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 1101–1150 of 1337 papers

Title	Date	Tasks	Status
Multivariate Conformal Selection	May 1, 2025	Drug DiscoveryUncertainty Quantification	—Unverified
nach0-pc: Multi-task Language Model with Molecular Point Cloud Encoder	Oct 11, 2024	Drug DiscoveryLanguage Modeling	—Unverified
Leveraging Large Language Models for enzymatic reaction prediction and characterization	May 8, 2025	Drug DiscoveryIn-Context Learning	CodeCode Available
Assay2Mol: large language model-based drug design using BioAssay context	Jul 16, 2025	DescriptiveDrug Design	CodeCode Available
Visualizing Deep Graph Generative Models for Drug Discovery	Jul 20, 2020	Drug Discovery	CodeCode Available
CLDR: Contrastive Learning Drug Response Models from Natural Language Supervision	Dec 17, 2023	Common Sense ReasoningContrastive Learning	CodeCode Available
DrugChat: Towards Enabling ChatGPT-Like Capabilities on Drug Molecule Graphs	May 18, 2023	Drug DiscoveryGraph Neural Network	CodeCode Available
Drug cell line interaction prediction	Dec 28, 2018	Drug DiscoveryPrediction	CodeCode Available
Ligand Pose Optimization with Atomic Grid-Based Convolutional Neural Networks	Oct 20, 2017	Drug Discovery	CodeCode Available
Adversarial Learned Molecular Graph Inference and Generation	May 24, 2019	Drug Discovery	CodeCode Available
Inductive-Associative Meta-learning Pipeline with Human Cognitive Patterns for Unseen Drug-Target Interaction Prediction	Jan 26, 2025	Drug DiscoveryMeta-Learning	CodeCode Available
CheMixNet: Mixed DNN Architectures for Predicting Chemical Properties using Multiple Molecular Representations	Nov 14, 2018	ClusteringDrug Discovery	CodeCode Available
A Self-feedback Knowledge Elicitation Approach for Chemical Reaction Predictions	Apr 15, 2024	Chemical Reaction PredictionDrug Discovery	CodeCode Available
LITE: Efficiently Estimating Gaussian Probability of Maximality	Jan 23, 2025	Bayesian OptimizationDrug Discovery	CodeCode Available
Learning to Denoise Biomedical Knowledge Graph for Robust Molecular Interaction Prediction	Dec 9, 2023	DenoisingDrug Discovery	CodeCode Available
Learning Hierarchical Interaction for Accurate Molecular Property Prediction	Apr 28, 2025	Drug DiscoveryMolecular Property Prediction	CodeCode Available
Learning Graph-Level Representation for Drug Discovery	Sep 12, 2017	AllDrug Discovery	CodeCode Available
Neural Atoms: Propagating Long-range Interaction in Molecular Graphs through Efficient Communication Channel	Nov 2, 2023	Drug Discovery	CodeCode Available
Chemical-protein Interaction Extraction via Gaussian Probability Distribution and External Biomedical Knowledge	Nov 21, 2019	Chemical-Protein Interaction ExtractionDrug Discovery	CodeCode Available
Transferable Graph Neural Fingerprint Models for Quick Response to Future Bio-Threats	Jul 17, 2023	Drug DiscoveryMolecular Docking	CodeCode Available
Machine learning analysis of cocaine addiction informed by DAT, SERT, and NET-based interactome networks	Jan 1, 2022	Drug Discovery	CodeCode Available
ChemGrapher: Optical Graph Recognition of Chemical Compounds by Deep Learning	Feb 23, 2020	ArticlesDeep Learning	CodeCode Available
Predicting Novel Functional Roles of Designed Small Biomolecules: An ML Approach Utilizing PubChem Compound and Substance Identifiers (CID-SID ML model)	Jan 4, 2025	Drug Discovery	CodeCode Available
UniMatch: Universal Matching from Atom to Task for Few-Shot Drug Discovery	Feb 18, 2025	Drug DiscoveryFew-Shot Learning	CodeCode Available
TF3P: Three-dimensional Force Fields Fingerprint Learned by Deep Capsular Network	Dec 24, 2019	Drug Discovery	CodeCode Available
