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 401–450 of 1337 papers

Title	Date	Tasks	Status	Score
Massively Multitask Networks for Drug Discovery	Feb 6, 2015	Drug Discovery	CodeCode Available	5
Multi-View Self-Attention for Interpretable Drug-Target Interaction Prediction	May 1, 2020	BIG-bench Machine LearningDrug Discovery	CodeCode Available	5
Protein Language Models and Machine Learning Facilitate the Identification of Antimicrobial Peptides	Aug 14, 2024	Binary ClassificationDrug Discovery	CodeCode Available	5
Differentially Private Federated Learning via Reconfigurable Intelligent Surface	Mar 31, 2022	Drug DiscoveryFederated Learning	CodeCode Available	5
Inductive-Associative Meta-learning Pipeline with Human Cognitive Patterns for Unseen Drug-Target Interaction Prediction	Jan 26, 2025	Drug DiscoveryMeta-Learning	CodeCode Available	5
Bayesian neural network with pretrained protein embedding enhances prediction accuracy of drug-protein interaction	Dec 15, 2020	Bayesian InferenceDeep Learning	CodeCode Available	5
D-GRIL: End-to-End Topological Learning with 2-parameter Persistence	Jun 11, 2024	Activity PredictionDrug Discovery	CodeCode Available	5
Learning to Denoise Biomedical Knowledge Graph for Robust Molecular Interaction Prediction	Dec 9, 2023	DenoisingDrug Discovery	CodeCode Available	5
Leveraging Large Language Models for enzymatic reaction prediction and characterization	May 8, 2025	Drug DiscoveryIn-Context Learning	CodeCode Available	5
Learning Graph-Level Representation for Drug Discovery	Sep 12, 2017	AllDrug Discovery	CodeCode Available	5
Learning Hierarchical Interaction for Accurate Molecular Property Prediction	Apr 28, 2025	Drug DiscoveryMolecular Property Prediction	CodeCode Available	5
BatmanNet: Bi-branch Masked Graph Transformer Autoencoder for Molecular Representation	Nov 25, 2022	Drug DiscoveryMolecular Property Prediction	CodeCode Available	5
Development and evaluation of a deep learning model for protein-ligand binding affinity prediction	Dec 19, 2017	Drug Discovery	CodeCode Available	5
Learning Cross-Domain Representations for Transferable Drug Perturbations on Single-Cell Transcriptional Responses	Dec 26, 2024	DecoderDrug Discovery	CodeCode Available	5
Latent Guided Sampling for Combinatorial Optimization	Jun 4, 2025	Combinatorial OptimizationDrug Discovery	CodeCode Available	5
BART: Bayesian additive regression trees	Jun 19, 2008	Causal InferenceDrug Discovery	CodeCode Available	5
Leak Proof CMap; a framework for training and evaluation of cell line agnostic L1000 similarity methods	Apr 29, 2024	BenchmarkingDrug Discovery	CodeCode Available	5
Improving detection of protein-ligand binding sites with 3D segmentation	Apr 13, 2019	Drug Discovery	CodeCode Available	5
Ligand Pose Optimization with Atomic Grid-Based Convolutional Neural Networks	Oct 20, 2017	Drug Discovery	CodeCode Available	5
BAPULM: Binding Affinity Prediction using Language Models	Nov 6, 2024	Drug Discoverymolecular representation	CodeCode Available	5
ChemBoost: A chemical language based approach for protein-ligand binding affinity prediction	Nov 2, 2018	Drug DiscoveryWord Embeddings	CodeCode Available	5
Drug Discovery SMILES-to-Pharmacokinetics Diffusion Models with Deep Molecular Understanding	Aug 14, 2024	Drug Discovery	CodeCode Available	5
KekuleScope: prediction of cancer cell line sensitivity and compound potency using convolutional neural networks trained on compound images	Nov 22, 2018	Drug DiscoveryPrediction Of Cancer Cell Line Sensitivity	CodeCode Available	5
LaGDif: Latent Graph Diffusion Model for Efficient Protein Inverse Folding with Self-Ensemble	Nov 4, 2024	Drug Discovery	CodeCode Available	5
Analysis of Gene Regulatory Networks from Gene Expression Using Graph Neural Networks	Sep 20, 2024	Drug DiscoveryGraph Attention	CodeCode Available	5
