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 901–950 of 1337 papers

Title	Date	Tasks	Status
Scaffold Splits Overestimate Virtual Screening Performance	Jun 2, 2024	BenchmarkingClustering	—Unverified
Scalable Fragment-Based 3D Molecular Design with Reinforcement Learning	Feb 1, 2022	Drug Discoveryreinforcement-learning	—Unverified
Scalable lipid droplet microarray fabrication, validation, and screening	Oct 13, 2022	Cultural Vocal Bursts Intensity PredictionDrug Discovery	—Unverified
Scalable Variational Quantum Circuits for Autoencoder-based Drug Discovery	Nov 15, 2021	Drug DiscoveryQuantum Machine Learning	—Unverified
Scaling Laws of Graph Neural Networks for Atomistic Materials Modeling	Apr 10, 2025	Drug Discoveryscientific discovery	—Unverified
Schrödinger-ANI: An Eight-Element Neural Network Interaction Potential with Greatly Expanded Coverage of Druglike Chemical Space	Nov 22, 2019	Drug Discovery	—Unverified
Scoreformer: A Surrogate Model For Large-Scale Prediction of Docking Scores	Jun 13, 2024	Drug DiscoveryGraph Neural Network	—Unverified
Evaluating Molecule Synthesizability via Retrosynthetic Planning and Reaction Prediction	Nov 13, 2024	Drug DesignDrug Discovery	—Unverified
SE(3)-Invariant Multiparameter Persistent Homology for Chiral-Sensitive Molecular Property Prediction	Dec 12, 2023	Active LearningDrug Discovery	—Unverified
Season combinatorial intervention predictions with Salt & Peper	Apr 25, 2024	Drug DiscoveryNavigate	—Unverified
Self-Attention Based Molecule Representation for Predicting Drug-Target Interaction	Aug 15, 2019	Drug Discovery	—Unverified
Self-Organizing Maps of Unbiased Ligand-Target Binding Pathways and Kinetics	Sep 19, 2024	Drug DesignDrug Discovery	—Unverified
Self-supervised Learning for Label Sparsity in Computational Drug Repositioning	Jun 1, 2022	Data AugmentationDrug Discovery	—Unverified
Semantic Judgement of Medical Concepts: Combining Syntagmatic and Paradigmatic Information with the Tensor Encoding Model	Dec 1, 2012	Drug DiscoveryInformation Retrieval	—Unverified
Semi-supervised regression with skewed data via adversarially forcing the distribution of predicted values	Jan 1, 2021	Drug Discoveryregression	—Unverified
Sequence Analysis Using the Bezier Curve	Mar 18, 2025	Drug Discovery	—Unverified
Sequence-based deep learning antibody design for in silico antibody affinity maturation	Feb 21, 2021	Computational EfficiencyDrug Discovery	—Unverified
Similarity-Quantized Relative Difference Learning for Improved Molecular Activity Prediction	Jan 15, 2025	Activity PredictionBenchmarking	—Unverified
Simulations meet Machine Learning in Structural Biology	Oct 19, 2018	BIG-bench Machine LearningDrug Discovery	—Unverified
Site2Vec: a reference frame invariant algorithm for vector embedding of protein-ligand binding sites	Mar 18, 2020	BenchmarkingDrug Discovery	—Unverified
Sliced Denoising: A Physics-Informed Molecular Pre-Training Method	Nov 3, 2023	DenoisingDrug Discovery	—Unverified
0/1 Deep Neural Networks via Block Coordinate Descent	Jun 19, 2022	10-shot image generation	—Unverified
SMILES-Mamba: Chemical Mamba Foundation Models for Drug ADMET Prediction	Aug 11, 2024	Drug DiscoveryMamba	—Unverified
S-MolSearch: 3D Semi-supervised Contrastive Learning for Bioactive Molecule Search	Aug 27, 2024	Contrastive LearningData Augmentation	—Unverified
