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 901–950 of 1337 papers

Title	Date	Tasks	Status	Hype
A Survey of Pretraining on Graphs: Taxonomy, Methods, and Applications	Feb 16, 2022	Drug DiscoveryGraph Representation Learning	CodeCode Available	2
TorchDrug: A Powerful and Flexible Machine Learning Platform for Drug Discovery	Feb 16, 2022	BIG-bench Machine LearningDrug Discovery	CodeCode Available	3
Modular multi-source prediction of drug side-effects with DruGNN	Feb 15, 2022	Drug Discovery	—Unverified	0
MGCVAE: Multi-objective Inverse Design via Molecular Graph Conditional Variational Autoencoder	Feb 14, 2022	Drug Discovery	CodeCode Available	1
Novel prediction methods for virtual drug screening	Feb 14, 2022	Drug DiscoveryPrediction	—Unverified	0
Learning to Discover Medicines	Feb 14, 2022	Drug DiscoveryKnowledge Graphs	—Unverified	0
Automated Architecture Search for Brain-inspired Hyperdimensional Computing	Feb 11, 2022	Drug Discovery	—Unverified	0
Learning Causally Invariant Representations for Out-of-Distribution Generalization on Graphs	Feb 11, 2022	Drug DiscoveryGraph Learning	CodeCode Available	2
Target-aware Molecular Graph Generation	Feb 10, 2022	Drug DiscoveryGraph Generation	—Unverified	0
Interactivity: the missing link between virtual reality technology and drug discovery pipelines	Feb 8, 2022	Drug DesignDrug Discovery	—Unverified	0
Nonmyopic Multiclass Active Search with Diminishing Returns for Diverse Discovery	Feb 8, 2022	DiversityDrug Discovery	—Unverified	0
EquiBind: Geometric Deep Learning for Drug Binding Structure Prediction	Feb 7, 2022	Blind DockingDeep Learning	CodeCode Available	2
Scalable Fragment-Based 3D Molecular Design with Reinforcement Learning	Feb 1, 2022	Drug Discoveryreinforcement-learning	—Unverified	0
SUGAR: Efficient Subgraph-level Training via Resource-aware Graph Partitioning	Jan 31, 2022	Drug DiscoveryEdge-computing	—Unverified	0
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	0
Reinforcement Learning for Personalized Drug Discovery and Design for Complex Diseases: A Systems Pharmacology Perspective	Jan 21, 2022	Drug DesignDrug Discovery	—Unverified	0
AlphaFold Accelerates Artificial Intelligence Powered Drug Discovery: Efficient Discovery of a Novel Cyclin-dependent Kinase 20 (CDK20) Small Molecule Inhibitor	Jan 21, 2022	Drug DesignDrug Discovery	—Unverified	0
GenGNN: A Generic FPGA Framework for Graph Neural Network Acceleration	Jan 20, 2022	CPUDrug Discovery	CodeCode Available	1
Deep Graph Convolutional Network and LSTM based approach for predicting drug-target binding affinity	Jan 18, 2022	Drug Discovery	CodeCode Available	1
Mitigating cold start problems in drug-target affinity prediction with interaction knowledge transferring	Jan 16, 2022	BIG-bench Machine LearningDrug Discovery	CodeCode Available	0
A robust kernel machine regression towards biomarker selection in multi-omics datasets of osteoporosis for drug discovery	Jan 13, 2022	Causal InferenceData Integration	—Unverified	0
Multi-task Joint Strategies of Self-supervised Representation Learning on Biomedical Networks for Drug Discovery	Jan 12, 2022	Drug DiscoveryGraph Attention	CodeCode Available	1
Riemannian Geometry and Molecular Surfaces I: Spectrum of the Laplacian	Jan 10, 2022	Drug Discovery	CodeCode Available	1
Machine Learning-enhanced Efficient Spectroscopic Ellipsometry Modeling	Jan 1, 2022	BIG-bench Machine LearningDrug Discovery	—Unverified	0
Machine learning analysis of cocaine addiction informed by DAT, SERT, and NET-based interactome networks	Jan 1, 2022	Drug Discovery	CodeCode Available	0