JAX MD: End-to-End Differentiable, Hardware Accelerated, Molecular Dynamics in Pure Python	Sep 25, 2019	BIG-bench Machine LearningCPU	CodeCode Available	5
DrugGen enhances drug discovery with large language models and reinforcement learning	Apr 18, 2025	Drug DesignDrug Discovery	CodeCode Available	5
Blend the Separated: Mixture of Synergistic Experts for Data-Scarcity Drug-Target Interaction Prediction	Mar 20, 2025	Drug Discovery	CodeCode Available	5
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	5
DeepSIBA: Chemical Structure-based Inference of Biological Alterations	Apr 1, 2020	Drug Discovery	CodeCode Available	5
Auxiliary Discrminator Sequence Generative Adversarial Networks (ADSeqGAN) for Few Sample Molecule Generation	Feb 23, 2025	DiversityDrug Discovery	CodeCode Available	5
Automatic Annotation Augmentation Boosts Translation between Molecules and Natural Language	Feb 10, 2025	Drug DiscoveryMolecule Captioning	CodeCode Available	5
Accelerating the Generation of Molecular Conformations with Progressive Distillation of Equivariant Latent Diffusion Models	Apr 21, 2024	Drug Discovery	CodeCode Available	5
DeeplyTough: Learning Structural Comparison of Protein Binding Sites	Apr 5, 2019	Drug Discovery	CodeCode Available	5
Deeply learning molecular structure-property relationships using attention- and gate-augmented graph convolutional network	May 28, 2018	Drug Discovery	CodeCode Available	5
Interpretable Deep Learning in Drug Discovery	Mar 7, 2019	Deep LearningDrug Discovery	CodeCode Available	5
Bridging Quantum and Classical Computing in Drug Design: Architecture Principles for Improved Molecule Generation	Jun 1, 2025	Bayesian OptimizationDrug Design	CodeCode Available	5
Drug-target interaction prediction by integrating heterogeneous information with mutual attention network	Apr 3, 2024	Drug DiscoveryGraph Attention	CodeCode Available	5
Large-Scale Knowledge Integration for Enhanced Molecular Property Prediction	Oct 15, 2024	Drug DiscoveryMolecular Property Prediction	CodeCode Available	5
Adversarial Learned Molecular Graph Inference and Generation	May 24, 2019	Drug Discovery	CodeCode Available	5
Injecting Domain Knowledge from Empirical Interatomic Potentials to Neural Networks for Predicting Material Properties	Oct 14, 2022	Drug DiscoveryTransfer Learning	CodeCode Available	5
Improving Molecular Pretraining with Complementary Featurizations	Sep 29, 2022	Computational chemistryDrug Discovery	CodeCode Available	5
AMPL: A Data-Driven Modeling Pipeline for Drug Discovery	Nov 13, 2019	BIG-bench Machine LearningDrug Discovery	CodeCode Available	5
Independent Vector Analysis for Data Fusion Prior to Molecular Property Prediction with Machine Learning	Nov 1, 2018	BIG-bench Machine LearningDrug Discovery	CodeCode Available	5
Improved antibody structure prediction by deep learning of side chain conformations	Sep 22, 2021	Deep LearningDrug Discovery	CodeCode Available	5
Improving Compound Activity Classification via Deep Transfer and Representation Learning	Nov 14, 2021	Drug DiscoveryRepresentation Learning	CodeCode Available	5
Integrating convolutional layers and biformer network with forward-forward and backpropagation training	Feb 28, 2025	Computational chemistryDrug Discovery	CodeCode Available	5
iBitter-Stack: A Multi-Representation Ensemble Learning Model for Accurate Bitter Peptide Identification	May 21, 2025	Drug DiscoveryEnsemble Learning	CodeCode Available	5
Hyperbolic Benchmarking Unveils Network Topology-Feature Relationship in GNN Performance	Jun 4, 2024	BenchmarkingDrug Discovery	CodeCode Available	5
Deep Inverse Reinforcement Learning for Structural Evolution of Small Molecules	Jul 24, 2020	Drug DiscoveryGenerative Adversarial Network	CodeCode Available	5

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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