| Uni-QSAR: an Auto-ML Tool for Molecular Property Prediction | Apr 24, 2023 | Drug DiscoveryModel Selection | CodeCode Available | 3 |
| Analyzing Learned Molecular Representations for Property Prediction | Apr 2, 2019 | Molecular Property Predictionmolecular representation | CodeCode Available | 2 |
| One Transformer Can Understand Both 2D & 3D Molecular Data | Oct 4, 2022 | Graph Regressionmolecular representation | CodeCode Available | 2 |
| A Systematic Survey of Chemical Pre-trained Models | Oct 29, 2022 | Drug Designmolecular representation | CodeCode Available | 2 |
| Multi-Modal Representation Learning for Molecular Property Prediction: Sequence, Graph, Geometry | Jan 7, 2024 | Data AugmentationDrug Discovery | CodeCode Available | 2 |
| SSI–DDI: Substructure–Substructure Interactions for Drug–Drug Interaction Prediction | Nov 7, 2021 | Drug–drug Interaction Extractionmolecular representation | CodeCode Available | 1 |
| GeoMFormer: A General Architecture for Geometric Molecular Representation Learning | Jun 24, 2024 | molecular representationRepresentation Learning | CodeCode Available | 1 |
| SubGDiff: A Subgraph Diffusion Model to Improve Molecular Representation Learning | May 9, 2024 | DenoisingDrug Discovery | CodeCode Available | 1 |
| MolSets: Molecular Graph Deep Sets Learning for Mixture Property Modeling | Dec 27, 2023 | Graph Neural Networkmixture property prediction | CodeCode Available | 1 |
| Molecular Representation Learning via Heterogeneous Motif Graph Neural Networks | Feb 1, 2022 | graph constructionGraph Neural Network | CodeCode Available | 1 |
| Fractional Denoising for 3D Molecular Pre-training | Jul 20, 2023 | DenoisingDrug Discovery | CodeCode Available | 1 |
| Multi-view biomedical foundation models for molecule-target and property prediction | Oct 25, 2024 | Drug Discoverymolecular representation | CodeCode Available | 1 |
| SELFormer: Molecular Representation Learning via SELFIES Language Models | Apr 10, 2023 | Dimensionality ReductionDrug Discovery | CodeCode Available | 1 |
| Semi-Supervised Junction Tree Variational Autoencoder for Molecular Property Prediction | Aug 10, 2022 | Computational chemistryDrug Discovery | CodeCode Available | 1 |
| MolSpectra: Pre-training 3D Molecular Representation with Multi-modal Energy Spectra | Feb 22, 2025 | molecular representation | CodeCode Available | 1 |
| JANUS: Parallel Tempered Genetic Algorithm Guided by Deep Neural Networks for Inverse Molecular Design | Jun 7, 2021 | Active LearningEvolutionary Algorithms | CodeCode Available | 1 |
| Improving Self-supervised Molecular Representation Learning using Persistent Homology | Nov 29, 2023 | Molecular Property Predictionmolecular representation | CodeCode Available | 1 |
| Learning Attributed Graph Representations with Communicative Message Passing Transformer | Jul 19, 2021 | Inductive Biasmolecular representation | CodeCode Available | 1 |
| Learning Over Molecular Conformer Ensembles: Datasets and Benchmarks | Sep 29, 2023 | Drug DiscoveryEnsemble Learning | CodeCode Available | 1 |
| Molecular Geometry Pretraining with SE(3)-Invariant Denoising Distance Matching | Jun 27, 2022 | Denoisingmolecular representation | CodeCode Available | 1 |
| Molecular representation learning with language models and domain-relevant auxiliary tasks | Nov 26, 2020 | Drug Discoverymolecular representation | CodeCode Available | 1 |
| MOL-Mamba: Enhancing Molecular Representation with Structural & Electronic Insights | Dec 21, 2024 | Drug DesignMamba | CodeCode Available | 1 |
| t-SMILES: A Scalable Fragment-based Molecular Representation Framework for De Novo Molecule Generation | Jan 4, 2023 | Language Modellingmolecular representation | CodeCode Available | 1 |
| MolTrans: Molecular Interaction Transformer for Drug Target Interaction Prediction | Apr 23, 2020 | Drug Discoverymolecular representation | CodeCode Available | 1 |
