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 501–550 of 1337 papers

Title	Date	Tasks	Status	Score
ChemBO: Bayesian Optimization of Small Organic Molecules with Synthesizable Recommendations	Aug 5, 2019	Bayesian OptimizationDrug Discovery	CodeCode Available	5
Advancing Drug Discovery with Enhanced Chemical Understanding via Asymmetric Contrastive Multimodal Learning	Nov 11, 2023	Contrastive LearningDrug Discovery	CodeCode Available	5
Learning Hierarchical Interaction for Accurate Molecular Property Prediction	Apr 28, 2025	Drug DiscoveryMolecular Property Prediction	CodeCode Available	5
Constrained Multi-objective Bayesian Optimization through Optimistic Constraints Estimation	Nov 6, 2024	Active LearningBayesian Optimization	CodeCode Available	5
JAX MD: End-to-End Differentiable, Hardware Accelerated, Molecular Dynamics in Pure Python	Sep 25, 2019	BIG-bench Machine LearningCPU	CodeCode Available	5
Confidence on the Focal: Conformal Prediction with Selection-Conditional Coverage	Mar 6, 2024	Conformal PredictionDrug Discovery	CodeCode Available	5
Integration of Genetic Algorithms and Deep Learning for the Generation and Bioactivity Prediction of Novel Tyrosine Kinase Inhibitors	Aug 13, 2024	Deep LearningDrug Discovery	CodeCode Available	5
Transferable Graph Neural Fingerprint Models for Quick Response to Future Bio-Threats	Jul 17, 2023	Drug DiscoveryMolecular Docking	CodeCode Available	5
Accelerating Drug Safety Assessment using Bidirectional-LSTM for SMILES Data	Jul 8, 2024	Drug Discovery	CodeCode Available	5
Conditional Prediction ROC Bands for Graph Classification	Oct 20, 2024	ClassificationDrug Discovery	CodeCode Available	5
Integrating convolutional layers and biformer network with forward-forward and backpropagation training	Feb 28, 2025	Computational chemistryDrug Discovery	CodeCode Available	5
Interpretable Deep Learning in Drug Discovery	Mar 7, 2019	Deep LearningDrug Discovery	CodeCode Available	5
Injecting Domain Knowledge from Empirical Interatomic Potentials to Neural Networks for Predicting Material Properties	Oct 14, 2022	Drug DiscoveryTransfer Learning	CodeCode Available	5
Improving Molecular Pretraining with Complementary Featurizations	Sep 29, 2022	Computational chemistryDrug Discovery	CodeCode Available	5
A Latent Diffusion Model for Protein Structure Generation	May 6, 2023	Drug Discoverymodel	CodeCode Available	5
Independent Vector Analysis for Data Fusion Prior to Molecular Property Prediction with Machine Learning	Nov 1, 2018	BIG-bench Machine LearningDrug Discovery	CodeCode Available	5
COMRECGC: Global Graph Counterfactual Explainer through Common Recourse	May 11, 2025	Binary Classificationcounterfactual	CodeCode Available	5
Improved antibody structure prediction by deep learning of side chain conformations	Sep 22, 2021	Deep LearningDrug Discovery	CodeCode Available	5
Improving Compound Activity Classification via Deep Transfer and Representation Learning	Nov 14, 2021	Drug DiscoveryRepresentation Learning	CodeCode Available	5
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	5
How Explanations Leak the Decision Logic: Stealing Graph Neural Networks via Explanation Alignment	Jun 3, 2025	Data AugmentationDrug Discovery	CodeCode Available	5
Hyperbolic Benchmarking Unveils Network Topology-Feature Relationship in GNN Performance	Jun 4, 2024	BenchmarkingDrug Discovery	CodeCode Available	5
iBitter-Stack: A Multi-Representation Ensemble Learning Model for Accurate Bitter Peptide Identification	May 21, 2025	Drug DiscoveryEnsemble Learning	CodeCode Available	5
Assay2Mol: large language model-based drug design using BioAssay context	Jul 16, 2025	DescriptiveDrug Design	CodeCode Available	5
Heter-LP: A heterogeneous label propagation algorithm and its application in drug repositioning	Nov 8, 2016	Data IntegrationDrug Discovery	CodeCode Available	5