Sparse hierarchical representation learning on molecular graphs	Aug 6, 2019	Drug DiscoveryRepresentation Learning	—Unverified
SPECTRe: Substructure Processing, Enumeration, and Comparison Tool Resource: An efficient tool to encode all substructures of molecules represented in SMILES	Nov 5, 2021	AllDrug Discovery	—Unverified
Spherical Message Passing for 3D Graph Networks	Feb 9, 2021	Drug DiscoveryRepresentation Learning	—Unverified
Statistical thermodynamic basis in drug-receptor interactions: double annihilation and double decoupling alchemical theories, revisited	Jul 13, 2016	Drug Discovery	—Unverified
STELLA: Towards Protein Function Prediction with Multimodal LLMs Integrating Sequence-Structure Representations	Jun 4, 2025	Drug DiscoveryGeneral Knowledge	—Unverified
STRIDE: Structure-guided Generation for Inverse Design of Molecules	Nov 6, 2023	Drug DesignDrug Discovery	—Unverified
Structure-based drug design with geometric deep learning	Oct 19, 2022	Deep LearningDrug Design	—Unverified
Structure-based drug discovery with deep learning	Dec 26, 2022	Deep LearningDrug Discovery	—Unverified
Structure-Function Dynamics Hybrid Modeling: RNA Degradation	May 6, 2023	Drug Discovery	—Unverified
Structure Language Models for Protein Conformation Generation	Oct 24, 2024	Drug DiscoveryLanguage Modeling	—Unverified
Substructure-Atom Cross Attention for Molecular Representation Learning	Oct 15, 2022	Drug DiscoveryGraph Neural Network	—Unverified
SUGAR: Efficient Subgraph-level Training via Resource-aware Graph Partitioning	Jan 31, 2022	Drug DiscoveryEdge-computing	—Unverified
SupSiam: Non-contrastive Auxiliary Loss for Learning from Molecular Conformers	Feb 15, 2023	Activity PredictionDrug Discovery	—Unverified
Surrogate modeling for Bayesian optimization beyond a single Gaussian process	May 27, 2022	Bayesian OptimizationDrug Discovery	—Unverified
SwiftDossier: Tailored Automatic Dossier for Drug Discovery with LLMs and Agents	Sep 24, 2024	Drug DiscoveryRAG	—Unverified
Symbiotic Message Passing Model for Transfer Learning between Anti-Fungal and Anti-Bacterial Domains	Apr 14, 2023	Drug DiscoveryGraph Neural Network	—Unverified
Symmetry-Aware Generative Modeling through Learned Canonicalization	Jan 14, 2025	Drug Discovery	—Unverified
Synergistic Fusion of Graph and Transformer Features for Enhanced Molecular Property Prediction	Aug 25, 2023	Drug DiscoveryMolecular Property Prediction	—Unverified
Synthesis-driven design of 3D molecules for structure-based drug discovery using geometric transformers	Dec 31, 2022	Drug DesignDrug Discovery	—Unverified
Synthetic Data from Diffusion Models Improve Drug Discovery Prediction	May 6, 2024	Drug DiscoveryPrediction	—Unverified
SynthFormer: Equivariant Pharmacophore-based Generation of Synthesizable Molecules for Ligand-Based Drug Design	Oct 3, 2024	Drug DesignDrug Discovery	—Unverified
Systems-Structure-Based Drug Design	Oct 14, 2024	Drug DesignDrug Discovery	—Unverified
Target-aware Molecular Graph Generation	Feb 10, 2022	Drug DiscoveryGraph Generation	—Unverified
Target-Free Compound Activity Prediction via Few-Shot Learning	Nov 27, 2023	Activity PredictionDrug Discovery	—Unverified
TEDDY: A Family Of Foundation Models For Understanding Single Cell Biology	Mar 5, 2025	Drug Discovery	—Unverified
Coverage Guided Testing for Recurrent Neural Networks	Nov 5, 2019	Defect DetectionDrug 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