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 1201–1250 of 1337 papers

Title	Date	Tasks	Status
GraPPI: A Retrieve-Divide-Solve GraphRAG Framework for Large-scale Protein-protein Interaction Exploration	Jan 24, 2025	Drug DiscoveryRAG	CodeCode Available
Reinforcement Learning for Molecular Dynamics Optimization: A Stochastic Pontryagin Maximum Principle Approach	Dec 6, 2022	Decision MakingDrug Discovery	CodeCode Available
An Overview of Multi-Task Learning in Deep Neural Networks	Jun 15, 2017	BIG-bench Machine LearningDrug Discovery	CodeCode Available
GraphVF: Controllable Protein-Specific 3D Molecule Generation with Variational Flow	Feb 23, 2023	3D geometry3D Molecule Generation	CodeCode Available
MolecularRNN: Generating realistic molecular graphs with optimized properties	May 31, 2019	Drug DiscoveryMolecular Graph Generation	CodeCode Available
Molecular Sets (MOSES): A Benchmarking Platform for Molecular Generation Models	Nov 29, 2018	BenchmarkingDiversity	CodeCode Available
GraphDTA: prediction of drug–target binding affinity using graph convolutional networks	Jul 2, 2019	Deep LearningDrug Discovery	CodeCode Available
MoleculeCLA: Rethinking Molecular Benchmark via Computational Ligand-Target Binding Analysis	Jun 13, 2024	Drug DiscoveryMolecular Property Prediction	CodeCode Available
GRAN is superior to GraphRNN: node orderings, kernel- and graph embeddings-based metrics for graph generators	Jul 13, 2023	Drug DiscoveryGraph Embedding	CodeCode Available
Grad-CAMO: Learning Interpretable Single-Cell Morphological Profiles from 3D Cell Painting Images	Mar 26, 2024	Drug DiscoveryRepresentation Learning	CodeCode Available
BridgeDPI: A Novel Graph Neural Network for Predicting Drug-Protein Interactions	Jan 29, 2021	Drug DiscoveryGraph Neural Network	CodeCode Available
Accelerating Prototype-Based Drug Discovery using Conditional Diversity Networks	Apr 8, 2018	DiversityDrug Discovery	CodeCode Available
GLADMamba: Unsupervised Graph-Level Anomaly Detection Powered by Selective State Space Model	Mar 23, 2025	Anomaly DetectionDrug Discovery	CodeCode Available
GGL-PPI: Geometric Graph Learning to Predict Mutation-Induced Binding Free Energy Changes	Sep 23, 2023	Drug DesignDrug Discovery	CodeCode Available
Therapeutic target discovery using Boolean network attractors: improvements of kali	Nov 10, 2016	Drug Discovery	CodeCode Available
Physics-informed generative real-time lens-free imaging	Mar 12, 2024	Drug DiscoveryImage Reconstruction	CodeCode Available
Molecule Property Prediction Based on Spatial Graph Embedding	Aug 22, 2019	Drug DiscoveryGraph Embedding	CodeCode Available
Spline refinement with differentiable rendering	Mar 15, 2025	Drug Discovery	CodeCode Available
BoKDiff: Best-of-K Diffusion Alignment for Target-Specific 3D Molecule Generation	Jan 26, 2025	3D Molecule GenerationDrug Design	CodeCode Available
Deep Inverse Reinforcement Learning for Structural Evolution of Small Molecules	Jul 24, 2020	Drug DiscoveryGenerative Adversarial Network	CodeCode Available
Stacked Ensemble Machine Learning for Range-Separation Parameters	Sep 24, 2021	DiversityDrug Discovery	CodeCode Available
RAGPPI: RAG Benchmark for Protein-Protein Interactions in Drug Discovery	May 28, 2025	Drug DiscoveryRAG	CodeCode Available
From Theory to Therapy: Reframing SBDD Model Evaluation via Practical Metrics	Jun 13, 2024	Drug DesignDrug Discovery	CodeCode Available
Unveiling Molecular Moieties through Hierarchical Grad-CAM Graph Explainability	Jan 29, 2024	Drug DiscoveryExplainable artificial intelligence	CodeCode Available
From Abstract to Actionable: Pairwise Shapley Values for Explainable AI	Feb 18, 2025	Drug DiscoveryFairness	CodeCode Available
