| ET-Flow: Equivariant Flow-Matching for Molecular Conformer Generation | Oct 29, 2024 | Drug Discovery | CodeCode Available | 2 | 5 |
| Multi-Objective Molecule Generation using Interpretable Substructures | Feb 8, 2020 | DiversityDrug Design | CodeCode Available | 2 | 5 |
| Equivariant 3D-Conditional Diffusion Models for Molecular Linker Design | Oct 11, 2022 | Drug Discoveryvalid | CodeCode Available | 2 | 5 |
| Multi-Modal Representation Learning for Molecular Property Prediction: Sequence, Graph, Geometry | Jan 7, 2024 | Data AugmentationDrug Discovery | CodeCode Available | 2 | 5 |
| FABind+: Enhancing Molecular Docking through Improved Pocket Prediction and Pose Generation | Mar 29, 2024 | Blind DockingDrug Discovery | CodeCode Available | 2 | 5 |
| GFT: Graph Foundation Model with Transferable Tree Vocabulary | Nov 9, 2024 | Drug DiscoveryGraph Learning | CodeCode Available | 2 | 5 |
| ChemCrow: Augmenting large-language models with chemistry tools | Apr 11, 2023 | Computational chemistryDrug Discovery | CodeCode Available | 2 | 5 |
| Generative Flows on Synthetic Pathway for Drug Design | Oct 6, 2024 | Drug DesignDrug Discovery | CodeCode Available | 2 | 5 |
| Generative Artificial Intelligence for Navigating Synthesizable Chemical Space | Oct 4, 2024 | Drug DiscoveryNavigate | CodeCode Available | 2 | 5 |
| Multi-modal Molecule Structure-text Model for Text-based Retrieval and Editing | Dec 21, 2022 | Contrastive LearningDrug Design | CodeCode Available | 2 | 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 |
| Drug–target affinity prediction using graph neural network and contact maps | Jun 1, 2020 | Drug DesignDrug Discovery | CodeCode Available | 1 | 5 |
| DTIAM: A unified framework for predicting drug-target interactions, binding affinities and activation/inhibition mechanisms | Dec 23, 2023 | Drug Discovery | CodeCode Available | 1 | 5 |
| A Group Symmetric Stochastic Differential Equation Model for Molecule Multi-modal Pretraining | May 28, 2023 | 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 |
| DrugPilot: LLM-based Parameterized Reasoning Agent for Drug Discovery | May 20, 2025 | Drug Discovery | CodeCode Available | 1 | 5 |
| EDBench: Large-Scale Electron Density Data for Molecular Modeling | May 14, 2025 | Drug Discovery | CodeCode Available | 1 | 5 |
| Drug Discovery under Covariate Shift with Domain-Informed Prior Distributions over Functions | Jul 14, 2023 | Domain AdaptationDrug Discovery | CodeCode Available | 1 | 5 |
| Drug Discovery with Dynamic Goal-aware Fragments | Oct 2, 2023 | Drug Discovery | CodeCode Available | 1 | 5 |
| Agentomics-ML: Autonomous Machine Learning Experimentation Agent for Genomic and Transcriptomic Data | Jun 5, 2025 | Drug DiscoveryLarge Language Model | CodeCode Available | 1 | 5 |
| ChiENN: Embracing Molecular Chirality with Graph Neural Networks | Jul 5, 2023 | Drug DiscoveryMolecular Property Prediction | CodeCode Available | 1 | 5 |
| DrugCLIP: Contrastive Protein-Molecule Representation Learning for Virtual Screening | Oct 10, 2023 | Contrastive LearningData Augmentation | 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 |
| EGR: Equivariant Graph Refinement and Assessment of 3D Protein Complex Structures | May 20, 2022 | Drug DiscoveryGraph Neural Network | 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 |
| Achieving Robustness to Aleatoric Uncertainty with Heteroscedastic Bayesian Optimisation | Oct 17, 2019 | Bayesian OptimisationDecision Making | CodeCode Available | 1 | 5 |