Guided Multi-objective Generative AI to Enhance Structure-based Drug Design	May 20, 2024	Drug DesignDrug Discovery	CodeCode Available	5
ComENet: Towards Complete and Efficient Message Passing for 3D Molecular Graphs	Jun 17, 2022	Drug DiscoveryGraph Neural Network	CodeCode Available	5
GraPPI: A Retrieve-Divide-Solve GraphRAG Framework for Large-scale Protein-protein Interaction Exploration	Jan 24, 2025	Drug DiscoveryRAG	CodeCode Available	5
GSHOT: Few-shot Generative Modeling of Labeled Graphs	Jun 6, 2023	Drug DiscoveryFew-Shot Learning	CodeCode Available	5
De Novo Generation of Hit-like Molecules from Gene Expression Profiles via Deep Learning	Dec 27, 2024	Drug Discoveryvalid	CodeCode Available	5
GraphVF: Controllable Protein-Specific 3D Molecule Generation with Variational Flow	Feb 23, 2023	3D geometry3D Molecule Generation	CodeCode Available	5
FMint: Bridging Human Designed and Data Pretrained Models for Differential Equation Foundation Model	Apr 23, 2024	Drug DiscoveryIn-Context Learning	CodeCode Available	5
GraphDTA: prediction of drug–target binding affinity using graph convolutional networks	Jul 2, 2019	Deep LearningDrug Discovery	CodeCode Available	5
A Self-feedback Knowledge Elicitation Approach for Chemical Reaction Predictions	Apr 15, 2024	Chemical Reaction PredictionDrug Discovery	CodeCode Available	5
Implementation and Application of an Intelligibility Protocol for Interaction with an LLM	Oct 27, 2024	Drug DiscoveryLarge Language Model	CodeCode Available	5
GLADMamba: Unsupervised Graph-Level Anomaly Detection Powered by Selective State Space Model	Mar 23, 2025	Anomaly DetectionDrug Discovery	CodeCode Available	5
FlexMol: A Flexible Toolkit for Benchmarking Molecular Relational Learning	Oct 19, 2024	BenchmarkingDrug Discovery	CodeCode Available	5
GGL-PPI: Geometric Graph Learning to Predict Mutation-Induced Binding Free Energy Changes	Sep 23, 2023	Drug DesignDrug Discovery	CodeCode Available	5
FIMBA: Evaluating the Robustness of AI in Genomics via Feature Importance Adversarial Attacks	Jan 19, 2024	Decision MakingDrug Discovery	CodeCode Available	5
Grad-CAMO: Learning Interpretable Single-Cell Morphological Profiles from 3D Cell Painting Images	Mar 26, 2024	Drug DiscoveryRepresentation Learning	CodeCode Available	5
Few-shot link prediction via graph neural networks for Covid-19 drug-repurposing	Jul 20, 2020	Drug DiscoveryFew-Shot Learning	CodeCode Available	5
Few-shot Conformal Prediction with Auxiliary Tasks	Feb 17, 2021	Computational chemistryConformal Prediction	CodeCode Available	5
Federated Learning in Chemical Engineering: A Tutorial on a Framework for Privacy-Preserving Collaboration Across Distributed Data Sources	Nov 23, 2024	Data IntegrationDrug Discovery	CodeCode Available	5
CoarsenConf: Equivariant Coarsening with Aggregated Attention for Molecular Conformer Generation	Jun 26, 2023	Drug DiscoveryProperty Prediction	CodeCode Available	5
Faster Lead Optimization Mapper Algorithm for Large-Scale Relative Free Energy Perturbation	Apr 10, 2023	Drug Discovery	CodeCode Available	5
Physics-informed generative real-time lens-free imaging	Mar 12, 2024	Drug DiscoveryImage Reconstruction	CodeCode Available	5
ShennongAlpha: an AI-driven sharing and collaboration platform for intelligent curation, acquisition, and translation of natural medicinal material knowledge	Dec 27, 2023	Drug DiscoveryMachine Translation	CodeCode Available	5
Fast Direct: Query-Efficient Online Black-box Guidance for Diffusion-model Target Generation	Feb 2, 2025	Drug DiscoveryImage Generation	CodeCode Available	5
Fast Bayesian Optimization of Function Networks with Partial Evaluations	Jun 13, 2025	Bayesian OptimizationDrug Discovery	CodeCode Available	5
CLDR: Contrastive Learning Drug Response Models from Natural Language Supervision	Dec 17, 2023	Common Sense ReasoningContrastive Learning	CodeCode Available	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