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 1201–1250 of 1337 papers

Title	Date	Tasks	Status	Hype
Data-Driven Approach to Encoding and Decoding 3-D Crystal Structures	Sep 3, 2019	DecoderDrug Discovery	CodeCode Available	0
Gated Graph Recursive Neural Networks for Molecular Property Prediction	Aug 31, 2019	Drug DiscoveryMolecular Property Prediction	—Unverified	0
Triclustering of Gene Expression Microarray Data Using Coarse-Grained Parallel Genetic Algorithm	Aug 31, 2019	ClusteringDrug Discovery	—Unverified	0
Deep Learning for Estimating Synaptic Health of Primary Neuronal Cell Culture	Aug 29, 2019	Binary ClassificationClassification	—Unverified	0
Molecule Property Prediction Based on Spatial Graph Embedding	Aug 22, 2019	Drug DiscoveryGraph Embedding	CodeCode Available	0
DeepScaffold: a comprehensive tool for scaffold-based de novo drug discovery using deep learning	Aug 20, 2019	Drug DesignDrug Discovery	—Unverified	0
Self-Attention Based Molecule Representation for Predicting Drug-Target Interaction	Aug 15, 2019	Drug Discovery	—Unverified	0
Concepts and Applications of Conformal Prediction in Computational Drug Discovery	Aug 9, 2019	Conformal PredictionDecision Making	—Unverified	0
Sparse hierarchical representation learning on molecular graphs	Aug 6, 2019	Drug DiscoveryRepresentation Learning	—Unverified	0
ChemBO: Bayesian Optimization of Small Organic Molecules with Synthesizable Recommendations	Aug 5, 2019	Bayesian OptimizationDrug Discovery	CodeCode Available	0
GraphDTA: prediction of drug–target binding affinity using graph convolutional networks	Jul 2, 2019	Deep LearningDrug Discovery	CodeCode Available	0
Constructing large scale biomedical knowledge bases from scratch with rapid annotation of interpretable patterns	Jul 2, 2019	Drug DiscoveryKnowledge Base Completion	—Unverified	0
Sequential Experimental Design for Transductive Linear Bandits	Jun 20, 2019	Drug DiscoveryExperimental Design	CodeCode Available	0
Utilizing Edge Features in Graph Neural Networks via Variational Information Maximization	Jun 13, 2019	Drug DiscoveryQuantum Chemistry Regression	—Unverified	0
Attention-based Multi-Input Deep Learning Architecture for Biological Activity Prediction: An Application in EGFR Inhibitors	Jun 12, 2019	Activity PredictionBIG-bench Machine Learning	CodeCode Available	0
Hierarchical Graph-to-Graph Translation for Molecules	Jun 11, 2019	DecoderDrug Discovery	CodeCode Available	1
A Bayesian Model of Dose-Response for Cancer Drug Studies	Jun 10, 2019	DenoisingDrug Discovery	CodeCode Available	1
Diameter-based Interactive Structure Discovery	Jun 5, 2019	Active LearningDrug Discovery	—Unverified	0
MolecularRNN: Generating realistic molecular graphs with optimized properties	May 31, 2019	Drug DiscoveryMolecular Graph Generation	CodeCode Available	0
Scaffold-based molecular design using graph generative model	May 31, 2019	Drug Discoverymodel	CodeCode Available	0
All SMILES Variational Autoencoder	May 30, 2019	AllDrug Discovery	—Unverified	0
Towards Interpretable Sparse Graph Representation Learning with Laplacian Pooling	May 28, 2019	Drug DesignDrug Discovery	—Unverified	0
Adaptive Deep Kernel Learning	May 28, 2019	BenchmarkingDrug Discovery	—Unverified	0
Leveraging binding-site structure for drug discovery with point-cloud methods	May 28, 2019	Drug Discovery	—Unverified	0
Validating the Validation: Reanalyzing a large-scale comparison of Deep Learning and Machine Learning models for bioactivity prediction	May 28, 2019	BIG-bench Machine LearningDrug Discovery	CodeCode Available	0
