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 251–300 of 1337 papers

Title	Date	Tasks	Status	Hype
Graph Fourier Neural ODEs: Modeling Spatial-temporal Multi-scales in Molecular Dynamics	Nov 3, 2024	Computational chemistryDrug Discovery	—Unverified	0
Pre-trained Molecular Language Models with Random Functional Group Masking	Nov 3, 2024	Computational chemistryDrug Discovery	—Unverified	0
Pin-Tuning: Parameter-Efficient In-Context Tuning for Few-Shot Molecular Property Prediction	Nov 2, 2024	AttributeDrug Discovery	CodeCode Available	0
Lung tumor segmentation in MRI mice scans using 3D nnU-Net with minimum annotations	Nov 1, 2024	Drug DiscoverySegmentation	—Unverified	0
Conditional Synthesis of 3D Molecules with Time Correction Sampler	Nov 1, 2024	Drug Discovery	—Unverified	0
ET-Flow: Equivariant Flow-Matching for Molecular Conformer Generation	Oct 29, 2024	Drug Discovery	CodeCode Available	2
Pushing the Limits of All-Atom Geometric Graph Neural Networks: Pre-Training, Scaling and Zero-Shot Transfer	Oct 29, 2024	AllDrug Discovery	—Unverified	0
A Perspective for Adapting Generalist AI to Specialized Medical AI Applications and Their Challenges	Oct 28, 2024	Drug DiscoveryHallucination	—Unverified	0
MAMMAL -- Molecular Aligned Multi-Modal Architecture and Language	Oct 28, 2024	Drug DiscoveryProperty Prediction	CodeCode Available	1
TurboHopp: Accelerated Molecule Scaffold Hopping with Consistency Models	Oct 28, 2024	Drug DesignDrug Discovery	CodeCode Available	0
Contextual Representation Anchor Network to Alleviate Selection Bias in Few-Shot Drug Discovery	Oct 28, 2024	Drug DiscoveryFew-Shot Learning	—Unverified	0
E(3)-invariant diffusion model for pocket-aware peptide generation	Oct 27, 2024	Activity PredictionDrug Discovery	—Unverified	0
Implementation and Application of an Intelligibility Protocol for Interaction with an LLM	Oct 27, 2024	Drug DiscoveryLarge Language Model	CodeCode Available	0
FoldMark: Protecting Protein Generative Models with Watermarking	Oct 27, 2024	Drug DiscoveryProtein Structure Prediction	CodeCode Available	1
PatentAgent: Intelligent Agent for Automated Pharmaceutical Patent Analysis	Oct 25, 2024	Drug DiscoveryQuestion Answering	—Unverified	0
Multi-view biomedical foundation models for molecule-target and property prediction	Oct 25, 2024	Drug Discoverymolecular representation	CodeCode Available	1
Efficient Biological Data Acquisition through Inference Set Design	Oct 25, 2024	Active LearningDrug Discovery	—Unverified	0
Structure Language Models for Protein Conformation Generation	Oct 24, 2024	Drug DiscoveryLanguage Modeling	—Unverified	0
Publishing Neural Networks in Drug Discovery Might Compromise Training Data Privacy	Oct 22, 2024	Drug DiscoveryMolecular Property Prediction	CodeCode Available	1
QuickBind: A Light-Weight And Interpretable Molecular Docking Model	Oct 21, 2024	Drug DiscoveryMolecular Docking	CodeCode Available	1
Conditional Prediction ROC Bands for Graph Classification	Oct 20, 2024	ClassificationDrug Discovery	CodeCode Available	0
Explaining Graph Neural Networks with Large Language Models: A Counterfactual Perspective for Molecular Property Prediction	Oct 19, 2024	counterfactualCounterfactual Explanation	CodeCode Available	0
FlexMol: A Flexible Toolkit for Benchmarking Molecular Relational Learning	Oct 19, 2024	BenchmarkingDrug Discovery	CodeCode Available	0
JAMUN: Transferable Molecular Conformational Ensemble Generation with Walk-Jump Sampling	Oct 18, 2024	Drug Discovery	—Unverified	0
MultiOrg: A Multi-rater Organoid-detection Dataset	Oct 18, 2024	Autonomous DrivingDisease Prediction	—Unverified	0
