| 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 Improved Metric and Benchmark for Assessing the Performance of Virtual Screening Models | Mar 15, 2024 | BenchmarkingDrug Discovery | CodeCode Available | 1 | 5 |
| Empowering Graph Representation Learning with Test-Time Graph Transformation | Oct 7, 2022 | Drug DiscoveryGraph Representation Learning | CodeCode Available | 1 | 5 |
| MGCVAE: Multi-objective Inverse Design via Molecular Graph Conditional Variational Autoencoder | Feb 14, 2022 | Drug Discovery | CodeCode Available | 1 | 5 |
| Biomedical NER for the Enterprise with Distillated BERN2 and the Kazu Framework | Dec 1, 2022 | Drug DiscoveryNER | CodeCode Available | 1 | 5 |
| An Open and Large-Scale Dataset for Multi-Modal Climate Change-aware Crop Yield Predictions | Jun 10, 2024 | Deep LearningDrug Discovery | CodeCode Available | 1 | 5 |
| HAC-Net: A Hybrid Attention-Based Convolutional Neural Network for Highly Accurate Protein-Ligand Binding Affinity Prediction | Dec 23, 2022 | Drug DiscoveryProperty Prediction | 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 |
| HiGNN: Hierarchical Informative Graph Neural Networks for Molecular Property Prediction Equipped with Feature-Wise Attention | Aug 30, 2022 | Drug DesignDrug Discovery | CodeCode Available | 1 | 5 |
| InstructMol: Multi-Modal Integration for Building a Versatile and Reliable Molecular Assistant in Drug Discovery | Nov 27, 2023 | Drug DiscoveryMolecule Captioning | CodeCode Available | 1 | 5 |
| Conditional Diffusion Based on Discrete Graph Structures for Molecular Graph Generation | Jan 1, 2023 | Drug DiscoveryGraph Generation | CodeCode Available | 1 | 5 |
| EquiCPI: SE(3)-Equivariant Geometric Deep Learning for Structure-Aware Prediction of Compound-Protein Interactions | Apr 7, 2025 | Drug DiscoveryRe-Ranking | CodeCode Available | 1 | 5 |
| EquiPocket: an E(3)-Equivariant Geometric Graph Neural Network for Ligand Binding Site Prediction | Feb 23, 2023 | Drug DiscoveryGraph Neural Network | CodeCode Available | 1 | 5 |
| Mol-AIR: Molecular Reinforcement Learning with Adaptive Intrinsic Rewards for Goal-directed Molecular Generation | Mar 29, 2024 | Drug Discoveryreinforcement-learning | CodeCode Available | 1 | 5 |
| Molecule Generation by Principal Subgraph Mining and Assembling | Jun 29, 2021 | Drug DiscoveryGraph Generation | CodeCode Available | 1 | 5 |
| Equivariant message passing for the prediction of tensorial properties and molecular spectra | Feb 5, 2021 | Drug Discovery | CodeCode Available | 1 | 5 |
| Molecular Mechanics-Driven Graph Neural Network with Multiplex Graph for Molecular Structures | Nov 15, 2020 | Drug DiscoveryFormation Energy | CodeCode Available | 1 | 5 |
| Molecular representation learning with language models and domain-relevant auxiliary tasks | Nov 26, 2020 | Drug Discoverymolecular representation | CodeCode Available | 1 | 5 |
| Exploring Chemical Space with Score-based Out-of-distribution Generation | Jun 6, 2022 | Drug Discovery | CodeCode Available | 1 | 5 |
| Comprehensive evaluation of deep and graph learning on drug-drug interactions prediction | Jun 8, 2023 | Drug DiscoveryGraph Learning | CodeCode Available | 1 | 5 |
| 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 | 5 |
| Advanced Graph and Sequence Neural Networks for Molecular Property Prediction and Drug Discovery | Dec 2, 2020 | BIG-bench Machine LearningDrug Discovery | CodeCode Available | 1 | 5 |
| GraphAF: a Flow-based Autoregressive Model for Molecular Graph Generation | Jan 26, 2020 | Density EstimationDrug Discovery | CodeCode Available | 1 | 5 |
| Graph Neural Networks for Quantifying Compatibility Mechanisms in Traditional Chinese Medicine | Nov 18, 2024 | Drug DiscoveryFeature Engineering | CodeCode Available | 1 | 5 |
| FABind: Fast and Accurate Protein-Ligand Binding | Oct 10, 2023 | Blind DockingDrug Discovery | CodeCode Available | 1 | 5 |
| Genetic algorithms are strong baselines for molecule generation | Oct 13, 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 |
| Fast and Uncertainty-Aware Directional Message Passing for Non-Equilibrium Molecules | Nov 28, 2020 | Drug DiscoveryUncertainty Quantification | CodeCode Available | 1 | 5 |
| Can LLMs Convert Graphs to Text-Attributed Graphs? | Dec 13, 2024 | Drug DiscoveryRecommendation Systems | CodeCode Available | 1 | 5 |
| Graph Prototypical Networks for Few-shot Learning on Attributed Networks | Jun 23, 2020 | ClassificationDrug Discovery | CodeCode Available | 1 | 5 |
| Can Large Language Models Understand Molecules? | Jan 5, 2024 | Drug DiscoveryLanguage Modelling | CodeCode Available | 1 | 5 |
| Fractional Denoising for 3D Molecular Pre-training | Jul 20, 2023 | DenoisingDrug Discovery | 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 |
| Multi-view biomedical foundation models for molecule-target and property prediction | Oct 25, 2024 | Drug Discoverymolecular representation | 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 |
| GNN-VPA: A Variance-Preserving Aggregation Strategy for Graph Neural Networks | Mar 7, 2024 | 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 |
| FoldMark: Protecting Protein Generative Models with Watermarking | Oct 27, 2024 | Drug DiscoveryProtein Structure Prediction | CodeCode Available | 1 | 5 |
| Cell Morphology-Guided Small Molecule Generation with GFlowNets | Aug 9, 2024 | Drug Discovery | CodeCode Available | 1 | 5 |
| FragXsiteDTI: Revealing Responsible Segments in Drug-Target Interaction with Transformer-Driven Interpretation | Nov 4, 2023 | BenchmarkingDrug Discovery | CodeCode Available | 1 | 5 |
| Multi-channel learning for integrating structural hierarchies into context-dependent molecular representation | Nov 5, 2023 | Drug DiscoveryMolecular Property Prediction | 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 |
| A Group Symmetric Stochastic Differential Equation Model for Molecule Multi-modal Pretraining | May 28, 2023 | Drug Discovery | CodeCode Available | 1 | 5 |
| GIT-Mol: A Multi-modal Large Language Model for Molecular Science with Graph, Image, and Text | Aug 14, 2023 | Drug DiscoveryImage Captioning | CodeCode Available | 1 | 5 |
| FusionDTI: Fine-grained Binding Discovery with Token-level Fusion for Drug-Target Interaction | Jun 3, 2024 | Drug DesignDrug 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 |
| Generalist Equivariant Transformer Towards 3D Molecular Interaction Learning | Jun 2, 2023 | Drug Discovery | CodeCode Available | 1 | 5 |
| Generalizing in the Real World with Representation Learning | Oct 18, 2022 | Drug DiscoveryRepresentation Learning | CodeCode Available | 1 | 5 |
| Gradual Optimization Learning for Conformational Energy Minimization | Nov 5, 2023 | Drug Discovery | CodeCode Available | 1 | 5 |
| GraphXForm: Graph transformer for computer-aided molecular design | Nov 3, 2024 | Drug DesignDrug Discovery | CodeCode Available | 1 | 5 |
