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 226–250 of 1337 papers

Title	Date	Tasks	Status	Hype
Investigating Graph Neural Networks and Classical Feature-Extraction Techniques in Activity-Cliff and Molecular Property Prediction	Nov 20, 2024	Drug DiscoveryMolecular Property Prediction	—Unverified	0
DrugGen: Advancing Drug Discovery with Large Language Models and Reinforcement Learning Feedback	Nov 20, 2024	Drug DesignDrug Discovery	CodeCode Available	1
Energy-based generative models for monoclonal antibodies	Nov 20, 2024	Drug Discovery	CodeCode Available	0
NPGPT: Natural Product-Like Compound Generation with GPT-based Chemical Language Models	Nov 19, 2024	DiversityDrug Discovery	CodeCode Available	1
GNNAS-Dock: Budget Aware Algorithm Selection with Graph Neural Networks for Molecular Docking	Nov 19, 2024	Blind DockingDrug Discovery	—Unverified	0
Molecule Generation with Fragment Retrieval Augmentation	Nov 18, 2024	Drug DiscoveryRAG	—Unverified	0
SCOP: A Sequence-Structure Contrast-Aware Framework for Protein Function Prediction	Nov 18, 2024	Drug DiscoveryProtein Function Prediction	CodeCode Available	0
A Modular Open Source Framework for Genomic Variant Calling	Nov 18, 2024	Drug DiscoveryImage Generation	—Unverified	0
Graph Neural Networks for Quantifying Compatibility Mechanisms in Traditional Chinese Medicine	Nov 18, 2024	Drug DiscoveryFeature Engineering	CodeCode Available	1
BioNeMo Framework: a modular, high-performance library for AI model development in drug discovery	Nov 15, 2024	Drug Discovery	—Unverified	0
WelQrate: Defining the Gold Standard in Small Molecule Drug Discovery Benchmarking	Nov 14, 2024	BenchmarkingDrug Discovery	—Unverified	0
Evaluating Molecule Synthesizability via Retrosynthetic Planning and Reaction Prediction	Nov 13, 2024	Drug DesignDrug Discovery	—Unverified	0
Concept Bottleneck Language Models For protein design	Nov 9, 2024	Decision MakingDrug Discovery	CodeCode Available	2
GFT: Graph Foundation Model with Transferable Tree Vocabulary	Nov 9, 2024	Drug DiscoveryGraph Learning	CodeCode Available	2
A Comprehensive Guide to Enhancing Antibiotic Discovery Using Machine Learning Derived Bio-computation	Nov 8, 2024	Drug Discovery	—Unverified	0
OneProt: Towards Multi-Modal Protein Foundation Models	Nov 7, 2024	Drug DiscoveryRetrieval	CodeCode Available	1
Bio-xLSTM: Generative modeling, representation and in-context learning of biological and chemical sequences	Nov 6, 2024	Drug DiscoveryIn-Context Learning	CodeCode Available	1
BAPULM: Binding Affinity Prediction using Language Models	Nov 6, 2024	Drug Discoverymolecular representation	CodeCode Available	0
Constrained Multi-objective Bayesian Optimization through Optimistic Constraints Estimation	Nov 6, 2024	Active LearningBayesian Optimization	CodeCode Available	0
Character-level Tokenizations as Powerful Inductive Biases for RNA Foundational Models	Nov 5, 2024	Drug Discovery	—Unverified	0
LaGDif: Latent Graph Diffusion Model for Efficient Protein Inverse Folding with Self-Ensemble	Nov 4, 2024	Drug Discovery	CodeCode Available	0
Persistent Directed Flag Laplacian (PDFL)-Based Machine Learning for Protein-Ligand Binding Affinity Prediction	Nov 4, 2024	Drug DiscoveryTopological Data Analysis	CodeCode Available	0
ViTally Consistent: Scaling Biological Representation Learning for Cell Microscopy	Nov 4, 2024	Drug DiscoveryRepresentation Learning	—Unverified	0
GraphXForm: Graph transformer for computer-aided molecular design	Nov 3, 2024	Drug DesignDrug Discovery	CodeCode Available	1
GramSeq-DTA: A grammar-based drug-target affinity prediction approach fusing gene expression information	Nov 3, 2024	Drug DiscoveryPrediction	—Unverified	0

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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