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 501–550 of 1337 papers

Title	Date	Tasks	Status
Expanding Chemical Representation with k-mers and Fragment-based Fingerprints for Molecular Fingerprinting	Mar 28, 2024	Drug Discovery	—Unverified
Explainable Artificial Intelligence for Drug Discovery and Development -- A Comprehensive Survey	Sep 21, 2023	Drug DiscoveryExplainable artificial intelligence	—Unverified
GraphPrint: Extracting Features from 3D Protein Structure for Drug Target Affinity Prediction	Jul 15, 2024	Drug Discovery	—Unverified
Differential Privacy-Driven Framework for Enhancing Heart Disease Prediction	Apr 25, 2025	Decision MakingDisease Prediction	—Unverified
BEACON: A Bayesian Optimization Strategy for Novelty Search in Expensive Black-Box Systems	Jun 5, 2024	Bayesian OptimizationDrug Discovery	—Unverified
Explainable Molecular Property Prediction: Aligning Chemical Concepts with Predictions via Language Models	May 25, 2024	Drug DiscoveryMolecular Property Prediction	—Unverified
Differentiable Scaffolding Tree for Molecule Optimization	Sep 29, 2021	Combinatorial OptimizationDrug Discovery	—Unverified
Exploring Chemical Space using Natural Language Processing Methodologies for Drug Discovery	Feb 10, 2020	Drug Discovery	—Unverified
Differentiable Scaffolding Tree for Molecular Optimization	Sep 22, 2021	Combinatorial OptimizationDrug Discovery	—Unverified
Exploring Deep Recurrent Models with Reinforcement Learning for Molecule Design	Jan 1, 2018	Drug DiscoveryOpenAI Gym	—Unverified
Bayesian semi-supervised learning for uncertainty-calibrated prediction of molecular properties and active learning	Feb 3, 2019	Active LearningDrug Discovery	—Unverified
Diameter-based Interactive Structure Discovery	Jun 5, 2019	Active LearningDrug Discovery	—Unverified
Anchoring to Exemplars for Training Mixture-of-Expert Cell Embeddings	Dec 6, 2021	Drug DiscoveryGPU	—Unverified
A deep-learning view of chemical space designed to facilitate drug discovery	Feb 7, 2020	Design SynthesisDrug Discovery	—Unverified
Geometric-informed GFlowNets for Structure-Based Drug Design	Jun 16, 2024	Drug DesignDrug Discovery	—Unverified
DG-GL: Differential geometry based geometric learning of molecular datasets	Jun 11, 2018	DescriptiveDimensionality Reduction	—Unverified
DGFN: Double Generative Flow Networks	Oct 30, 2023	Drug DiscoveryQ-Learning	—Unverified
Bayesian Multi Plate High Throughput Screening of Compounds	Sep 28, 2017	Drug DiscoverySpecificity	—Unverified
Boosting drug-disease association prediction for drug repositioning via dual-feature extraction and cross-dual-domain decoding	Jul 16, 2024	Drug Discovery	—Unverified
An Autonomous Large Language Model Agent for Chemical Literature Data Mining	Feb 20, 2024	AI AgentDrug Discovery	—Unverified
A Deep Learning Approach to the Prediction of Drug Side-Effects on Molecular Graphs	Nov 30, 2022	Drug Discovery	—Unverified
GeoDirDock: Guiding Docking Along Geodesic Paths	Apr 9, 2024	Blind DockingDenoising	—Unverified
Developing novel ligands with enhanced binding affinity for the sphingosine 1-phosphate receptor 1 using machine learning	Jul 29, 2023	Drug Discovery	—Unverified
Determining Multifunctional Genes and Diseases in Human Using Gene Ontology	Jan 11, 2019	Drug Discovery	—Unverified
BatGPT-Chem: A Foundation Large Model For Retrosynthesis Prediction	Aug 19, 2024	Drug DiscoveryLanguage Modelling	—Unverified
