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 1301–1337 of 1337 papers

Title	Date	Tasks	Status
FARM: Functional Group-Aware Representations for Small Molecules	Oct 2, 2024	Contrastive LearningDrug Discovery	—Unverified
DeepIso: A Deep Learning Model for Peptide Feature Detection	Dec 9, 2017	Deep LearningDrug Design	—Unverified
DeepHE: Accurately Predicting Human Essential Genes based on Deep Learning	Feb 15, 2020	BIG-bench Machine LearningDeep Learning	—Unverified
Advances of Deep Learning in Protein Science: A Comprehensive Survey	Mar 8, 2024	Deep LearningDrug Discovery	—Unverified
Structure-Function Dynamics Hybrid Modeling: RNA Degradation	May 6, 2023	Drug Discovery	—Unverified
Fast Dual-Regularized Autoencoder for Sparse Biological Data	Jan 30, 2024	Drug DiscoveryMatrix Completion	—Unverified
Faster and more diverse de novo molecular optimization with double-loop reinforcement learning using augmented SMILES	Oct 22, 2022	DiversityDrug Discovery	—Unverified
Structure Language Models for Protein Conformation Generation	Oct 24, 2024	Drug DiscoveryLanguage Modeling	—Unverified
Handling Missing Data in Downstream Tasks With Distribution-Preserving Guarantees	Jan 23, 2025	Drug DiscoveryHandwritten Digit Recognition	—Unverified
DeepGeneMD: A Joint Deep Learning Model for Extracting Gene Mutation-Disease Knowledge from PubMed Literature	Nov 1, 2019	Drug DiscoveryMulti-Task Learning	—Unverified
Feature Selection through Minimization of the VC dimension	Oct 27, 2014	Drug Discoveryfeature selection	—Unverified
Advances in Protein Representation Learning: Methods, Applications, and Future Directions	Mar 20, 2025	Drug DiscoveryRepresentation Learning	—Unverified
Variational Autoencoding Molecular Graphs with Denoising Diffusion Probabilistic Model	Jul 2, 2023	DenoisingDrug Discovery	—Unverified
DeepConv-DTI: Prediction of drug-target interactions via deep learning with convolution on protein sequences	Nov 6, 2018	Drug DiscoveryPrediction	—Unverified
Advancements in Molecular Property Prediction: A Survey of Single and Multimodal Approaches	Aug 18, 2024	Drug DiscoveryMolecular Property Prediction	—Unverified
Substructure-Atom Cross Attention for Molecular Representation Learning	Oct 15, 2022	Drug DiscoveryGraph Neural Network	—Unverified
FineMolTex: Towards Fine-grained Molecular Graph-Text Pre-training	Sep 21, 2024	Drug Discoverymolecular representation	—Unverified
SUGAR: Efficient Subgraph-level Training via Resource-aware Graph Partitioning	Jan 31, 2022	Drug DiscoveryEdge-computing	—Unverified
FlexSBDD: Structure-Based Drug Design with Flexible Protein Modeling	Sep 29, 2024	Data AugmentationDrug Design	—Unverified
Deep Confidence: A Computationally Efficient Framework for Calculating Reliable Errors for Deep Neural Networks	Sep 24, 2018	Conformal PredictionDeep Learning	—Unverified
Deep asymmetric mixture model for unsupervised cell segmentation	Jun 3, 2024	Cell SegmentationDrug Discovery	—Unverified
SupSiam: Non-contrastive Auxiliary Loss for Learning from Molecular Conformers	Feb 15, 2023	Activity PredictionDrug Discovery	—Unverified
FOBE and HOBE: First- and High-Order Bipartite Embeddings	May 27, 2019	Data VisualizationDrug Discovery	—Unverified
Deep2Lead: A distributed deep learning application for small molecule lead optimization	Aug 9, 2021	Drug Discovery	—Unverified
DecompOpt: Controllable and Decomposed Diffusion Models for Structure-based Molecular Optimization	Mar 7, 2024	Drug DesignDrug Discovery	—Unverified
Decoding Interpretable Logic Rules from Neural Networks	Jan 14, 2025	Autonomous DrivingDrug Discovery	—Unverified
FragFM: Hierarchical Framework for Efficient Molecule Generation via Fragment-Level Discrete Flow Matching	Feb 19, 2025	DiversityDrug Discovery	—Unverified
Fragment-based Sequential Translation for Molecular Optimization	Oct 26, 2021	Drug DiscoveryReinforcement Learning (RL)	—Unverified
Fragment-Masked Diffusion for Molecular Optimization	Aug 17, 2024	Drug Discovery	—Unverified
Decoding Drug Discovery: Exploring A-to-Z In silico Methods for Beginners	Dec 15, 2024	Drug DesignDrug Discovery	—Unverified
Current Methods for Drug Property Prediction in the Real World	Jul 25, 2023	Decision MakingDeep Learning	—Unverified
Surrogate modeling for Bayesian optimization beyond a single Gaussian process	May 27, 2022	Bayesian OptimizationDrug Discovery	—Unverified
Variational Quantum Algorithms for Chemical Simulation and Drug Discovery	Nov 15, 2022	Drug DiscoveryProtein Folding	—Unverified
From Bench to Bedside: A Review of Clinical Trials in Drug Discovery and Development	Dec 12, 2024	Drug DiscoveryMarketing	—Unverified
From Byte to Bench to Bedside: Molecular Dynamics Simulations and Drug Discovery	Nov 28, 2023	Drug DesignDrug Discovery	—Unverified
From Data to Action: Charting A Data-Driven Path to Combat Antimicrobial Resistance	Jan 30, 2025	DenoisingDrug Discovery	—Unverified
From large language models to multimodal AI: A scoping review on the potential of generative AI in medicine	Feb 13, 2025	DiagnosticDrug Discovery	—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