| Lo-Hi: Practical ML Drug Discovery Benchmark | Oct 10, 2023 | Drug DiscoveryMolecular Property Prediction | CodeCode Available | 1 | 5 |
| DeepNoise: Signal and Noise Disentanglement based on Classifying Fluorescent Microscopy Images via Deep Learning | Sep 13, 2022 | DisentanglementDrug Discovery | CodeCode Available | 1 | 5 |
| A hybrid quantum-classical fusion neural network to improve protein-ligand binding affinity predictions for drug discovery | Sep 6, 2023 | Drug DiscoveryPrediction | CodeCode Available | 1 | 5 |
| Strain Problems got you in a Twist? Try StrainRelief: A Quantum-Accurate Tool for Ligand Strain Calculations | Mar 17, 2025 | Drug DesignDrug Discovery | CodeCode Available | 1 | 5 |
| Learning Subpocket Prototypes for Generalizable Structure-based Drug Design | May 22, 2023 | 3D Molecule GenerationDrug Design | CodeCode Available | 1 | 5 |
| Learning to Extend Molecular Scaffolds with Structural Motifs | Mar 5, 2021 | Drug Discovery | CodeCode Available | 1 | 5 |
| Learning Joint 2D & 3D Diffusion Models for Complete Molecule Generation | May 21, 2023 | 3D Molecule GenerationDrug Discovery | CodeCode Available | 1 | 5 |
| 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 | 5 |
| Learning Over Molecular Conformer Ensembles: Datasets and Benchmarks | Sep 29, 2023 | Drug DiscoveryEnsemble Learning | CodeCode Available | 1 | 5 |
| Learning to Navigate in Synthetically Accessible Chemical Space Using Reinforcement Learning | Jan 1, 2020 | Drug DiscoveryNavigate | CodeCode Available | 1 | 5 |
| Machine learning modeling of family wide enzyme-substrate specificity screens | Sep 8, 2021 | BIG-bench Machine LearningDrug Discovery | CodeCode Available | 1 | 5 |
| K-Paths: Reasoning over Graph Paths for Drug Repurposing and Drug Interaction Prediction | Feb 18, 2025 | Drug DiscoveryKnowledge Graphs | CodeCode Available | 1 | 5 |
| Artificial Intelligence in Drug Discovery: Applications and Techniques | Jun 9, 2021 | Drug DesignDrug Discovery | CodeCode Available | 1 | 5 |
| Coarse-to-Fine: a Hierarchical Diffusion Model for Molecule Generation in 3D | May 5, 2023 | Drug Discovery | CodeCode Available | 1 | 5 |
| Knowledge-augmented Graph Machine Learning for Drug Discovery: A Survey | Feb 16, 2023 | Drug DiscoverySurvey | CodeCode Available | 1 | 5 |
| Large-scale ligand-based virtual screening for SARS-CoV-2 inhibitors using deep neural networks | Mar 25, 2020 | Drug Discovery | CodeCode Available | 1 | 5 |
| Cross-Domain Few-Shot Learning by Representation Fusion | Oct 13, 2020 | Cross-Domain Few-Shotcross-domain few-shot learning | CodeCode Available | 1 | 5 |
| Junction Tree Variational Autoencoder for Molecular Graph Generation | Feb 12, 2018 | Drug DiscoveryGraph Generation | CodeCode Available | 1 | 5 |
| KinDEL: DNA-Encoded Library Dataset for Kinase Inhibitors | Oct 11, 2024 | Drug Discovery | CodeCode Available | 1 | 5 |
| Learning a Continuous Representation of 3D Molecular Structures with Deep Generative Models | Oct 17, 2020 | Drug Discoveryvalid | CodeCode Available | 1 | 5 |
| DeepGS: Deep Representation Learning of Graphs and Sequences for Drug-Target Binding Affinity Prediction | Mar 31, 2020 | Drug DiscoveryRepresentation Learning | CodeCode Available | 1 | 5 |
| DeepGG: a Deep Graph Generator | Jun 7, 2020 | Drug DiscoveryGraph Embedding | CodeCode Available | 1 | 5 |
| Transition Path Sampling with Improved Off-Policy Training of Diffusion Path Samplers | May 30, 2024 | Drug Discovery | CodeCode Available | 1 | 5 |
| Contrastive Dual-Interaction Graph Neural Network for Molecular Property Prediction | May 4, 2024 | Drug DiscoveryGraph Neural Network | CodeCode Available | 1 | 5 |
| DEEPScreen: high performance drug–target interaction prediction with convolutional neural networks using 2-D structural compound representations | Jan 8, 2020 | Drug DiscoveryMolecular Docking | CodeCode Available | 1 | 5 |
| Learning Neural Set Functions Under the Optimal Subset Oracle | Mar 3, 2022 | Anomaly DetectionDrug Discovery | CodeCode Available | 1 | 5 |
