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 551–600 of 1337 papers

Title	Date	Tasks	Status	Score
GRAN is superior to GraphRNN: node orderings, kernel- and graph embeddings-based metrics for graph generators	Jul 13, 2023	Drug DiscoveryGraph Embedding	CodeCode Available	5
GLADMamba: Unsupervised Graph-Level Anomaly Detection Powered by Selective State Space Model	Mar 23, 2025	Anomaly DetectionDrug Discovery	CodeCode Available	5
CheMixNet: Mixed DNN Architectures for Predicting Chemical Properties using Multiple Molecular Representations	Nov 14, 2018	ClusteringDrug 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
Grad-CAMO: Learning Interpretable Single-Cell Morphological Profiles from 3D Cell Painting Images	Mar 26, 2024	Drug DiscoveryRepresentation Learning	CodeCode Available	5
From Abstract to Actionable: Pairwise Shapley Values for Explainable AI	Feb 18, 2025	Drug DiscoveryFairness	CodeCode Available	5
Chemical-protein Interaction Extraction via Gaussian Probability Distribution and External Biomedical Knowledge	Nov 21, 2019	Chemical-Protein Interaction ExtractionDrug 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
Exploring Latent Space for Generating Peptide Analogs Using Protein Language Models	Aug 15, 2024	Drug Discovery	CodeCode Available	5
GraphVF: Controllable Protein-Specific 3D Molecule Generation with Variational Flow	Feb 23, 2023	3D geometry3D Molecule Generation	CodeCode Available	5
Hyperbolic Benchmarking Unveils Network Topology-Feature Relationship in GNN Performance	Jun 4, 2024	BenchmarkingDrug Discovery	CodeCode Available	5
Exploring Deep Recurrent Models with Reinforcement Learning for Molecule Design	Jan 1, 2018	Drug DiscoveryOpenAI Gym	—Unverified	0
Exploring Chemical Space using Natural Language Processing Methodologies for Drug Discovery	Feb 10, 2020	Drug Discovery	—Unverified	0
Exploiting Pre-trained Models for Drug Target Affinity Prediction with Nearest Neighbors	Jul 21, 2024	Drug DiscoveryPrediction	—Unverified	0
Chemical classification program synthesis using generative artificial intelligence	May 24, 2025	ClassificationDrug Discovery	—Unverified	0
Explainable Molecular Property Prediction: Aligning Chemical Concepts with Predictions via Language Models	May 25, 2024	Drug DiscoveryMolecular Property Prediction	—Unverified	0
Explainable Deep Relational Networks for Predicting Compound-Protein Affinities and Contacts	Dec 29, 2019	BIG-bench Machine LearningDrug Discovery	—Unverified	0
Explainable Biomedical Recommendations via Reinforcement Learning Reasoning on Knowledge Graphs	Nov 20, 2021	Drug DiscoveryKnowledge Graphs	—Unverified	0
A Quantum-Inspired Method for Three-Dimensional Ligand-Based Virtual Screening	Jan 28, 2019	Drug Discovery	—Unverified	0
Explainable Artificial Intelligence for Drug Discovery and Development -- A Comprehensive Survey	Sep 21, 2023	Drug DiscoveryExplainable artificial intelligence	—Unverified	0
Expanding Chemical Representation with k-mers and Fragment-based Fingerprints for Molecular Fingerprinting	Mar 28, 2024	Drug Discovery	—Unverified	0
Evolutionary Algorithm for Drug Discovery Interim Design Report	Mar 19, 2014	Drug Discovery	—Unverified	0
Everything is Connected: Graph Neural Networks	Jan 19, 2023	Drug DiscoveryGraph Representation Learning	—Unverified	0
A Proposed Artificial Neural Network based Approach for Molecules Bitter Prediction	Nov 15, 2023	Computational chemistryDrug Discovery	—Unverified	0
Chem42: a Family of chemical Language Models for Target-aware Ligand Generation	Mar 20, 2025	Drug DiscoveryProperty Prediction	—Unverified	0
