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 451–500 of 1337 papers

Title	Date	Tasks	Status	Score
DeeplyTough: Learning Structural Comparison of Protein Binding Sites	Apr 5, 2019	Drug Discovery	CodeCode Available	5
Deeply learning molecular structure-property relationships using attention- and gate-augmented graph convolutional network	May 28, 2018	Drug Discovery	CodeCode Available	5
Learning Hierarchical Interaction for Accurate Molecular Property Prediction	Apr 28, 2025	Drug DiscoveryMolecular Property Prediction	CodeCode Available	5
LITE: Efficiently Estimating Gaussian Probability of Maximality	Jan 23, 2025	Bayesian OptimizationDrug Discovery	CodeCode Available	5
Latent Guided Sampling for Combinatorial Optimization	Jun 4, 2025	Combinatorial OptimizationDrug Discovery	CodeCode Available	5
Leak Proof CMap; a framework for training and evaluation of cell line agnostic L1000 similarity methods	Apr 29, 2024	BenchmarkingDrug Discovery	CodeCode Available	5
Large-Scale Knowledge Integration for Enhanced Molecular Property Prediction	Oct 15, 2024	Drug DiscoveryMolecular Property Prediction	CodeCode Available	5
AMPL: A Data-Driven Modeling Pipeline for Drug Discovery	Nov 13, 2019	BIG-bench Machine LearningDrug Discovery	CodeCode Available	5
LaGDif: Latent Graph Diffusion Model for Efficient Protein Inverse Folding with Self-Ensemble	Nov 4, 2024	Drug Discovery	CodeCode Available	5
Learning Cross-Domain Representations for Transferable Drug Perturbations on Single-Cell Transcriptional Responses	Dec 26, 2024	DecoderDrug Discovery	CodeCode Available	5
JAX MD: End-to-End Differentiable, Hardware Accelerated, Molecular Dynamics in Pure Python	Sep 25, 2019	BIG-bench Machine LearningCPU	CodeCode Available	5
Deep Inverse Reinforcement Learning for Structural Evolution of Small Molecules	Jul 24, 2020	Drug DiscoveryGenerative Adversarial Network	CodeCode Available	5
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	5
Interpretable Deep Learning in Drug Discovery	Mar 7, 2019	Deep LearningDrug Discovery	CodeCode Available	5
Protein Language Models and Machine Learning Facilitate the Identification of Antimicrobial Peptides	Aug 14, 2024	Binary ClassificationDrug Discovery	CodeCode Available	5
Learning Graph-Level Representation for Drug Discovery	Sep 12, 2017	AllDrug Discovery	CodeCode Available	5
A Unified Approach to Inferring Chemical Compounds with the Desired Aqueous Solubility	Sep 6, 2024	Drug Discoveryregression	CodeCode Available	5
AugWard: Augmentation-Aware Representation Learning for Accurate Graph Classification	Mar 27, 2025	DiversityDrug Discovery	CodeCode Available	5
DeepAtom: A Framework for Protein-Ligand Binding Affinity Prediction	Dec 1, 2019	Drug DesignDrug Discovery	CodeCode Available	5
Integrating convolutional layers and biformer network with forward-forward and backpropagation training	Feb 28, 2025	Computational chemistryDrug Discovery	CodeCode Available	5
Improving Molecular Pretraining with Complementary Featurizations	Sep 29, 2022	Computational chemistryDrug Discovery	CodeCode Available	5
DeepAffinity: Interpretable Deep Learning of Compound-Protein Affinity through Unified Recurrent and Convolutional Neural Networks	Jun 20, 2018	Drug DiscoveryTransfer Learning	CodeCode Available	5
Independent Vector Analysis for Data Fusion Prior to Molecular Property Prediction with Machine Learning	Nov 1, 2018	BIG-bench Machine LearningDrug Discovery	CodeCode Available	5
Adapting Differential Molecular Representation with Hierarchical Prompts for Multi-label Property Prediction	May 29, 2024	Drug Discoverymolecular representation	CodeCode Available	5
Improving Compound Activity Classification via Deep Transfer and Representation Learning	Nov 14, 2021	Drug DiscoveryRepresentation Learning	CodeCode Available	5