| Multiresolution Equivariant Graph Variational Autoencoder | Jun 2, 2021 | Graph GenerationImage Generation | CodeCode Available | 1 |
| ChemBERTa: Large-Scale Self-Supervised Pretraining for Molecular Property Prediction | Oct 19, 2020 | Molecular Property Predictionmolecular representation | CodeCode Available | 1 |
| Predictive Chemistry Augmented with Text Retrieval | Dec 8, 2023 | molecular representationRetrieval | CodeCode Available | 1 |
| Self-Referencing Embedded Strings (SELFIES): A 100% robust molecular string representation | May 31, 2019 | molecular representationvalid | CodeCode Available | 1 |
| Can Large Language Models Understand Molecules? | Jan 5, 2024 | Drug DiscoveryLanguage Modelling | CodeCode Available | 1 |
| Comprehensive evaluation of deep and graph learning on drug-drug interactions prediction | Jun 8, 2023 | Drug DiscoveryGraph Learning | CodeCode Available | 1 |
| 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 |
| Energy-Motivated Equivariant Pretraining for 3D Molecular Graphs | Jul 18, 2022 | 3D geometrymolecular representation | CodeCode Available | 1 |
| Graph-based Molecular Representation Learning | Jul 8, 2022 | Graph Learningmolecular representation | CodeCode Available | 1 |
| Multi-channel learning for integrating structural hierarchies into context-dependent molecular representation | Nov 5, 2023 | Drug DiscoveryMolecular Property Prediction | CodeCode Available | 1 |
| GeomGCL: Geometric Graph Contrastive Learning for Molecular Property Prediction | Sep 24, 2021 | Contrastive LearningData Augmentation | CodeCode Available | 1 |
| Large-Scale Chemical Language Representations Capture Molecular Structure and Properties | Jun 17, 2021 | Drug DiscoveryMolecular Property Prediction | CodeCode Available | 1 |
| Atomas: Hierarchical Alignment on Molecule-Text for Unified Molecule Understanding and Generation | Apr 23, 2024 | Drug Discoverymolecular representation | CodeCode Available | 1 |
| InstructBio: A Large-scale Semi-supervised Learning Paradigm for Biochemical Problems | Apr 8, 2023 | molecular representationRepresentation Learning | CodeCode Available | 1 |
| FunQG: Molecular Representation Learning Via Quotient Graphs | Jul 18, 2022 | Molecular Property Predictionmolecular representation | CodeCode Available | 1 |
| Learning Molecular Representation in a Cell | Jun 17, 2024 | Molecular Property Predictionmolecular representation | CodeCode Available | 1 |
| Improving Molecular Representation Learning with Metric Learning-enhanced Optimal Transport | Feb 13, 2022 | Domain AdaptationMetric Learning | CodeCode Available | 1 |
| Molecular Contrastive Learning with Chemical Element Knowledge Graph | Dec 1, 2021 | Contrastive LearningDrug Design | CodeCode Available | 1 |
| Exploring QSAR Models for Activity-Cliff Prediction | Jan 31, 2023 | molecular representationPrediction | CodeCode Available | 1 |
| GDiffRetro: Retrosynthesis Prediction with Dual Graph Enhanced Molecular Representation and Diffusion Generation | Jan 14, 2025 | molecular representationRetrosynthesis | CodeCode Available | 1 |
| Few-Shot Graph Learning for Molecular Property Prediction | Feb 16, 2021 | AttributeDrug Discovery | CodeCode Available | 1 |
| Molecule-Morphology Contrastive Pretraining for Transferable Molecular Representation | Apr 27, 2023 | Molecular Property Predictionmolecular representation | CodeCode Available | 1 |
| Self-Supervised Graph Transformer on Large-Scale Molecular Data | Jun 18, 2020 | Drug DesignMolecular Property Prediction | CodeCode Available | 1 |
| Learning Harmonic Molecular Representations on Riemannian Manifold | Mar 27, 2023 | Drug Discoverymolecular representation | CodeCode Available | 1 |
| C5T5: Controllable Generation of Organic Molecules with Transformers | Aug 23, 2021 | Drug Discoverymolecular representation | CodeCode Available | 1 |
| MolTailor: Tailoring Chemical Molecular Representation to Specific Tasks via Text Prompts | Jan 21, 2024 | Drug DiscoveryLanguage Modeling | CodeCode Available | 1 |
