| Machine learning modeling of family wide enzyme-substrate specificity screens | Sep 8, 2021 | BIG-bench Machine LearningDrug Discovery | CodeCode Available | 1 |
| Machine learning on DNA-encoded library count data using an uncertainty-aware probabilistic loss function | Aug 27, 2021 | DenoisingDrug Discovery | CodeCode Available | 1 |
| C5T5: Controllable Generation of Organic Molecules with Transformers | Aug 23, 2021 | Drug Discoverymolecular representation | CodeCode Available | 1 |
| Modeling Protein Using Large-scale Pretrain Language Model | Aug 17, 2021 | Drug DiscoveryLanguage Modeling | CodeCode Available | 1 |
| Structure-aware Interactive Graph Neural Networks for the Prediction of Protein-Ligand Binding Affinity | Jul 21, 2021 | Drug DiscoveryGraph Attention | CodeCode Available | 1 |
| DPPIN: A Biological Repository of Dynamic Protein-Protein Interaction Network Data | Jul 5, 2021 | AttributeDrug Discovery | CodeCode Available | 1 |
| Quantitative Evaluation of Explainable Graph Neural Networks for Molecular Property Prediction | Jul 1, 2021 | Drug DiscoveryExplainable artificial intelligence | CodeCode Available | 1 |
| Molecule Generation by Principal Subgraph Mining and Assembling | Jun 29, 2021 | Drug DiscoveryGraph Generation | CodeCode Available | 1 |
| Large-Scale Chemical Language Representations Capture Molecular Structure and Properties | Jun 17, 2021 | Drug DiscoveryMolecular Property Prediction | CodeCode Available | 1 |
| Artificial Intelligence in Drug Discovery: Applications and Techniques | Jun 9, 2021 | Drug DesignDrug Discovery | CodeCode Available | 1 |
| GeoMol: Torsional Geometric Generation of Molecular 3D Conformer Ensembles | Jun 8, 2021 | Drug Discovery | CodeCode Available | 1 |
| DIPS-Plus: The Enhanced Database of Interacting Protein Structures for Interface Prediction | Jun 6, 2021 | Drug DiscoveryProtein Interface Prediction | CodeCode Available | 1 |
| Spatial Graph Attention and Curiosity-driven Policy for Antiviral Drug Discovery | Jun 4, 2021 | Drug DiscoveryGraph Attention | CodeCode Available | 1 |
| Quantifying sources of uncertainty in drug discovery predictions with probabilistic models | May 18, 2021 | BIG-bench Machine LearningDecision Making | CodeCode Available | 1 |
| Understanding the Performance of Knowledge Graph Embeddings in Drug Discovery | May 17, 2021 | Drug DiscoveryGraph Embedding | CodeCode Available | 1 |
| Best practices for constructing, preparing, and evaluating protein-ligand binding affinity benchmarks | May 13, 2021 | BenchmarkingDrug Discovery | CodeCode Available | 1 |
| Evening the Score: Targeting SARS-CoV-2 Protease Inhibition in Graph Generative Models for Therapeutic Candidates | May 7, 2021 | Drug DesignDrug Discovery | CodeCode Available | 1 |
| An effective self-supervised framework for learning expressive molecular global representations to drug discovery | May 3, 2021 | Drug DiscoveryGraph Neural Network | CodeCode Available | 1 |
| Learning to Extend Molecular Scaffolds with Structural Motifs | Mar 5, 2021 | Drug Discovery | CodeCode Available | 1 |
| Molecular Contrastive Learning of Representations via Graph Neural Networks | Feb 19, 2021 | BIG-bench Machine LearningContrastive Learning | CodeCode Available | 1 |
| A Review of Biomedical Datasets Relating to Drug Discovery: A Knowledge Graph Perspective | Feb 19, 2021 | BIG-bench Machine LearningDrug Discovery | CodeCode Available | 1 |
| Few-Shot Graph Learning for Molecular Property Prediction | Feb 16, 2021 | AttributeDrug Discovery | CodeCode Available | 1 |
| Equivariant message passing for the prediction of tensorial properties and molecular spectra | Feb 5, 2021 | Drug Discovery | CodeCode Available | 1 |
| Drug and Disease Interpretation Learning with Biomedical Entity Representation Transformer | Jan 22, 2021 | Drug DiscoveryMetric Learning | CodeCode Available | 1 |
