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 1301–1337 of 1337 papers

Title	Date	Tasks	Status	Hype
Reverse-engineering biological networks from large data sets	May 25, 2017	Drug Discovery	—Unverified	0
Molecular Generation with Recurrent Neural Networks (RNNs)	May 12, 2017	Drug Discovery	—Unverified	0
Link Mining for Kernel-based Compound-Protein Interaction Predictions Using a Chemogenomics Approach	May 4, 2017	Drug DiscoveryPrediction	—Unverified	0
Neural Message Passing for Quantum Chemistry	Apr 4, 2017	Drug DiscoveryFormation Energy	CodeCode Available	1
Atomic Convolutional Networks for Predicting Protein-Ligand Binding Affinity	Mar 30, 2017	Drug DiscoveryMolecular Docking	CodeCode Available	3
Machine learning prediction errors better than DFT accuracy	Feb 17, 2017	BIG-bench Machine LearningDrug Discovery	—Unverified	0
Generating Focussed Molecule Libraries for Drug Discovery with Recurrent Neural Networks	Jan 5, 2017	Drug DesignDrug Discovery	CodeCode Available	1
Protein-Ligand Scoring with Convolutional Neural Networks	Dec 8, 2016	Drug DesignDrug Discovery	CodeCode Available	0
Therapeutic target discovery using Boolean network attractors: improvements of kali	Nov 10, 2016	Drug Discovery	CodeCode Available	0
Low Data Drug Discovery with One-shot Learning	Nov 10, 2016	Drug DiscoveryMolecular Property Prediction	—Unverified	0
Heter-LP: A heterogeneous label propagation algorithm and its application in drug repositioning	Nov 8, 2016	Data IntegrationDrug Discovery	CodeCode Available	0
Semi-Supervised Classification with Graph Convolutional Networks	Sep 9, 2016	Document ClassificationDrug Discovery	CodeCode Available	1
Inferring Implicit Causal Relationships in Biomedical Literature	Aug 1, 2016	Drug DiscoveryNamed Entity Recognition (NER)	—Unverified	0
Statistical thermodynamic basis in drug-receptor interactions: double annihilation and double decoupling alchemical theories, revisited	Jul 13, 2016	Drug Discovery	—Unverified	0
Modeling Industrial ADMET Data with Multitask Networks	Jun 28, 2016	Drug Discovery	—Unverified	0
Towards protein-protein docking with significant structural changes using CABS-dock	May 30, 2016	Drug DiscoveryMolecular Docking	—Unverified	0
An unbiased metric of antiproliferative drug effect in vitro	May 22, 2016	Drug Discovery	—Unverified	0
Molecular Graph Convolutions: Moving Beyond Fingerprints	Mar 2, 2016	BIG-bench Machine LearningDrug Discovery	CodeCode Available	0
Gated Graph Sequence Neural Networks	Nov 17, 2015	Drug DiscoveryGraph Classification	CodeCode Available	1
AtomNet: A Deep Convolutional Neural Network for Bioactivity Prediction in Structure-based Drug Discovery	Oct 10, 2015	Drug Discovery	CodeCode Available	0
Convolutional Networks on Graphs for Learning Molecular Fingerprints	Sep 30, 2015	Drug DiscoveryGraph Regression	CodeCode Available	0
Differential protein expression and peak selection in mass spectrometry data by binary discriminant analysis	May 27, 2015	Drug Discovery	—Unverified	0
PopED lite: an optimal design software for preclinical pharmacokinetic and pharmacodynamic studies	May 25, 2015	Drug DiscoveryExperimental Design	—Unverified	0
Therapeutic target discovery using Boolean network attractors: avoiding pathological phenotypes	May 23, 2015	Drug Discovery	—Unverified	0
iTreePack: Protein Complex Side-Chain Packing by Dual Decomposition	Apr 21, 2015	Drug DiscoveryTree Decomposition	—Unverified	0
Rectified Factor Networks	Feb 23, 2015	Drug Discovery	—Unverified	0
Classification and its applications for drug-target interaction identification	Feb 16, 2015	ClassificationClustering	—Unverified	0
Massively Multitask Networks for Drug Discovery	Feb 6, 2015	Drug Discovery	CodeCode Available	0
On the String Kernel Pre-Image Problem with Applications in Drug Discovery	Dec 3, 2014	Combinatorial OptimizationDrug Discovery	—Unverified	0
Feature Selection through Minimization of the VC dimension	Oct 27, 2014	Drug Discoveryfeature selection	—Unverified	0
Evolutionary Algorithm for Drug Discovery Interim Design Report	Mar 19, 2014	Drug Discovery	—Unverified	0
Performance Analysis Of Neural Network Models For Oxazolines And Oxazoles Derivatives Descriptor Dataset	Dec 10, 2013	Drug DiscoveryMedical Diagnosis	—Unverified	0
Generating Explanations for Biomedical Queries	Sep 24, 2013	Drug Discovery	—Unverified	0
Ensembling classification models based on phalanxes of variables with applications in drug discovery	Mar 20, 2013	Computational chemistryDrug Discovery	—Unverified	0
Semantic Judgement of Medical Concepts: Combining Syntagmatic and Paradigmatic Information with the Tensor Encoding Model	Dec 1, 2012	Drug DiscoveryInformation Retrieval	—Unverified	0
Extracting and Visualizing Semantic Relationships from Chinese Biomedical Text	Nov 1, 2012	Drug DiscoveryRelation Extraction	—Unverified	0
BART: Bayesian additive regression trees	Jun 19, 2008	Causal InferenceDrug Discovery	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