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 551–600 of 1337 papers

Title	Date	Tasks	Status
Structure Language Models for Protein Conformation Generation	Oct 24, 2024	Drug DiscoveryLanguage Modeling	—Unverified
Conditional Prediction ROC Bands for Graph Classification	Oct 20, 2024	ClassificationDrug Discovery	CodeCode Available
Explaining Graph Neural Networks with Large Language Models: A Counterfactual Perspective for Molecular Property Prediction	Oct 19, 2024	counterfactualCounterfactual Explanation	CodeCode Available
FlexMol: A Flexible Toolkit for Benchmarking Molecular Relational Learning	Oct 19, 2024	BenchmarkingDrug Discovery	CodeCode Available
JAMUN: Transferable Molecular Conformational Ensemble Generation with Walk-Jump Sampling	Oct 18, 2024	Drug Discovery	—Unverified
MultiOrg: A Multi-rater Organoid-detection Dataset	Oct 18, 2024	Autonomous DrivingDisease Prediction	—Unverified
Text-Guided Multi-Property Molecular Optimization with a Diffusion Language Model	Oct 17, 2024	Drug DiscoveryLanguage Modeling	—Unverified
Utilizing Large Language Models in an iterative paradigm with domain feedback for zero-shot molecule optimization	Oct 17, 2024	Drug DiscoveryHallucination	—Unverified
What Do LLMs Need to Understand Graphs: A Survey of Parametric Representation of Graphs	Oct 16, 2024	Drug DiscoveryGraph Generation	—Unverified
RapidDock: Unlocking Proteome-scale Molecular Docking	Oct 16, 2024	Drug DiscoveryGPU	—Unverified
Position Specific Scoring Is All You Need? Revisiting Protein Sequence Classification Tasks	Oct 16, 2024	AllDrug Discovery	—Unverified
MF-LAL: Drug Compound Generation Using Multi-Fidelity Latent Space Active Learning	Oct 15, 2024	Active LearningActivity Prediction	CodeCode Available
KA-GNN: Kolmogorov-Arnold Graph Neural Networks for Molecular Property Prediction	Oct 15, 2024	Drug DiscoveryGraph Attention	—Unverified
Large-Scale Knowledge Integration for Enhanced Molecular Property Prediction	Oct 15, 2024	Drug DiscoveryMolecular Property Prediction	CodeCode Available
UniGEM: A Unified Approach to Generation and Property Prediction for Molecules	Oct 14, 2024	Drug DiscoveryMolecular Property Prediction	—Unverified
Systems-Structure-Based Drug Design	Oct 14, 2024	Drug DesignDrug Discovery	—Unverified
On Divergence Measures for Training GFlowNets	Oct 12, 2024	Causal DiscoveryDrug Discovery	—Unverified
nach0-pc: Multi-task Language Model with Molecular Point Cloud Encoder	Oct 11, 2024	Drug DiscoveryLanguage Modeling	—Unverified
CryoFM: A Flow-based Foundation Model for Cryo-EM Densities	Oct 11, 2024	Drug DiscoveryElectron Tomography	—Unverified
Unveiling Molecular Secrets: An LLM-Augmented Linear Model for Explainable and Calibratable Molecular Property Prediction	Oct 11, 2024	CPUDimensionality Reduction	CodeCode Available
InstructBioMol: Advancing Biomolecule Understanding and Design Following Human Instructions	Oct 10, 2024	Data IntegrationDrug Discovery	—Unverified
OWPCP: A Deep Learning Model to Predict Octanol-Water Partition Coefficient	Oct 10, 2024	Drug DiscoveryHyperparameter Optimization	—Unverified
DLGNet: Hyperedge Classification through Directed Line Graphs for Chemical Reactions	Oct 9, 2024	Drug DiscoveryGraph Neural Network	—Unverified
Pullback Flow Matching on Data Manifolds	Oct 6, 2024	Drug Discovery	—Unverified
Can LLMs Generate Diverse Molecules? Towards Alignment with Structural Diversity	Oct 4, 2024	DiversityDrug Discovery	—Unverified
