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 101–150 of 1337 papers

Title	Date	Tasks	Status	Hype
EquiCPI: SE(3)-Equivariant Geometric Deep Learning for Structure-Aware Prediction of Compound-Protein Interactions	Apr 7, 2025	Drug DiscoveryRe-Ranking	CodeCode Available	1
An Open and Large-Scale Dataset for Multi-Modal Climate Change-aware Crop Yield Predictions	Jun 10, 2024	Deep LearningDrug Discovery	CodeCode Available	1
Large-Scale Chemical Language Representations Capture Molecular Structure and Properties	Jun 17, 2021	Drug DiscoveryMolecular Property Prediction	CodeCode Available	1
Drug and Disease Interpretation Learning with Biomedical Entity Representation Transformer	Jan 22, 2021	Drug DiscoveryMetric Learning	CodeCode Available	1
Evening the Score: Targeting SARS-CoV-2 Protease Inhibition in Graph Generative Models for Therapeutic Candidates	May 7, 2021	Drug DesignDrug Discovery	CodeCode Available	1
Exploring Chemical Space with Score-based Out-of-distribution Generation	Jun 6, 2022	Drug Discovery	CodeCode Available	1
An adaptive graph learning method for automated molecular interactions and properties predictions	Jun 23, 2022	Drug DiscoveryGraph Learning	CodeCode Available	1
A Multi-Grained Symmetric Differential Equation Model for Learning Protein-Ligand Binding Dynamics	Jan 26, 2024	Drug Discovery	CodeCode Available	1
Fast and Uncertainty-Aware Directional Message Passing for Non-Equilibrium Molecules	Nov 28, 2020	Drug DiscoveryUncertainty Quantification	CodeCode Available	1
Feature Overcorrelation in Deep Graph Neural Networks: A New Perspective	Jun 15, 2022	Drug DiscoveryFeature Correlation	CodeCode Available	1
DOCKSTRING: easy molecular docking yields better benchmarks for ligand design	Oct 29, 2021	Drug DesignDrug Discovery	CodeCode Available	1
Forward Learning of Graph Neural Networks	Mar 16, 2024	Drug DiscoveryGraph Learning	CodeCode Available	1
Agentomics-ML: Autonomous Machine Learning Experimentation Agent for Genomic and Transcriptomic Data	Jun 5, 2025	Drug DiscoveryLarge Language Model	CodeCode Available	1
FragNet: A Graph Neural Network for Molecular Property Prediction with Four Levels of Interpretability	Oct 16, 2024	Drug DiscoveryGraph Neural Network	CodeCode Available	1
DrugAssist: A Large Language Model for Molecule Optimization	Dec 28, 2023	Drug DiscoveryLanguage Modeling	CodeCode Available	1
FusionDTI: Fine-grained Binding Discovery with Token-level Fusion for Drug-Target Interaction	Jun 3, 2024	Drug DesignDrug Discovery	CodeCode Available	1
GeneDisco: A Benchmark for Experimental Design in Drug Discovery	Oct 22, 2021	Active LearningDrug Discovery	CodeCode Available	1
Generalist Equivariant Transformer Towards 3D Molecular Interaction Learning	Jun 2, 2023	Drug Discovery	CodeCode Available	1
Drug–target affinity prediction using graph neural network and contact maps	Jun 1, 2020	Drug DesignDrug Discovery	CodeCode Available	1
DIPS-Plus: The Enhanced Database of Interacting Protein Structures for Interface Prediction	Jun 6, 2021	Drug DiscoveryProtein Interface Prediction	CodeCode Available	1
A Group Symmetric Stochastic Differential Equation Model for Molecule Multi-modal Pretraining	May 28, 2023	Drug Discovery	CodeCode Available	1
Genetic algorithms are strong baselines for molecule generation	Oct 13, 2023	Drug Discovery	CodeCode Available	1
Amortized Tree Generation for Bottom-up Synthesis Planning and Synthesizable Molecular Design	Oct 12, 2021	Drug Discovery	CodeCode Available	1
Geometric Transformers for Protein Interface Contact Prediction	Oct 6, 2021	Drug DiscoveryPrediction	CodeCode Available	1
Directional Message Passing for Molecular Graphs	Mar 6, 2020	Drug DiscoveryFormation Energy	CodeCode Available	1