Utilizing Large Language Models in an iterative paradigm with domain feedback for zero-shot molecule optimization	Oct 17, 2024	Drug DiscoveryHallucination	—Unverified	0
Text-Guided Multi-Property Molecular Optimization with a Diffusion Language Model	Oct 17, 2024	Drug DiscoveryLanguage Modeling	—Unverified	0
RapidDock: Unlocking Proteome-scale Molecular Docking	Oct 16, 2024	Drug DiscoveryGPU	—Unverified	0
Position Specific Scoring Is All You Need? Revisiting Protein Sequence Classification Tasks	Oct 16, 2024	AllDrug Discovery	—Unverified	0
FragNet: A Graph Neural Network for Molecular Property Prediction with Four Levels of Interpretability	Oct 16, 2024	Drug DiscoveryGraph Neural Network	CodeCode Available	1
What Do LLMs Need to Understand Graphs: A Survey of Parametric Representation of Graphs	Oct 16, 2024	Drug DiscoveryGraph Generation	—Unverified	0
Large-Scale Knowledge Integration for Enhanced Molecular Property Prediction	Oct 15, 2024	Drug DiscoveryMolecular Property Prediction	CodeCode Available	0
MF-LAL: Drug Compound Generation Using Multi-Fidelity Latent Space Active Learning	Oct 15, 2024	Active LearningActivity Prediction	CodeCode Available	0
KA-GNN: Kolmogorov-Arnold Graph Neural Networks for Molecular Property Prediction	Oct 15, 2024	Drug DiscoveryGraph Attention	—Unverified	0
It Takes Two to Tango: Directly Optimizing for Constrained Synthesizability in Generative Molecular Design	Oct 15, 2024	Drug Discoveryreinforcement-learning	CodeCode Available	2
Systems-Structure-Based Drug Design	Oct 14, 2024	Drug DesignDrug Discovery	—Unverified	0
UniGEM: A Unified Approach to Generation and Property Prediction for Molecules	Oct 14, 2024	Drug DiscoveryMolecular Property Prediction	—Unverified	0
On Divergence Measures for Training GFlowNets	Oct 12, 2024	Causal DiscoveryDrug Discovery	—Unverified	0
nach0-pc: Multi-task Language Model with Molecular Point Cloud Encoder	Oct 11, 2024	Drug DiscoveryLanguage Modeling	—Unverified	0
Unveiling Molecular Secrets: An LLM-Augmented Linear Model for Explainable and Calibratable Molecular Property Prediction	Oct 11, 2024	CPUDimensionality Reduction	CodeCode Available	0
KinDEL: DNA-Encoded Library Dataset for Kinase Inhibitors	Oct 11, 2024	Drug Discovery	CodeCode Available	1
CryoFM: A Flow-based Foundation Model for Cryo-EM Densities	Oct 11, 2024	Drug DiscoveryElectron Tomography	—Unverified	0
OWPCP: A Deep Learning Model to Predict Octanol-Water Partition Coefficient	Oct 10, 2024	Drug DiscoveryHyperparameter Optimization	—Unverified	0
InstructBioMol: Advancing Biomolecule Understanding and Design Following Human Instructions	Oct 10, 2024	Data IntegrationDrug Discovery	—Unverified	0
DLGNet: Hyperedge Classification through Directed Line Graphs for Chemical Reactions	Oct 9, 2024	Drug DiscoveryGraph Neural Network	—Unverified	0
Generative Flows on Synthetic Pathway for Drug Design	Oct 6, 2024	Drug DesignDrug Discovery	CodeCode Available	2
Pullback Flow Matching on Data Manifolds	Oct 6, 2024	Drug Discovery	—Unverified	0
Can LLMs Generate Diverse Molecules? Towards Alignment with Structural Diversity	Oct 4, 2024	DiversityDrug Discovery	—Unverified	0
Text-guided Diffusion Model for 3D Molecule Generation	Oct 4, 2024	3D Molecule GenerationDiversity	—Unverified	0
Generative Artificial Intelligence for Navigating Synthesizable Chemical Space	Oct 4, 2024	Drug DiscoveryNavigate	CodeCode Available	2

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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