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 1151–1200 of 1337 papers

Title	Date	Tasks	Status
Interpretable Deep Learning in Drug Discovery	Mar 7, 2019	Deep LearningDrug Discovery	CodeCode Available
Protein Interface Prediction using Graph Convolutional Networks	Dec 1, 2017	Drug DiscoveryPrediction	CodeCode Available
Accelerating the Generation of Molecular Conformations with Progressive Distillation of Equivariant Latent Diffusion Models	Apr 21, 2024	Drug Discovery	CodeCode Available
Integration of Genetic Algorithms and Deep Learning for the Generation and Bioactivity Prediction of Novel Tyrosine Kinase Inhibitors	Aug 13, 2024	Deep LearningDrug Discovery	CodeCode Available
Integrating convolutional layers and biformer network with forward-forward and backpropagation training	Feb 28, 2025	Computational chemistryDrug Discovery	CodeCode Available
Protein Language Models and Machine Learning Facilitate the Identification of Antimicrobial Peptides	Aug 14, 2024	Binary ClassificationDrug Discovery	CodeCode Available
Injecting Domain Knowledge from Empirical Interatomic Potentials to Neural Networks for Predicting Material Properties	Oct 14, 2022	Drug DiscoveryTransfer Learning	CodeCode Available
Independent Vector Analysis for Data Fusion Prior to Molecular Property Prediction with Machine Learning	Nov 1, 2018	BIG-bench Machine LearningDrug Discovery	CodeCode Available
Characterizing the Conformational States of G Protein Coupled Receptors Generated with AlphaFold	Feb 24, 2025	Drug Discovery	CodeCode Available
XMolCap: Advancing Molecular Captioning through Multimodal Fusion and Explainable Graph Neural Networks	May 23, 2025	Drug DiscoveryMolecule Captioning	CodeCode Available
Protein-Ligand Scoring with Convolutional Neural Networks	Dec 8, 2016	Drug DesignDrug Discovery	CodeCode Available
Transformers for molecular property prediction: Lessons learned from the past five years	Apr 5, 2024	Drug DiscoveryMolecular Property Prediction	CodeCode Available
Improving Molecular Pretraining with Complementary Featurizations	Sep 29, 2022	Computational chemistryDrug Discovery	CodeCode Available
B-XAIC Dataset: Benchmarking Explainable AI for Graph Neural Networks Using Chemical Data	May 28, 2025	BenchmarkingDrug Discovery	CodeCode Available
MF-LAL: Drug Compound Generation Using Multi-Fidelity Latent Space Active Learning	Oct 15, 2024	Active LearningActivity Prediction	CodeCode Available
Improving Compound Activity Classification via Deep Transfer and Representation Learning	Nov 14, 2021	Drug DiscoveryRepresentation Learning	CodeCode Available
MicroBundleCompute: Automated segmentation, tracking, and analysis of subdomain deformation in cardiac microbundles	Aug 8, 2023	Drug Discovery	CodeCode Available
Improved antibody structure prediction by deep learning of side chain conformations	Sep 22, 2021	Deep LearningDrug Discovery	CodeCode Available
PSBench: a large-scale benchmark for estimating the accuracy of protein complex structural models	May 13, 2025	Drug DiscoveryProtein Design	CodeCode Available
Mitigating cold start problems in drug-target affinity prediction with interaction knowledge transferring	Jan 16, 2022	BIG-bench Machine LearningDrug Discovery	CodeCode Available
Mitigating Molecular Aggregation in Drug Discovery with Predictive Insights from Explainable AI	Jun 3, 2023	Drug Discovery	CodeCode Available
MLT-LE: predicting drug-target binding affinity with multi-task residual neural networks	Sep 13, 2022	Drug DiscoveryMulti-Task Learning	CodeCode Available
Implementation and Application of an Intelligibility Protocol for Interaction with an LLM	Oct 27, 2024	Drug DiscoveryLarge Language Model	CodeCode Available
Do Deep Learning Methods Really Perform Better in Molecular Conformation Generation?	Feb 14, 2023	Deep LearningDrug Discovery	CodeCode Available
