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 51–100 of 1337 papers

Title	Date	Tasks	Status	Hype
GeoDiff: a Geometric Diffusion Model for Molecular Conformation Generation	Mar 6, 2022	Drug Discovery	CodeCode Available	2
A Survey of Pretraining on Graphs: Taxonomy, Methods, and Applications	Feb 16, 2022	Drug DiscoveryGraph Representation Learning	CodeCode Available	2
Learning Causally Invariant Representations for Out-of-Distribution Generalization on Graphs	Feb 11, 2022	Drug DiscoveryGraph Learning	CodeCode Available	2
EquiBind: Geometric Deep Learning for Drug Binding Structure Prediction	Feb 7, 2022	Blind DockingDeep Learning	CodeCode Available	2
Therapeutics Data Commons: Machine Learning Datasets and Tasks for Drug Discovery and Development	Feb 18, 2021	BIG-bench Machine LearningDrug Discovery	CodeCode Available	2
DeepPurpose: a Deep Learning Library for Drug-Target Interaction Prediction	Apr 19, 2020	Deep LearningDrug Discovery	CodeCode Available	2
Multi-Objective Molecule Generation using Interpretable Substructures	Feb 8, 2020	DiversityDrug Design	CodeCode Available	2
JAX, M.D.: A Framework for Differentiable Physics	Dec 9, 2019	Drug DiscoveryGPU	CodeCode Available	2
DeepDTA: Deep Drug-Target Binding Affinity Prediction	Jan 30, 2018	Binary ClassificationDrug Discovery	CodeCode Available	2
Self-Normalizing Neural Networks	Jun 8, 2017	AstronomyBIG-bench Machine Learning	CodeCode Available	2
Agentomics-ML: Autonomous Machine Learning Experimentation Agent for Genomic and Transcriptomic Data	Jun 5, 2025	Drug DiscoveryLarge Language Model	CodeCode Available	1
MTPNet: Multi-Grained Target Perception for Unified Activity Cliff Prediction	Jun 5, 2025	Drug DiscoveryPrediction	CodeCode Available	1
DrugPilot: LLM-based Parameterized Reasoning Agent for Drug Discovery	May 20, 2025	Drug Discovery	CodeCode Available	1
EDBench: Large-Scale Electron Density Data for Molecular Modeling	May 14, 2025	Drug Discovery	CodeCode Available	1
scDrugMap: Benchmarking Large Foundation Models for Drug Response Prediction	May 8, 2025	BenchmarkingDrug Discovery	CodeCode Available	1
Heterogeneous networks in drug-target interaction prediction	Apr 22, 2025	Drug DiscoveryPrediction	CodeCode Available	1
Rethinking the generalization of drug target affinity prediction algorithms via similarity aware evaluation	Apr 13, 2025	Drug Discovery	CodeCode Available	1
BioChemInsight: An Open-Source Toolkit for Automated Identification and Recognition of Optical Chemical Structures and Activity Data in Scientific Publications	Apr 12, 2025	ArticlesDrug Design	CodeCode Available	1
EquiCPI: SE(3)-Equivariant Geometric Deep Learning for Structure-Aware Prediction of Compound-Protein Interactions	Apr 7, 2025	Drug DiscoveryRe-Ranking	CodeCode Available	1
Strain Problems got you in a Twist? Try StrainRelief: A Quantum-Accurate Tool for Ligand Strain Calculations	Mar 17, 2025	Drug DesignDrug Discovery	CodeCode Available	1
SynLlama: Generating Synthesizable Molecules and Their Analogs with Large Language Models	Mar 16, 2025	Drug Discovery	CodeCode Available	1
InversionGNN: A Dual Path Network for Multi-Property Molecular Optimization	Mar 3, 2025	Drug DiscoveryGraph Neural Network	CodeCode Available	1
Molecule Generation for Target Protein Binding with Hierarchical Consistency Diffusion Model	Mar 2, 2025	Drug DesignDrug Discovery	CodeCode Available	1
SE(3)-Equivariant Ternary Complex Prediction Towards Target Protein Degradation	Feb 26, 2025	Blind DockingDecoder	CodeCode Available	1
K-Paths: Reasoning over Graph Paths for Drug Repurposing and Drug Interaction Prediction	Feb 18, 2025	Drug DiscoveryKnowledge Graphs	CodeCode Available	1