The Role of Model Architecture and Scale in Predicting Molecular Properties: Insights from Fine-Tuning RoBERTa, BART, and LLaMA	May 2, 2024	BenchmarkingDrug Discovery	CodeCode Available
Fréchet ChemNet Distance: A metric for generative models for molecules in drug discovery	Mar 26, 2018	Drug DesignDrug Discovery	CodeCode Available
FMint: Bridging Human Designed and Data Pretrained Models for Differential Equation Foundation Model	Apr 23, 2024	Drug DiscoveryIn-Context Learning	CodeCode Available
MUBen: Benchmarking the Uncertainty of Molecular Representation Models	Jun 14, 2023	BenchmarkingDrug Discovery	CodeCode Available
ReactEmbed: A Cross-Domain Framework for Protein-Molecule Representation Learning via Biochemical Reaction Networks	Jan 30, 2025	Contrastive LearningDrug Discovery	CodeCode Available
Blend the Separated: Mixture of Synergistic Experts for Data-Scarcity Drug-Target Interaction Prediction	Mar 20, 2025	Drug Discovery	CodeCode Available
An open unified deep graph learning framework for discovering drug leads	Dec 6, 2022	BenchmarkingDrug Discovery	CodeCode Available
BioAct-Het: A Heterogeneous Siamese Neural Network for Bioactivity Prediction Using Novel Bioactivity Representatio	Oct 15, 2023	Drug DiscoveryMeta-Learning	CodeCode Available
A generalized method toward drug-target interaction prediction via low-rank matrix projection	Jun 6, 2017	BIG-bench Machine LearningDrug Discovery	CodeCode Available
Multi-Fidelity Cost-Aware Bayesian Optimization	Nov 4, 2022	Bayesian OptimizationDrug Discovery	CodeCode Available
AGATHA: Automatic Graph-mining And Transformer based Hypothesis generation Approach	Feb 13, 2020	Drug DiscoveryGraph Mining	CodeCode Available
Recursive Tree Grammar Autoencoders	Dec 3, 2020	DecoderDrug Discovery	CodeCode Available
Bayesian neural network with pretrained protein embedding enhances prediction accuracy of drug-protein interaction	Dec 15, 2020	Bayesian InferenceDeep Learning	CodeCode Available
Unveiling Molecular Secrets: An LLM-Augmented Linear Model for Explainable and Calibratable Molecular Property Prediction	Oct 11, 2024	CPUDimensionality Reduction	CodeCode Available
FlexMol: A Flexible Toolkit for Benchmarking Molecular Relational Learning	Oct 19, 2024	BenchmarkingDrug Discovery	CodeCode Available
Top-N: Equivariant set and graph generation without exchangeability	Oct 5, 2021	Drug DiscoveryGenerative Adversarial Network	CodeCode Available
FIMBA: Evaluating the Robustness of AI in Genomics via Feature Importance Adversarial Attacks	Jan 19, 2024	Decision MakingDrug Discovery	CodeCode Available
Few-shot link prediction via graph neural networks for Covid-19 drug-repurposing	Jul 20, 2020	Drug DiscoveryFew-Shot Learning	CodeCode Available
BatmanNet: Bi-branch Masked Graph Transformer Autoencoder for Molecular Representation	Nov 25, 2022	Drug DiscoveryMolecular Property Prediction	CodeCode Available
Study of Deep Generative Models for Inorganic Chemical Compositions	Oct 25, 2019	Drug DiscoveryImage Generation	CodeCode Available
Few-shot Conformal Prediction with Auxiliary Tasks	Feb 17, 2021	Computational chemistryConformal Prediction	CodeCode Available
DeepAtom: A Framework for Protein-Ligand Binding Affinity Prediction	Dec 1, 2019	Drug DesignDrug Discovery	CodeCode Available
Multiscale Topology in Interactomic Network: From Transcriptome to Antiaddiction Drug Repurposing	Dec 3, 2023	Drug DiscoveryTopological Data Analysis	CodeCode Available
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
BART: Bayesian additive regression trees	Jun 19, 2008	Causal InferenceDrug Discovery	CodeCode Available

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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