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 151–175 of 1337 papers

Title	Date	Tasks	Status	Hype	Score
3D Interaction Geometric Pre-training for Molecular Relational Learning	Dec 4, 2024	Contrastive LearningDrug Discovery	CodeCode Available	1	5
ChemSpaceAL: An Efficient Active Learning Methodology Applied to Protein-Specific Molecular Generation	Sep 11, 2023	Active LearningDrug Discovery	CodeCode Available	1	5
CausalBench: A Large-scale Benchmark for Network Inference from Single-cell Perturbation Data	Oct 31, 2022	Causal DiscoveryCausal Inference	CodeCode Available	1	5
Geometric Deep Learning for Structure-Based Drug Design: A Survey	Jun 20, 2023	BenchmarkingDeep Learning	CodeCode Available	1	5
Atomas: Hierarchical Alignment on Molecule-Text for Unified Molecule Understanding and Generation	Apr 23, 2024	Drug Discoverymolecular representation	CodeCode Available	1	5
FlowGNN: A Dataflow Architecture for Real-Time Workload-Agnostic Graph Neural Network Inference	Apr 27, 2022	CPUDrug Discovery	CodeCode Available	1	5
Activity Cliff Prediction: Dataset and Benchmark	Feb 15, 2023	Drug DiscoveryPrediction	CodeCode Available	1	5
ChiENN: Embracing Molecular Chirality with Graph Neural Networks	Jul 5, 2023	Drug DiscoveryMolecular Property Prediction	CodeCode Available	1	5
EquiCPI: SE(3)-Equivariant Geometric Deep Learning for Structure-Aware Prediction of Compound-Protein Interactions	Apr 7, 2025	Drug DiscoveryRe-Ranking	CodeCode Available	1	5
EquiPocket: an E(3)-Equivariant Geometric Graph Neural Network for Ligand Binding Site Prediction	Feb 23, 2023	Drug DiscoveryGraph Neural Network	CodeCode Available	1	5
AttentionSiteDTI: an interpretable graph-based model for drug-target interaction prediction using NLP sentence-level relation classification	Jul 12, 2022	Drug DiscoveryRelation Classification	CodeCode Available	1	5
Conditional Diffusion Based on Discrete Graph Structures for Molecular Graph Generation	Jan 1, 2023	Drug DiscoveryGraph Generation	CodeCode Available	1	5
Enhancing Activity Prediction Models in Drug Discovery with the Ability to Understand Human Language	Mar 6, 2023	Activity PredictionAttribute	CodeCode Available	1	5
End-to-End Differentiable Molecular Mechanics Force Field Construction	Oct 2, 2020	Computational chemistryDrug Discovery	CodeCode Available	1	5
Fractional Denoising for 3D Molecular Pre-training	Jul 20, 2023	DenoisingDrug Discovery	CodeCode Available	1	5
FragNet: A Graph Neural Network for Molecular Property Prediction with Four Levels of Interpretability	Oct 16, 2024	Drug DiscoveryGraph Neural Network	CodeCode Available	1	5
Barlow Twins Deep Neural Network for Advanced 1D Drug-Target Interaction Prediction	Jul 31, 2024	Drug Discovery	CodeCode Available	1	5
Contrastive Dual-Interaction Graph Neural Network for Molecular Property Prediction	May 4, 2024	Drug DiscoveryGraph Neural Network	CodeCode Available	1	5
Context-Guided Diffusion for Out-of-Distribution Molecular and Protein Design	Jul 16, 2024	Drug DiscoveryOut-of-Distribution Generalization	CodeCode Available	1	5
Context-enriched molecule representations improve few-shot drug discovery	Apr 24, 2023	Drug DiscoveryFew-Shot Learning	CodeCode Available	1	5
Enhancing Uncertainty Quantification in Drug Discovery with Censored Regression Labels	Sep 6, 2024	Drug Discoveryregression	CodeCode Available	1	5
Automated 3D Pre-Training for Molecular Property Prediction	Jun 13, 2023	Drug DiscoveryGraph Learning	CodeCode Available	1	5
Generalist Equivariant Transformer Towards 3D Molecular Interaction Learning	Jun 2, 2023	Drug Discovery	CodeCode Available	1	5
Generalizing in the Real World with Representation Learning	Oct 18, 2022	Drug DiscoveryRepresentation Learning	CodeCode Available	1	5
BioT5: Enriching Cross-modal Integration in Biology with Chemical Knowledge and Natural Language Associations	Oct 11, 2023	Drug DiscoveryMolecule Captioning	CodeCode Available	1	5

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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