3DMolFormer: A Dual-channel Framework for Structure-based Drug Discovery	Feb 7, 2025	Drug DesignDrug Discovery	CodeCode Available	1
Temporal Distribution Shift in Real-World Pharmaceutical Data: Implications for Uncertainty Quantification in QSAR Models	Feb 6, 2025	Drug DiscoveryUncertainty Quantification	CodeCode Available	1
QuantumBind-RBFE: Accurate Relative Binding Free Energy Calculations Using Neural Network Potentials	Jan 3, 2025	Drug Discovery	CodeCode Available	1
Can LLMs Convert Graphs to Text-Attributed Graphs?	Dec 13, 2024	Drug DiscoveryRecommendation Systems	CodeCode Available	1
3D Interaction Geometric Pre-training for Molecular Relational Learning	Dec 4, 2024	Contrastive LearningDrug Discovery	CodeCode Available	1
Scaling Structure Aware Virtual Screening to Billions of Molecules with SPRINT	Nov 23, 2024	Drug DiscoveryMolecular Docking	CodeCode Available	1
DrugGen: Advancing Drug Discovery with Large Language Models and Reinforcement Learning Feedback	Nov 20, 2024	Drug DesignDrug Discovery	CodeCode Available	1
NPGPT: Natural Product-Like Compound Generation with GPT-based Chemical Language Models	Nov 19, 2024	DiversityDrug Discovery	CodeCode Available	1
Graph Neural Networks for Quantifying Compatibility Mechanisms in Traditional Chinese Medicine	Nov 18, 2024	Drug DiscoveryFeature Engineering	CodeCode Available	1
OneProt: Towards Multi-Modal Protein Foundation Models	Nov 7, 2024	Drug DiscoveryRetrieval	CodeCode Available	1
Bio-xLSTM: Generative modeling, representation and in-context learning of biological and chemical sequences	Nov 6, 2024	Drug DiscoveryIn-Context Learning	CodeCode Available	1
GraphXForm: Graph transformer for computer-aided molecular design	Nov 3, 2024	Drug DesignDrug Discovery	CodeCode Available	1
MAMMAL -- Molecular Aligned Multi-Modal Architecture and Language	Oct 28, 2024	Drug DiscoveryProperty Prediction	CodeCode Available	1
FoldMark: Protecting Protein Generative Models with Watermarking	Oct 27, 2024	Drug DiscoveryProtein Structure Prediction	CodeCode Available	1
Multi-view biomedical foundation models for molecule-target and property prediction	Oct 25, 2024	Drug Discoverymolecular representation	CodeCode Available	1
Publishing Neural Networks in Drug Discovery Might Compromise Training Data Privacy	Oct 22, 2024	Drug DiscoveryMolecular Property Prediction	CodeCode Available	1
QuickBind: A Light-Weight And Interpretable Molecular Docking Model	Oct 21, 2024	Drug DiscoveryMolecular Docking	CodeCode Available	1
FragNet: A Graph Neural Network for Molecular Property Prediction with Four Levels of Interpretability	Oct 16, 2024	Drug DiscoveryGraph Neural Network	CodeCode Available	1
KinDEL: DNA-Encoded Library Dataset for Kinase Inhibitors	Oct 11, 2024	Drug Discovery	CodeCode Available	1
DeepProtein: Deep Learning Library and Benchmark for Protein Sequence Learning	Oct 2, 2024	Deep LearningDrug Discovery	CodeCode Available	1
Enhancing Uncertainty Quantification in Drug Discovery with Censored Regression Labels	Sep 6, 2024	Drug Discoveryregression	CodeCode Available	1
Cell Morphology-Guided Small Molecule Generation with GFlowNets	Aug 9, 2024	Drug Discovery	CodeCode Available	1
Barlow Twins Deep Neural Network for Advanced 1D Drug-Target Interaction Prediction	Jul 31, 2024	Drug Discovery	CodeCode Available	1
Context-Guided Diffusion for Out-of-Distribution Molecular and Protein Design	Jul 16, 2024	Drug DiscoveryOut-of-Distribution Generalization	CodeCode Available	1
Vision Language Model is NOT All You Need: Augmentation Strategies for Molecule Language Models	Jul 12, 2024	AllDrug Discovery	CodeCode Available	1

Show:10 25 50

← PrevPage 2 of 27Next →

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