Design Requirements for Human-Centered Graph Neural Network Explanations	May 11, 2024	Drug DiscoveryGraph Neural Network	—Unverified
An Assessment of PC-mer's Performance in Alignment-Free Phylogenetic Tree Construction	Nov 21, 2023	Drug Discovery	—Unverified
Geometric Deep Learning on Molecular Representations	Jul 26, 2021	Deep LearningDrug Discovery	—Unverified
GeoScatt-GNN: A Geometric Scattering Transform-Based Graph Neural Network Model for Ames Mutagenicity Prediction	Nov 22, 2024	Drug DiscoveryGraph Neural Network	—Unverified
De Novo Molecular Design Enabled by Direct Preference Optimization and Curriculum Learning	Apr 2, 2025	Drug DiscoveryReinforcement Learning (RL)	—Unverified
De novo design of protein target specific scaffold-based Inhibitors via Reinforcement Learning	May 21, 2022	Drug DiscoveryGraph Neural Network	—Unverified
Analysis of the Results of Metadynamics Simulations by metadynminer and metadynminer3d	Aug 22, 2020	Drug Discovery	—Unverified
Delta Score: Improving the Binding Assessment of Structure-Based Drug Design Methods	Nov 1, 2023	Drug DesignDrug Discovery	—Unverified
Delete: Deep Lead Optimization Enveloped in Protein Pocket through Unified Deleting Strategies and a Structure-aware Network	Aug 4, 2023	Drug Discovery	—Unverified
Backdoor Attacks on Discrete Graph Diffusion Models	Mar 8, 2025	Drug DiscoveryGraph Generation	—Unverified
A Bandit Approach to Sequential Experimental Design with False Discovery Control	Dec 1, 2018	Drug DiscoveryExperimental Design	—Unverified
DEFactor: Differentiable Edge Factorization-based Probabilistic Graph Generation	Nov 24, 2018	Drug DiscoveryGraph Generation	—Unverified
Backdiff: a diffusion model for generalized transferable protein backmapping	Oct 3, 2023	Drug DiscoveryProtein Design	—Unverified
A deep graph model for the signed interaction prediction in biological network	Jul 10, 2024	Drug DiscoveryTensor Decomposition	—Unverified
GENIE: Watermarking Graph Neural Networks for Link Prediction	Jun 7, 2024	Backdoor AttackDrug Discovery	—Unverified
GenMol: A Drug Discovery Generalist with Discrete Diffusion	Jan 10, 2025	Computational EfficiencyDrug Discovery	—Unverified
DeepScaffold: a comprehensive tool for scaffold-based de novo drug discovery using deep learning	Aug 20, 2019	Drug DesignDrug Discovery	—Unverified
Autonomous discovery in the chemical sciences part I: Progress	Mar 30, 2020	Drug Discovery	—Unverified
DeepPCM: Predicting Protein-Ligand Binding using Unsupervised Learned Representations	Sep 25, 2019	Computational chemistryDrug Discovery	—Unverified
Deep Mapper: Efficient Visualization of Plausible Conformational Pathways	Feb 29, 2024	Drug DiscoveryTopological Data Analysis	—Unverified
Automating reward function configuration for drug design	Dec 15, 2023	Drug DesignDrug Discovery	—Unverified
AdaptMol: Adaptive Fusion from Sequence String to Topological Structure for Few-shot Drug Discovery	May 17, 2025	Drug DiscoveryFew-Shot Learning	—Unverified
Genetic Constrained Graph Variational Autoencoder for COVID-19 Drug Discovery	Apr 23, 2021	Drug Discovery	—Unverified
GenShin:geometry-enhanced structural graph embodies binding pose can better predicting compound-protein interaction affinity	Mar 16, 2025	Drug DesignDrug Discovery	—Unverified
Deep Learning Prediction of Adverse Drug Reactions Using Open TG-GATEs and FAERS Databases	Oct 12, 2020	Drug Discovery	—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