| EquiCPI: SE(3)-Equivariant Geometric Deep Learning for Structure-Aware Prediction of Compound-Protein Interactions | Apr 7, 2025 | Drug DiscoveryRe-Ranking | CodeCode Available | 1 |
| An Open and Large-Scale Dataset for Multi-Modal Climate Change-aware Crop Yield Predictions | Jun 10, 2024 | Deep LearningDrug Discovery | CodeCode Available | 1 |
| Large-Scale Chemical Language Representations Capture Molecular Structure and Properties | Jun 17, 2021 | Drug DiscoveryMolecular Property Prediction | CodeCode Available | 1 |
| Drug and Disease Interpretation Learning with Biomedical Entity Representation Transformer | Jan 22, 2021 | Drug DiscoveryMetric Learning | 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 |
| Exploring Chemical Space with Score-based Out-of-distribution Generation | Jun 6, 2022 | Drug Discovery | CodeCode Available | 1 |
| An adaptive graph learning method for automated molecular interactions and properties predictions | Jun 23, 2022 | Drug DiscoveryGraph Learning | CodeCode Available | 1 |
| A Multi-Grained Symmetric Differential Equation Model for Learning Protein-Ligand Binding Dynamics | Jan 26, 2024 | Drug Discovery | CodeCode Available | 1 |
| Fast and Uncertainty-Aware Directional Message Passing for Non-Equilibrium Molecules | Nov 28, 2020 | Drug DiscoveryUncertainty Quantification | CodeCode Available | 1 |
| Feature Overcorrelation in Deep Graph Neural Networks: A New Perspective | Jun 15, 2022 | Drug DiscoveryFeature Correlation | CodeCode Available | 1 |
| AttentionSiteDTI: an interpretable graph-based model for drug-target interaction prediction using NLP sentence-level relation classification | Jul 12, 2022 | Drug DiscoveryRelation Classification | CodeCode Available | 1 |
| Forward Learning of Graph Neural Networks | Mar 16, 2024 | Drug DiscoveryGraph Learning | CodeCode Available | 1 |
| Agentomics-ML: Autonomous Machine Learning Experimentation Agent for Genomic and Transcriptomic Data | Jun 5, 2025 | Drug DiscoveryLarge Language Model | CodeCode Available | 1 |
| FragNet: A Graph Neural Network for Molecular Property Prediction with Four Levels of Interpretability | Oct 16, 2024 | Drug DiscoveryGraph Neural Network | CodeCode Available | 1 |
| DrugAssist: A Large Language Model for Molecule Optimization | Dec 28, 2023 | Drug DiscoveryLanguage Modeling | CodeCode Available | 1 |
| FusionDTI: Fine-grained Binding Discovery with Token-level Fusion for Drug-Target Interaction | Jun 3, 2024 | Drug DesignDrug Discovery | CodeCode Available | 1 |
| GeneDisco: A Benchmark for Experimental Design in Drug Discovery | Oct 22, 2021 | Active LearningDrug Discovery | CodeCode Available | 1 |
| Generalist Equivariant Transformer Towards 3D Molecular Interaction Learning | Jun 2, 2023 | 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 |
| Directional Message Passing for Molecular Graphs | Mar 6, 2020 | Drug DiscoveryFormation Energy | CodeCode Available | 1 |
| A Group Symmetric Stochastic Differential Equation Model for Molecule Multi-modal Pretraining | May 28, 2023 | Drug Discovery | CodeCode Available | 1 |
| Genetic algorithms are strong baselines for molecule generation | Oct 13, 2023 | Drug Discovery | CodeCode Available | 1 |
| Amortized Tree Generation for Bottom-up Synthesis Planning and Synthesizable Molecular Design | Oct 12, 2021 | Drug Discovery | CodeCode Available | 1 |
| Geometric Transformers for Protein Interface Contact Prediction | Oct 6, 2021 | Drug DiscoveryPrediction | CodeCode Available | 1 |
