| 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 |
| An Improved Metric and Benchmark for Assessing the Performance of Virtual Screening Models | Mar 15, 2024 | BenchmarkingDrug Discovery | CodeCode Available | 1 |
| ChiENN: Embracing Molecular Chirality with Graph Neural Networks | Jul 5, 2023 | Drug DiscoveryMolecular Property Prediction | CodeCode Available | 1 |
| 3D Interaction Geometric Pre-training for Molecular Relational Learning | Dec 4, 2024 | Contrastive LearningDrug Discovery | CodeCode Available | 1 |
| DPPIN: A Biological Repository of Dynamic Protein-Protein Interaction Network Data | Jul 5, 2021 | AttributeDrug Discovery | 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 |
| Drug–target affinity prediction using graph neural network and contact maps | Jun 1, 2020 | Drug DesignDrug Discovery | CodeCode Available | 1 |
| BioT5: Enriching Cross-modal Integration in Biology with Chemical Knowledge and Natural Language Associations | Oct 11, 2023 | Drug DiscoveryMolecule Captioning | CodeCode Available | 1 |
| EquiCPI: SE(3)-Equivariant Geometric Deep Learning for Structure-Aware Prediction of Compound-Protein Interactions | Apr 7, 2025 | Drug DiscoveryRe-Ranking | CodeCode Available | 1 |
| Large-scale ligand-based virtual screening for SARS-CoV-2 inhibitors using deep neural networks | Mar 25, 2020 | Drug Discovery | CodeCode Available | 1 |
| Bio-xLSTM: Generative modeling, representation and in-context learning of biological and chemical sequences | Nov 6, 2024 | Drug DiscoveryIn-Context Learning | CodeCode Available | 1 |
| Comprehensive evaluation of deep and graph learning on drug-drug interactions prediction | Jun 8, 2023 | Drug DiscoveryGraph Learning | CodeCode Available | 1 |
| Learning Over Molecular Conformer Ensembles: Datasets and Benchmarks | Sep 29, 2023 | Drug DiscoveryEnsemble Learning | CodeCode Available | 1 |
| Learning Neural Set Functions Under the Optimal Subset Oracle | Mar 3, 2022 | Anomaly DetectionDrug Discovery | CodeCode Available | 1 |
| Achieving Robustness to Aleatoric Uncertainty with Heteroscedastic Bayesian Optimisation | Oct 17, 2019 | Bayesian OptimisationDecision Making | CodeCode Available | 1 |
| DiffHopp: A Graph Diffusion Model for Novel Drug Design via Scaffold Hopping | Aug 14, 2023 | Drug DesignDrug Discovery | CodeCode Available | 1 |
| LIMO: Latent Inceptionism for Targeted Molecule Generation | Jun 17, 2022 | Drug DiscoveryGaussian Processes | CodeCode Available | 1 |
| Deep Surrogate Docking: Accelerating Automated Drug Discovery with Graph Neural Networks | Nov 4, 2022 | Drug Discovery | CodeCode Available | 1 |
| Machine learning modeling of family wide enzyme-substrate specificity screens | Sep 8, 2021 | BIG-bench Machine LearningDrug Discovery | CodeCode Available | 1 |
| Machine learning models to accelerate the design of polymeric long-acting injectables | Jan 10, 2023 | Drug 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 |
| MAMMAL -- Molecular Aligned Multi-Modal Architecture and Language | Oct 28, 2024 | Drug DiscoveryProperty Prediction | CodeCode Available | 1 |
| Conditional Diffusion Based on Discrete Graph Structures for Molecular Graph Generation | Jan 1, 2023 | Drug DiscoveryGraph Generation | CodeCode Available | 1 |
| C5T5: Controllable Generation of Organic Molecules with Transformers | Aug 23, 2021 | Drug Discoverymolecular representation | CodeCode Available | 1 |
| Meta-learning with an Adaptive Task Scheduler | Oct 26, 2021 | Drug DiscoveryMeta-Learning | CodeCode Available | 1 |
| FusionRetro: Molecule Representation Fusion via In-Context Learning for Retrosynthetic Planning | Sep 30, 2022 | Drug DiscoveryIn-Context 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 |
| Modeling Diverse Chemical Reactions for Single-step Retrosynthesis via Discrete Latent Variables | Aug 10, 2022 | DecoderDrug Discovery | CodeCode Available | 1 |
| Can LLMs Convert Graphs to Text-Attributed Graphs? | Dec 13, 2024 | Drug DiscoveryRecommendation Systems | CodeCode Available | 1 |
| Modelling Cellular Perturbations with the Sparse Additive Mechanism Shift Variational Autoencoder | Nov 5, 2023 | DisentanglementDrug Discovery | CodeCode Available | 1 |
| MolecularGPT: Open Large Language Model (LLM) for Few-Shot Molecular Property Prediction | Jun 18, 2024 | Drug DiscoveryGraph Neural Network | CodeCode Available | 1 |
| Molecular machine learning with conformer ensembles | Dec 15, 2020 | BIG-bench Machine LearningDeep Learning | CodeCode Available | 1 |
| CardioGenAI: A Machine Learning-Based Framework for Re-Engineering Drugs for Reduced hERG Liability | Mar 12, 2024 | Drug Discovery | CodeCode Available | 1 |
| Molecular representation learning with language models and domain-relevant auxiliary tasks | Nov 26, 2020 | Drug Discoverymolecular representation | CodeCode Available | 1 |
| CausalBench: A Large-scale Benchmark for Network Inference from Single-cell Perturbation Data | Oct 31, 2022 | Causal DiscoveryCausal Inference | CodeCode Available | 1 |
| Molecule Generation for Target Protein Binding with Hierarchical Consistency Diffusion Model | Mar 2, 2025 | Drug DesignDrug Discovery | 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 |
| Vision Language Model is NOT All You Need: Augmentation Strategies for Molecule Language Models | Jul 12, 2024 | AllDrug 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 |
| DeepNoise: Signal and Noise Disentanglement based on Classifying Fluorescent Microscopy Images via Deep Learning | Sep 13, 2022 | DisentanglementDrug 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 |
| Multi-Objective GFlowNets | Oct 23, 2022 | Active LearningDiversity | CodeCode Available | 1 |
| A Group Symmetric Stochastic Differential Equation Model for Molecule Multi-modal Pretraining | May 28, 2023 | Drug Discovery | CodeCode Available | 1 |
| Multi-task Joint Strategies of Self-supervised Representation Learning on Biomedical Networks for Drug Discovery | Jan 12, 2022 | Drug DiscoveryGraph Attention | CodeCode Available | 1 |
| DeepProtein: Deep Learning Library and Benchmark for Protein Sequence Learning | Oct 2, 2024 | Deep LearningDrug Discovery | CodeCode Available | 1 |
| ChatGPT-powered Conversational Drug Editing Using Retrieval and Domain Feedback | May 29, 2023 | Decision MakingDrug Discovery | 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 |
| NPGPT: Natural Product-Like Compound Generation with GPT-based Chemical Language Models | Nov 19, 2024 | DiversityDrug Discovery | CodeCode Available | 1 |
| Directional Message Passing for Molecular Graphs | Mar 6, 2020 | Drug DiscoveryFormation Energy | CodeCode Available | 1 |
| Artificial Intelligence in Drug Discovery: Applications and Techniques | Jun 9, 2021 | Drug DesignDrug Discovery | CodeCode Available | 1 |