Text-guided Diffusion Model for 3D Molecule Generation	Oct 4, 2024	3D Molecule GenerationDiversity	—Unverified
SynthFormer: Equivariant Pharmacophore-based Generation of Synthesizable Molecules for Ligand-Based Drug Design	Oct 3, 2024	Drug DesignDrug Discovery	—Unverified
MARS: A neurosymbolic approach for interpretable drug discovery	Oct 2, 2024	Drug Discovery	CodeCode Available
FARM: Functional Group-Aware Representations for Small Molecules	Oct 2, 2024	Contrastive LearningDrug Discovery	—Unverified
Binding Affinity Prediction: From Conventional to Machine Learning-Based Approaches	Sep 30, 2024	Drug DesignDrug Discovery	—Unverified
FlexSBDD: Structure-Based Drug Design with Flexible Protein Modeling	Sep 29, 2024	Data AugmentationDrug Design	—Unverified
Enhancing Robustness of Graph Neural Networks through p-Laplacian	Sep 27, 2024	Drug DiscoveryRecommendation Systems	—Unverified
Optimistic Games for Combinatorial Bayesian Optimization with Application to Protein Design	Sep 27, 2024	Bayesian OptimizationDrug Discovery	—Unverified
SwiftDossier: Tailored Automatic Dossier for Drug Discovery with LLMs and Agents	Sep 24, 2024	Drug DiscoveryRAG	—Unverified
Quantum Machine Learning in Drug Discovery: Applications in Academia and Pharmaceutical Industries	Sep 24, 2024	Drug DiscoveryMolecular Property Prediction	—Unverified
Dumpling GNN: Hybrid GNN Enables Better ADC Payload Activity Prediction Based on Chemical Structure	Sep 23, 2024	Activity PredictionDrug Discovery	—Unverified
GATher: Graph Attention Based Predictions of Gene-Disease Links	Sep 23, 2024	Drug DiscoveryGraph Attention	—Unverified
Protein-Mamba: Biological Mamba Models for Protein Function Prediction	Sep 22, 2024	Drug DiscoveryMamba	—Unverified
FineMolTex: Towards Fine-grained Molecular Graph-Text Pre-training	Sep 21, 2024	Drug Discoverymolecular representation	—Unverified
Analysis of Gene Regulatory Networks from Gene Expression Using Graph Neural Networks	Sep 20, 2024	Drug DiscoveryGraph Attention	CodeCode Available
Natural Language Processing Methods for the Study of Protein-Ligand Interactions	Sep 19, 2024	Drug Discovery	—Unverified
Discrimination vs. Generation: The Machine Learning Dichotomy for Dopaminergic Hit Discovery	Sep 19, 2024	Drug Discovery	—Unverified
Self-Organizing Maps of Unbiased Ligand-Target Binding Pathways and Kinetics	Sep 19, 2024	Drug DesignDrug Discovery	—Unverified
Quantum-inspired Reinforcement Learning for Synthesizable Drug Design	Sep 13, 2024	Drug DesignDrug Discovery	—Unverified
Open Source Infrastructure for Automatic Cell Segmentation	Sep 12, 2024	Cell SegmentationDrug Discovery	—Unverified
XMOL: Explainable Multi-property Optimization of Molecules	Sep 12, 2024	Drug Discovery	—Unverified
A Perspective on AI-Guided Molecular Simulations in VR: Exploring Strategies for Imitation Learning in Hyperdimensional Molecular Systems	Sep 11, 2024	Drug DesignDrug Discovery	—Unverified
PharmacoMatch: Efficient 3D Pharmacophore Screening via Neural Subgraph Matching	Sep 10, 2024	Contrastive LearningDrug Discovery	—Unverified
How Molecules Impact Cells: Unlocking Contrastive PhenoMolecular Retrieval	Sep 10, 2024	Contrastive LearningDrug Discovery	—Unverified
CRADLE-VAE: Enhancing Single-Cell Gene Perturbation Modeling with Counterfactual Reasoning-based Artifact Disentanglement	Sep 9, 2024	counterfactualCounterfactual Reasoning	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