Prediction Models in Drug Discovery with the Ability to Understand Human Language	Mar 6, 2023	Activity PredictionAttribute	CodeCode Available	1
DPPIN: A Biological Repository of Dynamic Protein-Protein Interaction Network Data	Jul 5, 2021	AttributeDrug Discovery	CodeCode Available	1
Large-Scale Chemical Language Representations Capture Molecular Structure and Properties	Jun 17, 2021	Drug DiscoveryMolecular Property Prediction	CodeCode Available	1
Drug and Disease Interpretation Learning with Biomedical Entity Representation Transformer	Jan 22, 2021	Drug DiscoveryMetric Learning	CodeCode Available	1
Drug Discovery with Dynamic Goal-aware Fragments	Oct 2, 2023	Drug Discovery	CodeCode Available	1
EGR: Equivariant Graph Refinement and Assessment of 3D Protein Complex Structures	May 20, 2022	Drug DiscoveryGraph Neural Network	CodeCode Available	1
Exploring Chemical Space with Score-based Out-of-distribution Generation	Jun 6, 2022	Drug Discovery	CodeCode Available	1
Directional Message Passing for Molecular Graphs	Mar 6, 2020	Drug DiscoveryFormation Energy	CodeCode Available	1
Class-Guided Image-to-Image Diffusion: Cell Painting from Brightfield Images with Class Labels	Mar 15, 2023	DenoisingDrug Discovery	CodeCode Available	1
Comprehensive evaluation of deep and graph learning on drug-drug interactions prediction	Jun 8, 2023	Drug DiscoveryGraph Learning	CodeCode Available	1
Fast and Uncertainty-Aware Directional Message Passing for Non-Equilibrium Molecules	Nov 28, 2020	Drug DiscoveryUncertainty Quantification	CodeCode Available	1
Few-Shot Graph Learning for Molecular Property Prediction	Feb 16, 2021	AttributeDrug Discovery	CodeCode Available	1
Discrete-state Continuous-time Diffusion for Graph Generation	May 19, 2024	Drug DiscoveryGraph Generation	CodeCode Available	1
3D Interaction Geometric Pre-training for Molecular Relational Learning	Dec 4, 2024	Contrastive LearningDrug Discovery	CodeCode Available	1
FragXsiteDTI: Revealing Responsible Segments in Drug-Target Interaction with Transformer-Driven Interpretation	Nov 4, 2023	BenchmarkingDrug Discovery	CodeCode Available	1
ChiENN: Embracing Molecular Chirality with Graph Neural Networks	Jul 5, 2023	Drug DiscoveryMolecular Property Prediction	CodeCode Available	1
ChemSpaceAL: An Efficient Active Learning Methodology Applied to Protein-Specific Molecular Generation	Sep 11, 2023	Active LearningDrug Discovery	CodeCode Available	1
3M-Diffusion: Latent Multi-Modal Diffusion for Language-Guided Molecular Structure Generation	Mar 11, 2024	DecoderDrug Discovery	CodeCode Available	1
Generalist Equivariant Transformer Towards 3D Molecular Interaction Learning	Jun 2, 2023	Drug Discovery	CodeCode Available	1
DiffHopp: A Graph Diffusion Model for Novel Drug Design via Scaffold Hopping	Aug 14, 2023	Drug DesignDrug Discovery	CodeCode Available	1
Conditional Diffusion Based on Discrete Graph Structures for Molecular Graph Generation	Jan 1, 2023	Drug DiscoveryGraph Generation	CodeCode Available	1
A Review of Biomedical Datasets Relating to Drug Discovery: A Knowledge Graph Perspective	Feb 19, 2021	BIG-bench Machine LearningDrug Discovery	CodeCode Available	1
AI-Bind: Improving Binding Predictions for Novel Protein Targets and Ligands	Dec 25, 2021	Drug DiscoveryUnsupervised Pre-training	CodeCode Available	1
Genetic algorithms are strong baselines for molecule generation	Oct 13, 2023	Drug Discovery	CodeCode Available	1
Genetic-guided GFlowNets for Sample Efficient Molecular Optimization	Feb 5, 2024	Bayesian OptimizationDrug Discovery	CodeCode Available	1
Geometric Transformers for Protein Interface Contact Prediction	Oct 6, 2021	Drug DiscoveryPrediction	CodeCode Available	1
DIPS-Plus: The Enhanced Database of Interacting Protein Structures for Interface Prediction	Jun 6, 2021	Drug DiscoveryProtein Interface Prediction	CodeCode Available	1

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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