| Quantum Generative Models for Small Molecule Drug Discovery | Jan 9, 2021 | Drug Discovery | CodeCode Available | 1 |
| Molecular machine learning with conformer ensembles | Dec 15, 2020 | BIG-bench Machine LearningDeep Learning | CodeCode Available | 1 |
| Accelerating high-throughput virtual screening through molecular pool-based active learning | Dec 13, 2020 | Active LearningBayesian Optimization | CodeCode Available | 1 |
| A Deep Generative Model for Molecule Optimization via One Fragment Modification | Dec 8, 2020 | Drug Discovery | CodeCode Available | 1 |
| Advanced Graph and Sequence Neural Networks for Molecular Property Prediction and Drug Discovery | Dec 2, 2020 | BIG-bench Machine LearningDrug Discovery | CodeCode Available | 1 |
| Fast and Uncertainty-Aware Directional Message Passing for Non-Equilibrium Molecules | Nov 28, 2020 | Drug DiscoveryUncertainty Quantification | CodeCode Available | 1 |
| Molecular representation learning with language models and domain-relevant auxiliary tasks | Nov 26, 2020 | Drug Discoverymolecular representation | CodeCode Available | 1 |
| Message Passing Networks for Molecules with Tetrahedral Chirality | Nov 24, 2020 | Drug Discovery | CodeCode Available | 1 |
| Molecular Mechanics-Driven Graph Neural Network with Multiplex Graph for Molecular Structures | Nov 15, 2020 | Drug DiscoveryFormation Energy | CodeCode Available | 1 |
| TrimNet: learning molecular representation from triplet messages for biomedicine | Nov 4, 2020 | Drug DiscoveryMolecular Property Prediction | CodeCode Available | 1 |
| COMO: A Pipeline for Multi-Omics Data Integration in Metabolic Modeling and Drug Discovery | Nov 4, 2020 | Data IntegrationDrug Discovery | CodeCode Available | 1 |
| Learning a Continuous Representation of 3D Molecular Structures with Deep Generative Models | Oct 17, 2020 | Drug Discoveryvalid | CodeCode Available | 1 |
| Cross-Domain Few-Shot Learning by Representation Fusion | Oct 13, 2020 | Cross-Domain Few-Shotcross-domain few-shot learning | CodeCode Available | 1 |
| MIMOSA: Multi-constraint Molecule Sampling for Molecule Optimization | Oct 5, 2020 | Drug DiscoveryType prediction | CodeCode Available | 1 |
| End-to-End Differentiable Molecular Mechanics Force Field Construction | Oct 2, 2020 | Computational chemistryDrug Discovery | CodeCode Available | 1 |
| PIGNet: A physics-informed deep learning model toward generalized drug-target interaction predictions | Aug 22, 2020 | Drug Discovery | CodeCode Available | 1 |
| Toward heterogeneous information fusion: bipartite graph convolutional networks for in silico drug repurposing | Jul 13, 2020 | Drug Discovery | CodeCode Available | 1 |
| Efficient Conformal Prediction via Cascaded Inference with Expanded Admission | Jul 6, 2020 | Computational chemistryConformal Prediction | CodeCode Available | 1 |
| Graph Prototypical Networks for Few-shot Learning on Attributed Networks | Jun 23, 2020 | ClassificationDrug Discovery | CodeCode Available | 1 |
| We Should at Least Be Able to Design Molecules That Dock Well | Jun 20, 2020 | Drug DesignDrug Discovery | CodeCode Available | 1 |
| MoFlow: An Invertible Flow Model for Generating Molecular Graphs | Jun 17, 2020 | Drug DiscoveryGraph Generation | CodeCode Available | 1 |
| Optimal Transport Graph Neural Networks | Jun 8, 2020 | Drug DiscoveryGraph Neural Network | CodeCode Available | 1 |
| DeepGG: a Deep Graph Generator | Jun 7, 2020 | Drug DiscoveryGraph Embedding | CodeCode Available | 1 |
| Causal Network Models of SARS-CoV-2 Expression and Aging to Identify Candidates for Drug Repurposing | Jun 5, 2020 | Drug Discovery | CodeCode Available | 1 |
| Drug–target affinity prediction using graph neural network and contact maps | Jun 1, 2020 | Drug DesignDrug Discovery | CodeCode Available | 1 |
| PaccMann^RL on SARS-CoV-2: Designing antiviral candidates with conditional generative models | May 27, 2020 | Drug Discovery | CodeCode Available | 1 |
