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 701–750 of 1337 papers

Title	Date	Tasks	Status	Hype
Enhancing Model Learning and Interpretation Using Multiple Molecular Graph Representations for Compound Property and Activity Prediction	Apr 13, 2023	Activity PredictionDrug Discovery	—Unverified	0
An Equivariant Generative Framework for Molecular Graph-Structure Co-Design	Apr 12, 2023	3D geometryDrug Design	CodeCode Available	0
ChemCrow: Augmenting large-language models with chemistry tools	Apr 11, 2023	Computational chemistryDrug Discovery	CodeCode Available	2
GraphGANFed: A Federated Generative Framework for Graph-Structured Molecules Towards Efficient Drug Discovery	Apr 11, 2023	Drug DiscoveryFederated Learning	—Unverified	0
Faster Lead Optimization Mapper Algorithm for Large-Scale Relative Free Energy Perturbation	Apr 10, 2023	Drug Discovery	CodeCode Available	0
SELFormer: Molecular Representation Learning via SELFIES Language Models	Apr 10, 2023	Dimensionality ReductionDrug Discovery	CodeCode Available	1
DiffDock-PP: Rigid Protein-Protein Docking with Diffusion Models	Apr 8, 2023	Drug DiscoveryProtein Design	CodeCode Available	2
Graph Representation Learning for Interactive Biomolecule Systems	Apr 5, 2023	Deep LearningDrug Discovery	—Unverified	0
The power of motifs as inductive bias for learning molecular distributions	Apr 4, 2023	Drug DiscoveryInductive Bias	—Unverified	0
Optimization of binding affinities in chemical space with generative pretrained transformer and deep reinforcement learning	Apr 3, 2023	Deep Reinforcement LearningDrug Discovery	CodeCode Available	0
A Survey on Federated Learning for the Healthcare Metaverse: Concepts, Applications, Challenges, and Future Directions	Apr 2, 2023	Drug DiscoveryEdge-computing	—Unverified	0
Learning Harmonic Molecular Representations on Riemannian Manifold	Mar 27, 2023	Drug Discoverymolecular representation	CodeCode Available	1
Large AI Models in Health Informatics: Applications, Challenges, and the Future	Mar 21, 2023	Decision MakingDrug Discovery	CodeCode Available	2
DSDP: A Blind Docking Strategy Accelerated by GPUs	Mar 16, 2023	Blind DockingDrug Discovery	—Unverified	0
Class-Guided Image-to-Image Diffusion: Cell Painting from Brightfield Images with Class Labels	Mar 15, 2023	DenoisingDrug Discovery	CodeCode Available	1
Intelligent diagnostic scheme for lung cancer screening with Raman spectra data by tensor network machine learning	Mar 11, 2023	DiagnosticDrug Discovery	—Unverified	0
Infinite Physical Monkey: Do Deep Learning Methods Really Perform Better in Conformation Generation?	Mar 8, 2023	Drug DesignDrug Discovery	—Unverified	0
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
Machine-learning Repurposing of DrugBank Compounds for Opioid Use Disorder	Mar 1, 2023	Drug Discovery	CodeCode Available	0
Deep Learning Methods for Small Molecule Drug Discovery: A Survey	Mar 1, 2023	Deep LearningDrug Discovery	—Unverified	0
GraphVF: Controllable Protein-Specific 3D Molecule Generation with Variational Flow	Feb 23, 2023	3D geometry3D Molecule Generation	CodeCode Available	0
EquiPocket: an E(3)-Equivariant Geometric Graph Neural Network for Ligand Binding Site Prediction	Feb 23, 2023	Drug DiscoveryGraph Neural Network	CodeCode Available	1
Machine learning for the prediction of safe and biologically active organophosphorus molecules	Feb 21, 2023	Drug DesignDrug Discovery	—Unverified	0
Don't guess what's true: choose what's optimal. A probability transducer for machine-learning classifiers	Feb 21, 2023	Drug Discovery	—Unverified	0
A Survey of Trustworthy Federated Learning with Perspectives on Security, Robustness, and Privacy	Feb 21, 2023	Drug DiscoveryFederated Learning	—Unverified	0
Boosting Convolutional Neural Networks' Protein Binding Site Prediction Capacity Using SE(3)-invariant transformers, Transfer Learning and Homology-based Augmentation	Feb 20, 2023	Drug DiscoveryTransfer Learning	—Unverified	0
Index analysis: an approach to understand signal transduction with application to the EGFR signalling pathway	Feb 17, 2023	Drug Discovery	—Unverified	0
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
SupSiam: Non-contrastive Auxiliary Loss for Learning from Molecular Conformers	Feb 15, 2023	Activity PredictionDrug Discovery	—Unverified	0
Do Deep Learning Methods Really Perform Better in Molecular Conformation Generation?	Feb 14, 2023	Deep LearningDrug Discovery	CodeCode Available	0
3D Molecular Generation via Virtual Dynamics	Feb 12, 2023	Drug DesignDrug Discovery	—Unverified	0
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	0
Beyond Statistical Similarity: Rethinking Metrics for Deep Generative Models in Engineering Design	Feb 6, 2023	Drug DiscoveryLearning Theory	—Unverified	0
PASSerRank: Prediction of Allosteric Sites with Learning to Rank	Feb 2, 2023	Drug DiscoveryLearning-To-Rank	CodeCode Available	0
Predicting Molecule-Target Interaction by Learning Biomedical Network and Molecule Representations	Feb 2, 2023	Drug DiscoveryGraph Neural Network	—Unverified	0
Retrosynthetic Planning with Dual Value Networks	Jan 31, 2023	Drug DiscoveryMulti-step retrosynthesis	CodeCode Available	1
Large Language Models for Biomedical Knowledge Graph Construction: Information extraction from EMR notes	Jan 29, 2023	DecoderDrug Discovery	—Unverified	0
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
The Clinical Trials Puzzle: How Network Effects Limit Drug Discovery	Jan 25, 2023	Drug Discovery	CodeCode Available	0
Everything is Connected: Graph Neural Networks	Jan 19, 2023	Drug DiscoveryGraph Representation Learning	—Unverified	0
Hybrid quantum-classical convolutional neural networks to improve molecular protein binding affinity predictions	Jan 16, 2023	Drug DiscoveryQuantum Machine Learning	—Unverified	0
Machine learning models to accelerate the design of polymeric long-acting injectables	Jan 10, 2023	Drug Discovery	CodeCode Available	1
A survey on Organoid Image Analysis Platforms	Jan 6, 2023	Cultural Vocal Bursts Intensity PredictionDrug Discovery	—Unverified	0
Protein-Ligand Complex Generator & Drug Screening via Tiered Tensor Transform	Jan 3, 2023	Drug Discovery	—Unverified	0
Conditional Diffusion Based on Discrete Graph Structures for Molecular Graph Generation	Jan 1, 2023	Drug DiscoveryGraph Generation	CodeCode Available	1
Synthesis-driven design of 3D molecules for structure-based drug discovery using geometric transformers	Dec 31, 2022	Drug DesignDrug Discovery	—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