Learning Cross-Domain Representations for Transferable Drug Perturbations on Single-Cell Transcriptional Responses	Dec 26, 2024	DecoderDrug Discovery	CodeCode Available
DProQ: A Gated-Graph Transformer for Protein Complex Structure Assessment	May 21, 2022	Drug Discovery	CodeCode Available
Leak Proof CMap; a framework for training and evaluation of cell line agnostic L1000 similarity methods	Apr 29, 2024	BenchmarkingDrug Discovery	CodeCode Available
Adaptive Batch Sizes for Active Learning A Probabilistic Numerics Approach	Jun 9, 2023	Active LearningBayesian Optimisation	CodeCode Available
Latent Guided Sampling for Combinatorial Optimization	Jun 4, 2025	Combinatorial OptimizationDrug Discovery	CodeCode Available
ChemGAN challenge for drug discovery: can AI reproduce natural chemical diversity?	Aug 28, 2017	DiversityDrug Discovery	CodeCode Available
Machine-learning Repurposing of DrugBank Compounds for Opioid Use Disorder	Mar 1, 2023	Drug Discovery	CodeCode Available
Preference Optimization for Molecule Synthesis with Conditional Residual Energy-based Models	Jun 4, 2024	Drug DiscoveryRetrosynthesis	CodeCode Available
Semi-supervised Ensemble Learning with Weak Supervision for Biomedical Relationship Extraction	Nov 17, 2018	Drug DiscoveryEnsemble Learning	CodeCode Available
ChemBO: Bayesian Optimization of Small Organic Molecules with Synthesizable Recommendations	Aug 5, 2019	Bayesian OptimizationDrug Discovery	CodeCode Available
Large-Scale Knowledge Integration for Enhanced Molecular Property Prediction	Oct 15, 2024	Drug DiscoveryMolecular Property Prediction	CodeCode Available
Transfer Learning for Temporal Link Prediction	Apr 15, 2025	Drug DiscoveryInformativeness	CodeCode Available
LaGDif: Latent Graph Diffusion Model for Efficient Protein Inverse Folding with Self-Ensemble	Nov 4, 2024	Drug Discovery	CodeCode Available
AMPL: A Data-Driven Modeling Pipeline for Drug Discovery	Nov 13, 2019	BIG-bench Machine LearningDrug Discovery	CodeCode Available
APACE: AlphaFold2 and advanced computing as a service for accelerated discovery in biophysics	Aug 15, 2023	Drug DiscoveryPrediction	CodeCode Available
MARS: A neurosymbolic approach for interpretable drug discovery	Oct 2, 2024	Drug Discovery	CodeCode Available
MARS: Markov Molecular Sampling for Multi-objective Drug Discovery	Mar 18, 2021	Drug DiscoveryGraph Neural Network	CodeCode Available
KekuleScope: prediction of cancer cell line sensitivity and compound potency using convolutional neural networks trained on compound images	Nov 22, 2018	Drug DiscoveryPrediction Of Cancer Cell Line Sensitivity	CodeCode Available
Principled Weight Initialisation for Input-Convex Neural Networks	Dec 19, 2023	Drug Discovery	CodeCode Available
Sequential Experimental Design for Transductive Linear Bandits	Jun 20, 2019	Drug DiscoveryExperimental Design	CodeCode Available
JAX MD: End-to-End Differentiable, Hardware Accelerated, Molecular Dynamics in Pure Python	Sep 25, 2019	BIG-bench Machine LearningCPU	CodeCode Available
Massively Multitask Networks for Drug Discovery	Feb 6, 2015	Drug Discovery	CodeCode Available
The Clinical Trials Puzzle: How Network Effects Limit Drug Discovery	Jan 25, 2023	Drug Discovery	CodeCode Available
Maximum Reward Formulation In Reinforcement Learning	Oct 8, 2020	Drug Discoveryreinforcement-learning	CodeCode Available
ChemBoost: A chemical language based approach for protein-ligand binding affinity prediction	Nov 2, 2018	Drug DiscoveryWord Embeddings	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