Injecting Domain Knowledge from Empirical Interatomic Potentials to Neural Networks for Predicting Material Properties	Oct 14, 2022	Drug DiscoveryTransfer Learning	CodeCode Available	5
RAGPPI: RAG Benchmark for Protein-Protein Interactions in Drug Discovery	May 28, 2025	Drug DiscoveryRAG	CodeCode Available	5
ReactEmbed: A Cross-Domain Framework for Protein-Molecule Representation Learning via Biochemical Reaction Networks	Jan 30, 2025	Contrastive LearningDrug 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
Accelerating Prototype-Based Drug Discovery using Conditional Diversity Networks	Apr 8, 2018	DiversityDrug Discovery	CodeCode Available	5
DebiasedDTA: A Framework for Improving the Generalizability of Drug-Target Affinity Prediction Models	Jul 4, 2021	Drug DiscoveryEnsemble Learning	CodeCode Available	5
Implementation and Application of an Intelligibility Protocol for Interaction with an LLM	Oct 27, 2024	Drug DiscoveryLarge Language Model	CodeCode Available	5
Improved antibody structure prediction by deep learning of side chain conformations	Sep 22, 2021	Deep LearningDrug Discovery	CodeCode Available	5
Data-Efficient Molecular Generation with Hierarchical Textual Inversion	May 5, 2024	Drug DiscoveryImage Generation	CodeCode Available	5
Attention-based Multi-Input Deep Learning Architecture for Biological Activity Prediction: An Application in EGFR Inhibitors	Jun 12, 2019	Activity PredictionBIG-bench Machine Learning	CodeCode Available	5
Data-Driven Approach to Encoding and Decoding 3-D Crystal Structures	Sep 3, 2019	DecoderDrug Discovery	CodeCode Available	5
iBitter-Stack: A Multi-Representation Ensemble Learning Model for Accurate Bitter Peptide Identification	May 21, 2025	Drug DiscoveryEnsemble Learning	CodeCode Available	5
AtomNet: A Deep Convolutional Neural Network for Bioactivity Prediction in Structure-based Drug Discovery	Oct 10, 2015	Drug Discovery	CodeCode Available	5
CRADLE-VAE: Enhancing Single-Cell Gene Perturbation Modeling with Counterfactual Reasoning-based Artifact Disentanglement	Sep 9, 2024	counterfactualCounterfactual Reasoning	CodeCode Available	5
Convolutional Networks on Graphs for Learning Molecular Fingerprints	Sep 30, 2015	Drug DiscoveryGraph Regression	CodeCode Available	5
Heter-LP: A heterogeneous label propagation algorithm and its application in drug repositioning	Nov 8, 2016	Data IntegrationDrug Discovery	CodeCode Available	5
Corresponding Projections for Orphan Screening	Nov 30, 2018	Drug DiscoveryTransfer Learning	CodeCode Available	5
Controlled Molecule Generator for Optimizing Multiple Chemical Properties	Oct 26, 2020	Drug DiscoveryProperty Prediction	CodeCode Available	5
Guided Multi-objective Generative AI to Enhance Structure-based Drug Design	May 20, 2024	Drug DesignDrug Discovery	CodeCode Available	5
A Systematic Assessment of Deep Learning Models for Molecule Generation	Aug 20, 2020	Deep LearningDrug Discovery	CodeCode Available	5
De Novo Generation of Hit-like Molecules from Gene Expression Profiles via Deep Learning	Dec 27, 2024	Drug Discoveryvalid	CodeCode Available	5
Advancing Drug Discovery with Enhanced Chemical Understanding via Asymmetric Contrastive Multimodal Learning	Nov 11, 2023	Contrastive LearningDrug Discovery	CodeCode Available	5
GraPPI: A Retrieve-Divide-Solve GraphRAG Framework for Large-scale Protein-protein Interaction Exploration	Jan 24, 2025	Drug DiscoveryRAG	CodeCode Available	5
GSHOT: Few-shot Generative Modeling of Labeled Graphs	Jun 6, 2023	Drug DiscoveryFew-Shot Learning	CodeCode Available	5
Constrained Multi-objective Bayesian Optimization through Optimistic Constraints Estimation	Nov 6, 2024	Active LearningBayesian Optimization	CodeCode Available	5

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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