Reversible Upper Confidence Bound Algorithm to Generate Diverse Optimized Candidates	Dec 30, 2021	Drug Discoveryreinforcement-learning	—Unverified	0
ToxTree: descriptor-based machine learning models for both hERG and Nav1.5 cardiotoxicity liability predictions	Dec 27, 2021	Binary ClassificationDrug Discovery	—Unverified	0
AI-Bind: Improving Binding Predictions for Novel Protein Targets and Ligands	Dec 25, 2021	Drug DiscoveryUnsupervised Pre-training	CodeCode Available	1
How Much Space Has Been Explored? Measuring the Chemical Space Covered by Databases and Machine-Generated Molecules	Dec 22, 2021	Drug Discovery	—Unverified	0
A molecular generative model with genetic algorithm and tree search for cancer samples	Dec 16, 2021	Drug Discovery	—Unverified	0
Implications of Topological Imbalance for Representation Learning on Biomedical Knowledge Graphs	Dec 13, 2021	Drug DiscoveryGraph Embedding	CodeCode Available	1
Multimodal Pre-Training Model for Sequence-based Prediction of Protein-Protein Interaction	Dec 9, 2021	Drug Discovery	—Unverified	0
Anchoring to Exemplars for Training Mixture-of-Expert Cell Embeddings	Dec 6, 2021	Drug DiscoveryGPU	—Unverified	0
Collective variable discovery in the age of machine learning: reality, hype and everything in between	Dec 6, 2021	Drug Discovery	—Unverified	0
Sample-Efficient Generation of Novel Photo-acid Generator Molecules using a Deep Generative Model	Dec 2, 2021	Drug Discovery	—Unverified	0
Towards understanding retrosynthesis by energy-based models	Dec 1, 2021	Drug DiscoveryRetrosynthesis	—Unverified	0
Functionally Regionalized Knowledge Transfer for Low-resource Drug Discovery	Dec 1, 2021	Drug DiscoveryMeta-Learning	—Unverified	0
HelixMO: Sample-Efficient Molecular Optimization in Scene-Sensitive Latent Space	Nov 30, 2021	Drug DesignDrug Discovery	—Unverified	0
Reliable Graph Neural Networks for Drug Discovery Under Distributional Shift	Nov 25, 2021	Drug Discovery	—Unverified	0
Explainable Biomedical Recommendations via Reinforcement Learning Reasoning on Knowledge Graphs	Nov 20, 2021	Drug DiscoveryKnowledge Graphs	—Unverified	0
Docking-based Virtual Screening with Multi-Task Learning	Nov 18, 2021	BIG-bench Machine LearningDrug Discovery	—Unverified	0
Scalable Variational Quantum Circuits for Autoencoder-based Drug Discovery	Nov 15, 2021	Drug DiscoveryQuantum Machine Learning	—Unverified	0
Improving Compound Activity Classification via Deep Transfer and Representation Learning	Nov 14, 2021	Drug DiscoveryRepresentation Learning	CodeCode Available	0
MassFormer: Tandem Mass Spectrum Prediction for Small Molecules using Graph Transformers	Nov 8, 2021	Drug Discovery	CodeCode Available	1
SPECTRe: Substructure Processing, Enumeration, and Comparison Tool Resource: An efficient tool to encode all substructures of molecules represented in SMILES	Nov 5, 2021	AllDrug Discovery	—Unverified	0
R-BERT-CNN: Drug-target interactions extraction from biomedical literature	Oct 31, 2021	ArticlesDrug Discovery	—Unverified	0
DOCKSTRING: easy molecular docking yields better benchmarks for ligand design	Oct 29, 2021	Drug DesignDrug Discovery	CodeCode Available	1
Learning physics confers pose-sensitivity in structure-based virtual screening	Oct 28, 2021	Drug DiscoverySensitivity	—Unverified	0
Generating 3D Molecules Conditional on Receptor Binding Sites with Deep Generative Models	Oct 28, 2021	Deep LearningDrug Discovery	CodeCode Available	1
The chemical space of terpenes: insights from data science and AI	Oct 27, 2021	ClusteringDimensionality Reduction	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