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 651–700 of 1337 papers

Title	Date	Tasks	Status	Hype
PIGNet2: A Versatile Deep Learning-based Protein-Ligand Interaction Prediction Model for Binding Affinity Scoring and Virtual Screening	Jul 3, 2023	Data AugmentationDrug Discovery	CodeCode Available	1
Variational Autoencoding Molecular Graphs with Denoising Diffusion Probabilistic Model	Jul 2, 2023	DenoisingDrug Discovery	—Unverified	0
Why Deep Models Often cannot Beat Non-deep Counterparts on Molecular Property Prediction?	Jun 30, 2023	Drug DiscoveryMolecular Property Prediction	—Unverified	0
A Unified View of Deep Learning for Reaction and Retrosynthesis Prediction: Current Status and Future Challenges	Jun 28, 2023	Computational chemistryDeep Learning	—Unverified	0
Augmenting Control over Exploration Space in Molecular Dynamics Simulators to Streamline De Novo Analysis through Generative Control Policies	Jun 26, 2023	Drug DiscoveryInductive Bias	—Unverified	0
CoarsenConf: Equivariant Coarsening with Aggregated Attention for Molecular Conformer Generation	Jun 26, 2023	Drug DiscoveryProperty Prediction	CodeCode Available	0
Otter-Knowledge: benchmarks of multimodal knowledge graph representation learning from different sources for drug discovery	Jun 22, 2023	Drug DiscoveryGraph Representation Learning	CodeCode Available	1
Geometric Deep Learning for Structure-Based Drug Design: A Survey	Jun 20, 2023	BenchmarkingDeep Learning	CodeCode Available	1
Size Matters: Large Graph Generation with HiGGs	Jun 20, 2023	Drug DiscoveryGraph Generation	—Unverified	0
MUBen: Benchmarking the Uncertainty of Molecular Representation Models	Jun 14, 2023	BenchmarkingDrug Discovery	CodeCode Available	0
MolCAP: Molecular Chemical reActivity pretraining and prompted-finetuning enhanced molecular representation learning	Jun 13, 2023	DiversityDrug Discovery	—Unverified	0
Automated 3D Pre-Training for Molecular Property Prediction	Jun 13, 2023	Drug DiscoveryGraph Learning	CodeCode Available	1
Molecule Design by Latent Space Energy-Based Modeling and Gradual Distribution Shifting	Jun 9, 2023	Drug Discovery	CodeCode Available	1
Adaptive Batch Sizes for Active Learning A Probabilistic Numerics Approach	Jun 9, 2023	Active LearningBayesian Optimisation	CodeCode Available	0
Gradient-Informed Quality Diversity for the Illumination of Discrete Spaces	Jun 8, 2023	DiversityDrug Discovery	—Unverified	0
Multi-task Bioassay Pre-training for Protein-ligand Binding Affinity Prediction	Jun 8, 2023	Drug DiscoveryPrediction	CodeCode Available	1
Comprehensive evaluation of deep and graph learning on drug-drug interactions prediction	Jun 8, 2023	Drug DiscoveryGraph Learning	CodeCode Available	1
XInsight: Revealing Model Insights for GNNs with Flow-based Explanations	Jun 7, 2023	Drug DiscoveryGraph Classification	—Unverified	0
Empowering Counterfactual Reasoning over Graph Neural Networks through Inductivity	Jun 7, 2023	counterfactualCounterfactual Explanation	CodeCode Available	0
Retrosynthesis Prediction with Local Template Retrieval	Jun 7, 2023	Drug DiscoveryPrediction	—Unverified	0
GSHOT: Few-shot Generative Modeling of Labeled Graphs	Jun 6, 2023	Drug DiscoveryFew-Shot Learning	CodeCode Available	0
Doubly Stochastic Graph-based Non-autoregressive Reaction Prediction	Jun 5, 2023	DecoderDrug Discovery	—Unverified	0
Mitigating Molecular Aggregation in Drug Discovery with Predictive Insights from Explainable AI	Jun 3, 2023	Drug Discovery	CodeCode Available	0
A Survey on Explainability of Graph Neural Networks	Jun 2, 2023	Drug DiscoveryRecommendation Systems	—Unverified	0
