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 1301–1337 of 1337 papers

Title	Date	Tasks	Status
Optimized Conformal Selection: Powerful Selective Inference After Conformity Score Optimization	Nov 27, 2024	Drug DiscoveryModel Optimization	CodeCode Available
Optimizing Area Under the Curve Measures via Matrix Factorization for Predicting Drug-Target Interaction with Multiple Similarities	May 1, 2021	Drug DiscoveryPrediction	CodeCode Available
AugWard: Augmentation-Aware Representation Learning for Accurate Graph Classification	Mar 27, 2025	DiversityDrug Discovery	CodeCode Available
Empirical Evidence for the Fragment level Understanding on Drug Molecular Structure of LLMs	Jan 15, 2024	Drug DesignDrug Discovery	CodeCode Available
Attention-based Multi-Input Deep Learning Architecture for Biological Activity Prediction: An Application in EGFR Inhibitors	Jun 12, 2019	Activity PredictionBIG-bench Machine Learning	CodeCode Available
Pandemic Drugs at Pandemic Speed: Infrastructure for Accelerating COVID-19 Drug Discovery with Hybrid Machine Learning- and Physics-based Simulations on High Performance Computers	Mar 4, 2021	Drug DiscoveryHybrid Machine Learning	CodeCode Available
Parallel Model Exploration for Tumor Treatment Simulations	Mar 25, 2021	Computational EfficiencyDrug Discovery	CodeCode Available
Scalable Bayesian Optimization Accelerates Process Optimization of Penicillin Production	Sep 24, 2021	Bayesian OptimizationDrug Discovery	CodeCode Available
PASSerRank: Prediction of Allosteric Sites with Learning to Rank	Feb 2, 2023	Drug DiscoveryLearning-To-Rank	CodeCode Available
Achieving Well-Informed Decision-Making in Drug Discovery: A Comprehensive Calibration Study using Neural Network-Based Structure-Activity Models	Jul 19, 2024	Decision MakingDrug Discovery	CodeCode Available
Linear-scaling kernels for protein sequences and small molecules outperform deep learning while providing uncertainty quantitation and improved interpretability	Feb 7, 2023	Data VisualizationDrug Discovery	CodeCode Available
PepHarmony: A Multi-View Contrastive Learning Framework for Integrated Sequence and Structure-Based Peptide Encoding	Jan 21, 2024	Contrastive LearningDrug Discovery	CodeCode Available
Perforated Backpropagation: A Neuroscience Inspired Extension to Artificial Neural Networks	Jan 29, 2025	Drug DiscoveryLanguage Modeling	CodeCode Available
AtomNet: A Deep Convolutional Neural Network for Bioactivity Prediction in Structure-based Drug Discovery	Oct 10, 2015	Drug Discovery	CodeCode Available
A Systematic Assessment of Deep Learning Models for Molecule Generation	Aug 20, 2020	Deep LearningDrug Discovery	CodeCode Available
Persistent Directed Flag Laplacian (PDFL)-Based Machine Learning for Protein-Ligand Binding Affinity Prediction	Nov 4, 2024	Drug DiscoveryTopological Data Analysis	CodeCode Available
Persistent Sheaf Laplacian Analysis of Protein Flexibility	Feb 12, 2025	Drug DiscoveryProtein Design	CodeCode Available
DynamicDTA: Drug-Target Binding Affinity Prediction Using Dynamic Descriptors and Graph Representation	May 13, 2025	Drug Discovery	CodeCode Available
PGraphDTA: Improving Drug Target Interaction Prediction using Protein Language Models and Contact Maps	Oct 6, 2023	Binary ClassificationDrug Discovery	CodeCode Available
Virtual screening of DrugBank database for hERG blockers using topological Laplacian-assisted AI models	Nov 2, 2022	Drug Discovery	CodeCode Available
Drug-Target Interaction Prediction via an Ensemble of Weighted Nearest Neighbors with Interaction Recovery	Dec 22, 2020	Drug DiscoveryPrediction	CodeCode Available
Conditional Prediction ROC Bands for Graph Classification	Oct 20, 2024	ClassificationDrug Discovery	CodeCode Available
Validating the Validation: Reanalyzing a large-scale comparison of Deep Learning and Machine Learning models for bioactivity prediction	May 28, 2019	BIG-bench Machine LearningDrug Discovery	CodeCode Available
COMRECGC: Global Graph Counterfactual Explainer through Common Recourse	May 11, 2025	Binary Classificationcounterfactual	CodeCode Available
Drug-target interaction prediction by integrating heterogeneous information with mutual attention network	Apr 3, 2024	Drug DiscoveryGraph Attention	CodeCode Available
SCOP: A Sequence-Structure Contrast-Aware Framework for Protein Function Prediction	Nov 18, 2024	Drug DiscoveryProtein Function Prediction	CodeCode Available
SCOPE-DTI: Semi-Inductive Dataset Construction and Framework Optimization for Practical Usability Enhancement in Deep Learning-Based Drug Target Interaction Prediction	Mar 12, 2025	DiversityDrug Discovery	CodeCode Available
SCORCH2: a generalised heterogeneous consensus model for high-enrichment interaction-based virtual screening	Apr 5, 2025	Drug Discovery	CodeCode Available
Drug-Target Indication Prediction by Integrating End-to-End Learning and Fingerprints	Dec 3, 2019	Deep LearningDrug Discovery	CodeCode Available
Physics-Constrained Predictive Molecular Latent Space Discovery with Graph Scattering Variational Autoencoder	Sep 29, 2020	Drug Discoverymolecular representation	CodeCode Available
DrugOOD: Out-of-Distribution (OOD) Dataset Curator and Benchmark for AI-aided Drug Discovery -- A Focus on Affinity Prediction Problems with Noise Annotations	Jan 24, 2022	BenchmarkingDrug Discovery	CodeCode Available
Advancing Drug Discovery with Enhanced Chemical Understanding via Asymmetric Contrastive Multimodal Learning	Nov 11, 2023	Contrastive LearningDrug Discovery	CodeCode Available
Pin-Tuning: Parameter-Efficient In-Context Tuning for Few-Shot Molecular Property Prediction	Nov 2, 2024	AttributeDrug Discovery	CodeCode Available
DrugGen enhances drug discovery with large language models and reinforcement learning	Apr 18, 2025	Drug DesignDrug Discovery	CodeCode Available
Drug Discovery SMILES-to-Pharmacokinetics Diffusion Models with Deep Molecular Understanding	Aug 14, 2024	Drug Discovery	CodeCode Available
About Graph Degeneracy, Representation Learning and Scalability	Sep 4, 2020	Drug DiscoveryEdge Detection	CodeCode Available
CoarsenConf: Equivariant Coarsening with Aggregated Attention for Molecular Conformer Generation	Jun 26, 2023	Drug DiscoveryProperty Prediction	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