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 1251–1300 of 1337 papers

Title	Date	Tasks	Status
Faster Lead Optimization Mapper Algorithm for Large-Scale Relative Free Energy Perturbation	Apr 10, 2023	Drug Discovery	CodeCode Available
An Equivariant Generative Framework for Molecular Graph-Structure Co-Design	Apr 12, 2023	3D geometryDrug Design	CodeCode Available
Analysis of Gene Regulatory Networks from Gene Expression Using Graph Neural Networks	Sep 20, 2024	Drug DiscoveryGraph Attention	CodeCode Available
Relation Extraction in underexplored biomedical domains: A diversity-optimised sampling and synthetic data generation approach	Nov 10, 2023	DiversityDrug Discovery	CodeCode Available
Fast Direct: Query-Efficient Online Black-box Guidance for Diffusion-model Target Generation	Feb 2, 2025	Drug DiscoveryImage Generation	CodeCode Available
Multi-View Self-Attention for Interpretable Drug-Target Interaction Prediction	May 1, 2020	BIG-bench Machine LearningDrug Discovery	CodeCode Available
Fast Bayesian Optimization of Function Networks with Partial Evaluations	Jun 13, 2025	Bayesian OptimizationDrug Discovery	CodeCode Available
DeepAffinity: Interpretable Deep Learning of Compound-Protein Affinity through Unified Recurrent and Convolutional Neural Networks	Jun 20, 2018	Drug DiscoveryTransfer Learning	CodeCode Available
NaFM: Pre-training a Foundation Model for Small-Molecule Natural Products	Mar 22, 2025	Contrastive LearningDrug Discovery	CodeCode Available
NaNa and MiGu: Semantic Data Augmentation Techniques to Enhance Protein Classification in Graph Neural Networks	Mar 21, 2024	Data AugmentationDrug Discovery	CodeCode Available
DebiasedDTA: A Framework for Improving the Generalizability of Drug-Target Affinity Prediction Models	Jul 4, 2021	Drug DiscoveryEnsemble Learning	CodeCode Available
TurboHopp: Accelerated Molecule Scaffold Hopping with Consistency Models	Oct 28, 2024	Drug DesignDrug Discovery	CodeCode Available
Natural Language Processing tools for Pharmaceutical Manufacturing Information Extraction from Patents	Apr 29, 2025	Drug Discoverynamed-entity-recognition	CodeCode Available
Using Molecular Embeddings in QSAR Modeling: Does it Make a Difference?	Mar 20, 2021	Drug DesignDrug Discovery	CodeCode Available
SVSBI: Sequence-based virtual screening of biomolecular interactions	Dec 27, 2022	Drug DesignDrug Discovery	CodeCode Available
TwinBooster: Synergising Large Language Models with Barlow Twins and Gradient Boosting for Enhanced Molecular Property Prediction	Jan 9, 2024	Drug DiscoveryLanguage Modeling	CodeCode Available
Exploring Latent Space for Generating Peptide Analogs Using Protein Language Models	Aug 15, 2024	Drug Discovery	CodeCode Available
NEBULA: Neural Empirical Bayes Under Latent Representations for Efficient and Controllable Design of Molecular Libraries	Jul 3, 2024	Drug Discoveryscientific discovery	CodeCode Available
Accelerating Drug Safety Assessment using Bidirectional-LSTM for SMILES Data	Jul 8, 2024	Drug Discovery	CodeCode Available
ResMGCN: Residual Message Graph Convolution Network for Fast Biomedical Interactions Discovering	Nov 13, 2023	Drug Discovery	CodeCode Available
Explaining Graph Neural Networks with Large Language Models: A Counterfactual Perspective for Molecular Property Prediction	Oct 19, 2024	counterfactualCounterfactual Explanation	CodeCode Available
Neural Message Passing with Edge Updates for Predicting Properties of Molecules and Materials	Jun 8, 2018	Drug DiscoveryFormation Energy	CodeCode Available
Everybody Needs a Little HELP: Explaining Graphs via Hierarchical Concepts	Nov 25, 2023	Drug DiscoveryTravel Time Estimation	CodeCode Available
Data-Efficient Molecular Generation with Hierarchical Textual Inversion	May 5, 2024	Drug DiscoveryImage Generation	CodeCode Available
Data-Driven Approach to Encoding and Decoding 3-D Crystal Structures	Sep 3, 2019	DecoderDrug Discovery	CodeCode Available