Generalist Equivariant Transformer Towards 3D Molecular Interaction Learning	Jun 2, 2023	Drug Discovery	CodeCode Available	1
Symmetric Replay Training: Enhancing Sample Efficiency in Deep Reinforcement Learning for Combinatorial Optimization	Jun 2, 2023	Combinatorial OptimizationDeep Reinforcement Learning	CodeCode Available	0
Causal Intervention for Measuring Confidence in Drug-Target Interaction Prediction	May 31, 2023	Drug DiscoveryGraph Embedding	—Unverified	0
MAGNet: Motif-Agnostic Generation of Molecules from Shapes	May 30, 2023	Drug Discovery	—Unverified	0
Graph Generation with K^2-trees	May 30, 2023	Drug DiscoveryGraph Generation	CodeCode Available	1
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	0
ChatGPT-powered Conversational Drug Editing Using Retrieval and Domain Feedback	May 29, 2023	Decision MakingDrug Discovery	CodeCode Available	1
A Group Symmetric Stochastic Differential Equation Model for Molecule Multi-modal Pretraining	May 28, 2023	Drug Discovery	CodeCode Available	1
Drugst.One -- A plug-and-play solution for online systems medicine and network-based drug repurposing	May 24, 2023	Drug Discovery	—Unverified	0
Learning Subpocket Prototypes for Generalizable Structure-based Drug Design	May 22, 2023	3D Molecule GenerationDrug Design	CodeCode Available	1
Learning Joint 2D & 3D Diffusion Models for Complete Molecule Generation	May 21, 2023	3D Molecule GenerationDrug Discovery	CodeCode Available	1
DrugChat: Towards Enabling ChatGPT-Like Capabilities on Drug Molecule Graphs	May 18, 2023	Drug DiscoveryGraph Neural Network	CodeCode Available	0
Augmented Memory: Capitalizing on Experience Replay to Accelerate De Novo Molecular Design	May 10, 2023	Data AugmentationDrug Discovery	—Unverified	0
Biophysical Model for Signal-Embedded Droplet Soaking into 2D Cell Culture	May 10, 2023	Cultural Vocal Bursts Intensity PredictionDrug Discovery	—Unverified	0
A Latent Diffusion Model for Protein Structure Generation	May 6, 2023	Drug Discoverymodel	—Unverified	0
Structure-Function Dynamics Hybrid Modeling: RNA Degradation	May 6, 2023	Drug Discovery	—Unverified	0
Coarse-to-Fine: a Hierarchical Diffusion Model for Molecule Generation in 3D	May 5, 2023	Drug Discovery	CodeCode Available	1
Optimizing Drug Design by Merging Generative AI With Active Learning Frameworks	May 4, 2023	Active LearningDrug Design	—Unverified	0
MolKD: Distilling Cross-Modal Knowledge in Chemical Reactions for Molecular Property Prediction	May 3, 2023	Drug DiscoveryMolecular Property Prediction	—Unverified	0
ALMERIA: Boosting pairwise molecular contrasts with scalable methods	Apr 28, 2023	Activity PredictionDrug Discovery	—Unverified	0
MUDiff: Unified Diffusion for Complete Molecule Generation	Apr 28, 2023	3D geometryDrug Discovery	—Unverified	0
Context-enriched molecule representations improve few-shot drug discovery	Apr 24, 2023	Drug DiscoveryFew-Shot Learning	CodeCode Available	1
Uni-QSAR: an Auto-ML Tool for Molecular Property Prediction	Apr 24, 2023	Drug DiscoveryModel Selection	CodeCode Available	3
Multidimensional Uncertainty Quantification for Deep Neural Networks	Apr 20, 2023	Decision MakingDrug Discovery	—Unverified	0
Towards Unified AI Drug Discovery with Multiple Knowledge Modalities	Apr 17, 2023	Drug DiscoveryKnowledge Graphs	—Unverified	0
Symbiotic Message Passing Model for Transfer Learning between Anti-Fungal and Anti-Bacterial Domains	Apr 14, 2023	Drug DiscoveryGraph Neural Network	—Unverified	0

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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