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 801–850 of 1337 papers

Title	Date	Tasks	Status
Offline Stochastic Optimization of Black-Box Objective Functions	Dec 3, 2024	Drug DiscoveryStochastic Optimization	—Unverified
On Divergence Measures for Training GFlowNets	Oct 12, 2024	Causal DiscoveryDrug Discovery	—Unverified
On How AI Needs to Change to Advance the Science of Drug Discovery	Dec 23, 2022	Drug DiscoveryProtein Structure Prediction	—Unverified
On Machine Learning Approaches for Protein-Ligand Binding Affinity Prediction	Jul 15, 2024	Active LearningBenchmarking	—Unverified
On the Adversarial Robustness of Benjamini Hochberg	Jan 6, 2025	Adversarial RobustnessAnomaly Detection	—Unverified
On the Scalability of GNNs for Molecular Graphs	Apr 17, 2024	DiversityDrug Discovery	—Unverified
On the String Kernel Pre-Image Problem with Applications in Drug Discovery	Dec 3, 2014	Combinatorial OptimizationDrug Discovery	—Unverified
Open Source Infrastructure for Automatic Cell Segmentation	Sep 12, 2024	Cell SegmentationDrug Discovery	—Unverified
Optimal compound downselection to promote diversity and parallel chemistry	Mar 17, 2025	Decision MakingDiversity	—Unverified
Optimal Decision Making in High-Throughput Virtual Screening Pipelines	Sep 23, 2021	Decision MakingDrug Discovery	—Unverified
Optimally Weighted Ensembles of Regression Models: Exact Weight Optimization and Applications	Jun 22, 2022	Drug DiscoveryModel Selection	—Unverified
Optimistic Games for Combinatorial Bayesian Optimization with Application to Protein Design	Sep 27, 2024	Bayesian OptimizationDrug Discovery	—Unverified
Optimizing Drug Design by Merging Generative AI With Active Learning Frameworks	May 4, 2023	Active LearningDrug Design	—Unverified
OWPCP: A Deep Learning Model to Predict Octanol-Water Partition Coefficient	Oct 10, 2024	Drug DiscoveryHyperparameter Optimization	—Unverified
What Do LLMs Need to Understand Graphs: A Survey of Parametric Representation of Graphs	Oct 16, 2024	Drug DiscoveryGraph Generation	—Unverified
PEMP: Leveraging Physics Properties to Enhance Molecular Property Prediction	Oct 18, 2022	Drug DiscoveryMolecular Property Prediction	—Unverified
PepGB: Facilitating peptide drug discovery via graph neural networks	Jan 26, 2024	Contrastive LearningDrug Discovery	—Unverified
Performance Analysis Of Neural Network Models For Oxazolines And Oxazoles Derivatives Descriptor Dataset	Dec 10, 2013	Drug DiscoveryMedical Diagnosis	—Unverified
Performance Heterogeneity in Graph Neural Networks: Lessons for Architecture Design and Preprocessing	Mar 1, 2025	Drug DiscoveryGraph Classification	—Unverified
PharmacoMatch: Efficient 3D Pharmacophore Screening via Neural Subgraph Matching	Sep 10, 2024	Contrastive LearningDrug Discovery	—Unverified
Pharmacophore-Conditioned Diffusion Model for Ligand-Based De Novo Drug Design	May 15, 2025	Drug DesignDrug Discovery	—Unverified
Pharmacophore-guided de novo drug design with diffusion bridge	Dec 10, 2024	Drug DesignDrug Discovery	—Unverified
PharmAgents: Building a Virtual Pharma with Large Language Model Agents	Mar 28, 2025	Drug DiscoveryLanguage Modeling	—Unverified
PhenoProfiler: Advancing Phenotypic Learning for Image-based Drug Discovery	Feb 26, 2025	Drug DiscoveryRepresentation Learning	—Unverified
Phenotypic Profiling of High Throughput Imaging Screens with Generic Deep Convolutional Features	Mar 15, 2019	ClusteringDrug Discovery	—Unverified
Physical formula enhanced multi-task learning for pharmacokinetics prediction	Apr 16, 2024	Drug DiscoveryMulti-Task Learning	—Unverified
