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 301–350 of 1337 papers

Title	Date	Tasks	Status	Hype
SynthFormer: Equivariant Pharmacophore-based Generation of Synthesizable Molecules for Ligand-Based Drug Design	Oct 3, 2024	Drug DesignDrug Discovery	—Unverified	0
MARS: A neurosymbolic approach for interpretable drug discovery	Oct 2, 2024	Drug Discovery	CodeCode Available	0
FARM: Functional Group-Aware Representations for Small Molecules	Oct 2, 2024	Contrastive LearningDrug Discovery	—Unverified	0
DeepProtein: Deep Learning Library and Benchmark for Protein Sequence Learning	Oct 2, 2024	Deep LearningDrug Discovery	CodeCode Available	1
Binding Affinity Prediction: From Conventional to Machine Learning-Based Approaches	Sep 30, 2024	Drug DesignDrug Discovery	—Unverified	0
FlexSBDD: Structure-Based Drug Design with Flexible Protein Modeling	Sep 29, 2024	Data AugmentationDrug Design	—Unverified	0
Enhancing Robustness of Graph Neural Networks through p-Laplacian	Sep 27, 2024	Drug DiscoveryRecommendation Systems	—Unverified	0
Optimistic Games for Combinatorial Bayesian Optimization with Application to Protein Design	Sep 27, 2024	Bayesian OptimizationDrug Discovery	—Unverified	0
Quantum Machine Learning in Drug Discovery: Applications in Academia and Pharmaceutical Industries	Sep 24, 2024	Drug DiscoveryMolecular Property Prediction	—Unverified	0
SwiftDossier: Tailored Automatic Dossier for Drug Discovery with LLMs and Agents	Sep 24, 2024	Drug DiscoveryRAG	—Unverified	0
GATher: Graph Attention Based Predictions of Gene-Disease Links	Sep 23, 2024	Drug DiscoveryGraph Attention	—Unverified	0
Dumpling GNN: Hybrid GNN Enables Better ADC Payload Activity Prediction Based on Chemical Structure	Sep 23, 2024	Activity PredictionDrug Discovery	—Unverified	0
Protein-Mamba: Biological Mamba Models for Protein Function Prediction	Sep 22, 2024	Drug DiscoveryMamba	—Unverified	0
FineMolTex: Towards Fine-grained Molecular Graph-Text Pre-training	Sep 21, 2024	Drug Discoverymolecular representation	—Unverified	0
Analysis of Gene Regulatory Networks from Gene Expression Using Graph Neural Networks	Sep 20, 2024	Drug DiscoveryGraph Attention	CodeCode Available	0
Discrimination vs. Generation: The Machine Learning Dichotomy for Dopaminergic Hit Discovery	Sep 19, 2024	Drug Discovery	—Unverified	0
Natural Language Processing Methods for the Study of Protein-Ligand Interactions	Sep 19, 2024	Drug Discovery	—Unverified	0
Self-Organizing Maps of Unbiased Ligand-Target Binding Pathways and Kinetics	Sep 19, 2024	Drug DesignDrug Discovery	—Unverified	0
Quantum-inspired Reinforcement Learning for Synthesizable Drug Design	Sep 13, 2024	Drug DesignDrug Discovery	—Unverified	0
XMOL: Explainable Multi-property Optimization of Molecules	Sep 12, 2024	Drug Discovery	—Unverified	0
Open Source Infrastructure for Automatic Cell Segmentation	Sep 12, 2024	Cell SegmentationDrug Discovery	—Unverified	0
A Perspective on AI-Guided Molecular Simulations in VR: Exploring Strategies for Imitation Learning in Hyperdimensional Molecular Systems	Sep 11, 2024	Drug DesignDrug Discovery	—Unverified	0
How Molecules Impact Cells: Unlocking Contrastive PhenoMolecular Retrieval	Sep 10, 2024	Contrastive LearningDrug Discovery	—Unverified	0
PharmacoMatch: Efficient 3D Pharmacophore Screening via Neural Subgraph Matching	Sep 10, 2024	Contrastive LearningDrug Discovery	—Unverified	0
Mapping Evolution of Molecules Across Biochemistry with Assembly Theory	Sep 9, 2024	Drug Discovery	—Unverified	0