Symmetric Replay Training: Enhancing Sample Efficiency in Deep Reinforcement Learning for Combinatorial Optimization	Jun 2, 2023	Combinatorial OptimizationDeep Reinforcement Learning	CodeCode Available
CRADLE-VAE: Enhancing Single-Cell Gene Perturbation Modeling with Counterfactual Reasoning-based Artifact Disentanglement	Sep 9, 2024	counterfactualCounterfactual Reasoning	CodeCode Available
Evaluation Framework for AI-driven Molecular Design of Multi-target Drugs: Brain Diseases as a Case Study	Aug 20, 2024	Drug DiscoveryEvolutionary Algorithms	CodeCode Available
WideDTA: prediction of drug-target binding affinity	Feb 4, 2019	Deep LearningDrug Discovery	CodeCode Available
Corresponding Projections for Orphan Screening	Nov 30, 2018	Drug DiscoveryTransfer Learning	CodeCode Available
Zero-shot Learning of Drug Response Prediction for Preclinical Drug Screening	Oct 5, 2023	Domain AdaptationDrug Discovery	CodeCode Available
BAPULM: Binding Affinity Prediction using Language Models	Nov 6, 2024	Drug Discoverymolecular representation	CodeCode Available
Entropy-Reinforced Planning with Large Language Models for Drug Discovery	Jun 11, 2024	Code GenerationDrug Discovery	CodeCode Available
Convolutional Networks on Graphs for Learning Molecular Fingerprints	Sep 30, 2015	Drug DiscoveryGraph Regression	CodeCode Available
Auxiliary Discrminator Sequence Generative Adversarial Networks (ADSeqGAN) for Few Sample Molecule Generation	Feb 23, 2025	DiversityDrug Discovery	CodeCode Available
Controlled Molecule Generator for Optimizing Multiple Chemical Properties	Oct 26, 2020	Drug DiscoveryProperty Prediction	CodeCode Available
Enhancing Drug-Target Interaction Prediction through Transfer Learning from Activity Cliff Prediction Tasks	Dec 11, 2024	Drug DiscoveryPrediction	CodeCode Available
Constrained Multi-objective Bayesian Optimization through Optimistic Constraints Estimation	Nov 6, 2024	Active LearningBayesian Optimization	CodeCode Available
Robust Molecular Property Prediction via Densifying Scarce Labeled Data	Jun 13, 2025	Drug DiscoveryMeta-Learning	CodeCode Available
Energy-based generative models for monoclonal antibodies	Nov 20, 2024	Drug Discovery	CodeCode Available
YZS-model: A Predictive Model for Organic Drug Solubility Based on Graph Convolutional Networks and Transformer-Attention	Jun 27, 2024	Drug DesignDrug Discovery	CodeCode Available
ADRNet: A Generalized Collaborative Filtering Framework Combining Clinical and Non-Clinical Data for Adverse Drug Reaction Prediction	Aug 3, 2023	Collaborative FilteringDrug Discovery	CodeCode Available
Adapting Differential Molecular Representation with Hierarchical Prompts for Multi-label Property Prediction	May 29, 2024	Drug Discoverymolecular representation	CodeCode Available
Confidence on the Focal: Conformal Prediction with Selection-Conditional Coverage	Mar 6, 2024	Conformal PredictionDrug Discovery	CodeCode Available
A Comparative Analysis of the Ensemble Methods for Drug Design	Dec 11, 2020	Drug DesignDrug Discovery	CodeCode Available
Scaffold-based molecular design using graph generative model	May 31, 2019	Drug Discoverymodel	CodeCode Available
Automatic Annotation Augmentation Boosts Translation between Molecules and Natural Language	Feb 10, 2025	Drug DiscoveryMolecule Captioning	CodeCode Available
Empowering Counterfactual Reasoning over Graph Neural Networks through Inductivity	Jun 7, 2023	counterfactualCounterfactual Explanation	CodeCode Available
A Unified Approach to Inferring Chemical Compounds with the Desired Aqueous Solubility	Sep 6, 2024	Drug Discoveryregression	CodeCode Available
Optimization of binding affinities in chemical space with generative pretrained transformer and deep reinforcement learning	Apr 3, 2023	Deep Reinforcement LearningDrug Discovery	CodeCode Available

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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