| DPPIN: A Biological Repository of Dynamic Protein-Protein Interaction Network Data | Jul 5, 2021 | AttributeDrug Discovery | CodeCode Available | 1 | 5 |
| ChatGPT-powered Conversational Drug Editing Using Retrieval and Domain Feedback | May 29, 2023 | Decision MakingDrug Discovery | CodeCode Available | 1 | 5 |
| Cell Morphology-Guided Small Molecule Generation with GFlowNets | Aug 9, 2024 | Drug 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 |
| Drug and Disease Interpretation Learning with Biomedical Entity Representation Transformer | Jan 22, 2021 | Drug DiscoveryMetric Learning | CodeCode Available | 1 | 5 |
| CardioGenAI: A Machine Learning-Based Framework for Re-Engineering Drugs for Reduced hERG Liability | Mar 12, 2024 | Drug Discovery | CodeCode Available | 1 | 5 |
| An Improved Metric and Benchmark for Assessing the Performance of Virtual Screening Models | Mar 15, 2024 | BenchmarkingDrug Discovery | CodeCode Available | 1 | 5 |
| CausalBench: A Large-scale Benchmark for Network Inference from Single-cell Perturbation Data | Oct 31, 2022 | Causal DiscoveryCausal Inference | CodeCode Available | 1 | 5 |
| C5T5: Controllable Generation of Organic Molecules with Transformers | Aug 23, 2021 | Drug Discoverymolecular representation | CodeCode Available | 1 | 5 |
| An efficient graph generative model for navigating ultra-large combinatorial synthesis libraries | Oct 19, 2022 | DecoderDrug Discovery | CodeCode Available | 1 | 5 |
| Can LLMs Convert Graphs to Text-Attributed Graphs? | Dec 13, 2024 | Drug DiscoveryRecommendation Systems | 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 |
| DrugAssist: A Large Language Model for Molecule Optimization | Dec 28, 2023 | Drug DiscoveryLanguage Modeling | CodeCode Available | 1 | 5 |
| Empowering Graph Representation Learning with Test-Time Graph Transformation | Oct 7, 2022 | Drug DiscoveryGraph Representation Learning | CodeCode Available | 1 | 5 |
| An effective self-supervised framework for learning expressive molecular global representations to drug discovery | May 3, 2021 | Drug DiscoveryGraph Neural Network | CodeCode Available | 1 | 5 |
| Bio-xLSTM: Generative modeling, representation and in-context learning of biological and chemical sequences | Nov 6, 2024 | Drug DiscoveryIn-Context Learning | 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 |
| BioT5: Enriching Cross-modal Integration in Biology with Chemical Knowledge and Natural Language Associations | Oct 11, 2023 | Drug DiscoveryMolecule Captioning | CodeCode Available | 1 | 5 |
| Accurate ADMET Prediction with XGBoost | Apr 15, 2022 | Drug DiscoveryMolecular Property Prediction | CodeCode Available | 1 | 5 |
| 3DMolFormer: A Dual-channel Framework for Structure-based Drug Discovery | Feb 7, 2025 | Drug DesignDrug Discovery | CodeCode Available | 1 | 5 |
| Deep Surrogate Docking: Accelerating Automated Drug Discovery with Graph Neural Networks | Nov 4, 2022 | Drug Discovery | CodeCode Available | 1 | 5 |
| Causal Network Models of SARS-CoV-2 Expression and Aging to Identify Candidates for Drug Repurposing | Jun 5, 2020 | Drug Discovery | CodeCode Available | 1 | 5 |
| BioChemInsight: An Open-Source Toolkit for Automated Identification and Recognition of Optical Chemical Structures and Activity Data in Scientific Publications | Apr 12, 2025 | ArticlesDrug Design | CodeCode Available | 1 | 5 |
| An adaptive graph learning method for automated molecular interactions and properties predictions | Jun 23, 2022 | Drug DiscoveryGraph Learning | CodeCode Available | 1 | 5 |