CRADLE-VAE: Enhancing Single-Cell Gene Perturbation Modeling with Counterfactual Reasoning-based Artifact Disentanglement	Sep 9, 2024	counterfactualCounterfactual Reasoning	CodeCode Available	0
Machine Learning-Based Prediction of Key Genes Correlated to the Subretinal Lesion Severity in a Mouse Model of Age-Related Macular Degeneration	Sep 8, 2024	Dimensionality ReductionDrug Discovery	—Unverified	0
Unlocking Potential Binders: Multimodal Pretraining DEL-Fusion for Denoising DNA-Encoded Libraries	Sep 7, 2024	DenoisingDrug Discovery	—Unverified	0
Large Language Models in Drug Discovery and Development: From Disease Mechanisms to Clinical Trials	Sep 6, 2024	Drug Discovery	—Unverified	0
A Unified Approach to Inferring Chemical Compounds with the Desired Aqueous Solubility	Sep 6, 2024	Drug Discoveryregression	CodeCode Available	0
Enhancing Uncertainty Quantification in Drug Discovery with Censored Regression Labels	Sep 6, 2024	Drug Discoveryregression	CodeCode Available	1
MaskMol: Knowledge-guided Molecular Image Pre-Training Framework for Activity Cliffs	Sep 2, 2024	Drug DiscoveryRepresentation Learning	—Unverified	0
A Survey for Large Language Models in Biomedicine	Aug 29, 2024	DiagnosticDrug Discovery	—Unverified	0
S-MolSearch: 3D Semi-supervised Contrastive Learning for Bioactive Molecule Search	Aug 27, 2024	Contrastive LearningData Augmentation	—Unverified	0
HyperSBINN: A Hypernetwork-Enhanced Systems Biology-Informed Neural Network for Efficient Drug Cardiosafety Assessment	Aug 26, 2024	Drug DiscoveryMeta-Learning	—Unverified	0
Quantum-machine-assisted Drug Discovery: Survey and Perspective	Aug 24, 2024	Drug DesignDrug Discovery	—Unverified	0
DrugAgent: Multi-Agent Large Language Model-Based Reasoning for Drug-Target Interaction Prediction	Aug 23, 2024	AI AgentDrug Discovery	—Unverified	0
Data-Driven Parametrization of Molecular Mechanics Force Fields for Expansive Chemical Space Coverage	Aug 23, 2024	Computational EfficiencyDrug Discovery	CodeCode Available	2
Evaluation Framework for AI-driven Molecular Design of Multi-target Drugs: Brain Diseases as a Case Study	Aug 20, 2024	Drug DiscoveryEvolutionary Algorithms	CodeCode Available	0
BatGPT-Chem: A Foundation Large Model For Retrosynthesis Prediction	Aug 19, 2024	Drug DiscoveryLanguage Modelling	—Unverified	0
Learning Regularization for Graph Inverse Problems	Aug 19, 2024	Drug Discovery	—Unverified	0
Molecular Graph Representation Learning Integrating Large Language Models with Domain-specific Small Models	Aug 19, 2024	DescriptiveDrug Discovery	CodeCode Available	0
Advancements in Molecular Property Prediction: A Survey of Single and Multimodal Approaches	Aug 18, 2024	Drug DiscoveryMolecular Property Prediction	—Unverified	0
Fragment-Masked Diffusion for Molecular Optimization	Aug 17, 2024	Drug Discovery	—Unverified	0
Exploring Latent Space for Generating Peptide Analogs Using Protein Language Models	Aug 15, 2024	Drug Discovery	CodeCode Available	0
Protein Language Models and Machine Learning Facilitate the Identification of Antimicrobial Peptides	Aug 14, 2024	Binary ClassificationDrug Discovery	CodeCode Available	0
Drug Discovery SMILES-to-Pharmacokinetics Diffusion Models with Deep Molecular Understanding	Aug 14, 2024	Drug Discovery	CodeCode Available	0
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	0
SMILES-Mamba: Chemical Mamba Foundation Models for Drug ADMET Prediction	Aug 11, 2024	Drug DiscoveryMamba	—Unverified	0
Cell Morphology-Guided Small Molecule Generation with GFlowNets	Aug 9, 2024	Drug Discovery	CodeCode Available	1

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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