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 151–200 of 1337 papers

Title	Date	Tasks	Status	Hype
A hybrid quantum-classical fusion neural network to improve protein-ligand binding affinity predictions for drug discovery	Sep 6, 2023	Drug DiscoveryPrediction	CodeCode Available	1
Hierarchical Grammar-Induced Geometry for Data-Efficient Molecular Property Prediction	Sep 4, 2023	Drug DiscoveryMolecular Property Prediction	CodeCode Available	1
DiffHopp: A Graph Diffusion Model for Novel Drug Design via Scaffold Hopping	Aug 14, 2023	Drug DesignDrug Discovery	CodeCode Available	1
GIT-Mol: A Multi-modal Large Language Model for Molecular Science with Graph, Image, and Text	Aug 14, 2023	Drug DiscoveryImage Captioning	CodeCode Available	1
Target-aware Variational Auto-encoders for Ligand Generation with Multimodal Protein Representation Learning	Aug 2, 2023	Drug DiscoveryRepresentation Learning	CodeCode Available	1
Fractional Denoising for 3D Molecular Pre-training	Jul 20, 2023	DenoisingDrug Discovery	CodeCode Available	1
Uncertainty Quantification for Molecular Property Predictions with Graph Neural Architecture Search	Jul 19, 2023	Decision MakingDrug Discovery	CodeCode Available	1
Drug Discovery under Covariate Shift with Domain-Informed Prior Distributions over Functions	Jul 14, 2023	Domain AdaptationDrug Discovery	CodeCode Available	1
ChiENN: Embracing Molecular Chirality with Graph Neural Networks	Jul 5, 2023	Drug DiscoveryMolecular Property Prediction	CodeCode Available	1
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
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
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
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
Generalist Equivariant Transformer Towards 3D Molecular Interaction Learning	Jun 2, 2023	Drug Discovery	CodeCode Available	1
Graph Generation with K^2-trees	May 30, 2023	Drug DiscoveryGraph Generation	CodeCode Available	1
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
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
Coarse-to-Fine: a Hierarchical Diffusion Model for Molecule Generation in 3D	May 5, 2023	Drug Discovery	CodeCode Available	1
Context-enriched molecule representations improve few-shot drug discovery	Apr 24, 2023	Drug DiscoveryFew-Shot Learning	CodeCode Available	1
SELFormer: Molecular Representation Learning via SELFIES Language Models	Apr 10, 2023	Dimensionality ReductionDrug Discovery	CodeCode Available	1
Learning Harmonic Molecular Representations on Riemannian Manifold	Mar 27, 2023	Drug Discoverymolecular representation	CodeCode Available	1
Class-Guided Image-to-Image Diffusion: Cell Painting from Brightfield Images with Class Labels	Mar 15, 2023	DenoisingDrug Discovery	CodeCode Available	1
Extrapolative Controlled Sequence Generation via Iterative Refinement	Mar 8, 2023	AttributeDrug Discovery	CodeCode Available	1
Enhancing Activity Prediction Models in Drug Discovery with the Ability to Understand Human Language	Mar 6, 2023	Activity PredictionAttribute	CodeCode Available	1
EquiPocket: an E(3)-Equivariant Geometric Graph Neural Network for Ligand Binding Site Prediction	Feb 23, 2023	Drug DiscoveryGraph Neural Network	CodeCode Available	1
Knowledge-augmented Graph Machine Learning for Drug Discovery: A Survey	Feb 16, 2023	Drug DiscoverySurvey	CodeCode Available	1
Activity Cliff Prediction: Dataset and Benchmark	Feb 15, 2023	Drug DiscoveryPrediction	CodeCode Available	1
Retrosynthetic Planning with Dual Value Networks	Jan 31, 2023	Drug DiscoveryMulti-step retrosynthesis	CodeCode Available	1
On Pre-trained Language Models for Antibody	Jan 28, 2023	Drug DiscoveryLanguage Modelling	CodeCode Available	1
SOBER: Highly Parallel Bayesian Optimization and Bayesian Quadrature over Discrete and Mixed Spaces	Jan 27, 2023	Bayesian OptimisationBayesian Optimization	CodeCode Available	1
Unsupervised Protein-Ligand Binding Energy Prediction via Neural Euler's Rotation Equation	Jan 25, 2023	DenoisingDrug Discovery	CodeCode Available	1
Machine learning models to accelerate the design of polymeric long-acting injectables	Jan 10, 2023	Drug Discovery	CodeCode Available	1
Conditional Diffusion Based on Discrete Graph Structures for Molecular Graph Generation	Jan 1, 2023	Drug DiscoveryGraph Generation	CodeCode Available	1
HAC-Net: A Hybrid Attention-Based Convolutional Neural Network for Highly Accurate Protein-Ligand Binding Affinity Prediction	Dec 23, 2022	Drug DiscoveryProperty Prediction	CodeCode Available	1
Pushing the boundaries of molecular property prediction for drug discovery with multitask learning BERT enhanced by SMILES enumeration	Dec 15, 2022	Drug DiscoveryFeature Engineering	CodeCode Available	1
Accelerating Inverse Learning via Intelligent Localization with Exploratory Sampling	Dec 2, 2022	Drug Discovery	CodeCode Available	1
Biomedical NER for the Enterprise with Distillated BERN2 and the Kazu Framework	Dec 1, 2022	Drug DiscoveryNER	CodeCode Available	1
Reinforced Genetic Algorithm for Structure-based Drug Design	Nov 28, 2022	Combinatorial OptimizationDrug Design	CodeCode Available	1
Deep Surrogate Docking: Accelerating Automated Drug Discovery with Graph Neural Networks	Nov 4, 2022	Drug Discovery	CodeCode Available	1
CausalBench: A Large-scale Benchmark for Network Inference from Single-cell Perturbation Data	Oct 31, 2022	Causal DiscoveryCausal Inference	CodeCode Available	1
Physics-aware Graph Neural Network for Accurate RNA 3D Structure Prediction	Oct 28, 2022	Drug DiscoveryGraph Neural Network	CodeCode Available	1
Multi-Objective GFlowNets	Oct 23, 2022	Active LearningDiversity	CodeCode Available	1
An efficient graph generative model for navigating ultra-large combinatorial synthesis libraries	Oct 19, 2022	DecoderDrug Discovery	CodeCode Available	1
Generalizing in the Real World with Representation Learning	Oct 18, 2022	Drug DiscoveryRepresentation Learning	CodeCode Available	1
Empowering Graph Representation Learning with Test-Time Graph Transformation	Oct 7, 2022	Drug DiscoveryGraph Representation Learning	CodeCode Available	1

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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