Evaluating Point-Prediction Uncertainties in Neural Networks for Drug Discovery	Oct 31, 2022	Drug DiscoveryUncertainty Quantification	—Unverified	0
ChatMol: A Versatile Molecule Designer Based on the Numerically Enhanced Large Language Model	Feb 27, 2025	Bayesian OptimizationDrug Discovery	—Unverified	0
Applying computational protein design to therapeutic antibody discovery -- current state and perspectives	Mar 2, 2025	Drug DiscoveryProtein Design	—Unverified	0
A Hitchhiker's Guide to Deep Chemical Language Processing for Bioactivity Prediction	Jul 16, 2024	Drug DiscoveryHyperparameter Optimization	—Unverified	0
A Comprehensive Benchmarking Platform for Deep Generative Models in Molecular Design	May 19, 2025	BenchmarkingDrug Discovery	—Unverified	0
ETDock: A Novel Equivariant Transformer for Protein-Ligand Docking	Oct 12, 2023	Drug DiscoveryPose Prediction	—Unverified	0
An Equivariant Pretrained Transformer for Unified 3D Molecular Representation Learning	Feb 20, 2024	DenoisingDrug Discovery	—Unverified	0
ChatGPT in Drug Discovery: A Case Study on Anti-Cocaine Addiction Drug Development with Chatbots	Aug 14, 2023	ChatbotDrug Discovery	—Unverified	0
Applications of Modular Co-Design for De Novo 3D Molecule Generation	May 23, 2025	3D Molecule GenerationDenoising	—Unverified	0
Equivariant Graph Attention Networks for Molecular Property Prediction	Feb 20, 2022	Drug DiscoveryGraph Attention	—Unverified	0
Character-level Tokenizations as Powerful Inductive Biases for RNA Foundational Models	Nov 5, 2024	Drug Discovery	—Unverified	0
Applications of Large Models in Medicine	Feb 24, 2025	DiagnosticDisease Prediction	—Unverified	0
Characterizing interdisciplinarity in drug research: a translational science perspective	Sep 4, 2021	Drug Discovery	—Unverified	0
Data-centric challenges with the application and adoption of artificial intelligence for drug discovery	Jul 6, 2024	Drug DiscoveryUncertainty Quantification	—Unverified	0
Application of Information Spectrum Method on Small Molecules and Target Recognition	Apr 15, 2020	Drug DiscoveryMolecular Docking	—Unverified	0
Ensembling classification models based on phalanxes of variables with applications in drug discovery	Mar 20, 2013	Computational chemistryDrug Discovery	—Unverified	0
Enhancing Robustness of Graph Neural Networks through p-Laplacian	Sep 27, 2024	Drug DiscoveryRecommendation Systems	—Unverified	0
Enhancing Neural Subset Selection: Integrating Background Information into Set Representations	Feb 5, 2024	Drug Discovery	—Unverified	0
HelixMO: Sample-Efficient Molecular Optimization in Scene-Sensitive Latent Space	Nov 30, 2021	Drug DesignDrug Discovery	—Unverified	0
Application of Graph Neural Networks and graph descriptors for graph classification	Nov 7, 2022	ClassificationDrug Discovery	—Unverified	0
A Graph Neural Network Approach for Product Relationship Prediction	May 12, 2021	Drug DiscoveryGraph Neural Network	—Unverified	0
A compendium of data sources for data science, machine learning, and artificial intelligence	Sep 10, 2023	Drug Discovery	—Unverified	0
Enhancing Molecular Design through Graph-based Topological Reinforcement Learning	Nov 22, 2024	Drug DesignDrug Discovery	—Unverified	0
Enhancing Model Learning and Interpretation Using Multiple Molecular Graph Representations for Compound Property and Activity Prediction	Apr 13, 2023	Activity PredictionDrug Discovery	—Unverified	0
CCS Explorer: Relevance Prediction, Extractive Summarization, and Named Entity Recognition from Clinical Cohort Studies	Nov 1, 2022	ArticlesDrug Discovery	—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