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 1–50 of 1337 papers

Title	Date	Tasks	Status	Hype
Assay2Mol: large language model-based drug design using BioAssay context	Jul 16, 2025	DescriptiveDrug Design	CodeCode Available	0
A Graph-in-Graph Learning Framework for Drug-Target Interaction Prediction	Jul 15, 2025	Drug DiscoveryGraph Learning	—Unverified	0
Graph Learning	Jul 8, 2025	Drug DiscoveryFairness	—Unverified	0
Exploring Modularity of Agentic Systems for Drug Discovery	Jun 27, 2025	Drug Discovery	—Unverified	0
Large Language Model Agent for Modular Task Execution in Drug Discovery	Jun 26, 2025	Drug DiscoveryLanguage Modeling	—Unverified	0
Diverse Mini-Batch Selection in Reinforcement Learning for Efficient Chemical Exploration in de novo Drug Design	Jun 26, 2025	Drug DesignDrug Discovery	—Unverified	0
A standard transformer and attention with linear biases for molecular conformer generation	Jun 24, 2025	Drug Discovery	—Unverified	0
PocketVina Enables Scalable and Highly Accurate Physically Valid Docking through Multi-Pocket Conditioning	Jun 24, 2025	BenchmarkingDrug Discovery	CodeCode Available	2
Context-Aware Scientific Knowledge Extraction on Linked Open Data using Large Language Models	Jun 21, 2025	Drug Discovery	—Unverified	0
Active Learning-Guided Seq2Seq Variational Autoencoder for Multi-target Inhibitor Generation	Jun 18, 2025	Active LearningDiversity	—Unverified	0
Q2SAR: A Quantum Multiple Kernel Learning Approach for Drug Discovery	Jun 17, 2025	BenchmarkingDrug Discovery	—Unverified	0
Reimagining Target-Aware Molecular Generation through Retrieval-Enhanced Aligned Diffusion	Jun 17, 2025	Drug DesignDrug Discovery	—Unverified	0
Exploring Non-contrastive Self-supervised Representation Learning for Image-based Profiling	Jun 17, 2025	Data AugmentationDrug Discovery	—Unverified	0
Bures-Wasserstein Flow Matching for Graph Generation	Jun 16, 2025	3D Molecule GenerationDrug Discovery	—Unverified	0
Learning Causality for Modern Machine Learning	Jun 13, 2025	Drug Discovery	—Unverified	0
Robust Molecular Property Prediction via Densifying Scarce Labeled Data	Jun 13, 2025	Drug DiscoveryMeta-Learning	CodeCode Available	0
Fast Bayesian Optimization of Function Networks with Partial Evaluations	Jun 13, 2025	Bayesian OptimizationDrug Discovery	CodeCode Available	0
Generalization Analysis for Bayesian Optimal Experiment Design under Model Misspecification	Jun 9, 2025	Drug DiscoveryExperimental Design	—Unverified	0
CaliciBoost: Performance-Driven Evaluation of Molecular Representations for Caco-2 Permeability Prediction	Jun 9, 2025	AutoMLDiversity	—Unverified	0
Graph Neural Networks in Modern AI-aided Drug Discovery	Jun 7, 2025	Drug Discoverygraph construction	—Unverified	0
AANet: Virtual Screening under Structural Uncertainty via Alignment and Aggregation	Jun 6, 2025	Contrastive LearningDrug Discovery	—Unverified	0
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
Latent Guided Sampling for Combinatorial Optimization	Jun 4, 2025	Combinatorial OptimizationDrug Discovery	CodeCode Available	0
STELLA: Towards Protein Function Prediction with Multimodal LLMs Integrating Sequence-Structure Representations	Jun 4, 2025	Drug DiscoveryGeneral Knowledge	—Unverified	0
AUTOCT: Automating Interpretable Clinical Trial Prediction with LLM Agents	Jun 4, 2025	Drug DiscoveryPrediction	—Unverified	0
