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 601–650 of 1337 papers

Title	Date	Tasks	Status
CRADLE-VAE: Enhancing Single-Cell Gene Perturbation Modeling with Counterfactual Reasoning-based Artifact Disentanglement	Sep 9, 2024	counterfactualCounterfactual Reasoning	CodeCode Available
Machine Learning-Based Prediction of Key Genes Correlated to the Subretinal Lesion Severity in a Mouse Model of Age-Related Macular Degeneration	Sep 8, 2024	Dimensionality ReductionDrug Discovery	—Unverified
Unlocking Potential Binders: Multimodal Pretraining DEL-Fusion for Denoising DNA-Encoded Libraries	Sep 7, 2024	DenoisingDrug Discovery	—Unverified
Large Language Models in Drug Discovery and Development: From Disease Mechanisms to Clinical Trials	Sep 6, 2024	Drug Discovery	—Unverified
A Unified Approach to Inferring Chemical Compounds with the Desired Aqueous Solubility	Sep 6, 2024	Drug Discoveryregression	CodeCode Available
MaskMol: Knowledge-guided Molecular Image Pre-Training Framework for Activity Cliffs	Sep 2, 2024	Drug DiscoveryRepresentation Learning	—Unverified
A Survey for Large Language Models in Biomedicine	Aug 29, 2024	DiagnosticDrug Discovery	—Unverified
S-MolSearch: 3D Semi-supervised Contrastive Learning for Bioactive Molecule Search	Aug 27, 2024	Contrastive LearningData Augmentation	—Unverified
HyperSBINN: A Hypernetwork-Enhanced Systems Biology-Informed Neural Network for Efficient Drug Cardiosafety Assessment	Aug 26, 2024	Drug DiscoveryMeta-Learning	—Unverified
Quantum-machine-assisted Drug Discovery: Survey and Perspective	Aug 24, 2024	Drug DesignDrug Discovery	—Unverified
DrugAgent: Multi-Agent Large Language Model-Based Reasoning for Drug-Target Interaction Prediction	Aug 23, 2024	AI AgentDrug Discovery	—Unverified
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
Learning Regularization for Graph Inverse Problems	Aug 19, 2024	Drug Discovery	—Unverified
BatGPT-Chem: A Foundation Large Model For Retrosynthesis Prediction	Aug 19, 2024	Drug DiscoveryLanguage Modelling	—Unverified
Molecular Graph Representation Learning Integrating Large Language Models with Domain-specific Small Models	Aug 19, 2024	DescriptiveDrug Discovery	CodeCode Available
Advancements in Molecular Property Prediction: A Survey of Single and Multimodal Approaches	Aug 18, 2024	Drug DiscoveryMolecular Property Prediction	—Unverified
Fragment-Masked Diffusion for Molecular Optimization	Aug 17, 2024	Drug Discovery	—Unverified
Exploring Latent Space for Generating Peptide Analogs Using Protein Language Models	Aug 15, 2024	Drug Discovery	CodeCode Available
Drug Discovery SMILES-to-Pharmacokinetics Diffusion Models with Deep Molecular Understanding	Aug 14, 2024	Drug Discovery	CodeCode Available
Protein Language Models and Machine Learning Facilitate the Identification of Antimicrobial Peptides	Aug 14, 2024	Binary ClassificationDrug 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
SMILES-Mamba: Chemical Mamba Foundation Models for Drug ADMET Prediction	Aug 11, 2024	Drug DiscoveryMamba	—Unverified
Towards Evolutionary-based Automated Machine Learning for Small Molecule Pharmacokinetic Prediction	Aug 1, 2024	AutoMLDrug Discovery	—Unverified
Hashing based Contrastive Learning for Virtual Screening	Jul 29, 2024	Contrastive LearningDrug Discovery	—Unverified
Quantum Long Short-Term Memory for Drug Discovery	Jul 29, 2024	Drug DiscoveryQuantum Machine Learning	—Unverified
Generative artificial intelligence in dentistry: Current approaches and future challenges	Jul 24, 2024	Drug DiscoveryText Generation	—Unverified
Exploiting Pre-trained Models for Drug Target Affinity Prediction with Nearest Neighbors	Jul 21, 2024	Drug DiscoveryPrediction	—Unverified
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
A Hitchhiker's Guide to Deep Chemical Language Processing for Bioactivity Prediction	Jul 16, 2024	Drug DiscoveryHyperparameter Optimization	—Unverified
Repurformer: Transformers for Repurposing-Aware Molecule Generation	Jul 16, 2024	DiversityDrug Discovery	—Unverified
Directly Optimizing for Synthesizability in Generative Molecular Design using Retrosynthesis Models	Jul 16, 2024	Drug DiscoveryRetrosynthesis	—Unverified
Boosting drug-disease association prediction for drug repositioning via dual-feature extraction and cross-dual-domain decoding	Jul 16, 2024	Drug Discovery	—Unverified
On Machine Learning Approaches for Protein-Ligand Binding Affinity Prediction	Jul 15, 2024	Active LearningBenchmarking	—Unverified
GraphPrint: Extracting Features from 3D Protein Structure for Drug Target Affinity Prediction	Jul 15, 2024	Drug Discovery	—Unverified
Pre-training with Fractional Denoising to Enhance Molecular Property Prediction	Jul 14, 2024	DenoisingDrug Discovery	—Unverified
A deep graph model for the signed interaction prediction in biological network	Jul 10, 2024	Drug DiscoveryTensor Decomposition	—Unverified
Token-Mol 1.0: Tokenized drug design with large language model	Jul 10, 2024	Drug DesignDrug Discovery	—Unverified
Accelerating Drug Safety Assessment using Bidirectional-LSTM for SMILES Data	Jul 8, 2024	Drug Discovery	CodeCode Available
Data-centric challenges with the application and adoption of artificial intelligence for drug discovery	Jul 6, 2024	Drug DiscoveryUncertainty Quantification	—Unverified
NEBULA: Neural Empirical Bayes Under Latent Representations for Efficient and Controllable Design of Molecular Libraries	Jul 3, 2024	Drug Discoveryscientific discovery	CodeCode Available
Reinforcement Learning for Sequence Design Leveraging Protein Language Models	Jul 3, 2024	DiversityDrug Discovery	—Unverified
AI-driven Alternative Medicine: A Novel Approach to Drug Discovery and Repurposing	Jul 2, 2024	Drug Discovery	—Unverified
Leveraging Latent Evolutionary Optimization for Targeted Molecule Generation	Jul 2, 2024	Drug DesignDrug Discovery	—Unverified
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
Enabling Regional Explainability by Automatic and Model-agnostic Rule Extraction	Jun 25, 2024	Drug Discovery	—Unverified
A Comprehensive Review of Emerging Approaches in Machine Learning for De Novo PROTAC Design	Jun 24, 2024	Drug DesignDrug Discovery	—Unverified
AntibodyFlow: Normalizing Flow Model for Designing Antibody Complementarity-Determining Regions	Jun 19, 2024	Drug Discoveryvalid	—Unverified
Geometric-informed GFlowNets for Structure-Based Drug Design	Jun 16, 2024	Drug DesignDrug Discovery	—Unverified
Scoreformer: A Surrogate Model For Large-Scale Prediction of Docking Scores	Jun 13, 2024	Drug DiscoveryGraph Neural Network	—Unverified
Automatically Labeling $200B Life-Saving Datasets: A Large Clinical Trial Outcome Benchmark	Jun 13, 2024	Drug DiscoveryLarge Language Model	—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