Incidence Networks for Geometric Deep Learning	May 27, 2019	Deep LearningDrug Discovery	—Unverified	0
FOBE and HOBE: First- and High-Order Bipartite Embeddings	May 27, 2019	Data VisualizationDrug Discovery	—Unverified	0
Adversarial Learned Molecular Graph Inference and Generation	May 24, 2019	Drug Discovery	CodeCode Available	0
Deep learning to generate in silico chemical property libraries and candidate molecules for small molecule identification in complex samples	May 21, 2019	Drug DiscoveryTransfer Learning	CodeCode Available	1
End-to-end learning of pharmacological assays from high-resolution microscopy images	May 1, 2019	Cell SegmentationDrug Discovery	—Unverified	0
Improving detection of protein-ligand binding sites with 3D segmentation	Apr 13, 2019	Drug Discovery	CodeCode Available	0
Reliable Prediction Errors for Deep Neural Networks Using Test-Time Dropout	Apr 12, 2019	Conformal PredictionDecision Making	—Unverified	0
DeeplyTough: Learning Structural Comparison of Protein Binding Sites	Apr 5, 2019	Drug Discovery	CodeCode Available	0
Phenotypic Profiling of High Throughput Imaging Screens with Generic Deep Convolutional Features	Mar 15, 2019	ClusteringDrug Discovery	—Unverified	0
Interpretable Deep Learning in Drug Discovery	Mar 7, 2019	Deep LearningDrug Discovery	CodeCode Available	0
Clustering Bioactive Molecules in 3D Chemical Space with Unsupervised Deep Learning	Feb 9, 2019	ClusteringDiversity	—Unverified	0
WideDTA: prediction of drug-target binding affinity	Feb 4, 2019	Deep LearningDrug Discovery	CodeCode Available	0
Bayesian semi-supervised learning for uncertainty-calibrated prediction of molecular properties and active learning	Feb 3, 2019	Active LearningDrug Discovery	—Unverified	0
A Quantum-Inspired Method for Three-Dimensional Ligand-Based Virtual Screening	Jan 28, 2019	Drug Discovery	—Unverified	0
Hybrid Modelling in Oncology: Sucesses, Challenges and Hopes	Jan 17, 2019	Data IntegrationDrug Discovery	—Unverified	0
Determining Multifunctional Genes and Diseases in Human Using Gene Ontology	Jan 11, 2019	Drug Discovery	—Unverified	0
Drug cell line interaction prediction	Dec 28, 2018	Drug DiscoveryPrediction	CodeCode Available	0
An Integrated Transfer Learning and Multitask Learning Approach for Pharmacokinetic Parameter Prediction	Dec 21, 2018	Drug DiscoveryParameter Prediction	—Unverified	0
Efficient nonmyopic batch active search	Dec 1, 2018	DiversityDrug Discovery	—Unverified	0
A Bandit Approach to Sequential Experimental Design with False Discovery Control	Dec 1, 2018	Drug DiscoveryExperimental Design	—Unverified	0
Corresponding Projections for Orphan Screening	Nov 30, 2018	Drug DiscoveryTransfer Learning	CodeCode Available	0
Molecular Sets (MOSES): A Benchmarking Platform for Molecular Generation Models	Nov 29, 2018	BenchmarkingDiversity	CodeCode Available	0
DEFactor: Differentiable Edge Factorization-based Probabilistic Graph Generation	Nov 24, 2018	Drug DiscoveryGraph Generation	—Unverified	0
GuacaMol: Benchmarking Models for De Novo Molecular Design	Nov 22, 2018	BenchmarkingDrug Discovery	CodeCode Available	1
KekuleScope: prediction of cancer cell line sensitivity and compound potency using convolutional neural networks trained on compound images	Nov 22, 2018	Drug DiscoveryPrediction Of Cancer Cell Line Sensitivity	CodeCode Available	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