PubChemQC B3LYP/6-31G//PM6 dataset: the Electronic Structures of 86 Million Molecules using B3LYP/6-31G calculations	May 29, 2023	Drug Discovery	CodeCode Available
iBitter-Stack: A Multi-Representation Ensemble Learning Model for Accurate Bitter Peptide Identification	May 21, 2025	Drug DiscoveryEnsemble Learning	CodeCode Available
Distance-aware Molecule Graph Attention Network for Drug-Target Binding Affinity Prediction	Dec 17, 2020	Drug DiscoveryGraph Attention	CodeCode Available
Hyperbolic Benchmarking Unveils Network Topology-Feature Relationship in GNN Performance	Jun 4, 2024	BenchmarkingDrug Discovery	CodeCode Available
Transition Path Sampling with Boltzmann Generator-based MCMC Moves	Dec 8, 2023	Drug Discovery	CodeCode Available
Differentially Private Federated Learning via Reconfigurable Intelligent Surface	Mar 31, 2022	Drug DiscoveryFederated Learning	CodeCode Available
How Explanations Leak the Decision Logic: Stealing Graph Neural Networks via Explanation Alignment	Jun 3, 2025	Data AugmentationDrug Discovery	CodeCode Available
D-GRIL: End-to-End Topological Learning with 2-parameter Persistence	Jun 11, 2024	Activity PredictionDrug Discovery	CodeCode Available
SMILES Transformer: Pre-trained Molecular Fingerprint for Low Data Drug Discovery	Nov 12, 2019	Drug DiscoveryLanguage Modeling	CodeCode Available
Heter-LP: A heterogeneous label propagation algorithm and its application in drug repositioning	Nov 8, 2016	Data IntegrationDrug Discovery	CodeCode Available
ShennongAlpha: an AI-driven sharing and collaboration platform for intelligent curation, acquisition, and translation of natural medicinal material knowledge	Dec 27, 2023	Drug DiscoveryMachine Translation	CodeCode Available
Bridging Quantum and Classical Computing in Drug Design: Architecture Principles for Improved Molecule Generation	Jun 1, 2025	Bayesian OptimizationDrug Design	CodeCode Available
Bridging Generalization Gaps in High Content Imaging Through Online Self-Supervised Domain Adaptation	Nov 21, 2023	Domain AdaptationDrug Discovery	CodeCode Available
De Novo Generation of Hit-like Molecules from Gene Expression Profiles via Deep Learning	Dec 27, 2024	Drug Discoveryvalid	CodeCode Available
Quality-Weighted Vendi Scores And Their Application To Diverse Experimental Design	May 3, 2024	Bayesian OptimizationDiversity	CodeCode Available
SOC-DGL: Social Interaction Behavior Inspired Dual Graph Learning Framework for Drug-Target Interaction Identification	Jun 2, 2025	Drug DiscoveryGraph Learning	CodeCode Available
Development and evaluation of a deep learning model for protein-ligand binding affinity prediction	Dec 19, 2017	Drug Discovery	CodeCode Available
Improving detection of protein-ligand binding sites with 3D segmentation	Apr 13, 2019	Drug Discovery	CodeCode Available
DeepSIBA: Chemical Structure-based Inference of Biological Alterations	Apr 1, 2020	Drug Discovery	CodeCode Available
Guided Multi-objective Generative AI to Enhance Structure-based Drug Design	May 20, 2024	Drug DesignDrug Discovery	CodeCode Available
Molecular Graph Convolutions: Moving Beyond Fingerprints	Mar 2, 2016	BIG-bench Machine LearningDrug Discovery	CodeCode Available
DeeplyTough: Learning Structural Comparison of Protein Binding Sites	Apr 5, 2019	Drug Discovery	CodeCode Available
Deeply learning molecular structure-property relationships using attention- and gate-augmented graph convolutional network	May 28, 2018	Drug Discovery	CodeCode Available
Molecular Graph Representation Learning Integrating Large Language Models with Domain-specific Small Models	Aug 19, 2024	DescriptiveDrug Discovery	CodeCode Available
Social and environmental impact of recent developments in machine learning on biology and chemistry research	Oct 1, 2022	DiversityDrug Discovery	CodeCode Available
GSHOT: Few-shot Generative Modeling of Labeled Graphs	Jun 6, 2023	Drug DiscoveryFew-Shot Learning	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