| Class-Guided Image-to-Image Diffusion: Cell Painting from Brightfield Images with Class Labels | Mar 15, 2023 | DenoisingDrug Discovery | CodeCode Available | 1 | 5 |
| DeepProtein: Deep Learning Library and Benchmark for Protein Sequence Learning | Oct 2, 2024 | Deep LearningDrug Discovery | CodeCode Available | 1 | 5 |
| ChiENN: Embracing Molecular Chirality with Graph Neural Networks | Jul 5, 2023 | Drug DiscoveryMolecular Property Prediction | CodeCode Available | 1 | 5 |
| Deep Surrogate Docking: Accelerating Automated Drug Discovery with Graph Neural Networks | Nov 4, 2022 | Drug Discovery | CodeCode Available | 1 | 5 |
| ChemSpaceAL: An Efficient Active Learning Methodology Applied to Protein-Specific Molecular Generation | Sep 11, 2023 | Active LearningDrug Discovery | CodeCode Available | 1 | 5 |
| Learning To Navigate The Synthetically Accessible Chemical Space Using Reinforcement Learning | Apr 26, 2020 | Drug DesignDrug Discovery | CodeCode Available | 1 | 5 |
| 3M-Diffusion: Latent Multi-Modal Diffusion for Language-Guided Molecular Structure Generation | Mar 11, 2024 | DecoderDrug Discovery | CodeCode Available | 1 | 5 |
| Context-enriched molecule representations improve few-shot drug discovery | Apr 24, 2023 | Drug DiscoveryFew-Shot Learning | CodeCode Available | 1 | 5 |
| A Review of Biomedical Datasets Relating to Drug Discovery: A Knowledge Graph Perspective | Feb 19, 2021 | BIG-bench Machine LearningDrug Discovery | CodeCode Available | 1 | 5 |
| DiffHopp: A Graph Diffusion Model for Novel Drug Design via Scaffold Hopping | Aug 14, 2023 | Drug DesignDrug Discovery | CodeCode Available | 1 | 5 |
| 3D Interaction Geometric Pre-training for Molecular Relational Learning | Dec 4, 2024 | Contrastive LearningDrug Discovery | CodeCode Available | 1 | 5 |
| DOCKSTRING: easy molecular docking yields better benchmarks for ligand design | Oct 29, 2021 | Drug DesignDrug Discovery | CodeCode Available | 1 | 5 |
| Discrete-state Continuous-time Diffusion for Graph Generation | May 19, 2024 | Drug DiscoveryGraph Generation | CodeCode Available | 1 | 5 |
| Context-Guided Diffusion for Out-of-Distribution Molecular and Protein Design | Jul 16, 2024 | Drug DiscoveryOut-of-Distribution Generalization | CodeCode Available | 1 | 5 |
| Large-Scale Chemical Language Representations Capture Molecular Structure and Properties | Jun 17, 2021 | Drug DiscoveryMolecular Property Prediction | CodeCode Available | 1 | 5 |
| DPPIN: A Biological Repository of Dynamic Protein-Protein Interaction Network Data | Jul 5, 2021 | AttributeDrug Discovery | CodeCode Available | 1 | 5 |
| AI-Bind: Improving Binding Predictions for Novel Protein Targets and Ligands | Dec 25, 2021 | Drug DiscoveryUnsupervised Pre-training | CodeCode Available | 1 | 5 |
| Deep Graph Convolutional Network and LSTM based approach for predicting drug-target binding affinity | Jan 18, 2022 | Drug Discovery | CodeCode Available | 1 | 5 |
| Drug and Disease Interpretation Learning with Biomedical Entity Representation Transformer | Jan 22, 2021 | Drug DiscoveryMetric Learning | CodeCode Available | 1 | 5 |
| DrugGen: Advancing Drug Discovery with Large Language Models and Reinforcement Learning Feedback | Nov 20, 2024 | Drug DesignDrug Discovery | CodeCode Available | 1 | 5 |
| DrugAssist: A Large Language Model for Molecule Optimization | Dec 28, 2023 | Drug DiscoveryLanguage Modeling | CodeCode Available | 1 | 5 |
| Meta-learning Adaptive Deep Kernel Gaussian Processes for Molecular Property Prediction | May 5, 2022 | Bilevel OptimizationDrug Discovery | CodeCode Available | 1 | 5 |
| DrugCLIP: Contrastive Protein-Molecule Representation Learning for Virtual Screening | Oct 10, 2023 | Contrastive LearningData Augmentation | CodeCode Available | 1 | 5 |
| Interpretable bilinear attention network with domain adaptation improves drug-target prediction | Aug 3, 2022 | Domain AdaptationDrug Discovery | CodeCode Available | 1 | 5 |