PILOT: Equivariant diffusion for pocket conditioned de novo ligand generation with multi-objective guidance via importance sampling	May 23, 2024	Drug DesignDrug Discovery	—Unverified
POINT: a web-based platform for pharmacological investigation enhanced by multi-omics networks and knowledge graphs	Mar 10, 2025	Drug DiscoveryKnowledge Graphs	—Unverified
PopED lite: an optimal design software for preclinical pharmacokinetic and pharmacodynamic studies	May 25, 2015	Drug DiscoveryExperimental Design	—Unverified
Position Specific Scoring Is All You Need? Revisiting Protein Sequence Classification Tasks	Oct 16, 2024	AllDrug Discovery	—Unverified
PotentialNet for Molecular Property Prediction	Mar 12, 2018	ARCBIG-bench Machine Learning	—Unverified
Powerful, transferable representations for molecules through intelligent task selection in deep multitask networks	Sep 17, 2018	Drug DiscoveryMulti-Task Learning	—Unverified
Predicting drug properties with parameter-free machine learning: Pareto-Optimal Embedded Modeling (POEM)	Feb 11, 2020	BIG-bench Machine LearningDrug Discovery	—Unverified
KGML-xDTD: A Knowledge Graph-based Machine Learning Framework for Drug Treatment Prediction and Mechanism Description	Nov 30, 2022	Drug Discovery	—Unverified
Predicting gene essentiality and drug response from perturbation screens in preclinical cancer models with LEAP: Layered Ensemble of Autoencoders and Predictors	Feb 21, 2025	Drug Discovery	—Unverified
Predicting Molecule-Target Interaction by Learning Biomedical Network and Molecule Representations	Feb 2, 2023	Drug DiscoveryGraph Neural Network	—Unverified
Predicting Nanoparticle Effects on Small Biomolecule Functionalities Using the Capability of Scikit-learn and PyTorch: A Case Study on Inhibitors of the DNA Damage-Inducible Transcript 3 (CHOP)	Apr 13, 2025	Drug Discovery	—Unverified
A Knowledge Graph-Enhanced Tensor Factorisation Model for Discovering Drug Targets	May 20, 2021	BIG-bench Machine LearningDrug Discovery	—Unverified
Predicting RNA-small molecule binding sites by 3D structure	Oct 29, 2023	Drug Discovery	—Unverified
Prediction of Binding Affinity for ErbB Inhibitors Using Deep Neural Network Model with Morgan Fingerprints as Features	Jan 9, 2025	Drug Discovery	—Unverified
Preferential Multi-Objective Bayesian Optimization for Drug Discovery	Mar 21, 2025	Bayesian OptimizationDrug Discovery	—Unverified
Pre-trained Molecular Language Models with Random Functional Group Masking	Nov 3, 2024	Computational chemistryDrug Discovery	—Unverified
Pre-Training on Large-Scale Generated Docking Conformations with HelixDock to Unlock the Potential of Protein-ligand Structure Prediction Models	Oct 21, 2023	CPUDrug Discovery	—Unverified
Pre-training Transformers for Molecular Property Prediction Using Reaction Prediction	Jul 6, 2022	Drug DiscoveryMolecular Property Prediction	—Unverified
Pre-training with Fractional Denoising to Enhance Molecular Property Prediction	Jul 14, 2024	DenoisingDrug Discovery	—Unverified
ProNet DB: A proteome-wise database for protein surface property representations and RNA-binding profiles	May 16, 2022	Drug Discovery	—Unverified
Property-Aware Relation Networks for Few-Shot Molecular Property Prediction	Jul 16, 2021	Drug DiscoveryGraph Learning	—Unverified
Protecting Genomic Privacy by a Sequence-Similarity Based Obfuscation Method	Aug 8, 2017	Drug Discovery	—Unverified
Protein Language Model-Powered 3D Ligand Binding Site Prediction from Protein Sequence	Dec 5, 2023	Drug DiscoveryGraph Neural Network	—Unverified
Protein-ligand binding representation learning from fine-grained interactions	Nov 9, 2023	Drug DiscoveryPrediction	—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