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 451–500 of 1337 papers

Title	Date	Tasks	Status
Efficient and Scalable Batch Bayesian Optimization Using K-Means	Jun 4, 2018	Bayesian Optimizationcompressed sensing	—Unverified
Efficient Biological Data Acquisition through Inference Set Design	Oct 25, 2024	Active LearningDrug Discovery	—Unverified
Efficient Fine-Tuning of Single-Cell Foundation Models Enables Zero-Shot Molecular Perturbation Prediction	Dec 18, 2024	Drug DiscoveryZero-shot Generalization	—Unverified
Efficient Nonmyopic Active Search	Aug 1, 2017	Active LearningDrug Discovery	—Unverified
Beyond Simple Concatenation: Fairly Assessing PLM Architectures for Multi-Chain Protein-Protein Interactions Prediction	May 26, 2025	Drug Discovery	—Unverified
Discrimination vs. Generation: The Machine Learning Dichotomy for Dopaminergic Hit Discovery	Sep 19, 2024	Drug Discovery	—Unverified
A Deep Subgrouping Framework for Precision Drug Repurposing via Emulating Clinical Trials on Real-world Patient Data	Dec 29, 2024	Drug Discovery	—Unverified
Embracing assay heterogeneity with neural processes for markedly improved bioactivity predictions	Aug 17, 2023	Drug DiscoveryMeta-Learning	—Unverified
0/1 Deep Neural Networks via Block Coordinate Descent	Jun 19, 2022	10-shot image generation	—Unverified
Emerging Opportunities of Using Large Language Models for Translation Between Drug Molecules and Indications	Feb 14, 2024	Drug DiscoveryLanguage Modelling	—Unverified
Can LLMs Generate Diverse Molecules? Towards Alignment with Structural Diversity	Oct 4, 2024	DiversityDrug Discovery	—Unverified
Towards Unified AI Drug Discovery with Multiple Knowledge Modalities	Apr 17, 2023	Drug DiscoveryKnowledge Graphs	—Unverified
Discovering intrinsic multi-compartment pharmacometric models using Physics Informed Neural Networks	Apr 30, 2024	Drug DiscoveryModel Discovery	—Unverified
Beyond Correlation: Towards Causal Large Language Model Agents in Biomedicine	May 22, 2025	Causal InferenceDrug Discovery	—Unverified
Enabling Regional Explainability by Automatic and Model-agnostic Rule Extraction	Jun 25, 2024	Drug Discovery	—Unverified
An Energy-Adaptive Elastic Equivariant Transformer Framework for Protein Structure Representation	Mar 21, 2025	Drug DiscoveryRepresentation Learning	—Unverified
Accurate, reliable and interpretable solubility prediction of druglike molecules with attention pooling and Bayesian learning	Sep 29, 2022	Bayesian InferenceDecision Making	—Unverified
EndToEndML: An Open-Source End-to-End Pipeline for Machine Learning Applications	Mar 27, 2024	Drug Discovery	—Unverified
CASTELO: Clustered Atom Subtypes aidEd Lead Optimization -- a combined machine learning and molecular modeling method	Nov 27, 2020	BIG-bench Machine LearningClustering	—Unverified
Energy-based Generative Models for Target-specific Drug Discovery	Dec 5, 2022	Drug Discovery	—Unverified
Direct Generation of Protein Conformational Ensembles via Machine Learning	Jun 19, 2022	BIG-bench Machine LearningBiomedical Information Retrieval	—Unverified
Diffusion Models in De Novo Drug Design	Jun 7, 2024	Computational chemistryDenoising	—Unverified
Enhancing Chemical Reaction and Retrosynthesis Prediction with Large Language Model and Dual-task Learning	May 5, 2025	Drug DesignDrug Discovery	—Unverified
Enhancing Drug Discovery: Autoencoder-Based Latent Space Augmentation for Improved Molecular Solubility Prediction using LatMixSol	May 30, 2025	Drug DiscoveryFeature Compression	—Unverified
BERT Learns (and Teaches) Chemistry	Jul 11, 2020	Drug Discovery	—Unverified