| Discrete-state Continuous-time Diffusion for Graph Generation | May 19, 2024 | Drug DiscoveryGraph Generation | CodeCode Available | 1 |
| Barlow Twins Deep Neural Network for Advanced 1D Drug-Target Interaction Prediction | Jul 31, 2024 | 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 |
| DiffHopp: A Graph Diffusion Model for Novel Drug Design via Scaffold Hopping | Aug 14, 2023 | Drug DesignDrug Discovery | CodeCode Available | 1 |
| 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 |
| Accelerating Inverse Learning via Intelligent Localization with Exploratory Sampling | Dec 2, 2022 | Drug Discovery | CodeCode Available | 1 |
| Deep Surrogate Docking: Accelerating Automated Drug Discovery with Graph Neural Networks | Nov 4, 2022 | Drug Discovery | CodeCode Available | 1 |
| DOCKSTRING: easy molecular docking yields better benchmarks for ligand design | Oct 29, 2021 | Drug DesignDrug Discovery | CodeCode Available | 1 |
| DTIAM: A unified framework for predicting drug-target interactions, binding affinities and activation/inhibition mechanisms | Dec 23, 2023 | Drug Discovery | CodeCode Available | 1 |
| Activity Cliff Prediction: Dataset and Benchmark | Feb 15, 2023 | Drug DiscoveryPrediction | CodeCode Available | 1 |
| AlphaFold Distillation for Protein Design | Oct 5, 2022 | DiversityDrug Discovery | CodeCode Available | 1 |
| 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 |
| DeepGS: Deep Representation Learning of Graphs and Sequences for Drug-Target Binding Affinity Prediction | Mar 31, 2020 | Drug DiscoveryRepresentation Learning | CodeCode Available | 1 |
| Accelerating high-throughput virtual screening through molecular pool-based active learning | Dec 13, 2020 | Active LearningBayesian Optimization | CodeCode Available | 1 |
| DeepNoise: Signal and Noise Disentanglement based on Classifying Fluorescent Microscopy Images via Deep Learning | Sep 13, 2022 | DisentanglementDrug Discovery | CodeCode Available | 1 |
| Contrastive Dual-Interaction Graph Neural Network for Molecular Property Prediction | May 4, 2024 | Drug DiscoveryGraph Neural Network | CodeCode Available | 1 |
| Deep Graph Convolutional Network and LSTM based approach for predicting drug-target binding affinity | Jan 18, 2022 | Drug Discovery | CodeCode Available | 1 |
| Conditional Diffusion Based on Discrete Graph Structures for Molecular Graph Generation | Jan 1, 2023 | Drug DiscoveryGraph Generation | CodeCode Available | 1 |
| Context-enriched molecule representations improve few-shot drug discovery | Apr 24, 2023 | Drug DiscoveryFew-Shot Learning | CodeCode Available | 1 |
| Geometric Deep Learning for Structure-Based Drug Design: A Survey | Jun 20, 2023 | BenchmarkingDeep Learning | CodeCode Available | 1 |
| 3D Interaction Geometric Pre-training for Molecular Relational Learning | Dec 4, 2024 | Contrastive LearningDrug Discovery | CodeCode Available | 1 |
| Context-Guided Diffusion for Out-of-Distribution Molecular and Protein Design | Jul 16, 2024 | Drug DiscoveryOut-of-Distribution Generalization | CodeCode Available | 1 |
| DeepGG: a Deep Graph Generator | Jun 7, 2020 | Drug DiscoveryGraph Embedding | 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 |
| DeepProtein: Deep Learning Library and Benchmark for Protein Sequence Learning | Oct 2, 2024 | Deep LearningDrug Discovery | CodeCode Available | 1 |
| Coarse-to-Fine: a Hierarchical Diffusion Model for Molecule Generation in 3D | May 5, 2023 | Drug Discovery | CodeCode Available | 1 |