How Explanations Leak the Decision Logic: Stealing Graph Neural Networks via Explanation Alignment	Jun 3, 2025	Data AugmentationDrug Discovery	CodeCode Available	0
Recent Developments in GNNs for Drug Discovery	Jun 2, 2025	Drug DiscoveryMolecular Property Prediction	—Unverified	0
SOC-DGL: Social Interaction Behavior Inspired Dual Graph Learning Framework for Drug-Target Interaction Identification	Jun 2, 2025	Drug DiscoveryGraph Learning	CodeCode Available	0
Bridging Quantum and Classical Computing in Drug Design: Architecture Principles for Improved Molecule Generation	Jun 1, 2025	Bayesian OptimizationDrug Design	CodeCode Available	0
Enhancing Drug Discovery: Autoencoder-Based Latent Space Augmentation for Improved Molecular Solubility Prediction using LatMixSol	May 30, 2025	Drug DiscoveryFeature Compression	—Unverified	0
Aligning Protein Conformation Ensemble Generation with Physical Feedback	May 30, 2025	DenoisingDrug Discovery	—Unverified	0
DistMLIP: A Distributed Inference Platform for Machine Learning Interatomic Potentials	May 28, 2025	Drug Discoverygraph partitioning	CodeCode Available	2
RAGPPI: RAG Benchmark for Protein-Protein Interactions in Drug Discovery	May 28, 2025	Drug DiscoveryRAG	CodeCode Available	0
B-XAIC Dataset: Benchmarking Explainable AI for Graph Neural Networks Using Chemical Data	May 28, 2025	BenchmarkingDrug Discovery	CodeCode Available	0
A Graph Completion Method that Jointly Predicts Geometry and Topology Enables Effective Molecule Assembly	May 27, 2025	DenoisingDrug Design	—Unverified	0
Beyond Simple Concatenation: Fairly Assessing PLM Architectures for Multi-Chain Protein-Protein Interactions Prediction	May 26, 2025	Drug Discovery	—Unverified	0
Transformers in Protein: A Survey	May 26, 2025	BenchmarkingDrug Discovery	—Unverified	0
Chemical classification program synthesis using generative artificial intelligence	May 24, 2025	ClassificationDrug Discovery	—Unverified	0
Conformal Prediction for Uncertainty Estimation in Drug-Target Interaction Prediction	May 24, 2025	ClusteringConformal Prediction	—Unverified	0
Applications of Modular Co-Design for De Novo 3D Molecule Generation	May 23, 2025	3D Molecule GenerationDenoising	—Unverified	0
XMolCap: Advancing Molecular Captioning through Multimodal Fusion and Explainable Graph Neural Networks	May 23, 2025	Drug DiscoveryMolecule Captioning	CodeCode Available	0
Can Large Language Models Design Biological Weapons? Evaluating Moremi Bio	May 22, 2025	Drug Discovery	—Unverified	0
Beyond Correlation: Towards Causal Large Language Model Agents in Biomedicine	May 22, 2025	Causal InferenceDrug Discovery	—Unverified	0
iBitter-Stack: A Multi-Representation Ensemble Learning Model for Accurate Bitter Peptide Identification	May 21, 2025	Drug DiscoveryEnsemble Learning	CodeCode Available	0
Multi-omic Causal Discovery using Genotypes and Gene Expression	May 21, 2025	Causal DiscoveryDrug Discovery	—Unverified	0
DrugPilot: LLM-based Parameterized Reasoning Agent for Drug Discovery	May 20, 2025	Drug Discovery	CodeCode Available	1
Virtual Cells: Predict, Explain, Discover	May 20, 2025	Drug Discovery	—Unverified	0
A Comprehensive Benchmarking Platform for Deep Generative Models in Molecular Design	May 19, 2025	BenchmarkingDrug Discovery	—Unverified	0
Active Learning on Synthons for Molecular Design	May 19, 2025	Active LearningDiversity	—Unverified	0

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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