Enhancing Few-Shot Learning with Integrated Data and GAN Model Approaches	Nov 25, 2024	Data AugmentationDrug Discovery	—Unverified
Enhancing Model Learning and Interpretation Using Multiple Molecular Graph Representations for Compound Property and Activity Prediction	Apr 13, 2023	Activity PredictionDrug Discovery	—Unverified
Enhancing Molecular Design through Graph-based Topological Reinforcement Learning	Nov 22, 2024	Drug DesignDrug Discovery	—Unverified
DiffNMR2: NMR Guided Sampling Acquisition Through Diffusion Model Uncertainty	Feb 6, 2025	Drug Discovery	—Unverified
Benchmarking Toxic Molecule Classification using Graph Neural Networks and Few Shot Learning	Nov 22, 2023	BenchmarkingDrug Discovery	—Unverified
DiffEx: Explaining a Classifier with Diffusion Models to Identify Microscopic Cellular Variations	Feb 12, 2025	Drug Discovery	—Unverified
Ensembling classification models based on phalanxes of variables with applications in drug discovery	Mar 20, 2013	Computational chemistryDrug Discovery	—Unverified
Data-centric challenges with the application and adoption of artificial intelligence for drug discovery	Jul 6, 2024	Drug DiscoveryUncertainty Quantification	—Unverified
Differential protein expression and peak selection in mass spectrometry data by binary discriminant analysis	May 27, 2015	Drug Discovery	—Unverified
Benchmarking AlphaFold3's protein-protein complex accuracy and machine learning prediction reliability for binding free energy changes upon mutation	Jun 6, 2024	BenchmarkingDrug Discovery	—Unverified
An Empirical Study of the Effectiveness of Using a Replay Buffer on Mode Discovery in GFlowNets	Jul 15, 2023	Drug DiscoveryReinforcement Learning (RL)	—Unverified
From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering	Jan 5, 2025	DenoisingDrug Discovery	—Unverified
G^3: Representation Learning and Generation for Geometric Graphs	Sep 29, 2021	Drug DiscoveryMolecular Property Prediction	—Unverified
Equivariant Graph Attention Networks for Molecular Property Prediction	Feb 20, 2022	Drug DiscoveryGraph Attention	—Unverified
Generative chemistry: drug discovery with deep learning generative models	Aug 20, 2020	Deep LearningDrug Discovery	—Unverified
An Equivariant Pretrained Transformer for Unified 3D Molecular Representation Learning	Feb 20, 2024	DenoisingDrug Discovery	—Unverified
Differential Privacy-Driven Framework for Enhancing Heart Disease Prediction	Apr 25, 2025	Decision MakingDisease Prediction	—Unverified
BEACON: A Bayesian Optimization Strategy for Novelty Search in Expensive Black-Box Systems	Jun 5, 2024	Bayesian OptimizationDrug Discovery	—Unverified
Differentiable Scaffolding Tree for Molecule Optimization	Sep 29, 2021	Combinatorial OptimizationDrug Discovery	—Unverified
Differentiable Scaffolding Tree for Molecular Optimization	Sep 22, 2021	Combinatorial OptimizationDrug Discovery	—Unverified
Bayesian semi-supervised learning for uncertainty-calibrated prediction of molecular properties and active learning	Feb 3, 2019	Active LearningDrug Discovery	—Unverified
Diameter-based Interactive Structure Discovery	Jun 5, 2019	Active LearningDrug Discovery	—Unverified
Chem42: a Family of chemical Language Models for Target-aware Ligand Generation	Mar 20, 2025	Drug DiscoveryProperty Prediction	—Unverified
Anchoring to Exemplars for Training Mixture-of-Expert Cell Embeddings	Dec 6, 2021	Drug DiscoveryGPU	—Unverified
A deep-learning view of chemical space designed to facilitate drug discovery	Feb 7, 2020	Design SynthesisDrug Discovery	—Unverified

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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