Atomas: Hierarchical Alignment on Molecule-Text for Unified Molecule Understanding and Generation	Apr 23, 2024	Drug Discoverymolecular representation	CodeCode Available	1
Barlow Twins Deep Neural Network for Advanced 1D Drug-Target Interaction Prediction	Jul 31, 2024	Drug Discovery	CodeCode Available	1
Discrete-state Continuous-time Diffusion for Graph Generation	May 19, 2024	Drug DiscoveryGraph Generation	CodeCode Available	1
Deep Surrogate Docking: Accelerating Automated Drug Discovery with Graph Neural Networks	Nov 4, 2022	Drug Discovery	CodeCode Available	1
Accelerating Inverse Learning via Intelligent Localization with Exploratory Sampling	Dec 2, 2022	Drug Discovery	CodeCode Available	1
AttentionSiteDTI: an interpretable graph-based model for drug-target interaction prediction using NLP sentence-level relation classification	Jul 12, 2022	Drug DiscoveryRelation Classification	CodeCode Available	1
DiffHopp: A Graph Diffusion Model for Novel Drug Design via Scaffold Hopping	Aug 14, 2023	Drug DesignDrug Discovery	CodeCode Available	1
DTIAM: A unified framework for predicting drug-target interactions, binding affinities and activation/inhibition mechanisms	Dec 23, 2023	Drug Discovery	CodeCode Available	1
Activity Cliff Prediction: Dataset and Benchmark	Feb 15, 2023	Drug DiscoveryPrediction	CodeCode Available	1
AlphaFold Distillation for Protein Design	Oct 5, 2022	DiversityDrug Discovery	CodeCode Available	1
DeepNoise: Signal and Noise Disentanglement based on Classifying Fluorescent Microscopy Images via Deep Learning	Sep 13, 2022	DisentanglementDrug Discovery	CodeCode Available	1
Accelerating high-throughput virtual screening through molecular pool-based active learning	Dec 13, 2020	Active LearningBayesian Optimization	CodeCode Available	1
Deep learning to generate in silico chemical property libraries and candidate molecules for small molecule identification in complex samples	May 21, 2019	Drug DiscoveryTransfer Learning	CodeCode Available	1
DeepProtein: Deep Learning Library and Benchmark for Protein Sequence Learning	Oct 2, 2024	Deep LearningDrug Discovery	CodeCode Available	1
Deep Graph Convolutional Network and LSTM based approach for predicting drug-target binding affinity	Jan 18, 2022	Drug Discovery	CodeCode Available	1
Cross-Domain Few-Shot Learning by Representation Fusion	Oct 13, 2020	Cross-Domain Few-Shotcross-domain few-shot learning	CodeCode Available	1
DeepGG: a Deep Graph Generator	Jun 7, 2020	Drug DiscoveryGraph Embedding	CodeCode Available	1
Context-enriched molecule representations improve few-shot drug discovery	Apr 24, 2023	Drug DiscoveryFew-Shot Learning	CodeCode Available	1
Context-Guided Diffusion for Out-of-Distribution Molecular and Protein Design	Jul 16, 2024	Drug DiscoveryOut-of-Distribution Generalization	CodeCode Available	1
3D Interaction Geometric Pre-training for Molecular Relational Learning	Dec 4, 2024	Contrastive LearningDrug Discovery	CodeCode Available	1
Conditional Diffusion Based on Discrete Graph Structures for Molecular Graph Generation	Jan 1, 2023	Drug DiscoveryGraph Generation	CodeCode Available	1
Contrastive Dual-Interaction Graph Neural Network for Molecular Property Prediction	May 4, 2024	Drug DiscoveryGraph Neural Network	CodeCode Available	1
DeepGS: Deep Representation Learning of Graphs and Sequences for Drug-Target Binding Affinity Prediction	Mar 31, 2020	Drug DiscoveryRepresentation Learning	CodeCode Available	1
Coarse-to-Fine: a Hierarchical Diffusion Model for Molecule Generation in 3D	May 5, 2023	Drug Discovery	CodeCode Available	1
Class-Guided Image-to-Image Diffusion: Cell Painting from Brightfield Images with Class Labels	Mar 15, 2023	DenoisingDrug 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